Query 023458
Match_columns 282
No_of_seqs 188 out of 414
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:11:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023458hhsearch_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-103 2E-108 741.2 19.8 280 1-282 87-367 (477)
2 PF01650 Peptidase_C13: Peptid 100.0 1.7E-70 3.6E-75 504.1 18.4 215 1-232 42-256 (256)
3 KOG1349 Gpi-anchor transamidas 100.0 2.6E-54 5.6E-59 391.6 13.7 219 1-233 70-291 (309)
4 COG5206 GPI8 Glycosylphosphati 100.0 6.1E-44 1.3E-48 326.3 11.4 215 1-232 70-290 (382)
5 PF00656 Peptidase_C14: Caspas 98.7 3.8E-08 8.3E-13 87.2 6.2 142 36-202 43-230 (248)
6 smart00115 CASc Caspase, inter 97.1 0.0038 8.2E-08 57.1 9.6 123 66-203 71-214 (241)
7 cd00032 CASc Caspase, interleu 96.7 0.0097 2.1E-07 54.3 8.8 144 36-203 51-218 (243)
8 KOG1546 Metacaspase involved i 96.4 0.0066 1.4E-07 58.3 5.8 60 65-127 135-211 (362)
9 PF14538 Raptor_N: Raptor N-te 92.6 0.17 3.6E-06 43.8 4.2 73 37-128 70-152 (154)
10 PF12770 CHAT: CHAT domain 90.2 0.26 5.6E-06 44.7 3.2 67 33-123 123-201 (287)
11 PF01364 Peptidase_C25: Peptid 82.6 1.6 3.5E-05 42.0 4.2 104 69-202 238-351 (378)
12 TIGR02855 spore_yabG sporulati 73.6 2.9 6.3E-05 39.6 2.9 100 14-135 104-221 (283)
13 COG4249 Uncharacterized protei 70.6 3.2 7E-05 40.9 2.6 63 67-130 132-207 (380)
14 PF05582 Peptidase_U57: YabG p 68.6 4.5 9.8E-05 38.5 2.9 101 13-135 104-222 (287)
15 PF07999 RHSP: Retrotransposon 41.9 1.5E+02 0.0032 29.9 8.8 104 93-203 187-299 (439)
16 COG4566 TtrR Response regulato 36.2 37 0.00081 30.8 3.1 35 71-106 78-121 (202)
17 PF13709 DUF4159: Domain of un 34.9 84 0.0018 28.2 5.3 66 41-120 21-90 (207)
18 PF03415 Peptidase_C11: Clostr 28.4 42 0.0009 33.1 2.4 73 37-125 76-160 (397)
19 PRK10649 hypothetical protein; 27.5 36 0.00078 35.3 1.8 17 65-81 449-465 (577)
20 KOG1387 Glycosyltransferase [C 26.1 66 0.0014 32.2 3.2 37 30-75 78-115 (465)
21 KOG1654 Microtubule-associated 23.8 70 0.0015 26.6 2.5 34 37-81 53-86 (116)
22 PF01972 SDH_sah: Serine dehyd 23.5 2E+02 0.0044 27.5 5.8 55 65-119 45-99 (285)
23 COG2194 Predicted membrane-ass 23.2 46 0.00099 34.6 1.6 16 65-80 441-456 (555)
24 PF06866 DUF1256: Protein of u 23.1 1.2E+02 0.0025 26.8 3.9 31 91-122 67-97 (163)
25 PF10116 Host_attach: Protein 22.4 1.2E+02 0.0025 25.0 3.7 38 91-128 72-109 (138)
26 PRK09598 lipid A phosphoethano 21.4 53 0.0011 33.7 1.6 15 67-81 428-442 (522)
27 TIGR02841 spore_YyaC putative 21.3 1.1E+02 0.0024 26.3 3.3 31 91-122 43-73 (140)
28 cd03020 DsbA_DsbC_DsbG DsbA fa 20.0 2E+02 0.0044 24.8 4.9 35 14-48 21-57 (197)
29 cd01906 proteasome_protease_Hs 20.0 2.2E+02 0.0049 23.7 5.0 116 61-199 33-161 (182)
No 1
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-103 Score=741.16 Aligned_cols=280 Identities=61% Similarity=1.053 Sum_probs=269.1
Q ss_pred CCcccCCCCCCCCCCeEeeCCCCCCccCCccccCCCCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCC
Q 023458 1 MYDDIAMHELNPRPGVIINHPQGENLYDGVPKDYTGEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGG 80 (282)
