Query 016132
Match_columns 394
No_of_seqs 180 out of 428
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 04:05:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016132.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016132hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1348 Asparaginyl peptidases 100.0 1E-132 2E-137 969.2 30.9 391 1-393 87-477 (477)
2 PF01650 Peptidase_C13: Peptid 100.0 1E-67 2.2E-72 508.9 18.9 215 1-230 42-256 (256)
3 KOG1349 Gpi-anchor transamidas 100.0 2.4E-51 5.2E-56 384.6 11.7 216 1-231 70-291 (309)
4 COG5206 GPI8 Glycosylphosphati 100.0 1.4E-41 3E-46 320.7 11.1 215 1-230 70-290 (382)
5 PF00656 Peptidase_C14: Caspas 98.4 3.2E-07 7E-12 86.2 5.6 143 36-202 43-230 (248)
6 smart00115 CASc Caspase, inter 96.4 0.021 4.5E-07 54.9 9.5 144 37-203 50-214 (241)
7 cd00032 CASc Caspase, interleu 96.0 0.046 1E-06 52.4 9.7 144 36-203 51-218 (243)
8 KOG1546 Metacaspase involved i 94.9 0.07 1.5E-06 53.4 6.7 60 65-127 135-211 (362)
9 PF14538 Raptor_N: Raptor N-te 88.0 0.75 1.6E-05 41.6 4.5 73 37-128 70-152 (154)
10 PF12770 CHAT: CHAT domain 85.2 0.8 1.7E-05 44.0 3.3 67 33-123 123-201 (287)
11 PF01364 Peptidase_C25: Peptid 72.3 4.7 0.0001 41.0 4.3 104 69-202 238-351 (378)
12 TIGR02855 spore_yabG sporulati 59.0 8.6 0.00019 38.0 3.0 101 14-136 104-222 (283)
13 COG4249 Uncharacterized protei 54.4 9.7 0.00021 39.4 2.7 62 68-130 133-207 (380)
14 PF05582 Peptidase_U57: YabG p 51.6 14 0.00029 36.8 3.1 102 13-136 104-223 (287)
15 PF12554 MOZART1: Mitotic-spin 48.7 28 0.00061 25.5 3.6 26 350-375 21-46 (48)
16 PRK10649 hypothetical protein; 25.2 40 0.00086 36.7 1.7 19 63-81 447-465 (577)
17 KOG1387 Glycosyltransferase [C 23.7 75 0.0016 32.9 3.2 37 30-75 78-115 (465)
18 COG2194 Predicted membrane-ass 20.8 56 0.0012 35.5 1.8 18 63-80 439-456 (555)
19 KOG1654 Microtubule-associated 20.1 96 0.0021 26.7 2.6 35 37-82 53-87 (116)
No 1
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-132 Score=969.24 Aligned_cols=391 Identities=65% Similarity=1.131 Sum_probs=380.2
Q ss_pred CCcccCCCCCCCCCCeEeeCCCCCcccCCccccCCCCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCC
Q 016132 1 MYDDIAFNEENPRPGVIINHPHGDDVYKGVPKDYTGEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGG 80 (394)
Q Consensus 1 mydDia~~~~Np~pG~i~~~~~g~~vy~g~~iDY~g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~ 80 (394)
||||||+||+||+||+|||+|+|+|||+||++||+|++|||+||++||+|++++++|||||||+|+|||||||||+||||
T Consensus 87 MYDDIA~~~~NPrpG~iiN~P~G~DvY~GvpkDYtg~~Vt~~Nf~aVllGd~savkGGsGKV~~SgpnDhiFiYytDHG~ 166 (477)
T KOG1348|consen 87 MYDDIANNEENPRPGVIINRPNGKDVYQGVPKDYTGEDVTPQNFLAVLLGDASAVKGGSGKVLKSGPNDHIFIYYTDHGG 166 (477)
T ss_pred EehhhhcCCCCCCCceeecCCCchhhhcCCCCcccCCcCCHHHHHHHHhcccccccCCCceeeccCCCceEEEEEecCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCCCCCCCCHHHHHHHHHHHHHcCCCceEEEeeecccccccccccCCCCCcEEEEeecCCCCccccccCCCCCCCC
Q 016132 81 PGVLGMPTSRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSIFEGLLPEGLNIYATTASNAEESSWGTYCPGEIPGP 160 (394)
Q Consensus 81 ~g~l~fp~~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~~~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~~~ 160 (394)
||+|.||+++.|+++||+++|++||+.++|++||||+|||||||||+++||+++||||+||||+.||||++|||+++|.|
T Consensus 167 pGvl~mP~~~~l~akdlnevL~kmhk~k~Y~~mvfYlEACESGSmfegiLp~~lnIYatTAaNa~ESSwgtycp~~~psp 246 (477)
T KOG1348|consen 167 PGVLGMPTSPDLYAKDLNEVLKKMHKSKTYKKMVFYLEACESGSMFEGILPKNLNIYATTAANARESSWGTYCPGEYPSP 246 (477)
T ss_pred CceEecCCCcchhHHHHHHHHHHHHhccchheEEEEeeeccCcchhhhhccCCCcEEEeecCCccccccceeCCCCCCCC
Confidence 99999999889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccchhhhHhhhhhccccccCCCCcccHHHHHHHHHhhhccCCCCCCCceeecCCCcccccchhhcccCCCCCCcccc
Q 016132 161 PPEYSTCLGDLYSIAWMEDSDIHNLRTETLHQQYELVKTRTASYNSYGSHVMQYGDIGLSKNNLFTYLGTNPANDNYTFV 240 (394)
Q Consensus 161 ~~~~~t~lgD~fs~~wme~~~~~~~~~~tl~~~f~~v~~~t~~~~t~~Shv~~yGd~~~~~~~~~~f~g~~~~~~~~~~~ 240 (394)
+.++.|||||+||++||||||.+|+++|||.+||+.||++|+.....|||||||||..|++++|..|||.+|+++++++.
