Accession      Name                      Profile   Description
SM00001     EGF_like                    EGF_like.HMM  EGF domain, unclasssified subfamily
SM00002          PLP                         PLP.HMM  Myelin proteolipid protein (PLP or lipophilin)
SM00003           NH                          NH.HMM  Neurohypophysial hormones
SM00004           NL                          NL.HMM  Domain found in Notch and Lin-12
SM00005        DEATH                       DEATH.HMM  DEATH domain, found in proteins involved in cell death (apoptosis).
SM00006     A4_EXTRA                    A4_EXTRA.HMM  amyloid A4
SM00008        HormR                       HormR.HMM  Domain present in hormone receptors
SM00010 small_GTPase                small_GTPase.HMM  Small GTPase of the Ras superfamily; ill-defined subfamily
SM00011      VWC_def                     VWC_def.HMM  
SM00012    PTPc_DSPc                   PTPc_DSPc.HMM  Protein tyrosine phosphatase, catalytic domain, undefined specificity
SM00013        LRRNT                       LRRNT.HMM  Leucine rich repeat N-terminal domain
SM00014      acidPPc                     acidPPc.HMM  Acid phosphatase homologues
SM00015           IQ                          IQ.HMM  Short calmodulin-binding motif containing conserved Ile and Gln residues.
SM00017        OSTEO                       OSTEO.HMM  Osteopontin
SM00018           PD                          PD.HMM  P or trefoil or TFF domain
SM00019         SF_P                        SF_P.HMM  Pulmonary surfactant proteins
SM00020     Tryp_SPc                    Tryp_SPc.HMM  Trypsin-like serine protease
SM00021          DAX                         DAX.HMM  Domain present in Dishevelled and axin
SM00022         PLAc                        PLAc.HMM  Cytoplasmic phospholipase A2, catalytic subunit
SM00023     COLIPASE                    COLIPASE.HMM  Colipase
SM00025      Pumilio                     Pumilio.HMM  Pumilio-like repeats
SM00026        EPEND                       EPEND.HMM  Ependymins
SM00027           EH                          EH.HMM  Eps15 homology domain
SM00028          TPR                         TPR.HMM  Tetratricopeptide repeats
SM00029      GASTRIN                     GASTRIN.HMM  gastrin / cholecystokinin / caerulein family
SM00030          CLb                         CLb.HMM  CLUSTERIN Beta chain
SM00031          DED                         DED.HMM  Death effector domain
SM00032          CCP                         CCP.HMM  Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
SM00033           CH                          CH.HMM  Calponin homology domain
SM00034        CLECT                       CLECT.HMM  C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
SM00035          CLa                         CLa.HMM  CLUSTERIN alpha chain
SM00036          CNH                         CNH.HMM  Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2
SM00037          CNX                         CNX.HMM  Connexin homologues
SM00038        COLFI                       COLFI.HMM  Fibrillar collagens C-terminal domain
SM00039          CRF                         CRF.HMM  corticotropin-releasing factor
SM00040         CSF2                        CSF2.HMM  Granulocyte-macrophage colony-simulating factor (GM-CSF)
SM00041           CT                          CT.HMM  C-terminal cystine knot-like domain (CTCK)
SM00042          CUB                         CUB.HMM  Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein.
SM00043           CY                          CY.HMM  Cystatin-like domain
SM00044         CYCc                        CYCc.HMM  Adenylyl- / guanylyl cyclase, catalytic domain
SM00045        DAGKa                       DAGKa.HMM  Diacylglycerol kinase accessory domain (presumed)
SM00046        DAGKc                       DAGKc.HMM  Diacylglycerol kinase catalytic domain (presumed)
SM00047         LYZ2                        LYZ2.HMM  Lysozyme subfamily 2
SM00048        DEFSN                       DEFSN.HMM  Defensin/corticostatin family
SM00049          DEP                         DEP.HMM  Domain found in Dishevelled, Egl-10, and Pleckstrin
SM00050        DISIN                       DISIN.HMM  Homologues of snake disintegrins  
SM00051          DSL                         DSL.HMM  delta serrate ligand
SM00052          EAL                         EAL.HMM  Putative diguanylate phosphodiesterase
SM00053         DYNc                        DYNc.HMM  Dynamin, GTPase
SM00054          EFh                         EFh.HMM  EF-hand, calcium binding motif
SM00055          FCH                         FCH.HMM  Fes/CIP4 homology domain
SM00057        FIMAC                       FIMAC.HMM  factor I membrane attack complex
SM00058          FN1                         FN1.HMM  Fibronectin type 1 domain
SM00059          FN2                         FN2.HMM  Fibronectin type 2 domain
SM00060          FN3                         FN3.HMM  Fibronectin type 3 domain
SM00061         MATH                        MATH.HMM  meprin and TRAF homology
SM00062         PBPb                        PBPb.HMM  Bacterial periplasmic substrate-binding proteins
SM00063          FRI                         FRI.HMM  Frizzled
SM00064         FYVE                        FYVE.HMM  Protein present in Fab1, YOTB, Vac1, and EEA1
SM00065          GAF                         GAF.HMM  Domain present in phytochromes and cGMP-specific phosphodiesterases.
SM00066         GAL4                        GAL4.HMM  GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain
SM00067          GHA                         GHA.HMM  Glycoprotein hormone alpha chain homologues.
SM00068          GHB                         GHB.HMM  Glycoprotein hormone beta chain homologues.
SM00069          GLA                         GLA.HMM  Domain containing Gla (gamma-carboxyglutamate) residues.
SM00070        GLUCA                       GLUCA.HMM  Glucagon like hormones
SM00071      Galanin                     Galanin.HMM  Galanin
SM00072         GuKc                        GuKc.HMM  Guanylate kinase homologues.
SM00073          HPT                         HPT.HMM  Histidine Phosphotransfer domain
SM00075        HYDRO                       HYDRO.HMM  Hydrophobins
SM00076        IFabd                       IFabd.HMM  Interferon alpha, beta and delta.
SM00077         ITAM                        ITAM.HMM  Immunoreceptor tyrosine-based activation motif
SM00078         IlGF                        IlGF.HMM  Insulin / insulin-like growth factor / relaxin family.
SM00079         PBPe                        PBPe.HMM  Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
SM00080      LIF_OSM                     LIF_OSM.HMM  leukemia inhibitory factor 
SM00082        LRRCT                       LRRCT.HMM  Leucine rich repeat C-terminal domain
SM00084          NMU                         NMU.HMM  Neuromedin U 
SM00085         PA2c                        PA2c.HMM  Phospholipase A2
SM00086          PAC                         PAC.HMM  Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)
SM00087          PTH                         PTH.HMM  Parathyroid hormone
SM00088         PINT                        PINT.HMM  motif in proteasome subunits, Int-6, Nip-1 and TRIP-15
SM00089          PKD                         PKD.HMM  Repeats in polycystic kidney disease 1 (PKD1) and other proteins
SM00090          RIO                         RIO.HMM  RIO-like kinase
SM00091          PAS                         PAS.HMM  PAS domain
SM00092     RNAse_Pc                    RNAse_Pc.HMM  Pancreatic ribonuclease 
SM00093       SERPIN                      SERPIN.HMM  SERine  Proteinase INhibitors
SM00094       TR_FER                      TR_FER.HMM  Transferrin
SM00095       TR_THY                      TR_THY.HMM  Transthyretin
SM00096          UTG                         UTG.HMM  Uteroglobin
SM00097         WNT1                        WNT1.HMM  found in Wnt-1
SM00098       alkPPc                      alkPPc.HMM  Alkaline phosphatase homologues
SM00099         btg1                        btg1.HMM  tob/btg1 family
SM00100         cNMP                        cNMP.HMM  Cyclic nucleotide-monophosphate binding domain
SM00101       14_3_3                      14_3_3.HMM  14-3-3 homologues
SM00102          ADF                         ADF.HMM  Actin depolymerisation factor/cofilin -like domains
SM00103      ALBUMIN                     ALBUMIN.HMM  serum albumin
SM00104        ANATO                       ANATO.HMM  Anaphylatoxin homologous domain
SM00105       ArfGap                      ArfGap.HMM  Putative GTP-ase activating proteins for the small GTPase, ARF
SM00107          BTK                         BTK.HMM  Bruton's tyrosine kinase Cys-rich motif
SM00108     B_lectin                    B_lectin.HMM  Bulb-type mannose-specific lectin
SM00109           C1                          C1.HMM  Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains)
SM00110          C1Q                         C1Q.HMM  Complement component C1q domain.
SM00111           C4                          C4.HMM  C-terminal tandem repeated domain in type 4 procollagens
SM00112           CA                          CA.HMM  Cadherin repeats.
SM00113   CALCITONIN                  CALCITONIN.HMM  calcitonin
SM00114         CARD                        CARD.HMM  Caspase recruitment domain
SM00115         CASc                        CASc.HMM  Caspase, interleukin-1 beta converting enzyme (ICE) homologues
SM00116          CBS                         CBS.HMM  Domain in cystathionine beta-synthase and other proteins.
SM00119        HECTc                       HECTc.HMM  Domain Homologous to E6-AP Carboxyl Terminus with 
SM00120           HX                          HX.HMM  Hemopexin-like repeats.
SM00121           IB                          IB.HMM  Insulin growth factor-binding protein homologues
SM00125          IL1                         IL1.HMM  Interleukin-1 homologues 
SM00126          IL6                         IL6.HMM  Interleukin-6 homologues
SM00127          IL7                         IL7.HMM  Interleukin-7 and interleukin-9 family.
SM00128         IPPc                        IPPc.HMM  Inositol polyphosphate phosphatase, catalytic domain homologues
SM00129         KISc                        KISc.HMM  Kinesin motor, catalytic domain. ATPase.
SM00130           KR                          KR.HMM  Kringle domain
SM00131           KU                          KU.HMM  BPTI/Kunitz family of serine protease inhibitors.
SM00132          LIM                         LIM.HMM  Zinc-binding domain present in Lin-11, Isl-1, Mec-3.
SM00133       S_TK_X                      S_TK_X.HMM  Extension to Ser/Thr-type protein kinases
SM00134           LU                          LU.HMM  Ly-6 antigen / uPA receptor -like domain
SM00135           LY                          LY.HMM  Low-density lipoprotein-receptor YWTD domain
SM00136        LamNT                       LamNT.HMM  Laminin N-terminal domain (domain VI)
SM00137          MAM                         MAM.HMM  Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)
SM00138        MeTrc                       MeTrc.HMM  Methyltransferase, chemotaxis proteins 
SM00139        MyTH4                       MyTH4.HMM  Domain in Myosin and Kinesin Tails
SM00140          NGF                         NGF.HMM  Nerve growth factor (NGF or beta-NGF)
SM00141         PDGF                        PDGF.HMM  Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family
SM00142      PI3K_C2                     PI3K_C2.HMM  Phosphoinositide 3-kinase, region postulated to contain C2 domain
SM00143    PI3K_p85B                   PI3K_p85B.HMM  PI3-kinase family, p85-binding domain
SM00144     PI3K_rbd                    PI3K_rbd.HMM  PI3-kinase family, Ras-binding domain
SM00145        PI3Ka                       PI3Ka.HMM  Phosphoinositide 3-kinase family, accessory domain (PIK domain)
SM00146        PI3Kc                       PI3Kc.HMM  Phosphoinositide 3-kinase, catalytic domain
SM00147       RasGEF                      RasGEF.HMM  Guanine nucleotide exchange factor for Ras-like small GTPases
SM00148        PLCXc                       PLCXc.HMM  Phospholipase C, catalytic domain (part); domain X
SM00149        PLCYc                       PLCYc.HMM  Phospholipase C, catalytic domain (part); domain Y
SM00150         SPEC                        SPEC.HMM  Spectrin repeats
SM00151         SWIB                        SWIB.HMM  SWI complex, BAF60b domains
SM00152          THY                         THY.HMM  Thymosin beta actin-binding motif.
