Query psy3691
Match_columns 137
No_of_seqs 202 out of 1326
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 23:08:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00431 CUB: CUB domain CUB d 99.9 8.6E-24 1.9E-28 137.8 11.8 100 1-102 5-110 (110)
2 cd00041 CUB CUB domain; extrac 99.9 5.7E-23 1.2E-27 134.4 12.7 97 5-103 10-112 (113)
3 smart00042 CUB Domain first fo 99.9 3E-22 6.5E-27 129.4 12.6 95 6-102 1-102 (102)
4 KOG4586|consensus 99.8 2E-18 4.4E-23 114.6 6.2 98 5-104 49-153 (156)
5 KOG4292|consensus 98.8 1.6E-08 3.6E-13 80.0 6.9 76 4-81 299-380 (454)
6 PF05428 CRF-BP: Corticotropin 97.5 0.001 2.3E-08 50.5 9.3 85 16-104 76-176 (311)
7 PF02408 CUB_2: CUB-like domai 97.1 0.0092 2E-07 39.7 8.9 41 14-58 37-77 (120)
8 KOG4292|consensus 95.7 0.0098 2.1E-07 47.8 2.9 100 6-107 36-163 (454)
9 PF05547 Peptidase_M6: Immune 55.5 36 0.00079 29.2 5.7 29 24-54 359-388 (645)
10 PF07888 CALCOCO1: Calcium bin 40.8 1.5E+02 0.0032 25.1 6.9 33 5-37 5-42 (546)
11 PF05428 CRF-BP: Corticotropin 36.6 1.9E+02 0.0041 22.6 6.5 76 14-90 198-288 (311)
12 KOG3147|consensus 36.1 48 0.001 25.0 3.2 40 3-42 151-194 (252)
13 smart00166 UBX Domain present 23.4 1.6E+02 0.0034 17.5 3.5 31 19-51 3-34 (80)
14 PF12970 DUF3858: Domain of Un 22.6 66 0.0014 21.4 1.7 23 14-38 32-54 (116)
15 KOG4088|consensus 21.5 2.9E+02 0.0063 19.2 5.5 59 36-102 40-100 (167)
No 1
>PF00431 CUB: CUB domain CUB domain entry Spermadhesins family entry Link to schematic domain picture by Peer Bork. ; InterPro: IPR000859 The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found almost exclusively in extracellular and plasma membrane-associated proteins, many of which are developmentally regulated [, ]. These proteins are involved in a diverse range of functions, including complement activation, developmental patterning, tissue repair, axon guidance and angiogenesis, cell signalling, fertilisation, haemostasis, inflammation, neurotransmission, receptor-mediated endocytosis, and tumour suppression [, ]. Many CUB-containing proteins are peptidases belonging to MEROPS peptidase families M12A (astacin) and S1A (chymotrypsin). Proteins containing a CUB domain include: Mammalian complement subcomponents C1s/C1r, which form the calcium-dependent complex C1, the first component of the classical pathway of the complement system. Cricetidae sp. (Hamster) serine protease Casp, which degrades type I and IV collagen and fibronectin in the presence of calcium. Mammalian complement-activating component of Ra-reactive factor (RARF), a protease that cleaves the C4 component of complement. Vertebrate enteropeptidase (3.4.21.9 from EC), a type II membrane protein of the intestinal brush border, which activates trypsinogen. Vertebrate bone morphogenic protein 1 (BMP-1), a protein which induces cartilage and bone formation and expresses metalloendopeptidase activity. Sea urchin blastula proteins BP10 and SpAN. Caenorhabditis elegans hypothetical proteins F42A10.8 and R151.5. Neuropilin (A5 antigen), a calcium-independent cell adhesion molecule that functions during the formation of certain neuronal circuits. Fibropellins I and III from Strongylocentrotus purpuratus (Purple sea urchin). Mammalian hyaluronate-binding protein TSG-6 (or PS4), a serum and growth factor induced protein. Mammalian spermadhesins. Xenopus laevis embryonic protein UVS.2, which is expressed during dorsoanterior development. Several of the above proteins consist of a catalytic domain together with several CUB domains interspersed by calcium-binding EGF domains. Some CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding partners. For example, in the complement proteases, the CUB domains mediate dimerisation and binding to collagen-like regions of target proteins (e.g. C1q for C1r/C1s). The structure of CUB domains consists of a beta-sandwich with a jelly-roll fold. Almost all CUB domains contain four conserved cysteines that probably form two disulphide bridges (C1-C2, C3-C4). The CUB1 domains of C1s and Map19 have calcium-binding sites [].; PDB: 1SFP_A 3KQ4_B 2WNO_A 2QQK_A 2QQL_A 2QQO_B 2QQM_A 3POJ_A 3POB_A 3POG_B ....