T Consensus 247 pse~~tcLGDlySV~WmeDSd~hdL~kETL~qQYhlVK~rt~~s~s~gsHVmqyGd~~iske~l~lfqG~~pa~~nf~l~ 326 (477)
T KOG1348|consen 247 PSEYSTCLGDLYSVNWMEDSDVHDLKKETLHQQYHLVKKRTNTSYSYGSHVMQYGDKTISKEKLMLFQGMKPANENFTLP 326 (477)
T ss_pred hhhcccccccceeeeeeccCccccchHHHHHHHHHHHHHhcCCCCCCcceeeecCcchhhHHHHHHHcCCCcccCCCCCC
Confidence 99999999999999999999999999999999999999999998779999999999999999999999999999999886
Q ss_pred CCCCCCccCccccCcchhHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcccccccCCC
Q 016132 241 DENSLRPASKAVNQRDADLLHFWDKYRKAPEGTPRKAEAQKQFFEAMSHRMHVDHSIKLIGKLLFGIEKGPEILNTVRPA 320 (394)
Q Consensus 241 ~~~~l~~~~~~v~sRDa~L~~L~~k~~~~~~~~~~k~~a~~eL~~~l~~R~~id~~v~~I~~ll~g~~~~~~~l~~~r~~ 320 (394)
+.+..+++..||||||||++||+|++++++++.++.+++++|.++++||++||+++..|+.++||. ....+|+.+|+.
T Consensus 327 -~~s~~~~s~~~n~rD~~L~~l~~k~rka~dgs~~s~e~~k~i~~~~~hR~~id~sV~~I~~llf~~-~~~~~l~~vr~~ 404 (477)
T KOG1348|consen 327 -ASSHKSPSGLTNQRDAPLLHLWRKYRKANDGSAESRELQKEILRHKDHRKHIDKSVRLIVSLLFGS-EGEAVLNQVRSE 404 (477)
T ss_pred -ccCcCCccccCCCCCccHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-chHHHHHHhhcC
Confidence 445556778999999999999999999999999999999999999999999999999999999988 344688889999
Q ss_pred CCCCcCccchHHHHHHHHhhhcCCCchhhhhHHHHHHHHHccCCCHHHHHHHHHhhccCCCCCCCCCcccCCC
Q 016132 321 GQPLVDDWGCLKSLVRTFESHCGALSQYGMKHMRSLANICNTGIGKEKMAEASAQACENIPSGPWSSLDKGFS 393 (394)
Q Consensus 321 g~plv~d~dCyk~~V~~Fe~~Cg~l~eY~lk~~~~laNLC~~G~~~~~i~~Ai~~~C~~~~~~~~~~~~~~~~ 393 (394)
|+|+++||+|+|.+|++|++|||+++||||||||+|+||||.|++.++|.+|+.++|..+...+|+++.+|||
T Consensus 405 g~Plvddw~C~k~~v~~F~~hCg~~~~YglKh~~~~aN~Cn~g~~~e~~~~A~~~aC~~~~~~~~~~~~~gfs 477 (477)
T KOG1348|consen 405 GQPLVDDWDCLKSAVRHFETHCGSTYEYGLKHMRVLANMCNKGVPLEQIELAMDQACLGIYTEPWSSLRRGFS 477 (477)
T ss_pred CCCccchHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhcCccHHHHHHHHHhHhcCCccccchhhcccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=100.00 E-value=1e-67 Score=508.87 Aligned_cols=215 Identities=53% Similarity=0.889 Sum_probs=206.7
Q ss_pred CCcccCCCCCCCCCCeEeeCCCCCcccCCccccCCCCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCC
Q 016132 1 MYDDIAFNEENPRPGVIINHPHGDDVYKGVPKDYTGEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGG 80 (394)
Q Consensus 1 mydDia~~~~Np~pG~i~~~~~g~~vy~g~~iDY~g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~ 80 (394)
|||||||||+||+||+|||+|+|.|+|+||+|||+|.+||+++|++||+|+++ + +++|||+|+++|+|||||+||||
T Consensus 42 ~~dd~a~~~~Np~~g~i~~~~~~~n~y~~~~iDY~g~~v~~~~fl~vL~G~~~-~--~~~kvl~s~~~D~vfiy~~~HG~ 118 (256)
T PF01650_consen 42 MYDDIACNPRNPFPGKIFNDPDGTNVYKGVEIDYRGEDVTPENFLNVLTGDKS-V--PSGKVLNSTENDNVFIYFTGHGG 118 (256)
T ss_pred ecCCccchhhCCCCceEEeCCCcccccCCccccccccccCHHHHHHHhcCCCC-C--CccccccCCCCCeEEEEEeccCC
Confidence 79999999999999999999999999999999999999999999999999998 5 56899999999999999999999
Q ss_pred CCccCCCCCCCCCHHHHHHHHHHHHHcCCCceEEEeeecccccccccccCCCCCcEEEEeecCCCCccccccCCCCCCCC
Q 016132 81 PGVLGMPTSRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSIFEGLLPEGLNIYATTASNAEESSWGTYCPGEIPGP 160 (394)
Q Consensus 81 ~g~l~fp~~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~~~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~~~ 160 (394)
+|+|+||+.+.|+++||.++|++|+++++|+||||++|||||||||+. |++++||++||||+++|+||+|+|++
T Consensus 119 ~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs~~~~-L~~~~nv~~iTAa~~~e~Sy~~~~~~----- 192 (256)
T PF01650_consen 119 PGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYSGSFFEG-LLKSPNVYVITAANADESSYGCYCSD----- 192 (256)
T ss_pred CCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccccchhhc-cCCCCCEEEEecCCcccccccccccc-----
Confidence 999999988889999999999999999999999999999999999999 67889999999999999999999932
Q ss_pred CCCccchhhhHhhhhhccccccCCCCcccHHHHHHHHHhhhccCCCCCCCceeecCCCcccccchhhccc
Q 016132 161 PPEYSTCLGDLYSIAWMEDSDIHNLRTETLHQQYELVKTRTASYNSYGSHVMQYGDIGLSKNNLFTYLGT 230 (394)
Q Consensus 161 ~~~~~t~lgD~fs~~wme~~~~~~~~~~tl~~~f~~v~~~t~~~~t~~Shv~~yGd~~~~~~~~~~f~g~ 230 (394)
++++|||||+||.+||++++.++++.+||.+||+.||++|.. |||++|||.++.+++|++|||.