SM00153          VHP                         VHP.HMM  Villin headpiece domain
SM00154      ZnF_AN1                     ZnF_AN1.HMM  AN1-like Zinc finger
SM00155         PLDc                        PLDc.HMM  Phospholipase D. Active site motifs.
SM00156        PP2Ac                       PP2Ac.HMM  Protein phosphatase 2A homologues, catalytic domain.
SM00157          PRP                         PRP.HMM  Major prion protein
SM00159          PTX                         PTX.HMM  Pentraxin / C-reactive protein / pentaxin family
SM00160        RanBD                       RanBD.HMM  Ran-binding domain
SM00162         SAPA                        SAPA.HMM  Saposin/surfactant protein-B A-type DOMAIN
SM00164          TBC                         TBC.HMM  Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs.
SM00165          UBA                         UBA.HMM  Ubiquitin associated domain
SM00166          UBX                         UBX.HMM  Domain present in ubiquitin-regulatory proteins
SM00167         VPS9                        VPS9.HMM  Domain present in VPS9
SM00173          RAS                         RAS.HMM  Ras subfamily of RAS small GTPases
SM00174          RHO                         RHO.HMM  Rho (Ras homology) subfamily of Ras-like small GTPases
SM00175          RAB                         RAB.HMM  Rab subfamily of small GTPases
SM00176          RAN                         RAN.HMM  Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases
SM00177          ARF                         ARF.HMM  ARF-like small GTPases; ARF, ADP-ribosylation factor
SM00178          SAR                         SAR.HMM  Sar1p-like members of the Ras-family  of small GTPases
SM00179       EGF_CA                      EGF_CA.HMM  Calcium-binding EGF-like domain
SM00180      EGF_Lam                     EGF_Lam.HMM  Laminin-type epidermal growth factor-like domai
SM00181          EGF                         EGF.HMM  Epidermal growth factor-like domain.
SM00182       CULLIN                      CULLIN.HMM  Cullin
SM00183      NAT_PEP                     NAT_PEP.HMM  Natriuretic peptide
SM00184         RING                        RING.HMM  Ring finger
SM00185          ARM                         ARM.HMM  Armadillo/beta-catenin-like repeats
SM00186          FBG                         FBG.HMM  Fibrinogen-related domains (FReDs)
SM00187          INB                         INB.HMM  Integrin beta subunits (N-terminal portion of extracellular region)
SM00188         IL10                        IL10.HMM  Interleukin-10 family
SM00189          IL2                         IL2.HMM  Interleukin-2 family
SM00190       IL4_13                      IL4_13.HMM  Interleukins 4 and 13
SM00191    Int_alpha                   Int_alpha.HMM  Integrin alpha (beta-propellor repeats).
SM00192         LDLa                        LDLa.HMM  Low-density lipoprotein receptor domain class A
SM00193          PTN                         PTN.HMM  Pleiotrophin / midkine family
SM00194         PTPc                        PTPc.HMM  Protein tyrosine phosphatase, catalytic domain
SM00195         DSPc                        DSPc.HMM  Dual specificity phosphatase, catalytic domain
SM00197          SAA                         SAA.HMM  Serum amyloid A proteins
SM00198          SCP                         SCP.HMM  SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains.
SM00199          SCY                         SCY.HMM  Intercrine alpha family (small cytokine C-X-C) (chemokine CXC).
SM00200          SEA                         SEA.HMM  Domain found in sea urchin sperm protein, enterokinase, agrin
SM00201           SO                          SO.HMM  Somatomedin B -like domains
SM00202           SR                          SR.HMM  Scavenger receptor Cys-rich
SM00203           TK                          TK.HMM  Tachykinin family
SM00204         TGFB                        TGFB.HMM  Transforming growth  factor-beta (TGF-beta) family
SM00205          THN                         THN.HMM  Thaumatin family
SM00206          NTR                         NTR.HMM  Tissue inhibitor of metalloproteinase family.
SM00207          TNF                         TNF.HMM  Tumour necrosis factor family.
SM00208         TNFR                        TNFR.HMM  Tumor necrosis factor receptor / nerve growth factor receptor repeats.
SM00209         TSP1                        TSP1.HMM  Thrombospondin type 1 repeats
SM00210         TSPN                        TSPN.HMM  Thrombospondin N-terminal -like domains.
SM00211           TY                          TY.HMM  Thyroglobulin type I repeats.
SM00212         UBCc                        UBCc.HMM  Ubiquitin-conjugating enzyme E2, catalytic domain homologues
SM00213          UBQ                         UBQ.HMM  Ubiquitin homologues
SM00214          VWC                         VWC.HMM  von Willebrand factor (vWF) type C domain
SM00215      VWC_out                     VWC_out.HMM  von Willebrand factor (vWF) type C domain
SM00216          VWD                         VWD.HMM  von Willebrand factor (vWF) type D domain
SM00217          WAP                         WAP.HMM  Four-disulfide core domains
SM00218          ZU5                         ZU5.HMM  Domain present in ZO-1 and Unc5-like netrin receptors
SM00219        TyrKc                       TyrKc.HMM  Tyrosine kinase, catalytic domain
SM00220        S_TKc                       S_TKc.HMM  Serine/Threonine protein kinases, catalytic domain
SM00221        STYKc                       STYKc.HMM  Protein kinase; unclassified specificity.
SM00222         Sec7                        Sec7.HMM  Sec7 domain
SM00223        APPLE                       APPLE.HMM  APPLE domain
SM00224          GGL                         GGL.HMM  G protein gamma subunit-like motifs
SM00225          BTB                         BTB.HMM  Broad-Complex, Tramtrack and Bric a brac
SM00226        LMWPc                       LMWPc.HMM  Low molecular weight phosphatase family
SM00227         NEBU                        NEBU.HMM  
SM00228          PDZ                         PDZ.HMM  Domain present in PSD-95, Dlg, and ZO-1/2.
SM00229      RasGEFN                     RasGEFN.HMM  Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
SM00230        CysPc                       CysPc.HMM  Calpain-like thiol protease family.
SM00231        FA58C                       FA58C.HMM  Coagulation factor 5/8 C-terminal domain, discoidin domain
SM00232      JAB_MPN                     JAB_MPN.HMM  JAB/MPN domain
SM00233           PH                          PH.HMM  Pleckstrin homology domain.
SM00234        START                       START.HMM  in StAR and phosphatidylcholine transfer protein
SM00235         ZnMc                        ZnMc.HMM  Zinc-dependent metalloprotease
SM00236         fCBD                        fCBD.HMM  Fungal-type cellulose-binding domain
SM00237    Calx_beta                   Calx_beta.HMM  Domains in Na-Ca exchangers and integrin-beta4
SM00238          BIR                         BIR.HMM  Baculoviral inhibition of apoptosis protein repeat
SM00239           C2                          C2.HMM  Protein kinase C conserved region 2 (CalB)
SM00240          FHA                         FHA.HMM  Forkhead associated domain
SM00241           ZP                          ZP.HMM  Zona pellucida (ZP) domain
SM00242         MYSc                        MYSc.HMM  Myosin. Large ATPases.
SM00243         GAS2                        GAS2.HMM  Growth-Arrest-Specific Protein 2 Domain
SM00244          PHB                         PHB.HMM  prohibitin homologues
SM00245         TSPc                        TSPc.HMM  tail specific protease
SM00246          WH2                         WH2.HMM  Wiskott Aldrich syndrome homology region 2
SM00247       XTALbg                      XTALbg.HMM  Beta/gamma crystallins
SM00248          ANK                         ANK.HMM  ankyrin repeats
SM00249          PHD                         PHD.HMM  PHD zinc finger
SM00250         PLEC                        PLEC.HMM  Plectin repeat
SM00251      SAM_PNT                     SAM_PNT.HMM  SAM / Pointed domain
SM00252          SH2                         SH2.HMM  Src homology 2 domains
SM00253         SOCS                        SOCS.HMM  suppressors of cytokine signalling
SM00254         ShKT                        ShKT.HMM  ShK toxin domain
SM00255          TIR                         TIR.HMM  Toll - interleukin 1 - resistance
SM00256         FBOX                        FBOX.HMM  A Receptor for Ubiquitination Targets
SM00257         LysM                        LysM.HMM  Lysin motif
SM00258         SAND                        SAND.HMM  SAND domain
SM00259      ZnF_A20                     ZnF_A20.HMM  A20-like zinc fingers
SM00260         CheW                        CheW.HMM  Two component signalling adaptor domain
SM00261           FU                          FU.HMM  Furin-like repeats
SM00262          GEL                         GEL.HMM  Gelsolin homology domain
SM00263         LYZ1                        LYZ1.HMM   Alpha-lactalbumin / lysozyme C
SM00264          BAG                         BAG.HMM  BAG domains, present in regulator of Hsp70 proteins
SM00265          BH4                         BH4.HMM  BH4 Bcl-2 homology region 4
SM00266          CAD                         CAD.HMM  Domains present in proteins implicated in post-mortem DNA fragmentation
SM00267        GGDEF                       GGDEF.HMM  diguanylate cyclase
SM00268        ACTIN                       ACTIN.HMM  Actin
SM00269         BowB                        BowB.HMM  Bowman-Birk type proteinase inhibitor
SM00270       ChtBD1                      ChtBD1.HMM  Chitin binding domain
SM00271         DnaJ                        DnaJ.HMM  DnaJ molecular chaperone homology domain
SM00272          END                         END.HMM  Endothelin
SM00273         ENTH                        ENTH.HMM  Epsin N-terminal homology (ENTH) domain
SM00274         FOLN                        FOLN.HMM  Follistatin-N-terminal domain-like
SM00275      G_alpha                     G_alpha.HMM  G protein alpha subunit
SM00276        GLECT                       GLECT.HMM  Galectin
SM00277         GRAN                        GRAN.HMM  Granulin
SM00278         HhH1                        HhH1.HMM  Helix-hairpin-helix DNA-binding motif class 1
SM00279         HhH2                        HhH2.HMM  Helix-hairpin-helix class 2 (Pol1 family) motifs
SM00280        KAZAL                       KAZAL.HMM  Kazal type serine protease inhibitors
SM00281         LamB                        LamB.HMM  Laminin B domain
SM00282         LamG                        LamG.HMM  Laminin G domain
SM00283           MA                          MA.HMM  Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer).