Probab=99.91 E-value=8.6e-24 Score=137.82 Aligned_cols=100 Identities=32% Similarity=0.514 Sum_probs=90.4
Q ss_pred CCCCcEEEEe--CCCCCCCCCeeEEEEEeCCCCCcEEEEEeCeEEee----eeceEEEEecCCCCCCceeEEeeCCccCC
Q psy3691 1 LSDKSGIIID--GPGNYSIDVKCSWLIDASDTPNATIRLHFNSFATE----CGWDHLYIFDGDSVHAPLLGVFSGLMYEG 74 (137)
Q Consensus 1 lt~~~G~i~s--yP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~le----c~~D~l~I~dg~~~~~~~l~~~cG~~~p~ 74 (137)
+++.+|.|++ ||..|+.+.+|.|.|++++ +++|+|+|..|+++ |..|+|+|++|.......++++||...|.
T Consensus 5 ~~~~~g~i~Sp~yp~~y~~~~~C~w~i~~~~--~~~I~l~f~~~~~~~~~~c~~d~l~v~~g~~~~~~~~~~~cg~~~~~ 82 (110)
T PF00431_consen 5 LTNNSGIISSPNYPSNYPSNSDCTWTITAPP--GHRIRLTFLSFDLESSDSCCQDYLEVYDGNDESSPLLGRFCGSSPPP 82 (110)
T ss_dssp ECSSEEEEESTTTTS-SSSSEEEEEEEE-ST--TEEEEEEEEEEEB--TTTSTSSEEEEESSSSTTSEEEEEESSSSCCE
T ss_pred EECCeEEEECCCCCCCCCCCCcEeEEEEecc--cceeeeccccccceeeeeecccceeEEeeccccceeeeeccCCcCCc
Confidence 3678899996 9999999999999999998 99999999999998 88999999999988888999999987788
Q ss_pred CeEEeCCeEEEEEEcCCCcCCCCeEEEE
Q psy3691 75 DYSIHRVPDVKCFTITNELGNTGIQIVL 102 (137)
Q Consensus 75 ~~~s~~~~~~v~f~sd~~~~~~GF~~~y 102 (137)
.+.+.++.++|.|.++......||+++|
T Consensus 83 ~i~s~~~~l~i~f~s~~~~~~~gF~~~y 110 (110)
T PF00431_consen 83 SIISSSNSLFIRFHSDSSNSSRGFKATY 110 (110)
T ss_dssp EEEESSSEEEEEEEESSSSTTSEEEEEE
T ss_pred cEEECCCEEEEEEEECCCCCCccEEEEC
Confidence 8899999999999999999999999987
No 2
>cd00041 CUB CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
Probab=99.90 E-value=5.7e-23 Score=134.36 Aligned_cols=97 Identities=32% Similarity=0.552 Sum_probs=90.2
Q ss_pred cEEEEe--CCCCCCCCCeeEEEEEeCCCCCcEEEEEeCeEEee----eeceEEEEecCCCCCCceeEEeeCCccCCCeEE
Q psy3691 5 SGIIID--GPGNYSIDVKCSWLIDASDTPNATIRLHFNSFATE----CGWDHLYIFDGDSVHAPLLGVFSGLMYEGDYSI 78 (137)
Q Consensus 5 ~G~i~s--yP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~le----c~~D~l~I~dg~~~~~~~l~~~cG~~~p~~~~s 78 (137)
.|.|+| ||..|+++.+|.|.|+++. |.+|.|+|.+|+++ |..|+|+||||.......++++||...|..+.+
T Consensus 10 ~g~i~Sp~~p~~~~~~~~C~w~i~~~~--g~~i~l~f~~~~l~~~~~C~~d~l~i~~g~~~~~~~~~~~Cg~~~~~~~~s 87 (113)
T cd00041 10 SGTISSPNYPNNYPNNLNCVWTIEAPP--GYRIRLTFEDFDLESSPNCSYDYLEIYDGPSTSSPLLGRFCGSTLPPPIIS 87 (113)
T ss_pred CeEEECCCCCCCCCCCCcEEEEEEcCC--CCEEEEEEeCcccccCCCCCCcEEEEEcCCCCccccceeeECCCCCCCEEe