T Consensus 193 -~~~~~~l~d~fs~~~m~~~~~~~~~~~Tl~~~f~~v~~~~~~-----shv~~~gd~s~~~~~v~~f~g~ 256 (256)
T PF01650_consen 193 -DSIGTYLGDAFSYNWMEDSDSHPLSEETLDDQFEYVKRKTTG-----SHVQQYGDPSIPQLPVSEFQGT 256 (256)
T ss_pred -cccccEeHHHHHHHhhhhhccCCccccCHHHHHHHHHHhccc-----chHHhcCCCCccccCHHHhcCC
Confidence 489999999999999999999899999999999999999877 9999999999999999999984
No 3
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-51 Score=384.63 Aligned_cols=216 Identities=25% Similarity=0.441 Sum_probs=195.2
Q ss_pred CCcccCCCCCCCCCCeEeeCCC-CCcccC-CccccCCCCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecC
Q 016132 1 MYDDIAFNEENPRPGVIINHPH-GDDVYK-GVPKDYTGEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDH 78 (394)
Q Consensus 1 mydDia~~~~Np~pG~i~~~~~-g~~vy~-g~~iDY~g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~H 78 (394)
+|||+|||+|||+||+||++.| +.|||. .|++||+|.+||+|||++||+|+.+..+|+|+| |.+++.+|||||+|||
T Consensus 70 ladd~acn~RN~~pg~Vy~n~~~~~nlygd~vevdyrgyevtvEnflr~LTgR~~~~tprSKr-lltDe~SNIlIYmtGH 148 (309)
T KOG1349|consen 70 LADDMACNSRNPRPGTVYNNENHALNLYGDDVEVDYRGYEVTVENFLRVLTGRHPNNTPRSKR-LLTDEGSNILIYLTGH 148 (309)
T ss_pred eccccccccCCCCCcceeccccccccccCCcceeecccchhHHHHHHHHHcCCCCCCCchhhh-hcccCCCcEEEEEccC
Confidence 4899999999999999999997 589997 789999999999999999999999999999877 7799999999999999
Q ss_pred CCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCceEEEeeecccccccccccCCCCCcEEEEeecCCCCccccccCCCCCC
Q 016132 79 GGPGVLGMPTSRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSIFEGLLPEGLNIYATTASNAEESSWGTYCPGEIP 158 (394)
Q Consensus 79 G~~g~l~fp~~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~~~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~ 158 (394)
||+|||+|||.++|+.+||++++++|++++||++|+|+||||+|.||++++.+ |||+|+++|..+|+||+++.|+
T Consensus 149 Ggd~FlKFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQaasly~~~~s--PNVLav~SS~~ge~SySh~~d~--- 223 (309)
T KOG1349|consen 149 GGDGFLKFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQAASLYERFYS--PNVLAVASSLVGEPSYSHHSDS--- 223 (309)
T ss_pred CCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccchHHHHHhhcC--CCeEEEeecccCCcccccCCCc---
Confidence 99999999999999999999999999999999999999999999999999754 6999999999999999999876
Q ss_pred CCCCCccchhhhHhhhhhccccccC-CCCcccHHHHHHHHHhhhccCCCCCCCceeecCC---CcccccchhhcccC
Q 016132 159 GPPPEYSTCLGDLYSIAWMEDSDIH-NLRTETLHQQYELVKTRTASYNSYGSHVMQYGDI---GLSKNNLFTYLGTN 231 (394)
Q Consensus 159 ~~~~~~~t~lgD~fs~~wme~~~~~-~~~~~tl~~~f~~v~~~t~~~~t~~Shv~~yGd~---~~~~~~~~~f~g~~ 231 (394)
+||+++.|.|++..++..++. +....||+++|+..-.+... |+|-.--|+ ...+-++++|+|..
T Consensus 224 ----~Igv~vIDrftyy~l~flek~~~~~~~~l~dl~~s~~~~~~~-----St~gvr~dl~~r~~~~v~itDFFg~v 291 (309)
T KOG1349|consen 224 ----DIGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLFDSCPKRLLG-----STPGVRTDLYQRDPKDVLITDFFGSV 291 (309)
T ss_pred ----ccceeeeccchHHHHHHHHhcccchhhhHHHHHHhCChhhhc-----CCcCcccccccCCcccceeeeecccc
Confidence 899999999999888776653 44556899999999877765 888665554 45678899999964
No 4
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-41 Score=320.70 Aligned_cols=215 Identities=21% Similarity=0.351 Sum_probs=187.7
Q ss_pred CCcccCCCCCCCCCCeEeeCCC-CCcccC-CccccCCCCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecC
Q 016132 1 MYDDIAFNEENPRPGVIINHPH-GDDVYK-GVPKDYTGEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDH 78 (394)
Q Consensus 1 mydDia~~~~Np~pG~i~~~~~-g~~vy~-g~~iDY~g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~H 78 (394)
.|||.|||.||-|||.||++.+ +-++|. .++|||+|.+||+|+|.+.|+.+...-+|.|++ |.+++++||||||+||
T Consensus 70 ~~dd~acnsRnlfpgsvf~N~Dra~dlyge~~eidY~gyevTve~firLLt~r~~en~p~sKr-lltdE~SNIfIYmtGH 148 (382)
T COG5206 70 SYDDQACNSRNLFPGSVFNNSDRAGDLYGEDSEIDYSGYEVTVEVFIRLLTARSGENHPKSKR-LLTDESSNIFIYMTGH 148 (382)
T ss_pred echhhhhhhcccCCcccccCcccccceeCcccccccccccchHHHHHHHHHhhccCCChhhhh-hcccccCcEEEEEccC
Confidence 4899999999999999999988 578886 789999999999999999999998888888766 7789999999999999
Q ss_pred CCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCceEEEeeecccccccccccCCCCCcEEEEeecCCCCccccccCCCCCC
Q 016132 79 GGPGVLGMPTSRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSIFEGLLPEGLNIYATTASNAEESSWGTYCPGEIP 158 (394)
Q Consensus 79 G~~g~l~fp~~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~~~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~ 158 (394)
||++||+|+|.++++++||++++++|+++|||++++|+|||||+.+|+++... |||+|+++|.-++|||+++.+.