SM00284          OLF                         OLF.HMM  Olfactomedin-like domains
SM00285          PBD                         PBD.HMM  P21-Rho-binding domain
SM00286          PTI                         PTI.HMM  Plant trypsin inhibitors
SM00287         SH3b                        SH3b.HMM  Bacterial SH3 domain homologues
SM00288          VHS                         VHS.HMM  Domain present in VPS-27, Hrs and STAM
SM00289          WR1                         WR1.HMM  Worm-specific repeat type 1
SM00290      ZnF_UBP                     ZnF_UBP.HMM  Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger
SM00291       ZnF_ZZ                      ZnF_ZZ.HMM  Zinc-binding domain, present in Dystrophin, CREB-binding protein.
SM00292         BRCT                        BRCT.HMM  breast cancer carboxy-terminal domain
SM00293         PWWP                        PWWP.HMM  domain with conserved PWWP motif
SM00294         4.1m                        4.1m.HMM  putative band 4.1 homologues' binding motif
SM00295          B41                         B41.HMM  Band 4.1 homologues
SM00297        BROMO                       BROMO.HMM  bromo domain
SM00298       CHROMO                      CHROMO.HMM  Chromatin organization modifier domain
SM00299          CLH                         CLH.HMM  Clathrin heavy chain repeat homology
SM00300         ChSh                        ChSh.HMM  Chromo Shadow Domain
SM00301           DM                          DM.HMM  Doublesex DNA-binding motif
SM00302          GED                         GED.HMM  Dynamin GTPase effector domain
SM00303          GPS                         GPS.HMM  G-protein-coupled receptor proteolytic site domain
SM00304         HAMP                        HAMP.HMM  HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain
SM00305        HintC                       HintC.HMM  Hint (Hedgehog/Intein) domain C-terminal region
SM00306        HintN                       HintN.HMM  Hint (Hedgehog/Intein) domain N-terminal region
SM00307        ILWEQ                       ILWEQ.HMM  I/LWEQ domain
SM00308          LH2                         LH2.HMM  Lipoxygenase homology 2 (beta barrel) domain
SM00309          PAH                         PAH.HMM  Pancreatic hormones / neuropeptide F / peptide YY family 
SM00310         PTBI                        PTBI.HMM  Phosphotyrosine-binding domain (IRS1-like)
SM00311          PWI                         PWI.HMM  PWI, domain in splicing factors
SM00312           PX                          PX.HMM  PhoX homologous domain, present in p47phox and p40phox.
SM00313          PXA                         PXA.HMM  Domain associated with PX domains
SM00314           RA                          RA.HMM  Ras association (RalGDS/AF-6) domain
SM00315          RGS                         RGS.HMM  Regulator of G protein signalling domain
SM00316           S1                          S1.HMM  Ribosomal protein S1-like RNA-binding domain
SM00317          SET                         SET.HMM  SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
SM00318          SNc                         SNc.HMM  Staphylococcal nuclease homologues
SM00319         TarH                        TarH.HMM  Homologues of the ligand binding domain of Tar
SM00320         WD40                        WD40.HMM  WD40 repeats
SM00321          WSC                         WSC.HMM  present in yeast cell wall integrity and stress response component proteins
SM00322           KH                          KH.HMM  K homology RNA-binding domain
SM00323       RasGAP                      RasGAP.HMM  GTPase-activator protein for Ras-like GTPases
SM00324       RhoGAP                      RhoGAP.HMM  GTPase-activator protein for Rho-like GTPases
SM00325       RhoGEF                      RhoGEF.HMM  Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
SM00326          SH3                         SH3.HMM  Src homology 3 domains
SM00327          VWA                         VWA.HMM  von Willebrand factor (vWF) type A domain
SM00328         BPI1                        BPI1.HMM  BPI/LBP/CETP N-terminal domain
SM00329         BPI2                        BPI2.HMM  BPI/LBP/CETP C-terminal domain
SM00330        PIPKc                       PIPKc.HMM  Phosphatidylinositol phosphate kinases
SM00331     PP2C_SIG                    PP2C_SIG.HMM  Sigma factor PP2C-like phosphatases
SM00332        PP2Cc                       PP2Cc.HMM  Serine/threonine phosphatases, family 2C, catalytic domain
SM00333        TUDOR                       TUDOR.HMM  Tudor domain
SM00335          ANX                         ANX.HMM  Annexin repeats
SM00336         BBOX                        BBOX.HMM  B-Box-type zinc finger
SM00337          BCL                         BCL.HMM  BCL (B-Cell lymphoma); contains BH1, BH2 regions
SM00338         BRLZ                        BRLZ.HMM  basic region leucin zipper
SM00339           FH                          FH.HMM  FORKHEAD
SM00340         HALZ                        HALZ.HMM  homeobox associated leucin zipper
SM00341         HRDC                        HRDC.HMM  Helicase and RNase D C-terminal
SM00342     HTH_ARAC                    HTH_ARAC.HMM  helix_turn_helix, arabinose operon control protein
SM00343     ZnF_C2HC                    ZnF_C2HC.HMM  zinc finger
SM00344     HTH_ASNC                    HTH_ASNC.HMM  helix_turn_helix ASNC type
SM00345     HTH_GNTR                    HTH_GNTR.HMM  helix_turn_helix gluconate operon transcriptional repressor
SM00346     HTH_ICLR                    HTH_ICLR.HMM  helix_turn_helix isocitrate lyase regulation
SM00347     HTH_MARR                    HTH_MARR.HMM  helix_turn_helix multiple antibiotic resistance protein
SM00348          IRF                         IRF.HMM  interferon regulatory factor
SM00349         KRAB                        KRAB.HMM  krueppel associated box
SM00350          MCM                         MCM.HMM  minichromosome  maintenance proteins
SM00351          PAX                         PAX.HMM  Paired Box domain
SM00352          POU                         POU.HMM  Found in Pit-Oct-Unc transcription factors
SM00353          HLH                         HLH.HMM  helix loop helix domain
SM00354     HTH_LACI                    HTH_LACI.HMM  helix_turn _helix lactose operon repressor
SM00355     ZnF_C2H2                    ZnF_C2H2.HMM  zinc finger
SM00356     ZnF_C3H1                    ZnF_C3H1.HMM  zinc finger
SM00357          CSP                         CSP.HMM  Cold shock protein domain
SM00358         DSRM                        DSRM.HMM  Double-stranded RNA binding motif
SM00359          PUA                         PUA.HMM  Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
SM00360          RRM                         RRM.HMM  RNA recognition motif
SM00361        RRM_1                       RRM_1.HMM  RNA recognition motif
SM00362        RRM_2                       RRM_2.HMM  RNA recognition motif
SM00363           S4                          S4.HMM  S4 RNA-binding domain
SM00364      LRR_BAC                     LRR_BAC.HMM  Leucine-rich repeats, bacterial type
SM00365     LRR_SD22                    LRR_SD22.HMM  Leucine-rich repeat, SDS22-like subfamily
SM00367       LRR_CC                      LRR_CC.HMM  Leucine-rich repeat - CC (cysteine-containing) subfamily
SM00368       LRR_RI                      LRR_RI.HMM  Leucine rich repeat, ribonuclease inhibitor type
SM00369      LRR_TYP                     LRR_TYP.HMM  Leucine-rich repeats, typical (most populated) subfamily
SM00370          LRR                         LRR.HMM  Leucine-rich repeats, outliers
SM00380          AP2                         AP2.HMM  DNA-binding domain in plant proteins such as APETALA2 and EREBPs
SM00382          AAA                         AAA.HMM  ATPases associated with a variety of cellular activities
SM00384      AT_hook                     AT_hook.HMM  DNA binding domain with preference for A/T rich regions
SM00385       CYCLIN                      CYCLIN.HMM  domain present in cyclins, TFIIB and Retinoblastoma
SM00386          HAT                         HAT.HMM  HAT (Half-A-TPR) repeats
SM00387    HATPase_c                   HATPase_c.HMM  Histidine kinase-like ATPases
SM00388        HisKA                       HisKA.HMM  His Kinase A (phosphoacceptor) domain
SM00389          HOX                         HOX.HMM  Homeodomain
SM00390       GoLoco                      GoLoco.HMM  LGN motif, putative GEFs specific for G-alpha GTPases
SM00391          MBD                         MBD.HMM  Methyl-CpG binding domain
SM00392         PROF                        PROF.HMM  Profilin
SM00393          R3H                         R3H.HMM  Putative single-stranded nucleic acids-binding domain
SM00394         RIIa                        RIIa.HMM  RIIalpha, Regulatory subunit portion of type II PKA R-subunit
SM00396     ZnF_UBR1                    ZnF_UBR1.HMM  Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway
SM00397      t_SNARE                     t_SNARE.HMM  Helical region found in SNAREs
SM00398          HMG                         HMG.HMM  high mobility group
SM00399       ZnF_C4                      ZnF_C4.HMM  c4 zinc finger in nuclear hormone receptors
SM00400     ZnF_CHCC                    ZnF_CHCC.HMM  zinc finger
SM00401     ZnF_GATA                    ZnF_GATA.HMM  zinc finger binding to DNA consensus sequence [AT]GATA[AG] 
SM00404   PTPc_motif                  PTPc_motif.HMM  Protein tyrosine phosphatase, catalytic domain motif
SM00406          IGv                         IGv.HMM  Immunoglobulin V-Type
SM00407         IGc1                        IGc1.HMM  Immunoglobulin C-Type
SM00408         IGc2                        IGc2.HMM  Immunoglobulin C-2 Type
SM00409           IG                          IG.HMM  Immunoglobulin
SM00410      IG_like                     IG_like.HMM  Immunoglobulin like
SM00411          BHL                         BHL.HMM  bacterial (prokaryotic) histone like domain
SM00412      Cu_FIST                     Cu_FIST.HMM  Copper-Fist
SM00413          ETS                         ETS.HMM  erythroblast transformation specific domain
SM00414          H2A                         H2A.HMM  Histone 2A
SM00415          HSF                         HSF.HMM  heat shock factor
SM00417           H4                          H4.HMM  Histone H4
SM00418     HTH_ARSR                    HTH_ARSR.HMM  helix_turn_helix, Arsenical Resistance Operon Repressor
SM00419      HTH_CRP                     HTH_CRP.HMM  helix_turn_helix, cAMP Regulatory protein
SM00420     HTH_DEOR                    HTH_DEOR.HMM  helix_turn_helix, Deoxyribose operon repressor
SM00421     HTH_LUXR                    HTH_LUXR.HMM  helix_turn_helix, Lux Regulon
SM00422     HTH_MERR                    HTH_MERR.HMM  helix_turn_helix, mercury resistance
SM00423          PSI                         PSI.HMM  domain found in Plexins, Semaphorins and Integrins
SM00424          STE                         STE.HMM  STE like transcription factors
SM00425         TBOX                        TBOX.HMM  Domain first found  in the mice T locus (Brachyury) protein
SM00426          TEA                         TEA.HMM  TEA domain
SM00427          H2B                         H2B.HMM  Histone H2B
SM00428           H3                          H3.HMM  Histone H3
SM00429          IPT                         IPT.HMM  ig-like, plexins, transcription factors
SM00430         HOLI                        HOLI.HMM  Ligand binding domain of hormone receptors
SM00431         SCAN                        SCAN.HMM  leucine rich region
SM00432         MADS                        MADS.HMM  
SM00433        TOP2c                       TOP2c.HMM  TopoisomeraseII
SM00434        TOP4c                       TOP4c.HMM  DNA Topoisomerase IV
SM00435       TOPEUc                      TOPEUc.HMM  DNA Topoisomerase I (eukaryota)
SM00436       TOP1Bc                      TOP1Bc.HMM  Bacterial DNA topoisomeraes I ATP-binding domain
SM00437       TOP1Ac                      TOP1Ac.HMM  Bacterial DNA topoisomerase I DNA-binding domain
SM00438      ZnF_NFX                     ZnF_NFX.HMM  
SM00439          BAH                         BAH.HMM  Bromo adjacent homology domain
SM00440     ZnF_C2C2                    ZnF_C2C2.HMM  C2C2 Zinc finger
SM00441           FF                          FF.HMM  Contains two conserved F residues
SM00442          FGF                         FGF.HMM  Acidic and basic fibroblast growth factor family.