Confidence 899996 9999999999999999998 99999999999998 999999999998766678899999988888888
Q ss_pred eCCeEEEEEEcCCCcCCCCeEEEEE
Q psy3691 79 HRVPDVKCFTITNELGNTGIQIVLG 103 (137)
Q Consensus 79 ~~~~~~v~f~sd~~~~~~GF~~~y~ 103 (137)
.++.+.+.|.++....+.||++.|+
T Consensus 88 ~~~~~~i~f~s~~~~~~~GF~~~y~ 112 (113)
T cd00041 88 SGNSLTVRFRSDSSVTGRGFKATYS 112 (113)
T ss_pred cCCEEEEEEEeCCCCCCCCEEEEEE
Confidence 8899999999998889999999997
No 3
>smart00042 CUB Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
Probab=99.89 E-value=3e-22 Score=129.35 Aligned_cols=95 Identities=29% Similarity=0.518 Sum_probs=83.6
Q ss_pred EEEEe--CCCCCCCCCeeEEEEEeCCCCCcEEEEEeCeEEee----eeceEEEEecCCCCCCceeEEeeCCccCCC-eEE
Q psy3691 6 GIIID--GPGNYSIDVKCSWLIDASDTPNATIRLHFNSFATE----CGWDHLYIFDGDSVHAPLLGVFSGLMYEGD-YSI 78 (137)
Q Consensus 6 G~i~s--yP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~le----c~~D~l~I~dg~~~~~~~l~~~cG~~~p~~-~~s 78 (137)
|.|+| ||..||++.+|.|.|++++ |.+|+|+|..|+++ |..|+|+|++|.......++++||...|.. +.+
T Consensus 1 G~i~Sp~yP~~y~~~~~C~w~i~~~~--g~~i~l~f~~~~l~~~~~C~~d~l~i~~g~~~~~~~~~~~Cg~~~~~~~~~s 78 (102)
T smart00042 1 GTITSPNYPQSYPNNLDCVWTIRAPP--GYRIELQFTDFDLESSDNCEYDYVEIYDGPSASSPLLGRFCGSELPPPVISS 78 (102)
T ss_pred CEEeCCCCCcCCCCCCcEEEEEECCC--CeEEEEEEEEEeccCCCCeeEeEEEEEeCCCCCCceeEEEecCcCCCCeEEc
Confidence 67875 9999999999999999998 99999999999995 889999999998766677899999886554 566
Q ss_pred eCCeEEEEEEcCCCcCCCCeEEEE
Q psy3691 79 HRVPDVKCFTITNELGNTGIQIVL 102 (137)
Q Consensus 79 ~~~~~~v~f~sd~~~~~~GF~~~y 102 (137)
.++.+.+.|.++......||+++|
T Consensus 79 ~~n~~~i~f~s~~~~~~~GF~~~y 102 (102)
T smart00042 79 SSNSLTVTFVSDSSVQKRGFSARY 102 (102)
T ss_pred CCCEEEEEEEeCCCCCCCCeEEEC
Confidence 688899999999888889999986
No 4
>KOG4586|consensus
Probab=99.75 E-value=2e-18 Score=114.57 Aligned_cols=98 Identities=19% Similarity=0.291 Sum_probs=89.1
Q ss_pred cEEEE--eCCCCCCCCCeeEEEEEeCCCCCcEEEEEeC-eEEe----eeeceEEEEecCCCCCCceeEEeeCCccCCCeE
Q psy3691 5 SGIII--DGPGNYSIDVKCSWLIDASDTPNATIRLHFN-SFAT----ECGWDHLYIFDGDSVHAPLLGVFSGLMYEGDYS 77 (137)
Q Consensus 5 ~G~i~--syP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~-~f~l----ec~~D~l~I~dg~~~~~~~l~~~cG~~~p~~~~ 77 (137)
.+.++ |||+.||++.+|...|.+.. -+-|.+.|+ .|.+ ||..|++||.||+-..++++++|||...|+.+.