T Consensus 149 Ggd~FlKFqdaeemtseDladai~ql~~~kRyNeIlfmiDTCQAnaly~k~ys--PNvLavgsSeig~ssyShhsd~--- 223 (382)
T COG5206 149 GGDAFLKFQDAEEMTSEDLADAISQLAAKKRYNEILFMIDTCQANALYDKSYS--PNVLAVGSSEIGQSSYSHHSDS--- 223 (382)
T ss_pred CCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccccchhhhhccC--CceEEEeccccCCccccccchh---
Confidence 99999999999999999999999999999999999999999999999998754 5999999999999999999875
Q ss_pred CCCCCccchhhhHhhhhhccccccC-CCCcccHHHHHHHHHhhhccCCCCCCCceeec---CCCcccccchhhccc
Q 016132 159 GPPPEYSTCLGDLYSIAWMEDSDIH-NLRTETLHQQYELVKTRTASYNSYGSHVMQYG---DIGLSKNNLFTYLGT 230 (394)
Q Consensus 159 ~~~~~~~t~lgD~fs~~wme~~~~~-~~~~~tl~~~f~~v~~~t~~~~t~~Shv~~yG---d~~~~~~~~~~f~g~ 230 (394)
.+|.-+.|.|++.+++..+.- -.++.||++++...-.+. ++|||..-- |..-++-.+.+|+|.
T Consensus 224 ----~IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n~e~-----ihS~~gv~~~~fdr~p~d~litDFF~n 290 (382)
T COG5206 224 ----LIGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLNKEP-----IHSHVGVRELVFDRRPSDFLITDFFAN 290 (382)
T ss_pred ----hhhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcCccc-----ccCCCCcccccccCCccceeehHhhhh
Confidence 899999999999877766553 357889999998876544 459985422 223334557888875
No 5
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=98.41 E-value=3.2e-07 Score=86.20 Aligned_cols=143 Identities=22% Similarity=0.318 Sum_probs=95.0
Q ss_pred CCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCC--Cc----cCCCCCCCCCHHH---HHHHHHHHHH
Q 016132 36 GEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGP--GV----LGMPTSRYIYADE---LIDVLKKKHA 106 (394)
Q Consensus 36 g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~--g~----l~fp~~~~l~a~d---l~~~l~~m~~ 106 (394)
..++|.+++++.|+--.. ...++|.|+|||+|||.. +. +.-.++..+..+. +.+.|..+..
T Consensus 43 ~~~~t~~~i~~~l~~l~~----------~~~~~D~~~~yfsGHG~~~~~~~~~~~~~~d~~~~~~d~~~~~~~~l~~~~~ 112 (248)
T PF00656_consen 43 IDNATRANILKALRELLQ----------RAQPGDSVVFYFSGHGIQVDGEGGDEDSGYDGYLLPLDANLILDDELRDLLC 112 (248)
T ss_dssp EESSSHHHHHHHHHHHHT----------SGGTCSEEEEEEESEEETETTCCSTEEEETSSEEEEHHHHEEHHHHTSTTTT
T ss_pred ccchHHHHHHHHHhhhhc----------cCCCCCeeEEEEeccccccCCccCcccccccceeeecchhhhHHHHHhhhhh
Confidence 456999999999883211 123889999999999965 21 1111333344444 6777777666
Q ss_pred cCC-Cc-eEEEeeecccccccccccC----------------------------CCCCcEEEEeecCCCCccccccCCCC
Q 016132 107 SGN-YK-SLVFYLEACESGSIFEGLL----------------------------PEGLNIYATTASNAEESSWGTYCPGE 156 (394)
Q Consensus 107 ~~~-y~-~~v~~ieaC~SgSm~~~~l----------------------------~~~~nv~~~tAs~~~EsSy~~~~~~~ 156 (394)
+.. -+ + +|++|+|+||.+..... +...++++++|+.++|.||.. ++
T Consensus 113 ~~~~~~~k-~~ilD~C~sg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~as~~~~~s~e~--~~- 188 (248)
T PF00656_consen 113 KSLPKKPK-LFILDCCRSGGFIDGLSSSSGESSKREERKLSSSIPPEDPNRSDVPSPSGFIVLSASRPGQTSYED--SP- 188 (248)
T ss_dssp GGGTTS-E-EEEEESESSSBTBCEEEEEESSSTSS-EECHCCCCCCSSCCSEEEETTTSEEEEESSSTTBCEEEE--CT-
T ss_pred hhccCCcc-EEeeccccCCccCCccccccccccccccccccccccccccccccccCCCCcEEEEeccccceeecc--cC-
Confidence 522 22 4 99999999999866411 122489999999999999998 21
Q ss_pred CCCCCCCccchhhhHhhhhhcccccc------CCCCcccHHHHHHHHHhhhc
Q 016132 157 IPGPPPEYSTCLGDLYSIAWMEDSDI------HNLRTETLHQQYELVKTRTA 202 (394)
Q Consensus 157 ~~~~~~~~~t~lgD~fs~~wme~~~~------~~~~~~tl~~~f~~v~~~t~ 202 (394)
.. +-+|+..+++-... ......+|.+++..|++++.