Q Consensus 1 myDDiA~n~~Np~pG~i~n~~~g~nvY~gv~iDY~g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg 80 (282)
||||||+||+||+||+|||+|+|+|||+||+|||||++|||+||++||+|++++++|||||||+|+|||||||||+||||
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 CCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccccCCCCCCEEEEeccCCCCccccccCCCCCCCC
Q 023458 81 PGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEGVMPKDLDIYVTTASNAQESSFGTYCPGMDPSP 160 (282)
Q Consensus 81 ~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~~lp~~~nV~~iTAS~~~EsSya~~~~~~~~~~ 160 (282)
+|+|.||+++.|+++||+++|++||+.++|++||||+|||||||||+++||+++||||+||||+.||||++|||+++|+|
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 99999999989999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccchhhhhhhhhhhhhhccccCchhcHHHHHHHHHhhhccCCCCCCCCccceecCCccccccceeecccCCCCCCCC
Q 023458 161 PPEYITCLGDLYSVAWMEDSETHNLKRETISQQYQAVKERTSNFNNYNSGSHVMEYGNTSVKSEKLYLYQGFDPASTNFP 240 (282)
Q Consensus 161 ~~~~~t~lgD~fS~~wme~~~~~~~~~~Tl~~~f~~vk~~t~~~~~~~~~Shv~~yGd~~~~~~~l~~f~g~~~~~~~~~ 240 (282)
++++.|||||+||++||||++.+|+++|||.+||+.||++|+.+ |..|||||||||..|++++|..|||.+|++++++
T Consensus 247 pse~~tcLGDlySV~WmeDSd~hdL~kETL~qQYhlVK~rt~~s--~s~gsHVmqyGd~~iske~l~lfqG~~pa~~nf~ 324 (477)
T KOG1348|consen 247 PSEYSTCLGDLYSVNWMEDSDVHDLKKETLHQQYHLVKKRTNTS--YSYGSHVMQYGDKTISKEKLMLFQGMKPANENFT 324 (477)
T ss_pred hhhcccccccceeeeeeccCccccchHHHHHHHHHHHHHhcCCC--CCCcceeeecCcchhhHHHHHHHcCCCcccCCCC
Confidence 99999999999999999999999999999999999999999986 5578999999999999999999999999999876
Q ss_pred C-CCCCCCCCCCCCCCchhHHHHHHHHHhcCCcHHHHHHhhhC
Q 023458 241 P-NKLQPDQMGVVNQRDADLLFMWHMQRDQKRNQKCLSRLQRQ 282 (282)
Q Consensus 241 ~-~~~~~~~~~~~~~rd~~l~~~~~~~~~~~~~~~~~~~~~~~ 282 (282)
- +.+..+++..|||||++|++||+|++++++++.++.++|+|
T Consensus 325 l~~~s~~~~s~~~n~rD~~L~~l~~k~rka~dgs~~s~e~~k~ 367 (477)
T KOG1348|consen 325 LPASSHKSPSGLTNQRDAPLLHLWRKYRKANDGSAESRELQKE 367 (477)
T ss_pred CCccCcCCccccCCCCCccHHHHHHHHhcCcccchhhHHHHHH
Confidence 3 33444567789999999999999999999999888888764
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=1.7e-70 Score=504.14 Aligned_cols=215 Identities=49% Similarity=0.829 Sum_probs=206.4
Q ss_pred CCcccCCCCCCCCCCeEeeCCCCCCccCCccccCCCCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCC
Q 023458 1 MYDDIAMHELNPRPGVIINHPQGENLYDGVPKDYTGEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGG 80 (282)
Q Consensus 1 myDDiA~n~~Np~pG~i~n~~~g~nvY~gv~iDY~g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg 80 (282)
|||||||||+||+||+|||+|+|.|||+||+|||+|.+||+++|++||+|+++ + +++|||+|+++|+|||||+||||
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 57899999999999999999999
Q ss_pred CCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccccCCCCCCEEEEeccCCCCccccccCCCCCCCC
Q 023458 81 PGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEGVMPKDLDIYVTTASNAQESSFGTYCPGMDPSP 160 (282)
Q Consensus 81 ~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~~lp~~~nV~~iTAS~~~EsSya~~~~~~~~~~ 160 (282)
+|+|+||+.+.|++.||+++|++|+++++|+||||++|||+|||||+. |++++||++||||+++|+||+|+|.