T Consensus 49 ~~Iftspn~ps~ypp~r~cv~vi~~~p--~~~ve~~Fde~y~IEps~EC~fD~iEvrDGpfGFSPlI~rfCG~~nPp~Ir 126 (156)
T KOG4586|consen 49 FNIFTSPNFPSRYPPNRDCVRVIHSRP--QHDVEVKFDEVYHIEPSYECPFDFIEVRDGPFGFSPLIARFCGDRNPPEIR 126 (156)
T ss_pred cceEecCCccccCCCCcceEEeEeccc--ccceEEeeeeeEEecccccCCCCcccccCCCcCccHHHHHHhccCCChhhe
Confidence 34555 49999999999999999986 788999997 5776 599999999999999999999999999999999
Q ss_pred EeCCeEEEEEEcCCCcCCCCeEEEEEe
Q psy3691 78 IHRVPDVKCFTITNELGNTGIQIVLGN 104 (137)
Q Consensus 78 s~~~~~~v~f~sd~~~~~~GF~~~y~~ 104 (137)
+.+..+|+.|.+|++....||.++|.-
T Consensus 127 s~grFlWIkF~sD~ele~~gfsa~y~~ 153 (156)
T KOG4586|consen 127 SVGRFLWIKFRSDSELEYQGFSAEYAI 153 (156)
T ss_pred ecCcEEEEEEcccchhhhcccceeeec
Confidence 999999999999999999999999963
No 5
>KOG4292|consensus
Probab=98.79 E-value=1.6e-08 Score=80.01 Aligned_cols=76 Identities=26% Similarity=0.399 Sum_probs=60.6
Q ss_pred CcEEEEe--CCCCCCCCCeeEEEEEeCCCCCcEEEEEeCeEEe----eeeceEEEEecCCCCCCceeEEeeCCccCCCeE
Q psy3691 4 KSGIIID--GPGNYSIDVKCSWLIDASDTPNATIRLHFNSFAT----ECGWDHLYIFDGDSVHAPLLGVFSGLMYEGDYS 77 (137)
Q Consensus 4 ~~G~i~s--yP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~l----ec~~D~l~I~dg~~~~~~~l~~~cG~~~p~~~~ 77 (137)
..|.+++ ||..|+++.+|+|++.++. ++.|.+.|+.|.+ +|.+||+....|+.....++++.|+...+....
T Consensus 299 ~~G~~~Sp~yp~~y~~~l~Ct~~l~~~~--g~~l~v~fh~~~~~~s~~C~~d~l~~r~~~~~~~~l~g~~~~~ls~~~~s 376 (454)
T KOG4292|consen 299 KFGNLTSPGYPQNYPNNLDCTTHLTVPG--GHTLVVFFHEFSIENSRECINDYLVLRNGNSGNGPLLGPHGAGLSPELVS 376 (454)
T ss_pred ceeEEcCCCCcccCCCCCcceEEEEcCC--CCEEEEEeecccchhhhhhccceEEeccCCCCCCCccCcccCCCCccccc
Confidence 4688885 9999999999999999999 9999999888854 599999999999888888888844444444344
Q ss_pred EeCC
Q psy3691 78 IHRV 81 (137)
Q Consensus 78 s~~~ 81 (137)
+.+.
T Consensus 377 s~s~ 380 (454)
T KOG4292|consen 377 SASL 380 (454)
T ss_pred cccc
Confidence 4333
No 6
>PF05428 CRF-BP: Corticotropin-releasing factor binding protein (CRF-BP); InterPro: IPR008435 This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development [].