SM00443      G_patch                     G_patch.HMM  glycine rich nucleic binding domain
SM00444          GYF                         GYF.HMM  Contains conserved Gly-Tyr-Phe residues
SM00445         LINK                        LINK.HMM  Link (Hyaluronan-binding)
SM00446       LRRcap                      LRRcap.HMM  occurring C-terminal to leucine-rich repeats
SM00448          REC                         REC.HMM  cheY-homologous receiver domain
SM00449         SPRY                        SPRY.HMM  Domain in SPla and the RYanodine Receptor. 
SM00450         RHOD                        RHOD.HMM  Rhodanese Homology Domain
SM00451       ZnF_U1                      ZnF_U1.HMM  U1-like zinc finger
SM00452          STI                         STI.HMM  Soybean trypsin inhibitor (Kunitz) family of protease inhibitors
SM00453          WSN                         WSN.HMM  Worm-specific (usually) N-terminal domain
SM00454          SAM                         SAM.HMM  Sterile alpha motif.
SM00455          RBD                         RBD.HMM  Raf-like Ras-binding domain
SM00456           WW                          WW.HMM  Domain with 2 conserved Trp (W) residues
SM00457        MACPF                       MACPF.HMM  membrane-attack complex / perforin
SM00458        RICIN                       RICIN.HMM  Ricin-type beta-trefoil
SM00459         Sorb                        Sorb.HMM  Sorbin homologous domain
SM00460          TGc                         TGc.HMM  Transglutaminase/protease-like homologues
SM00461          WH1                         WH1.HMM  WASP homology region 1
SM00462          PTB                         PTB.HMM  Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain
SM00463          SMR                         SMR.HMM  Small MutS-related domain
SM00464          LON                         LON.HMM  Found in ATP-dependent protease La (LON)
SM00465         GIYc                        GIYc.HMM  GIY-YIG type nucleases (URI domain)
SM00466          SRA                         SRA.HMM  SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.
SM00467           GS                          GS.HMM  GS motif
SM00468       PreSET                      PreSET.HMM  N-terminal to some SET domains
SM00469          WIF                         WIF.HMM  Wnt-inhibitory factor-1 like domain
SM00470         ParB                        ParB.HMM  ParB-like nuclease domain
SM00471          HDc                         HDc.HMM  Metal dependent phosphohydrolases with conserved 'HD' motif.
SM00472          MIR                         MIR.HMM  Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases
SM00473       PAN_AP                      PAN_AP.HMM  divergent subfamily of APPLE domains
SM00474       35EXOc                      35EXOc.HMM  3'-5' exonuclease
SM00475       53EXOc                      53EXOc.HMM  5'-3' exonuclease
SM00476      DNaseIc                     DNaseIc.HMM  deoxyribonuclease I
SM00477          NUC                         NUC.HMM  DNA/RNA non-specific endonuclease
SM00478       ENDO3c                      ENDO3c.HMM  endonuclease III
SM00479       EXOIII                      EXOIII.HMM  
SM00480       POL3Bc                      POL3Bc.HMM  DNA polymerase III beta subunit
SM00481     POLIIIAc                    POLIIIAc.HMM  DNA polymerase alpha chain like domain
SM00482        POLAc                       POLAc.HMM  DNA polymerase A domain
SM00483        POLXc                       POLXc.HMM  DNA polymerase X family
SM00484         XPGI                        XPGI.HMM  Xeroderma pigmentosum G I-region
SM00485         XPGN                        XPGN.HMM  Xeroderma pigmentosum G N-region
SM00486        POLBc                       POLBc.HMM  DNA polymerase type-B family
SM00487        DEXDc                       DEXDc.HMM  DEAD-like helicases superfamily
SM00488       DEXDc2                      DEXDc2.HMM  
SM00489       DEXDc3                      DEXDc3.HMM  
SM00490       HELICc                      HELICc.HMM  helicase superfamily c-terminal domain
SM00491      HELICc2                     HELICc2.HMM  
SM00492      HELICc3                     HELICc3.HMM  
SM00493       TOPRIM                      TOPRIM.HMM  
SM00494       ChtBD2                      ChtBD2.HMM  Chitin-binding domain type 2
SM00495       ChtBD3                      ChtBD3.HMM  Chitin-binding domain type 3
SM00496        IENR2                       IENR2.HMM  Intron-encoded nuclease repeat 2
SM00497        IENR1                       IENR1.HMM  Intron encoded nuclease repeat motif
SM00498          FH2                         FH2.HMM  Formin Homology 2 Domain
SM00499          AAI                         AAI.HMM  Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family
SM00500          SFM                         SFM.HMM  Splicing Factor Motif, present in Prp18 and Pr04
SM00501       BRIGHT                      BRIGHT.HMM  BRIGHT, ARID (A/T-rich interaction domain) domain
SM00502          BBC                         BBC.HMM  B-Box C-terminal domain
SM00503         SynN                        SynN.HMM  Syntaxin N-terminal domain
SM00504         Ubox                        Ubox.HMM  Modified RING finger domain
SM00505        Knot1                       Knot1.HMM  Knottins
SM00506         A1pp                        A1pp.HMM  Appr-1"-p processing enzyme
SM00507         HNHc                        HNHc.HMM  HNH nucleases
SM00508      PostSET                     PostSET.HMM  Cysteine-rich motif following a subset of SET domains
SM00509        TFS2N                       TFS2N.HMM  Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) 
SM00510        TFS2M                       TFS2M.HMM  Domain in the central regions of transcription elongation factor S-II (and elsewhere)
SM00511       ORANGE                      ORANGE.HMM  Orange domain
SM00512         Skp1                        Skp1.HMM  Found in Skp1 protein family
SM00513          SAP                         SAP.HMM  Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
SM00515        eIF5C                       eIF5C.HMM  Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5
SM00516        SEC14                       SEC14.HMM  Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p)
SM00517        PolyA                       PolyA.HMM  C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein.
SM00518        AP2Ec                       AP2Ec.HMM  AP endonuclease family 2
SM00520        BASIC                       BASIC.HMM  Basic domain in HLH proteins of MYOD family
SM00521          CBF                         CBF.HMM  CCAAT-Binding transcription Factor
SM00523          DWA                         DWA.HMM  Domain A in dwarfin family proteins
SM00524          DWB                         DWB.HMM  Domain B in dwarfin family proteins
SM00525          FES                         FES.HMM  
SM00526          H15                         H15.HMM  Domain in histone families 1 and 5
SM00527        HMG17                       HMG17.HMM  domain in high mobilty group proteins HMG14 and HMG 17
SM00528          HNS                         HNS.HMM  Domain in histone-like proteins of HNS family
SM00529     HTH_DTXR                    HTH_DTXR.HMM  Helix-turn-helix diphteria tox regulatory element
SM00530      HTH_XRE                     HTH_XRE.HMM  Helix-turn-helix XRE-family like proteins 
SM00531        TFIIE                       TFIIE.HMM  Transcription initiation factor IIE
SM00532       LIGANc                      LIGANc.HMM  Ligase N family
SM00533        MUTSd                       MUTSd.HMM  DNA-binding domain of DNA mismatch repair MUTS family
SM00534       MUTSac                      MUTSac.HMM  ATPase domain of DNA mismatch repair MUTS family
SM00535        RIBOc                       RIBOc.HMM  Ribonuclease III family
SM00536          AXH                         AXH.HMM  domain in Ataxins and HMG containing proteins
SM00537          DCX                         DCX.HMM  Domain in the Doublecortin (DCX) gene product
SM00538         POP4                        POP4.HMM  A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
SM00539         NIDO                        NIDO.HMM  Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins.
SM00540          LEM                         LEM.HMM  in nuclear membrane-associated proteins
SM00541         FYRN                        FYRN.HMM  "FY-rich" domain, N-terminal region
SM00542         FYRC                        FYRC.HMM  "FY-rich" domain, C-terminal region
SM00543        MIF4G                       MIF4G.HMM  Middle domain of eukaryotic initiation factor 4G (eIF4G)
SM00544          MA3                         MA3.HMM  Domain in DAP-5, eIF4G, MA-3 and other proteins.
SM00545         JmjN                        JmjN.HMM  Small domain found in the jumonji family of transcription factors
SM00546          CUE                         CUE.HMM  Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs)
SM00547      ZnF_RBZ                     ZnF_RBZ.HMM  Zinc finger domain
SM00548          IRO                         IRO.HMM  Motif in Iroquois-class homeodomain proteins (only). Unknown function.
SM00549         TAFH                        TAFH.HMM  TAF homology
SM00550       Zalpha                      Zalpha.HMM  Z-DNA-binding domain in adenosine deaminases.
SM00551      ZnF_TAZ                     ZnF_TAZ.HMM  TAZ zinc finger, present in p300 and CBP 
SM00552       ADEAMc                      ADEAMc.HMM  tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)
SM00553          SEP                         SEP.HMM  Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
SM00554         FAS1                        FAS1.HMM  Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
SM00555          GIT                         GIT.HMM  Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins
SM00557      IG_FLMN                     IG_FLMN.HMM  Filamin-type immunoglobulin domains
SM00558         JmjC                        JmjC.HMM  A domain family that is part of the cupin metalloenzyme superfamily.