T Consensus 189 -----~~-----~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~~~v~~~~~ 230 (248)
T PF00656_consen 189 -----GS-----GGLFTYALLEALKGNAADDPNQSWDELLEELLTEVNQKVA 230 (248)
T ss_dssp -----TT-----EEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHHHHHHHHHH
T ss_pred -----cc-----CHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHhHCC
Confidence 12 23677777765422 12345789999999998873
No 6
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=96.37 E-value=0.021 Score=54.86 Aligned_cols=144 Identities=16% Similarity=0.223 Sum_probs=83.6
Q ss_pred CCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCCCccCCCCCCCCCHHHHHHHHHHHH-HcCCCceEEE
Q 016132 37 EDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGPGVLGMPTSRYIYADELIDVLKKKH-ASGNYKSLVF 115 (394)
Q Consensus 37 ~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~g~l~fp~~~~l~a~dl~~~l~~m~-~~~~y~~~v~ 115 (394)
.+.|.+.+.++|.-- . .+ .+-...|-+++||.+||+.|+|.-.|+..+.-++|.+.|..-. ..-+-|=-+|
T Consensus 50 ~dlt~~em~~~l~~~-~------~~-~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlf 121 (241)
T smart00115 50 NNLTAEEMLEELKEF-A------ER-PEHSDSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLF 121 (241)
T ss_pred cCCCHHHHHHHHHHH-H------hc-cccCCCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEE
Confidence 455666666666521 1 01 1223567889999999999988777776677777777763211 1112244688
Q ss_pred eeecccccccccc--------------------cCCCCCcEEEEeecCCCCccccccCCCCCCCCCCCccchhhhHhhhh
Q 016132 116 YLEACESGSIFEG--------------------LLPEGLNIYATTASNAEESSWGTYCPGEIPGPPPEYSTCLGDLYSIA 175 (394)
Q Consensus 116 ~ieaC~SgSm~~~--------------------~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~~~~~~~~t~lgD~fs~~ 175 (394)
+|+||...-+-.+ .+|...++++.=|+.++.-||-.- ..|+.+.-.+--.
T Consensus 122 fiqACRg~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~D~li~ysT~pG~va~r~~----------~~gS~fi~~L~~~ 191 (241)
T smart00115 122 FIQACRGDELDGGVPVEDDVDDPPTEFEDDAIYKIPVEADFLAAYSTTPGYVSWRNP----------TRGSWFIQSLCQV 191 (241)
T ss_pred EEeCCCCCCCCCCeecccccccccccccccccccCCCcCcEEEEEeCCCCeEeecCC----------CCCchHHHHHHHH
Confidence 9999975422111 123334677777777776666431 2233322222222
Q ss_pred hccccccCCCCcccHHHHHHHHHhhhcc
Q 016132 176 WMEDSDIHNLRTETLHQQYELVKTRTAS 203 (394)
Q Consensus 176 wme~~~~~~~~~~tl~~~f~~v~~~t~~ 203 (394)
+-+ ....+.|.++|..|.+++..
T Consensus 192 l~~-----~~~~~~l~~ilt~V~~~V~~ 214 (241)
T smart00115 192 LKE-----YARSLDLLDILTEVNRKVAV 214 (241)
T ss_pred HHH-----cCCCCCHHHHHHHHHHHHhh
Confidence 221 12457899999999998864
No 7
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=95.98 E-value=0.046 Score=52.44 Aligned_cols=144 Identities=15% Similarity=0.215 Sum_probs=88.0
Q ss_pred CCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCCCccCCCCCCCCCHHHHHHHHHHHH-HcCCCceEE
Q 016132 36 GEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGPGVLGMPTSRYIYADELIDVLKKKH-ASGNYKSLV 114 (394)
Q Consensus 36 g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~g~l~fp~~~~l~a~dl~~~l~~m~-~~~~y~~~v 114 (394)
..++|.+.+.+.|.--.. + +....|-+++||.+||..+.|.-.|...+.-++|.+.|..-. ..-+-|=-|
T Consensus 51 ~~nlt~~~~~~~l~~f~~-------~--~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl 121 (243)
T cd00032 51 KNNLTAEEILEELKEFAS-------P--DHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKL 121 (243)
T ss_pred eCCCCHHHHHHHHHHHHh-------c--cCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcE
Confidence 467788888888863211 1 235567789999999999988766755677777776665211 112235568
Q ss_pred Eeeecccccccccc-----------------------cCCCCCcEEEEeecCCCCccccccCCCCCCCCCCCccchhhhH
Q 016132 115 FYLEACESGSIFEG-----------------------LLPEGLNIYATTASNAEESSWGTYCPGEIPGPPPEYSTCLGDL 171 (394)
Q Consensus 115 ~~ieaC~SgSm~~~-----------------------~l~~~~nv~~~tAs~~~EsSy~~~~~~~~~~~~~~~~t~lgD~ 171 (394)
|+|+||...-+-.+ ..|...++++.=|+.++.-||-.- .-|+.
T Consensus 122 ~~iqACRg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~d~lv~ysT~pG~~a~r~~----------~~gS~---- 187 (243)
T cd00032 122 FFIQACRGDELDLGVEVDSGADEPPDVETEAEDDAVQTIPVEADFLVAYSTVPGYVSWRNT----------KKGSW---- 187 (243)
T ss_pred EEEECCCCCcCCCceeccCccccccccccccccccccCCCCcccEEEEecCCCCeEeecCC----------CCCCE----
Confidence 99999997654221 123334777777777777766441 12222
Q ss_pred hhhhhccccccCCCCcccHHHHHHHHHhhhcc
Q 016132 172 YSIAWMEDSDIHNLRTETLHQQYELVKTRTAS 203 (394)
Q Consensus 172 fs~~wme~~~~~~~~~~tl~~~f~~v~~~t~~ 203 (394)
|.-.+.+-.. +....+.|.+++..|.+++..