Probab=97.54 E-value=0.001 Score=50.52 Aligned_cols=85 Identities=16% Similarity=0.255 Sum_probs=63.4
Q ss_pred CCCCeeEEEEEeCCCCCcEEEEEeCeEEeeee-ceEEEEecCCCCCCc--------------eeEEeeCCccCC-CeEEe
Q psy3691 16 SIDVKCSWLIDASDTPNATIRLHFNSFATECG-WDHLYIFDGDSVHAP--------------LLGVFSGLMYEG-DYSIH 79 (137)
Q Consensus 16 p~~~~C~W~I~~~~~pg~~I~L~F~~f~lec~-~D~l~I~dg~~~~~~--------------~l~~~cG~~~p~-~~~s~ 79 (137)
.+...|-=.+.+.. +..|.++|..+|+.|. .|+|.|+||..-++. ....||+..... .+.|+
T Consensus 76 ~pq~~Ca~y~iaeP--d~~IeI~~~~vdidC~~G~ll~v~DGW~LnGe~FPs~~DHplpl~eR~~efC~~~~~~~~~rSS 153 (311)
T PF05428_consen 76 RPQLVCAAYFIAEP--DELIEIEFDHVDIDCEGGDLLKVFDGWELNGEKFPSSQDHPLPLEERYTEFCDSGPNRRSFRSS 153 (311)
T ss_pred CCCceeEEEEEeCC--CeEEEEEEEEeeccCCCCCEEEEEeceEECccCCcCcccCCCchHHHHHHhccCCCCcceeEec
Confidence 45778876666664 8999999999999999 799999999542221 124589985543 57888
Q ss_pred CCeEEEEEEcCCCcCCCCeEEEEEe
Q psy3691 80 RVPDVKCFTITNELGNTGIQIVLGN 104 (137)
Q Consensus 80 ~~~~~v~f~sd~~~~~~GF~~~y~~ 104 (137)
.|..+++|.-. ..++||.++.+.
T Consensus 154 QNvAmi~fRip--~~GsgFt~~vR~ 176 (311)
T PF05428_consen 154 QNVAMIQFRIP--SPGSGFTLTVRF 176 (311)
T ss_pred cceEEEEEEec--CCCCceEEEEEe
Confidence 99999999754 567788876653
No 7
>PF02408 CUB_2: CUB-like domain; InterPro: IPR003366 This domain is found in a family of hypothetical Caenorhabditis elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain (IPR000859 from INTERPRO). The aligned region is approximately 130 amino acids long and contains two conserved cysteine residues.
Probab=97.07 E-value=0.0092 Score=39.67 Aligned_cols=41 Identities=10% Similarity=0.318 Sum_probs=32.4
Q ss_pred CCCCCCeeEEEEEeCCCCCcEEEEEeCeEEeeeeceEEEEecCCC
Q psy3691 14 NYSIDVKCSWLIDASDTPNATIRLHFNSFATECGWDHLYIFDGDS 58 (137)
Q Consensus 14 ~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~lec~~D~l~I~dg~~ 58 (137)
.+|.+.+|.|.|.+|. |..++|++.. ++.- .|.+.|.|...
T Consensus 37 ~~p~n~~C~y~i~iP~--G~~a~v~~~~-~~~~-~d~i~v~D~~g 77 (120)
T PF02408_consen 37 QFPANQNCTYQINIPK--GYYAKVTLSA-NLND-NDSITVTDSNG 77 (120)
T ss_pred ccCCCCceEEEEEcCC--ceEEEEEEEE-ecCC-CCEEEEEecCC
Confidence 4789999999999998 9999998752 2222 79999998643
No 8
>KOG4292|consensus
Probab=95.67 E-value=0.0098 Score=47.80 Aligned_cols=100 Identities=21% Similarity=0.180 Sum_probs=77.4
Q ss_pred EEEEe--CCCCCCCCCeeEEEEEeCCCCCcEEEEEeCeEEe-------------------------e-eeceEEEEecCC
Q psy3691 6 GIIID--GPGNYSIDVKCSWLIDASDTPNATIRLHFNSFAT-------------------------E-CGWDHLYIFDGD 57 (137)
Q Consensus 6 G~i~s--yP~~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f~l-------------------------e-c~~D~l~I~dg~ 57 (137)
+.+.+ +|..|+...+|...|.-.. -..+.+.+..+++ . +....+.++.+.