SM00559         Ku78                        Ku78.HMM  Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen
SM00560        LamGL                       LamGL.HMM  LamG-like jellyroll fold domain
SM00561          MBT                         MBT.HMM  Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
SM00562          NDK                         NDK.HMM  
SM00563         PlsC                        PlsC.HMM  Phosphate acyltransferases
SM00564          PQQ                         PQQ.HMM  beta-propeller repeat
SM00567      EZ_HEAT                     EZ_HEAT.HMM  E-Z type HEAT repeats
SM00568         GRAM                        GRAM.HMM  domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins
SM00569          L27                         L27.HMM  domain in receptor targeting proteins Lin-2 and Lin-7
SM00570          AWS                         AWS.HMM  associated with SET domains
SM00571          DDT                         DDT.HMM  domain in different transcription and chromosome remodeling factors
SM00572          DZF                         DZF.HMM  domain in DSRM or ZnF_C2H2 domain containing proteins
SM00573          HSA                         HSA.HMM  domain in helicases and associated with SANT domains
SM00574          POX                         POX.HMM  domain associated with HOX domains
SM00575      ZnF_PMZ                     ZnF_PMZ.HMM  plant mutator transposase zinc finger
SM00576          BTP                         BTP.HMM  Bromodomain transcription factors and PHD domain containing proteins
SM00577         CPDc                        CPDc.HMM  catalytic domain of ctd-like phosphatases
SM00579          FBD                         FBD.HMM  domain in FBox and BRCT domain containing plant proteins
SM00580          PUG                         PUG.HMM  domain in protein kinases, N-glycanases and other nuclear proteins
SM00581          PSP                         PSP.HMM  proline-rich domain in spliceosome associated proteins
SM00582          RPR                         RPR.HMM  
SM00583          SPK                         SPK.HMM  
SM00584         TLDc                        TLDc.HMM  domain in TBC and LysM domain containing proteins
SM00586      ZnF_DBF                     ZnF_DBF.HMM  Zinc finger in DBF-like proteins
SM00587          CHK                         CHK.HMM  ZnF_C4 abd HLH domain containing kinases domain
SM00588         NEUZ                        NEUZ.HMM  
SM00589          PRY                         PRY.HMM  
SM00591          RWD                         RWD.HMM  
SM00592          BRK                         BRK.HMM  domain in transcription and CHROMO domain helicases
SM00593          RUN                         RUN.HMM  
SM00594          UAS                         UAS.HMM  
SM00595         MADF                        MADF.HMM  
SM00596     PRE_C2HC                    PRE_C2HC.HMM  
SM00597      ZnF_TTF                     ZnF_TTF.HMM  
SM00602        VPS10                       VPS10.HMM  
SM00603         LCCL                        LCCL.HMM  
SM00604           MD                          MD.HMM  
SM00605           CW                          CW.HMM  
SM00606       CBD_IV                      CBD_IV.HMM  Cellulose Binding Domain Type IV
SM00607          FTP                         FTP.HMM  eel-Fucolectin Tachylectin-4 Pentaxrin-1 Domain
SM00608          ACR                         ACR.HMM  ADAM Cysteine-Rich Domain
SM00609          VIT                         VIT.HMM  Vault protein Inter-alpha-Trypsin domain
SM00611        SEC63                       SEC63.HMM  Domain of unknown function in Sec63p, Brr2p and other proteins.
SM00612        Kelch                       Kelch.HMM  
SM00613          PAW                         PAW.HMM  domain present in PNGases and other hypothetical proteins
SM00614      ZnF_BED                     ZnF_BED.HMM  BED zinc finger
SM00615      EPH_lbd                     EPH_lbd.HMM  Ephrin receptor ligand binding domain
SM00630         Sema                        Sema.HMM  semaphorin domain
SM00631      Zn_pept                     Zn_pept.HMM  
SM00632       Aamy_C                      Aamy_C.HMM  
SM00633     Glyco_10                    Glyco_10.HMM  Glycosyl hydrolase family 10
SM00634        BID_1                       BID_1.HMM  Bacterial Ig-like domain (group 1)
SM00635        BID_2                       BID_2.HMM  Bacterial Ig-like domain 2
SM00636     Glyco_18                    Glyco_18.HMM  
SM00637       CBD_II                      CBD_II.HMM  
SM00638        LPD_N                       LPD_N.HMM  Lipoprotein N-terminal Domain
SM00639          PSA                         PSA.HMM  Paramecium Surface Antigen Repeat
SM00640     Glyco_32                    Glyco_32.HMM  Glycosyl hydrolases family 32
SM00641     Glyco_25                    Glyco_25.HMM  Glycosyl hydrolases family 25
SM00642         Aamy                        Aamy.HMM  Alpha-amylase domain
SM00643        C345C                       C345C.HMM  Netrin C-terminal Domain
SM00644        Ami_2                       Ami_2.HMM  
SM00645      Pept_C1                     Pept_C1.HMM  Papain family cysteine protease
SM00646        Ami_3                       Ami_3.HMM  
SM00647          IBR                         IBR.HMM  In Between Ring fingers
SM00648         SWAP                        SWAP.HMM  Suppressor-of-White-APricot splicing regulator
SM00649         RL11                        RL11.HMM  Ribosomal protein L11/L12
SM00650         rADc                        rADc.HMM  Ribosomal RNA adenine dimethylases
SM00651           Sm                          Sm.HMM  snRNP Sm proteins
SM00652        eIF1a                       eIF1a.HMM  eukaryotic translation initiation factor 1A
SM00653      eIF2B_5                     eIF2B_5.HMM  domain present in translation initiation factor eIF2B and eIF5
SM00654         eIF6                        eIF6.HMM  translation initiation factor 6
SM00656      Amb_all                     Amb_all.HMM  
SM00657       RPOL4c                      RPOL4c.HMM  DNA-directed RNA-polymerase II subunit 
SM00658       RPOL8c                      RPOL8c.HMM  RNA polymerase subunit 8
SM00659       RPOLCX                      RPOLCX.HMM  RNA polymerase subunit CX
SM00661        RPOL9                       RPOL9.HMM  RNA polymerase subunit 9
SM00662        RPOLD                       RPOLD.HMM  RNA polymerases D
SM00663      RPOLA_N                     RPOLA_N.HMM  RNA polymerase I subunit A N-terminus
SM00664          DoH                         DoH.HMM  Possible catecholamine-binding domain present in a variety of eukaryotic proteins.
SM00665         B561                        B561.HMM  Cytochrome b-561 / ferric reductase transmembrane domain.
SM00666          PB1                         PB1.HMM  PB1 domain 
SM00667         LisH                        LisH.HMM  Lissencephaly type-1-like homology motif
SM00668         CTLH                        CTLH.HMM  C-terminal to LisH motif. 
SM00670         PINc                        PINc.HMM  Large family of predicted nucleotide-binding domains
SM00671         SEL1                        SEL1.HMM  Sel1-like repeats.
SM00672        CAP10                       CAP10.HMM  Putative lipopolysaccharide-modifying enzyme.
SM00673         CARP                        CARP.HMM  Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product.
SM00674        CENPB                       CENPB.HMM  Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.
SM00675         DM11                        DM11.HMM  Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
SM00676         DM10                        DM10.HMM  Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
SM00678          WWE                         WWE.HMM  Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
SM00679         CTNS                        CTNS.HMM  Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins.
SM00680         CLIP                        CLIP.HMM  Clip or disulphide knot domain
SM00682          G2F                         G2F.HMM  G2 nidogen domain and fibulin
SM00683         DM16                        DM16.HMM  Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc.
SM00684         DM15                        DM15.HMM  Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.
SM00685         DM14                        DM14.HMM  Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
SM00686         DM13                        DM13.HMM  Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10.1 and Arabidopsis thaliana MBG8.9.
SM00688          DM7                         DM7.HMM  Domain of unknown function in Drosophila CG15332, CG15333 and CG18293
SM00689          DM6                         DM6.HMM  Cysteine-rich domain currently specific to Drosophila.
SM00690          DM5                         DM5.HMM  Domain of unknown function, currently peculiar to Drosophila.
SM00692          DM3                         DM3.HMM  Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK.
SM00693        DysFN                       DysFN.HMM  Dysferlin domain, N-terminal region.
SM00694        DysFC                       DysFC.HMM  Dysferlin domain, C-terminal region.
SM00695         DUSP                        DUSP.HMM  Domain in ubiquitin-specific proteases.
SM00696          DM9                         DM9.HMM  Repeats found in Drosophila proteins.
SM00697          DM8                         DM8.HMM  Repeats found in several Drosophila proteins.
SM00698         MORN                        MORN.HMM  Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
SM00700         JHBP                        JHBP.HMM  Juvenile hormone binding protein domains in insects.
SM00701         PGRP                        PGRP.HMM  Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme.
SM00702         P4Hc                        P4Hc.HMM  Prolyl 4-hydroxylase alpha subunit homologues.
SM00703          NRF                         NRF.HMM  N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4).
SM00704    ZnF_CDGSH                   ZnF_CDGSH.HMM  CDGSH-type zinc finger. Function unknown.
SM00705         THEG                        THEG.HMM  Repeats in THEG (testicular haploid expressed gene) and several fly proteins.
SM00706        TECPR                       TECPR.HMM  Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins.
SM00707         RPEL                        RPEL.HMM  Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
SM00708         PhBP                        PhBP.HMM  Insect pheromone/odorant binding protein domains.
SM00709         Zpr1                        Zpr1.HMM  Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
SM00710         PbH1                        PbH1.HMM  Parallel beta-helix repeats
SM00711          TDU                         TDU.HMM  Short repeats in human TONDU, fly vestigial and other proteins.
SM00712          PUR                         PUR.HMM  DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
SM00713          GYR                         GYR.HMM  Motif of unknown function with conserved Gly, Tyr, Arg tripeptide in Drosophila proteins.
SM00714        LITAF                       LITAF.HMM  Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
SM00715           LA                          LA.HMM  Domain in the RNA-binding Lupus La protein; unknown function
SM00717         SANT                        SANT.HMM  SANT  SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
SM00718       DM4_12                      DM4_12.HMM  DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function.
SM00719        Plus3                       Plus3.HMM  Short conserved domain in transcriptional regulators.
SM00720  calpain_III                 calpain_III.HMM  
SM00721          BAR                         BAR.HMM  
SM00722         CASH                        CASH.HMM   Domain present in carbohydrate binding proteins and sugar hydrolses
SM00723         AMOP                        AMOP.HMM  Adhesion-associated domain present in MUC4 and other proteins
SM00724          TLC                         TLC.HMM  TRAM, LAG1 and CLN8 homology domains.
SM00725         NEAT                        NEAT.HMM  NEAr Transporter domain
SM00726          UIM                         UIM.HMM  Ubiquitin-interacting motif.
SM00727         STI1                        STI1.HMM  Heat shock chaperonin-binding motif.
SM00728          ChW                         ChW.HMM  Clostridial hydrophobic, with a conserved W residue, domain.
SM00729         Elp3                        Elp3.HMM  Elongator protein 3, MiaB family, Radical SAM
SM00730          PSN                         PSN.HMM  Presenilin, signal peptide peptidase, family
SM00731         SprT                        SprT.HMM  SprT homologues.
SM00732        YqgFc                       YqgFc.HMM  Likely ribonuclease with RNase H fold.