T Consensus 188 fi~~l~~~l~-~~~~~~~l~~il~~V~~~V~~ 218 (243)
T cd00032 188 FIQSLCQVLR-KYAHSLDLLDILTKVNRKVAE 218 (243)
T ss_pred eHHHHHHHHH-HhCCCCcHHHHHHHHHHHHhh
Confidence 2222222111 112356899999999998865
No 8
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.07 Score=53.39 Aligned_cols=60 Identities=22% Similarity=0.352 Sum_probs=39.8
Q ss_pred CCCCCeEEEEeecCCCC-------CccCCCC----------CCCCCHHHHHHHHHHHHHcCCCceEEEeeeccccccccc
Q 016132 65 SGPNDHIFIFYSDHGGP-------GVLGMPT----------SRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSIFE 127 (394)
Q Consensus 65 s~~~d~vFiY~t~HG~~-------g~l~fp~----------~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~ 127 (394)
..++|-+|+=|||||+. ..-+|-+ +..|+.++.....+.+ ..=-++-.++|+|+||++.+
T Consensus 135 aq~gD~LvfHYSGHGtr~~~~~gDe~dG~DE~I~P~D~~t~G~iIdDe~~r~lV~pl---p~G~~lt~I~DSCHSGgliD 211 (362)
T KOG1546|consen 135 AQPGDSLVFHYSGHGTRQPDTNGDEVDGYDETIVPCDHNTQGPIIDDEIFRILVRPL---PKGCKLTAISDSCHSGGLID 211 (362)
T ss_pred CCCCCEEEEEecCCCCcCCCCCCCCCCCCcceeecccccccccccchHHHHHHHhcc---CCCceEEEEeecccCCCccc
Confidence 46789999999999983 1222211 1134455555555443 23357889999999999987
No 9
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=88.04 E-value=0.75 Score=41.55 Aligned_cols=73 Identities=18% Similarity=0.337 Sum_probs=54.0
Q ss_pred CCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCCC------ccCCCCCC----CCCHHHHHHHHHHHHH
Q 016132 37 EDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGPG------VLGMPTSR----YIYADELIDVLKKKHA 106 (394)
Q Consensus 37 ~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~g------~l~fp~~~----~l~a~dl~~~l~~m~~ 106 (394)
-+.|++.+.+.+..-. ...+++.|.+.|.|||-|. +..|.... .++-.||...+.
T Consensus 70 ~dpt~e~~~~~~~~~R-----------~~a~~~RvLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~dL~~~lg---- 134 (154)
T PF14538_consen 70 LDPTVEDLKRLCQSLR-----------RNAKDERVLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIYDLQSWLG---- 134 (154)
T ss_pred cCCCHHHHHHHHHHHH-----------hhCCCceEEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHHHHHHhcC----
Confidence 4778888888777421 1234578999999999984 45554432 378888888876
Q ss_pred cCCCceEEEeeecccccccccc
Q 016132 107 SGNYKSLVFYLEACESGSIFEG 128 (394)
Q Consensus 107 ~~~y~~~v~~ieaC~SgSm~~~ 128 (394)
.-.+|+.|...||++++.
T Consensus 135 ----~Psi~V~DC~~AG~il~~ 152 (154)
T PF14538_consen 135 ----SPSIYVFDCSNAGSILNA 152 (154)
T ss_pred ----CCEEEEEECCcHHHHHHh
Confidence 578999999999998764
No 10
>PF12770 CHAT: CHAT domain
Probab=85.21 E-value=0.8 Score=43.97 Aligned_cols=67 Identities=22% Similarity=0.362 Sum_probs=44.0
Q ss_pred cCCCCCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCCC-------ccCCC-----CCCCCCHHHHHHH
Q 016132 33 DYTGEDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGPG-------VLGMP-----TSRYIYADELIDV 100 (394)
Q Consensus 33 DY~g~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~g-------~l~fp-----~~~~l~a~dl~~~ 100 (394)
-..+.+.|.++|+..|.. ..-=.|.|++||... .|.+. ++..|++.+|..
T Consensus 123 ~~~~~~at~~~l~~~l~~-----------------~~~~ilH~a~Hg~~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~- 184 (287)
T PF12770_consen 123 VLVGPEATKDALLEALER-----------------RGPDILHFAGHGTFDPDPPDQSGLVLSDESGQEDGLLSAEELAQ- 184 (287)
T ss_pred EeeccCCCHHHHHhhhcc-----------------CCCCEEEEEcccccCCCCCCCCEEEEeccCCCCCcccCHHHHHh-
Confidence 345566677777666621 111268999999877 67775 345699999988
Q ss_pred HHHHHHcCCCceEEEeeeccccc
Q 016132 101 LKKKHASGNYKSLVFYLEACESG 123 (394)
Q Consensus 101 l~~m~~~~~y~~~v~~ieaC~Sg 123 (394)
++- .+ -+ ++++-||+||
T Consensus 185 l~l---~~--~~-lVvLsaC~s~ 201 (287)
T PF12770_consen 185 LDL---RG--PR-LVVLSACESA 201 (287)
T ss_pred hcC---CC--CC-EEEecCcCCc
Confidence 321 11 33 6689999999
No 11
>PF01364 Peptidase_C25: Peptidase family C25 This family belongs to family C25 of the peptidase classification.; InterPro: IPR001769 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C25 (gingipain, clan CD). The protein fold of the peptidase domain for members of this entry resembles that of caspase 1, the type example for clan CD. This is a protein family found only in the bacteria. Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=72.34 E-value=4.7 Score=40.96 Aligned_cols=104 Identities=22% Similarity=0.245 Sum_probs=49.1
Q ss_pred CeEEEEeecCCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCceEEEeeeccccccc-ccc-------c--CCCCCcEEE
Q 016132 69 DHIFIFYSDHGGPGVLGMPTSRYIYADELIDVLKKKHASGNYKSLVFYLEACESGSI-FEG-------L--LPEGLNIYA 138 (394)
Q Consensus 69 d~vFiY~t~HG~~g~l~fp~~~~l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm-~~~-------~--l~~~~nv~~ 138 (394)
...||.|.|||++..+ ..+.|+.+++. .| . +..|--|++.-||..|.+ ... + .|++--|-.