T Consensus 36 ~~v~~~~~~~~~~ap~~~~~~~s~~~--~~~~~~~~v~~~~s~~~~~~~~~~d~~~~~~~~a~~s~a~~~~~~~~~~v~~ 113 (454)
T KOG4292|consen 36 GFVESPGYPGAVNAPLDCIFNISDAA--SNVIQLSFVSFDLSIKNLLSKQCLDSNLLVALVARHSRASPLDRLLGLYVGL 113 (454)
T ss_pred ccccCCCCcccccCCcccccCCCCcc--cceeeeehhhhhhhhhhhhhhhhhhccchhhhhcccCcCccchhhhcccccc
Confidence 44443 7888888888888887776 6788877776643 1 335566788888
Q ss_pred CCCCceeEEeeCCccCCCeEEeCCeEEEEEEcCCCcCCCCeEEEEEeeee
Q psy3691 58 SVHAPLLGVFSGLMYEGDYSIHRVPDVKCFTITNELGNTGIQIVLGNDFV 107 (137)
Q Consensus 58 ~~~~~~l~~~cG~~~p~~~~s~~~~~~v~f~sd~~~~~~GF~~~y~~~~~ 107 (137)
+.+..+.+++||...|..+.+..++..+.|.++-.....||...++.-+.
T Consensus 114 s~n~~l~~~~~~~t~p~~~es~~~~~~q~~~~~l~a~~~~~~~t~~~~~~ 163 (454)
T KOG4292|consen 114 SENANLAGTQCGSTVPGPFESSRGFLGQQFISDLLAEREGFSATPTYMDM 163 (454)
T ss_pred cccccccccccCCcCCccccccCCccceEEechhhccccccCCccccccC
Confidence 88888999999999999999988888888888877888888777765443
No 9
>PF05547 Peptidase_M6: Immune inhibitor A peptidase M6; InterPro: IPR008757 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M6 (immune inhibitor A family, clan MA(M)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. InhA of Bacillus thuringiensis (an entomopathogenic bacterium) specifically cleaves antibacterial peptides produced by insect hosts []. B. thuringiensis is highly resistant to the insect immune system due to its production of two factors, inhibitor A (InhA or InA) and inhibitor B (InhB or InB), which selectively block the humoral defence system developed by insects against Escherichia coli and Bacillus cereus []. B. thuringiensis is especially resistant to cecropins and attacins, which are the main classes of inducible antibacterial peptides in various lepidopterans and dipterans [], []. InhA has been shown to specifically hydrolyze cecropins and attacins in the immune hemolymph of Hyalophora cecropia (Cecropia moth) in vitro []. However, it has been suggested that the role of InhA in resistance to the humoral defence system is not consistent with the time course of InhA production []. B. thuringiensis has two proteins belonging to this group (InhA and InhA2), and it has been shown that InhA2 has a vital role in virulence when the host is infected via the oral route []. The B. cereus member has been found as an exosporium component from endospores []. B. thuringiensis InhA is induced at the onset of sporulation and is regulated by Spo0A and AbrB []. Vibrio cholerae PrtV is thought to be encoded in the pathogenicity island []. However, PrtV mutants did not exhibit a reduced virulence phenotype, and thus PrtV is not an indispensable virulence factor []. Annotation note: due to the presence of PKD repeats in some of the members of this group (e.g., V. cholerae VCA0223), spurious similarity hits may appear (involving unrelated proteins), which may lead to the erroneous transfer of functional annotations and protein names. Also, please note that related Bacillus subtilis Bacillopeptidase F (Bpr or Bpf) contains two different protease domains: N-terminal IPR000209 from INTERPRO (peptidase S8, subtilase, a subtilisin-like serine protease) and this C-terminal domain (peptidase M6), which may also complicate annotation.; GO: 0008233 peptidase activity, 0006508 proteolysis
Probab=55.46 E-value=36 Score=29.25 Aligned_cols=29 Identities=21% Similarity=0.403 Sum_probs=23.8
Q ss_pred EEEeCCCCCcEEEEEeC-eEEeeeeceEEEEe
Q psy3691 24 LIDASDTPNATIRLHFN-SFATECGWDHLYIF 54 (137)
Q Consensus 24 ~I~~~~~pg~~I~L~F~-~f~lec~~D~l~I~ 54 (137)
.|..|. +....|+|. .+++|-.+||+.|.