SM00733        Mterf                       Mterf.HMM  Mitochondrial termination factor repeats
SM00734    ZnF_Rad18                   ZnF_Rad18.HMM  Rad18-like CCHC zinc finger
SM00735           ZM                          ZM.HMM  ZASP-like motif
SM00736         CADG                        CADG.HMM  Dystroglycan-type cadherin-like domains.
SM00737           ML                          ML.HMM  Domain involved in innate immunity and lipid metabolism.
SM00738          NGN                         NGN.HMM  In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold.
SM00739          KOW                         KOW.HMM  KOW (Kyprides, Ouzounis, Woese) motif.
SM00740        PASTA                       PASTA.HMM  
SM00741         SapB                        SapB.HMM  Saposin (B) Domains
SM00742          Hr1                         Hr1.HMM  Rho effector or protein kinase C-related kinase homology region 1 homologues
SM00743       Agenet                      Agenet.HMM  Tudor-like domain present in plant sequences.
SM00744        RINGv                       RINGv.HMM  The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity.
SM00745          MIT                         MIT.HMM  Microtubule Interacting and Trafficking molecule domain
SM00746        TRASH                       TRASH.HMM  metallochaperone-like domain
SM00747         CFEM                        CFEM.HMM  
SM00748         HEPN                        HEPN.HMM  Higher Eukarytoes and Prokaryotes Nucleotide-binding domain
SM00749          BON                         BON.HMM  bacterial OsmY and nodulation domain
SM00750         KIND                        KIND.HMM  kinase non-catalytic C-lobe domain
SM00751          BSD                         BSD.HMM  domain in transcription factors and synapse-associated proteins
SM00752         HTTM                        HTTM.HMM  Horizontally Transferred TransMembrane Domain
SM00753          PAM                         PAM.HMM  PCI/PINT associated module
SM00754         CHRD                        CHRD.HMM  A domain in the BMP inhibitor chordin and in microbial proteins.
SM00755         Grip                        Grip.HMM  golgin-97, RanBP2alpha,Imh1p and p230/golgin-245
SM00756          VKc                         VKc.HMM  
SM00757          CRA                         CRA.HMM  CT11-RanBPM
SM00758         PA14                        PA14.HMM  
SM00759     Flu_M1_C                    Flu_M1_C.HMM  Influenza Matrix protein (M1) C-terminal domain
SM00760   Bac_DnaA_C                  Bac_DnaA_C.HMM  Bacterial dnaA protein helix-turn-helix domain
SM00761 HDAC_interact               HDAC_interact.HMM  Histone deacetylase (HDAC) interacting
SM00762         Cog4                        Cog4.HMM  COG4 transport protein
SM00763     AAA_PrkA                    AAA_PrkA.HMM  PrkA AAA domain
SM00764 Citrate_ly_lig              Citrate_ly_lig.HMM  Citrate lyase ligase C-terminal domain
SM00765        MANEC                       MANEC.HMM  
SM00766 DnaG_DnaB_bind              DnaG_DnaB_bind.HMM  DNA primase DnaG DnaB-binding
SM00767          DCD                         DCD.HMM  
SM00768           X8                          X8.HMM  Possibly involved in carbohydrate binding
SM00769          WHy                         WHy.HMM  Water Stress and Hypersensitive response
SM00770  Zn_dep_PLPC                 Zn_dep_PLPC.HMM  Zinc dependent phospholipase C (alpha toxin)
SM00771       ZipA_C                      ZipA_C.HMM  ZipA, C-terminal domain (FtsZ-binding)
SM00773          WGR                         WGR.HMM  Proposed nucleic acid binding domain
SM00774         WRKY                        WRKY.HMM  DNA binding domain
SM00775         LNS2                        LNS2.HMM  
SM00776        NPCBM                       NPCBM.HMM  
SM00777  Mad3_BUB1_I                 Mad3_BUB1_I.HMM  Mad3/BUB1 hoMad3/BUB1 homology region 1
SM00778 Prim_Zn_Ribbon              Prim_Zn_Ribbon.HMM  Zinc-binding domain of primase-helicase
SM00780        PIG-X                       PIG-X.HMM  PIG-X / PBN1
SM00782 PhnA_Zn_Ribbon              PhnA_Zn_Ribbon.HMM  PhnA Zinc-Ribbon
SM00783 A_amylase_inhib             A_amylase_inhib.HMM  Alpha amylase inhibitor
SM00784         SPT2                        SPT2.HMM  SPT2 chromatin protein
SM00785      AARP2CN                     AARP2CN.HMM  AARP2CN (NUC121) domain
SM00786 SHR3_chaperone              SHR3_chaperone.HMM  ER membrane protein SH3
SM00787         Spc7                        Spc7.HMM  Spc7 kinetochore protein
SM00788 Adenylsucc_synt             Adenylsucc_synt.HMM  Adenylosuccinate synthetase
SM00789 Ad_cyc_g-alpha              Ad_cyc_g-alpha.HMM  Adenylate cyclase G-alpha binding domain
SM00790       AFOR_N                      AFOR_N.HMM  Aldehyde ferredoxin oxidoreductase, N-terminal domain
SM00791   Agglutinin                  Agglutinin.HMM  
SM00792       Agouti                      Agouti.HMM  Agouti protein
SM00793         AgrB                        AgrB.HMM  Accessory gene regulator B
SM00794         AgrD                        AgrD.HMM  Staphylococcal AgrD protein
SM00795   Agro_virD5                  Agro_virD5.HMM  Agrobacterium VirD5 protein
SM00796         AHS1                        AHS1.HMM  Allophanate hydrolase subunit 1
SM00797         AHS2                        AHS2.HMM  Allophanate hydrolase subunit 2
SM00798 AICARFT_IMPCHas             AICARFT_IMPCHas.HMM  AICARFT/IMPCHase bienzyme
SM00799         DENN                        DENN.HMM  Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
SM00800        uDENN                       uDENN.HMM  Domain always found upstream of DENN domain, found in a variety of signalling proteins
SM00801        dDENN                       dDENN.HMM  Domain always found downstream of DENN domain, found in a variety of signalling proteins
SM00802          UME                         UME.HMM  Domain in UVSB PI-3 kinase, MEI-41 and ESR-1
SM00803          TAF                         TAF.HMM  TATA box binding protein associated factor
SM00804        TAP_C                       TAP_C.HMM  C-terminal domain of vertebrate Tap protein
SM00805       AGTRAP                      AGTRAP.HMM  Angiotensin II, type I receptor-associated protein
SM00806         AIP3                        AIP3.HMM  Actin interacting protein 3
SM00807     AKAP_110                    AKAP_110.HMM  A-kinase anchor protein 110 kDa
SM00808         FABD                        FABD.HMM  F-actin binding domain (FABD) 
SM00809 Alpha_adaptinC2             Alpha_adaptinC2.HMM  Adaptin C-terminal domain
SM00810 Alpha-amyl_C2               Alpha-amyl_C2.HMM  Alpha-amylase C-terminal beta-sheet domain
SM00811 Alpha_kinase                Alpha_kinase.HMM  Alpha-kinase family
SM00812 Alpha_L_fucos               Alpha_L_fucos.HMM  Alpha-L-fucosidase
SM00813 Alpha-L-AF_C                Alpha-L-AF_C.HMM  Alpha-L-arabinofuranosidase C-terminus
SM00814    Alpha_TIF                   Alpha_TIF.HMM  Alpha trans-inducing protein (Alpha-TIF)
SM00815        AMA-1                       AMA-1.HMM  Apical membrane antigen 1
SM00816 Amb_V_allergen              Amb_V_allergen.HMM  Amb V Allergen
SM00817       Amelin                      Amelin.HMM  Ameloblastin precursor (Amelin)
SM00818   Amelogenin                  Amelogenin.HMM  
SM00822       PKS_KR                      PKS_KR.HMM  
SM00823       PKS_PP                      PKS_PP.HMM  Phosphopantetheine attachment site
SM00824       PKS_TE                      PKS_TE.HMM  Thioesterase
SM00825       PKS_KS                      PKS_KS.HMM  Beta-ketoacyl synthase
SM00826       PKS_DH                      PKS_DH.HMM  
SM00827       PKS_AT                      PKS_AT.HMM  Acyl transferase domain in polyketide synthase (PKS) enzymes.
SM00828       PKS_MT                      PKS_MT.HMM  Methyltransferase  in polyketide synthase (PKS) enzymes.