T Consensus 238 G~~~v~y~GHG~~~~w---~~~~~~~~d~~-~l---~--N~~~~p~~~s~~C~~g~fd~~~~~sl~E~~v~~~~gGAia~ 308 (378)
T PF01364_consen 238 GAGFVNYFGHGSPTSW---ADEDFTSSDIS-NL---N--NKNKLPVVISAACYTGNFDDPDNPSLGEALVLNPNGGAIAF 308 (378)
T ss_dssp --SEEEEES-B-SSBB---TTT--BTTTGG-G--------TT---EEEEESSSTT-TTSSS---HHHHHHTTEE-S-SEE
T ss_pred CCeEEEEecCCchhhc---ccCcccHhHHH-Hh---c--CCCCceEEEEeECCCcCCCCCCCCcHHHHheECCCCcEEEE
Confidence 3468899999999855 22224444432 11 1 223556778889999988 332 1 233223555
Q ss_pred EeecCCCCccccccCCCCCCCCCCCccchhhhHhhhhhccccccCCCCcccHHHHHHHHHhhhc
Q 016132 139 TTASNAEESSWGTYCPGEIPGPPPEYSTCLGDLYSIAWMEDSDIHNLRTETLHQQYELVKTRTA 202 (394)
Q Consensus 139 ~tAs~~~EsSy~~~~~~~~~~~~~~~~t~lgD~fs~~wme~~~~~~~~~~tl~~~f~~v~~~t~ 202 (394)
+++|. .+|... .+.|...|++....... .+|.+.+...|....
T Consensus 309 ig~s~---~~~~~~----------------~~~~~~~~~~~l~~~~~--~~lG~a~~~a~~~~~ 351 (378)
T PF01364_consen 309 IGSSR---VSYASP----------------NDRLNRGFYEALFNSNM--DTLGEALRQAKNYYL 351 (378)
T ss_dssp EEESS-----SSHH----------------HHHHHHHHTT-STT------BHHHHHHHHHHHHH
T ss_pred Eecce---eEecch----------------HHHHHHHHHHHHhccCC--CCHHHHHHHHHHHHH
Confidence 55544 444331 45566666654433211 289999888877554
No 12
>TIGR02855 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.
Probab=59.04 E-value=8.6 Score=38.00 Aligned_cols=101 Identities=22% Similarity=0.415 Sum_probs=65.5
Q ss_pred CCeEeeCCCC--------CcccCCccccCCCCCCC----HHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCC
Q 016132 14 PGVIINHPHG--------DDVYKGVPKDYTGEDVT----VENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGP 81 (394)
Q Consensus 14 pG~i~~~~~g--------~~vy~g~~iDY~g~~Vt----~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~ 81 (394)
||+|.+- +| .++|+-..|+-.|.-|. |+.....|.--+ |+ | +-+|||-|
T Consensus 104 PGrVLHi-DGD~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~~~~--------------PD--I-lViTGHD~- 164 (283)
T TIGR02855 104 PGRVLHI-DGDPEYLRKCLKLYKKIGVPVVGIHCKEKEMPEKVLDLIEEVR--------------PD--I-LVITGHDA- 164 (283)
T ss_pred CCcEEee-cCCHHHHHHHHHHHHHhCCceEEEEecchhchHHHHHHHHHhC--------------CC--E-EEEeCchh-
Confidence 9999874 44 25776444444444443 666666665221 11 2 45799954
Q ss_pred CccC----CCC-CCCCCHHHHHHHHHHHHHcC-CCceEEEeeecccccccccccCCCCCcE
Q 016132 82 GVLG----MPT-SRYIYADELIDVLKKKHASG-NYKSLVFYLEACESGSIFEGLLPEGLNI 136 (394)
Q Consensus 82 g~l~----fp~-~~~l~a~dl~~~l~~m~~~~-~y~~~v~~ieaC~SgSm~~~~l~~~~nv 136 (394)
+++ |.| ..+-.++.+.++++....-. -+-++|++.-|||| -||.||..+-|-
T Consensus 165 -~~K~~~d~~dl~~YrnSkyFVeaVk~aR~y~~~~D~LVIFAGACQS--~yEall~AGANF 222 (283)
T TIGR02855 165 -YSKNKGNYMDLNAYRHSKYFVETVREARKYVPSLDQLVIFAGACQS--HFESLIRAGANF 222 (283)
T ss_pred -hhcCCCChhhhhhhhhhHHHHHHHHHHHhcCCCcccEEEEcchhHH--HHHHHHHcCccc
Confidence 433 222 23678899999999876643 67899999999997 788887655553
No 13
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=54.45 E-value=9.7 Score=39.38 Aligned_cols=62 Identities=23% Similarity=0.364 Sum_probs=37.8
Q ss_pred CCeEEEEeecCCCCC-------ccCCCCCC--C----CCHHHHHHHHHHHHHcCCCceEEEeeecccccccccccC
Q 016132 68 NDHIFIFYSDHGGPG-------VLGMPTSR--Y----IYADELIDVLKKKHASGNYKSLVFYLEACESGSIFEGLL 130 (394)
Q Consensus 68 ~d~vFiY~t~HG~~g-------~l~fp~~~--~----l~a~dl~~~l~~m~~~~~y~~~v~~ieaC~SgSm~~~~l 130 (394)
.|+++.||+|||... |+.|-... . =+..-+......+|. ..-++-|.++++|.+|.+|....