T Consensus 359 ~vdLp~--~s~AtLsfk~wydIE~dyDy~~Ve 388 (645)
T PF05547_consen 359 SVDLPA--ASSATLSFKAWYDIEADYDYAYVE 388 (645)
T ss_pred eeccCC--CCCeEEEeehheecccCCceEEEE
Confidence 667776 667899996 68999989998887
No 10
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=40.77 E-value=1.5e+02 Score=25.11 Aligned_cols=33 Identities=18% Similarity=0.347 Sum_probs=20.3
Q ss_pred cEEEE-eCCCCCCCC--CeeEEEEEeCC--CCCcEEEE
Q psy3691 5 SGIII-DGPGNYSID--VKCSWLIDASD--TPNATIRL 37 (137)
Q Consensus 5 ~G~i~-syP~~Yp~~--~~C~W~I~~~~--~pg~~I~L 37 (137)
..+|. |-+..|.++ ..|.|++...- ++...|.|
T Consensus 5 ~~ViF~nV~~~Y~P~~~v~C~Ytlt~~~~ps~~DWIGi 42 (546)
T PF07888_consen 5 SQVIFNNVAKSYIPGTDVECHYTLTPGFHPSSKDWIGI 42 (546)
T ss_pred CeEEEeccccccCCCCCeEEEEecCCCCCCCCCCeeEE
Confidence 34454 677788665 68999987532 12444554
No 11
>PF05428 CRF-BP: Corticotropin-releasing factor binding protein (CRF-BP); InterPro: IPR008435 This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development [].
Probab=36.65 E-value=1.9e+02 Score=22.55 Aligned_cols=76 Identities=16% Similarity=0.130 Sum_probs=42.7
Q ss_pred CCCCCCeeEEEEEeCCCCCcEEEEEeCeE---Ee------eee--ceEEEEecCCCCCCc---eeEEeeCCcc-CCCeEE
Q psy3691 14 NYSIDVKCSWLIDASDTPNATIRLHFNSF---AT------ECG--WDHLYIFDGDSVHAP---LLGVFSGLMY-EGDYSI 78 (137)
Q Consensus 14 ~Yp~~~~C~W~I~~~~~pg~~I~L~F~~f---~l------ec~--~D~l~I~dg~~~~~~---~l~~~cG~~~-p~~~~s 78 (137)
+|....+|...|.-|.. -..+.|..-.. .+ .|. .|||+|.-|...... .+..+||... |.....
T Consensus 198 n~gq~rNCSfs~iyP~~-i~i~~L~lG~~~~l~~~~~~~~~C~~~~D~Vei~Gg~GlD~skM~~~~~lCg~~~~p~~~~I 276 (311)
T PF05428_consen 198 NPGQRRNCSFSIIYPVV-ISISDLSLGHTNGLELQRGVIHGCQGSGDFVEIGGGNGLDTSKMFPVADLCGSFSGPAQMKI 276 (311)
T ss_pred CCCcccCcEEEEEeeeE-EEEEEEecccccCcccccccccCCCCcCCeEEECCcCCcCcccCEEhhHhhccCCCCceEEE
Confidence 44567789998888751 12222333221 11 254 599999887653333 3477999764 433444
Q ss_pred eCCeEEEEEEcC
Q psy3691 79 HRVPDVKCFTIT 90 (137)
Q Consensus 79 ~~~~~~v~f~sd 90 (137)
.-...+|...+.
T Consensus 277 ~Cd~TvVRLVSS 288 (311)
T PF05428_consen 277 GCDNTVVRLVSS 288 (311)
T ss_pred ecCCcEEEEEec
Confidence 444455555544
No 12
>KOG3147|consensus
Probab=36.12 E-value=48 Score=25.03 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=31.3
Q ss_pred CCcEEEEe-CCCCCCCCCeeEEEEEeCC---CCCcEEEEEeCeE
Q psy3691 3 DKSGIIID-GPGNYSIDVKCSWLIDASD---TPNATIRLHFNSF 42 (137)
Q Consensus 3 ~~~G~i~s-yP~~Yp~~~~C~W~I~~~~---~pg~~I~L~F~~f 42 (137)
++.|-+-| ||+.|+-+..=.|.+-... .|-.||.|++.-.