SM00829       PKS_ER                      PKS_ER.HMM  Enoylreductase
SM00830         CM_2                        CM_2.HMM  Chorismate mutase type II
SM00831 Cation_ATPase_N             Cation_ATPase_N.HMM  Cation transporter/ATPase, N-terminus
SM00832           C8                          C8.HMM  
SM00833       CobW_C                      CobW_C.HMM   Cobalamin synthesis protein cobW C-terminal domain
SM00834 CxxC_CXXC_SSSS              CxxC_CXXC_SSSS.HMM   Putative regulatory protein
SM00835      Cupin_1                     Cupin_1.HMM  Cupin
SM00836       DALR_1                      DALR_1.HMM  DALR anticodon binding domain
SM00837       DPBB_1                      DPBB_1.HMM  Rare lipoprotein A (RlpA)-like double-psi beta-barrel
SM00838        EFG_C                       EFG_C.HMM  Elongation factor G C-terminus
SM00839 ELFV_dehydrog               ELFV_dehydrog.HMM  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
SM00840       DALR_2                      DALR_2.HMM  
SM00841 Elong-fact-P_C              Elong-fact-P_C.HMM  Elongation factor P, C-terminal
SM00842         FtsA                        FtsA.HMM  Cell division protein FtsA
SM00843   Ftsk_gamma                  Ftsk_gamma.HMM  
SM00844           GA                          GA.HMM  GA module
SM00845    GatB_Yqey                   GatB_Yqey.HMM  GatB domain
SM00846      Gp_dh_N                     Gp_dh_N.HMM  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
SM00847          HA2                         HA2.HMM  Helicase associated domain (HA2)  Add an annotation
SM00848 Inhibitor_I29               Inhibitor_I29.HMM  Cathepsin propeptide inhibitor domain (I29)
SM00849  Lactamase_B                 Lactamase_B.HMM  Metallo-beta-lactamase superfamily
SM00850        LytTR                       LytTR.HMM  LytTr DNA-binding domain
SM00851          MGS                         MGS.HMM  MGS-like domain
SM00852 MoCF_biosynth               MoCF_biosynth.HMM  Probable molybdopterin binding domain
SM00853       MutL_C                      MutL_C.HMM  MutL C terminal dimerisation domain
SM00854      PGA_cap                     PGA_cap.HMM  Bacterial capsule synthesis protein PGA_cap
SM00855         PGAM                        PGAM.HMM  Phosphoglycerate mutase family
SM00856         PMEI                        PMEI.HMM  Plant invertase/pectin methylesterase inhibitor
SM00857    Resolvase                   Resolvase.HMM   Resolvase, N terminal domain
SM00858          SAF                         SAF.HMM  
SM00859 Semialdhyde_dh              Semialdhyde_dh.HMM  Semialdehyde dehydrogenase, NAD binding domain
SM00860    SMI1_KNR4                   SMI1_KNR4.HMM  SMI1 / KNR4 family
SM00861 Transket_pyr                Transket_pyr.HMM  Transketolase, pyrimidine binding domain
SM00862  Trans_reg_C                 Trans_reg_C.HMM  Transcriptional regulatory protein, C terminal
SM00863     tRNA_SAD                    tRNA_SAD.HMM  Threonyl and Alanyl tRNA synthetase second additional domain
SM00864      Tubulin                     Tubulin.HMM  Tubulin/FtsZ family, GTPase domain
SM00865    Tubulin_C                   Tubulin_C.HMM  Tubulin/FtsZ family, C-terminal domain
SM00866         UTRA                        UTRA.HMM  
SM00867         YceI                        YceI.HMM  YceI-like domain 
SM00868        zf-AD                       zf-AD.HMM  Zinc-finger associated domain (zf-AD)
SM00869 Autotransporter             Autotransporter.HMM  Autotransporter beta-domain
SM00870 Asparaginase                Asparaginase.HMM  
SM00871  AraC_E_bind                 AraC_E_bind.HMM  Bacterial transcription activator, effector binding domain
SM00872 Alpha-mann_mid              Alpha-mann_mid.HMM  Alpha mannosidase, middle domain
SM00873         B3_4                        B3_4.HMM  B3/4 domain
SM00874           B5                          B5.HMM  tRNA synthetase B5 domain
SM00875         BACK                        BACK.HMM  BTB And C-terminal Kelch
SM00876         BATS                        BATS.HMM  Biotin and Thiamin Synthesis associated domain
SM00877          BMC                         BMC.HMM  
SM00878 Biotin_carb_C               Biotin_carb_C.HMM  Biotin carboxylase C-terminal domain
SM00879         Brix                        Brix.HMM  
SM00880         CHAD                        CHAD.HMM  
SM00881  CoA_binding                 CoA_binding.HMM  CoA binding domain
SM00882    CoA_trans                   CoA_trans.HMM  Coenzyme A transferase
SM00883        Cpn10                       Cpn10.HMM  Chaperonin 10 Kd subunit
SM00884 Cullin_Nedd8                Cullin_Nedd8.HMM  Cullin protein neddylation domain
SM00885         D5_N                        D5_N.HMM  D5 N terminal like
SM00886         Dabb                        Dabb.HMM  Stress responsive A/B Barrel Domain
SM00887        EB_dh                       EB_dh.HMM  Ethylbenzene dehydrogenase
SM00888      EF1_GNE                     EF1_GNE.HMM  EF-1 guanine nucleotide exchange domain
SM00889       EFG_IV                      EFG_IV.HMM  Elongation factor G, domain IV
SM00890          EKR                         EKR.HMM  Domain of unknown function
SM00891        ERCC4                       ERCC4.HMM  ERCC4 domain
SM00892 Endonuclease_NS             Endonuclease_NS.HMM  DNA/RNA non-specific endonuclease
SM00893          ETF                         ETF.HMM  Electron transfer flavoprotein domain
SM00894    Excalibur                   Excalibur.HMM  Excalibur calcium-binding domain
SM00895          FCD                         FCD.HMM  
SM00896      FDX-ACB                     FDX-ACB.HMM  Ferredoxin-fold anticodon binding domain
SM00897         FIST                        FIST.HMM  FIST N domain
SM00898 Fapy_DNA_glyco              Fapy_DNA_glyco.HMM  Formamidopyrimidine-DNA glycosylase N-terminal domain
SM00899         FeoA                        FeoA.HMM  
SM00900     FMN_bind                    FMN_bind.HMM  
SM00901          FRG                         FRG.HMM  
SM00902   Fe_hyd_SSU                  Fe_hyd_SSU.HMM  Iron hydrogenase small subunit
SM00903 Flavin_Reduct               Flavin_Reduct.HMM  Flavin reductase like domain
SM00904  Flavokinase                 Flavokinase.HMM  Riboflavin kinase
SM00905         FolB                        FolB.HMM  Dihydroneopterin aldolase
SM00906 Fungal_trans                Fungal_trans.HMM  Fungal specific transcription factor domain
SM00907         GDNF                        GDNF.HMM  GDNF/GAS1 domain
SM00908 Gal-bind_lectin             Gal-bind_lectin.HMM  Galactoside-binding lectin
SM00909      Germane                     Germane.HMM  Sporulation and spore germination
SM00910        HIRAN                       HIRAN.HMM  
SM00911       HWE_HK                      HWE_HK.HMM  HWE histidine kinase
SM00912  Haemagg_act                 Haemagg_act.HMM  haemagglutination activity domain
SM00913        IBN_N                       IBN_N.HMM  Importin-beta N-terminal domain
SM00914        IDEAL                       IDEAL.HMM  
SM00915      Jacalin                     Jacalin.HMM  Jacalin-like lectin domain
SM00916 L51_S25_CI-B8               L51_S25_CI-B8.HMM  Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
SM00917   LeuA_dimer                  LeuA_dimer.HMM  LeuA allosteric (dimerisation) domain
SM00918 Lig_chan-Glu_bd             Lig_chan-Glu_bd.HMM  Ligated ion channel L-glutamate- and glycine-binding site
SM00919      Malic_M                     Malic_M.HMM  Malic enzyme, NAD binding domain
SM00920 MHC_II_alpha                MHC_II_alpha.HMM  Class II histocompatibility antigen, alpha domain
SM00921  MHC_II_beta                 MHC_II_beta.HMM  Class II histocompatibility antigen, beta domain
SM00922       MR_MLE                      MR_MLE.HMM  Mandelate racemase / muconate lactonizing enzyme, C-terminal domain
SM00923         MbtH                        MbtH.HMM  MbtH-like protein
SM00924       MgtE_N                      MgtE_N.HMM  MgtE intracellular N domain
SM00925         MltA                        MltA.HMM  MltA specific insert domain
SM00926 Molybdop_Fe4S4              Molybdop_Fe4S4.HMM  Molybdopterin oxidoreductase Fe4S4 domain
SM00927         MutH                        MutH.HMM  DNA mismatch repair enzyme MutH
SM00928  NADH_4Fe-4S                 NADH_4Fe-4S.HMM  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
SM00929 NADH-G_4Fe-4S_3             NADH-G_4Fe-4S_3.HMM  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
SM00930          NIL                         NIL.HMM  
SM00931        NOSIC                       NOSIC.HMM  NOSIC (NUC001) domain
SM00932        Nfu_N                       Nfu_N.HMM  Scaffold protein Nfu/NifU N terminal
SM00933         NurA                        NurA.HMM  
SM00934    OMPdecase                   OMPdecase.HMM  Orotidine 5'-phosphate decarboxylase / HUMPS family
SM00935         OmpH                        OmpH.HMM  Outer membrane protein (OmpH-like)
SM00936       PBP5_C                      PBP5_C.HMM  Penicillin-binding protein 5, C-terminal domain 
SM00937         PCRF                        PCRF.HMM  
SM00938         P-II                        P-II.HMM  Nitrogen regulatory protein P-II
SM00939       PepX_C                      PepX_C.HMM  X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain
SM00940       PepX_N                      PepX_N.HMM  X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal
SM00941       PYNP_C                      PYNP_C.HMM  Pyrimidine nucleoside phosphorylase C-terminal domain
SM00942      PriCT_1                     PriCT_1.HMM  Primase C terminal 1 (PriCT-1)
SM00943     Prim-Pol                    Prim-Pol.HMM  Bifunctional DNA primase/polymerase, N-terminal
SM00944 Pro-kuma_activ              Pro-kuma_activ.HMM  Pro-kumamolisin, activation domain
SM00945         ProQ                        ProQ.HMM  ProQ/FINO family
SM00946    ProRS-C_1                   ProRS-C_1.HMM  Prolyl-tRNA synthetase, C-terminal
SM00947       Pro_CA                      Pro_CA.HMM  Carbonic anhydrase
SM00948 Proteasome_A_N              Proteasome_A_N.HMM  Proteasome subunit A N-terminal signature  Add an annotation
SM00949          PAZ                         PAZ.HMM  
SM00950         Piwi                        Piwi.HMM  
SM00951          QLQ                         QLQ.HMM  
SM00952          RAP                         RAP.HMM  
SM00953          RES                         RES.HMM  
SM00954    RelA_SpoT                   RelA_SpoT.HMM  Region found in RelA / SpoT proteins
SM00955          RNB                         RNB.HMM  
SM00956          RQC                         RQC.HMM  
SM00957    SecA_DEAD                   SecA_DEAD.HMM  SecA DEAD-like domain
SM00958 SecA_PP_bind                SecA_PP_bind.HMM  SecA preprotein cross-linking domain
SM00959        Rho_N                       Rho_N.HMM  Rho termination factor, N-terminal domain
SM00960     Robl_LC7                    Robl_LC7.HMM  Roadblock/LC7 domain
SM00961 RuBisCO_small               RuBisCO_small.HMM  Ribulose bisphosphate carboxylase, small chain
SM00962        SRP54                       SRP54.HMM  SRP54-type protein, GTPase domain
SM00963      SRP54_N                     SRP54_N.HMM  SRP54-type protein, helical bundle domain
SM00964     STAT_int                    STAT_int.HMM  STAT protein, protein interaction domain
SM00965          STN                         STN.HMM  Secretin and TonB N terminus short domain