T Consensus 133 ~d~~~~~fsG~g~~~~~d~~~~lia~~t~p~~~a~~~~~~~s~~~~~~~~~~-~~~~~ql~~~d~~~~~~~~~~~~ 207 (380)
T COG4249 133 ADTILFFFSGHGATPGADGRAYLIAFDTRPGAVAYDGEGGISPYSVAQALHL-SEPGNQLVDLDACVRGDVFKATA 207 (380)
T ss_pred hhhhhheeeccccccCCCCceeEEeecCChhhhcccCCCcccHHHHHHHHHh-ccCCceeehhhhhcchhhhcccc
Confidence 699999999999962 33332110 0 001112233333443 44466678999999999998764
No 14
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=51.65 E-value=14 Score=36.78 Aligned_cols=102 Identities=28% Similarity=0.531 Sum_probs=64.9
Q ss_pred CCCeEeeCCCC--------CcccCCccccCCCCCCC----HHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCC
Q 016132 13 RPGVIINHPHG--------DDVYKGVPKDYTGEDVT----VENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGG 80 (394)
Q Consensus 13 ~pG~i~~~~~g--------~~vy~g~~iDY~g~~Vt----~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~ 80 (394)
.||+|.+- || .++|+-.-|+=.|.-|. |+.....|.--+ |+ | +-+|||=|
T Consensus 104 ~PGkVLHl-DGD~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~~~~--------------PD--I-lViTGHD~ 165 (287)
T PF05582_consen 104 RPGKVLHL-DGDEEYLNKCLKVYKQLGIPAVGIHVPEKEQPEKIYRLLEEYR--------------PD--I-LVITGHDG 165 (287)
T ss_pred CCCeEEEe-cCCHHHHHHHHHHHHHcCCceEEEEechHHhhHHHHHHHHHcC--------------CC--E-EEEeCchh
Confidence 69998874 44 25776444444454444 555555555221 11 2 34799965
Q ss_pred CCccC----CCC-CCCCCHHHHHHHHHHHHH-cCCCceEEEeeecccccccccccCCCCCcE
Q 016132 81 PGVLG----MPT-SRYIYADELIDVLKKKHA-SGNYKSLVFYLEACESGSIFEGLLPEGLNI 136 (394)
Q Consensus 81 ~g~l~----fp~-~~~l~a~dl~~~l~~m~~-~~~y~~~v~~ieaC~SgSm~~~~l~~~~nv 136 (394)
+++ |.+ ..+=.++.+.++.+...+ ..-+-+||++.-|||| -||.||..+-|-
T Consensus 166 --~~K~~~d~~dl~~YrnSkyFVeaV~~aR~~ep~~D~LVIfAGACQS--~fEall~AGANF 223 (287)
T PF05582_consen 166 --YLKNKKDYSDLNNYRNSKYFVEAVKEARKYEPNLDDLVIFAGACQS--HFEALLEAGANF 223 (287)
T ss_pred --hhcCCCChhhhhhhhccHHHHHHHHHHHhcCCCcccEEEEcchhHH--HHHHHHHcCccc
Confidence 333 222 235678889999988765 4567899999999997 788887655553
No 15
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=48.72 E-value=28 Score=25.45 Aligned_cols=26 Identities=15% Similarity=0.409 Sum_probs=21.7
Q ss_pred hhHHHHHHHHHccCCCHHHHHHHHHh
Q 016132 350 MKHMRSLANICNTGIGKEKMAEASAQ 375 (394)
Q Consensus 350 lk~~~~laNLC~~G~~~~~i~~Ai~~ 375 (394)
...+.....||+.|+.++..++.|..
T Consensus 21 ~etL~ici~L~e~GVnPeaLA~vI~e 46 (48)
T PF12554_consen 21 RETLSICIELCENGVNPEALAAVIKE 46 (48)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 45677889999999999998887764
No 16
>PRK10649 hypothetical protein; Provisional
Probab=25.24 E-value=40 Score=36.73 Aligned_cols=19 Identities=21% Similarity=0.602 Sum_probs=14.9
Q ss_pred ccCCCCCeEEEEeecCCCC
Q 016132 63 VDSGPNDHIFIFYSDHGGP 81 (394)
Q Consensus 63 l~s~~~d~vFiY~t~HG~~ 81 (394)
|+...++.++||++|||..
T Consensus 447 Lk~~~~nt~iiy~SDHGe~ 465 (577)
T PRK10649 447 FKATDPNGFLVYFSDHGEE 465 (577)
T ss_pred HhcCCCCeEEEEECCCCcc
Confidence 3344578999999999975
No 17
>KOG1387 consensus Glycosyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=23.68 E-value=75 Score=32.94 Aligned_cols=37 Identities=27% Similarity=0.478 Sum_probs=26.9
Q ss_pred ccccCCCC-CCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEe
Q 016132 30 VPKDYTGE-DVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFY 75 (394)
Q Consensus 30 ~~iDY~g~-~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~ 75 (394)
+.+=|+|+ +|||+++|+=.+.+.. +.-+++.-.|||+
T Consensus 78 ~~viYsGD~n~t~~~IL~k~k~~F~---------idlDs~nI~Fi~L 115 (465)
T KOG1387|consen 78 VIVIYSGDFNVTPENILNKVKNKFD---------IDLDSDNIFFIYL 115 (465)
T ss_pred eEEEEeCCCCCCHHHHHHHHHHhcC---------ceecccceEEEEE
Confidence 34789999 9999999877664432 4446666678876
No 18
>COG2194 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]
Probab=20.80 E-value=56 Score=35.54 Aligned_cols=18 Identities=28% Similarity=0.709 Sum_probs=13.7
Q ss_pred ccCCCCCeEEEEeecCCC
Q 016132 63 VDSGPNDHIFIFYSDHGG 80 (394)
Q Consensus 63 l~s~~~d~vFiY~t~HG~ 80 (394)
|+....+-++||+||||-
T Consensus 439 Lk~~~~~~~liY~SDHGE 456 (555)
T COG2194 439 LKDKKDNTSLIYFSDHGE 456 (555)
T ss_pred HHhCCCCeEEEEEcCccH
Confidence 334444889999999996
No 19
>KOG1654 consensus Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton]
Probab=20.07 E-value=96 Score=26.73 Aligned_cols=35 Identities=29% Similarity=0.610 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHcCCCCCCCCCCCccccCCCCCeEEEEeecCCCCC
Q 016132 37 EDVTVENFFAVILGNKTALTGGSGKVVDSGPNDHIFIFYSDHGGPG 82 (394)
Q Consensus 37 ~~Vt~~nfl~vL~G~~~~~~~~s~kvl~s~~~d~vFiY~t~HG~~g 82 (394)
+++|+..|+.|++ |.|+-.|++-+|++..+|--+.
T Consensus 53 ~dltvgqfi~iIR-----------kRiqL~~~kA~flfVn~~~p~t 87 (116)
T KOG1654|consen 53 DDLTVGQFIKIIR-----------KRIQLSPEKAFFLFVNNTSPPT 87 (116)
T ss_pred ccccHHHHHHHHH-----------HHhccChhHeEEEEEcCcCCcc
Confidence 6899999999999 2377799999999999986443
Done!