T Consensus 151 GpDGHtaSLFP~~~~l~e~~~wV~~itdSPkpPp~RITlTLPvI 194 (252)
T KOG3147|consen 151 GPDGHTASLFPGHPLLNEKLKWVVPITDSPKPPPKRITLTLPVI 194 (252)
T ss_pred CCCCCeeecCCCchhhhcccCEEEEeCCCCCCCCccEEEehHHh
Confidence 56788888 9999998888888887655 3678999887543
No 13
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=23.41 E-value=1.6e+02 Score=17.51 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=23.8
Q ss_pred CeeEEEEEeCCCCCcEEEEEeCeE-EeeeeceEE
Q psy3691 19 VKCSWLIDASDTPNATIRLHFNSF-ATECGWDHL 51 (137)
Q Consensus 19 ~~C~W~I~~~~~pg~~I~L~F~~f-~lec~~D~l 51 (137)
..|.-.|+.|. |.+|.-+|..= .++.-++||
T Consensus 3 ~~~~I~iRlPd--G~ri~~~F~~~~tl~~v~~~v 34 (80)
T smart00166 3 DQCRLQIRLPD--GSRLVRRFPSSDTLRTVYEFV 34 (80)
T ss_pred CeEEEEEEcCC--CCEEEEEeCCCCcHHHHHHHH
Confidence 46999999998 99999999743 345556666
No 14
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=22.56 E-value=66 Score=21.35 Aligned_cols=23 Identities=13% Similarity=0.312 Sum_probs=14.4
Q ss_pred CCCCCCeeEEEEEeCCCCCcEEEEE
Q psy3691 14 NYSIDVKCSWLIDASDTPNATIRLH 38 (137)
Q Consensus 14 ~Yp~~~~C~W~I~~~~~pg~~I~L~ 38 (137)
+|..+-.|.|+|+.|+ |.++.-.
T Consensus 32 P~~~~E~ytyti~~pe--gm~l~t~ 54 (116)
T PF12970_consen 32 PYLVDETYTYTIELPE--GMKLVTP 54 (116)
T ss_dssp SS-EEEEEEEEEEE-T--T-EE-S-
T ss_pred ccccCcceEEEEEcCC--CCeeecC
Confidence 3556778999999999 8876543
No 15
>KOG4088|consensus
Probab=21.47 E-value=2.9e+02 Score=19.16 Aligned_cols=59 Identities=14% Similarity=0.252 Sum_probs=29.2
Q ss_pred EEEe-CeEEeeeeceEEEEecCCCCCCceeEEeeCCccCCCeEEeCCeEEEEEEcCCCcCCCC-eEEEE
Q psy3691 36 RLHF-NSFATECGWDHLYIFDGDSVHAPLLGVFSGLMYEGDYSIHRVPDVKCFTITNELGNTG-IQIVL 102 (137)
Q Consensus 36 ~L~F-~~f~lec~~D~l~I~dg~~~~~~~l~~~cG~~~p~~~~s~~~~~~v~f~sd~~~~~~G-F~~~y 102 (137)
++.| .+|.|.|... ..+..+...+-|...|....-..+.--|.++-|....+.| |++++
T Consensus 40 ~t~fi~EftLqCsn~--------~~n~~l~Aev~Gk~~PVs~~~d~~kyQVSW~ldhK~a~agt~~vr~ 100 (167)
T KOG4088|consen 40 KTTFITEFTLQCSNN--------PKNIQLTAEVNGKLIPVSISDDTAKYQVSWTLDHKDAGAGTFNVRI 100 (167)
T ss_pred EEEEEEEEEEEeCCC--------CcceEEEEecCCEEEeEEecCccceEEEEEEEeecccCCceEEEEE
Confidence 3445 5889999732 1223334455565555433333334445555555444444 44443
Done!