SM00966   SpoVT_AbrB                  SpoVT_AbrB.HMM  SpoVT / AbrB like domain 
SM00967 SpoU_sub_bind               SpoU_sub_bind.HMM  RNA 2'-O ribose methyltransferase substrate binding
SM00968    SMC_hinge                   SMC_hinge.HMM  SMC proteins Flexible Hinge Domain
SM00969     SOCS_box                    SOCS_box.HMM  
SM00970       s48_45                      s48_45.HMM  Sexual stage antigen s48/45 domain
SM00971     SATase_N                    SATase_N.HMM  Serine acetyltransferase, N-terminal
SM00972         SCPU                        SCPU.HMM  Spore Coat Protein U domain
SM00973        Sec63                       Sec63.HMM  Sec63 Brl domain  
SM00974     T5orf172                    T5orf172.HMM  
SM00975 Telomerase_RBD              Telomerase_RBD.HMM  Telomerase ribonucleoprotein complex - RNA binding domain
SM00976    Telo_bind                   Telo_bind.HMM  Telomeric single stranded DNA binding POT1/CDC13
SM00977       TilS_C                      TilS_C.HMM  TilS substrate C-terminal domain
SM00978        Tim44                       Tim44.HMM  
SM00979         TIFY                        TIFY.HMM  
SM00980         THAP                        THAP.HMM  
SM00981        THUMP                       THUMP.HMM  
SM00982         TRCF                        TRCF.HMM  
SM00983 TPK_B1_binding              TPK_B1_binding.HMM  Thiamin pyrophosphokinase, vitamin B1 binding domain
SM00984 UDPG_MGDP_dh_C              UDPG_MGDP_dh_C.HMM  UDP binding domain
SM00985     UBA_e1_C                    UBA_e1_C.HMM  Ubiquitin-activating enzyme e1 C-terminal domain
SM00986          UDG                         UDG.HMM  Uracil DNA glycosylase superfamily
SM00987       UreE_C                      UreE_C.HMM  UreE urease accessory protein, C-terminal domain 
SM00988       UreE_N                      UreE_N.HMM  UreE urease accessory protein, N-terminal domain
SM00989          V4R                         V4R.HMM  
SM00990      VRR_NUC                     VRR_NUC.HMM  
SM00991     WHEP-TRS                    WHEP-TRS.HMM  
SM00992    YccV-like                   YccV-like.HMM  Hemimethylated DNA-binding protein YccV like
SM00993        YL1_C                       YL1_C.HMM  YL1 nuclear protein C-terminal domain
SM00994   zf-C4_ClpX                  zf-C4_ClpX.HMM  ClpX C4-type zinc finger
SM00995           AD                          AD.HMM  Anticodon-binding domain
SM00996    AdoHcyase                   AdoHcyase.HMM  S-adenosyl-L-homocysteine hydrolase
SM00997 AdoHcyase_NAD               AdoHcyase_NAD.HMM  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
SM00998       ADSL_C                      ADSL_C.HMM  Adenylosuccinate lyase C-terminus
SM00999    Aerolysin                   Aerolysin.HMM  Aerolysin toxin
SM01000       Aha1_N                      Aha1_N.HMM  Activator of Hsp90 ATPase, N-terminal
SM01001         AIRC                        AIRC.HMM  AIR carboxylase
SM01002  AlaDh_PNT_C                 AlaDh_PNT_C.HMM  Alanine dehydrogenase/PNT, C-terminal domain
SM01003  AlaDh_PNT_N                 AlaDh_PNT_N.HMM  Alanine dehydrogenase/PNT, N-terminal domain
SM01004         ALAD                        ALAD.HMM  Delta-aminolevulinic acid dehydratase
SM01005 Ala_racemase_C              Ala_racemase_C.HMM  Alanine racemase, C-terminal domain
SM01006         AlcB                        AlcB.HMM  Siderophore biosynthesis protein domain
SM01007  Aldolase_II                 Aldolase_II.HMM  Class II Aldolase and Adducin N-terminal domain
SM01008 Ald_Xan_dh_C                Ald_Xan_dh_C.HMM  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
SM01009       AlkA_N                      AlkA_N.HMM  AlkA N-terminal domain
SM01010       AMPKBI                      AMPKBI.HMM  5'-AMP-activated protein kinase beta subunit, interation domain
SM01011        AMP_N                       AMP_N.HMM  Aminopeptidase P, N-terminal domain
SM01012        ANTAR                       ANTAR.HMM  
SM01013         APC2                        APC2.HMM  Anaphase promoting complex (APC) subunit 2
SM01014         ARID                        ARID.HMM  ARID/BRIGHT DNA binding domain
SM01015     Arfaptin                    Arfaptin.HMM  Arfaptin-like domain
SM01016 Arg_tRNA_synt_N             Arg_tRNA_synt_N.HMM  Arginyl tRNA synthetase N terminal dom
SM01017   Arrestin_C                  Arrestin_C.HMM  Arrestin (or S-antigen), C-terminal domain
SM01018 B12-binding_2               B12-binding_2.HMM  B12 binding domain
SM01019           B3                          B3.HMM  B3 DNA binding domain
SM01020 B2-adapt-app_C              B2-adapt-app_C.HMM  Beta2-adaptin appendage, C-terminal sub-domain
SM01021 Bac_rhodopsin               Bac_rhodopsin.HMM  Bacteriorhodopsin-like protein
SM01022         ASCH                        ASCH.HMM  
SM01023          BAF                         BAF.HMM  Barrier to autointegration factor
SM01024       BCS1_N                      BCS1_N.HMM  
SM01025          BEN                         BEN.HMM  
SM01026        Beach                       Beach.HMM  Beige/BEACH domain
SM01027    Beta-Casp                   Beta-Casp.HMM  Beta-Casp domain
SM01028  Beta-TrCP_D                 Beta-TrCP_D.HMM  D domain of beta-TrCP
SM01029 BetaGal_dom2                BetaGal_dom2.HMM  Beta-galactosidase, domain 2
SM01030        BHD_1                       BHD_1.HMM  Rad4 beta-hairpin domain 1
SM01031        BHD_2                       BHD_2.HMM  Rad4 beta-hairpin domain 2
SM01032        BHD_3                       BHD_3.HMM  Rad4 beta-hairpin domain 3
SM01033      BING4CT                     BING4CT.HMM  BING4CT (NUC141) domain
SM01034         BLUF                        BLUF.HMM  Sensors of blue-light using FAD
SM01035       BOP1NT                      BOP1NT.HMM  BOP1NT (NUC169) domain
SM01036       BP28CT                      BP28CT.HMM  BP28CT (NUC211) domain
SM01037      Bet_v_1                     Bet_v_1.HMM  Pathogenesis-related protein Bet v I family
SM01038 Bgal_small_N                Bgal_small_N.HMM  Beta galactosidase small chain
SM01039      BRICHOS                     BRICHOS.HMM  
SM01040        Bro-N                       Bro-N.HMM  BRO family, N-terminal domain
SM01041         BRO1                        BRO1.HMM  BRO1-like domain
SM01042 Brr6_like_C_C               Brr6_like_C_C.HMM  Di-sulfide bridge nucleocytoplasmic transport domain
SM01043         BTAD                        BTAD.HMM  Bacterial transcriptional activator domain
SM01044          Btz                         Btz.HMM  CASC3/Barentsz eIF4AIII binding
SM01045         BURP                        BURP.HMM  
SM01046 c-SKI_SMAD_bind             c-SKI_SMAD_bind.HMM  c-SKI Smad4 binding domain
SM01047         C1_4                        C1_4.HMM  TFIIH C1-like domain
SM01048           C6                          C6.HMM  
SM01049      Cache_2                     Cache_2.HMM  
SM01050 CactinC_cactus              CactinC_cactus.HMM  Cactus-binding C-terminus of cactin protein
SM01051   CAMSAP_CKK                  CAMSAP_CKK.HMM  Microtubule-binding calmodulin-regulated spectrin-associated
SM01052      CAP_GLY                     CAP_GLY.HMM  
SM01053        CaMBD                       CaMBD.HMM  Calmodulin binding domain
SM01054  CaM_binding                 CaM_binding.HMM  Plant calmodulin-binding domain
SM01055 Cadherin_pro                Cadherin_pro.HMM  Cadherin prodomain like
SM01056 Candida_ALS_N               Candida_ALS_N.HMM  Cell-wall agglutinin N-terminal ligand-sugar binding
SM01057 Carb_anhydrase              Carb_anhydrase.HMM  Eukaryotic-type carbonic anhydrase
SM01058    CarD_TRCF                   CarD_TRCF.HMM  CarD-like/TRCF domain
SM01059          CAT                         CAT.HMM  Chloramphenicol acetyltransferase
SM01060     Catalase                    Catalase.HMM  
SM01061      CAT_RBD                     CAT_RBD.HMM  CAT RNA binding domain
SM01062   Ca_chan_IQ                  Ca_chan_IQ.HMM  Voltage gated calcium channel IQ domain
SM01063        CBM49                       CBM49.HMM  Carbohydrate binding domain CBM49
SM01064       CBM_10                      CBM_10.HMM  Cellulose or protein binding domain
SM01065        CBM_2                       CBM_2.HMM  Starch binding domain
SM01066       CBM_25                      CBM_25.HMM  Carbohydrate binding domain
SM01067        CBM_3                       CBM_3.HMM  Cellulose binding domain
SM01068        CBM_X                       CBM_X.HMM  Putative carbohydrate binding domain
SM01069      CDC37_C                     CDC37_C.HMM  Cdc37 C terminal domain
SM01070      CDC37_M                     CDC37_M.HMM  Cdc37 Hsp90 binding domain
SM01071      CDC37_N                     CDC37_N.HMM  Cdc37 N terminal kinase binding
SM01072      CDC48_2                     CDC48_2.HMM  Cell division protein 48 (CDC48) domain 2
SM01073      CDC48_N                     CDC48_N.HMM  Cell division protein 48 (CDC48) N-terminal domain
SM01074       Cdc6_C                      Cdc6_C.HMM  CDC6, C terminal
SM01075         CDT1                        CDT1.HMM  DNA replication factor CDT1 like
SM01076         CG-1                        CG-1.HMM  
SM01077     Cg6151-P                    Cg6151-P.HMM  Uncharacterized conserved protein CG6151-P
SM01078         CGGC                        CGGC.HMM  
SM01079        CHASE                       CHASE.HMM  
SM01080       CHASE2                      CHASE2.HMM  
SM01081      CHB_HEX                     CHB_HEX.HMM  Putative carbohydrate binding domain
SM01082          CHZ                         CHZ.HMM  Histone chaperone domain CHZ
SM01083        Cir_N                       Cir_N.HMM  N-terminal domain of CBF1 interacting co-repressor CIR
SM01084          CKS                         CKS.HMM  Cyclin-dependent kinase regulatory subunit
SM01085   CK_II_beta                  CK_II_beta.HMM  Casein kinase II regulatory subunit
SM01086 ClpB_D2-small               ClpB_D2-small.HMM  C-terminal, D2-small domain, of ClpB protein
SM01087         COG6                        COG6.HMM  Conserved oligomeric complex COG6
SM01088 Col_cuticle_N               Col_cuticle_N.HMM  Nematode cuticle collagen N-terminal domain
SM01089 Connexin_CCC                Connexin_CCC.HMM  Gap junction channel protein cysteine-rich domain
SM01090  Copper-fist                 Copper-fist.HMM  
SM01091    CorC_HlyC                   CorC_HlyC.HMM  Transporter associated domain
SM01092 CO_deh_flav_C               CO_deh_flav_C.HMM  CO dehydrogenase flavoprotein C-terminal domain
SM01093         CP12                        CP12.HMM  
SM01094         CpcD                        CpcD.HMM  CpcD/allophycocyanin linker domain
SM01095        Cpl-7                       Cpl-7.HMM  Cpl-7 lysozyme C-terminal domain
SM01096  CPSase_L_D3                 CPSase_L_D3.HMM  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
SM01097 CPSase_sm_chain             CPSase_sm_chain.HMM  Carbamoyl-phosphate synthase small chain, CPSase domain
SM01098 CPSF73-100_C                CPSF73-100_C.HMM  
SM01099      CPW_WPC                     CPW_WPC.HMM  
SM01100  CRAL_TRIO_N                 CRAL_TRIO_N.HMM  CRAL/TRIO, N-terminal domain
SM01101 CRISPR_assoc                CRISPR_assoc.HMM  
SM01102       CRM1_C                      CRM1_C.HMM  CRM1 C terminal
SM01103    CRS1_YhbY                   CRS1_YhbY.HMM  
SM01104          CTD                         CTD.HMM  Spt5 C-terminal nonapeptide repeat binding Spt4