T Consensus 119 ~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs~~~~-L~~~~nv~~iTAa~~~e~Sy~~~~~------ 191 (256)
T PF01650_consen 119 PGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYSGSFFEG-LLKSPNVYVITAANADESSYGCYCS------ 191 (256)
T ss_pred CCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccccchhhc-cCCCCCEEEEecCCccccccccccc------
Confidence 999999988889999999999999999999999999999999999999 6788999999999999999999993
Q ss_pred CCCccchhhhhhhhhhhhhhccccCchhcHHHHHHHHHhhhccCCCCCCCCccceecCCccccccceeeccc
Q 023458 161 PPEYITCLGDLYSVAWMEDSETHNLKRETISQQYQAVKERTSNFNNYNSGSHVMEYGNTSVKSEKLYLYQGF 232 (282)
Q Consensus 161 ~~~~~t~lgD~fS~~wme~~~~~~~~~~Tl~~~f~~vk~~t~~~~~~~~~Shv~~yGd~~~~~~~l~~f~g~ 232 (282)
++++++||||+||.+||++++.++++++||.+||+.|+++|.. |||++|||.++.+++|++|||.
T Consensus 192 ~~~~~~~l~d~fs~~~m~~~~~~~~~~~Tl~~~f~~v~~~~~~-------shv~~~gd~s~~~~~v~~f~g~ 256 (256)
T PF01650_consen 192 DDSIGTYLGDAFSYNWMEDSDSHPLSEETLDDQFEYVKRKTTG-------SHVQQYGDPSIPQLPVSEFQGT 256 (256)
T ss_pred ccccccEeHHHHHHHhhhhhccCCccccCHHHHHHHHHHhccc-------chHHhcCCCCccccCHHHhcCC
Confidence 2599999999999999999999889999999999999999864 9999999999999999999985
No 3
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-54 Score=391.59 Aligned_cols=219 Identities=22% Similarity=0.359 Sum_probs=195.2
Q ss_pred CCcccCCCCCCCCCCeEeeCCC-CCCccC-CccccCCCCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecC
Q 023458 1 MYDDIAMHELNPRPGVIINHPQ-GENLYD-GVPKDYTGEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDH 78 (282)
Q Consensus 1 myDDiA~n~~Np~pG~i~n~~~-g~nvY~-gv~iDY~g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgH 78 (282)
++||+|||+|||+||+||++.+ +.|||. .|++||+|.+||+|||++||+||.+..+|+|+| |.+++.+|||||+|||
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 689997 778999999999999999999999999999987 6799999999999999
Q ss_pred CCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccccCCCCCCEEEEeccCCCCccccccCCCCCC
Q 023458 79 GGPGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEGVMPKDLDIYVTTASNAQESSFGTYCPGMDP 158 (282)
Q Consensus 79 Gg~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~~lp~~~nV~~iTAS~~~EsSya~~~~~~~~ 158 (282)
||+|||||||.++|+.+||++++++|++++||++|+|+||||+|.||++++.+ |||+|+++|..+|+||+++.|+
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 7999999999999999999874
Q ss_pred CCCCCccchhhhhhhhhhhhhhccc-cCchhcHHHHHHHHHhhhccCCCCCCCCccceecCCccccccceeecccC
Q 023458 159 SPPPEYITCLGDLYSVAWMEDSETH-NLKRETISQQYQAVKERTSNFNNYNSGSHVMEYGNTSVKSEKLYLYQGFD 233 (282)
Q Consensus 159 ~~~~~~~t~lgD~fS~~wme~~~~~-~~~~~Tl~~~f~~vk~~t~~~~~~~~~Shv~~yGd~~~~~~~l~~f~g~~ 233 (282)
.||++++|+|++..++..++. .....||+++|+.+.++...|+++ -..-.| .....+.++++|||..
T Consensus 224 ----~Igv~vIDrftyy~l~flek~~~~~~~~l~dl~~s~~~~~~~St~g---vr~dl~-~r~~~~v~itDFFg~v 291 (309)
T KOG1349|consen 224 ----DIGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLFDSCPKRLLGSTPG---VRTDLY-QRDPKDVLITDFFGSV 291 (309)
T ss_pred ----ccceeeeccchHHHHHHHHhcccchhhhHHHHHHhCChhhhcCCcC---cccccc-cCCcccceeeeecccc
Confidence 999999999999888877764 344568999999999998775432 121222 3356788999999975
No 4
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.1e-44 Score=326.29 Aligned_cols=215 Identities=18% Similarity=0.286 Sum_probs=189.6
Q ss_pred CCcccCCCCCCCCCCeEeeCCC-CCCccC-CccccCCCCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecC
Q 023458 1 MYDDIAMHELNPRPGVIINHPQ-GENLYD-GVPKDYTGEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDH 78 (282)
Q Consensus 1 myDDiA~n~~Np~pG~i~n~~~-g~nvY~-gv~iDY~g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgH 78 (282)
.|||.|||.||-|||.||++.+ +-++|. .++|||+|.+||+++|.+.|+.+...-+|.|+| +.+++++||||||+||
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 779999999999999999999998888887776 6799999999999999
Q ss_pred CCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccccCCCCCCEEEEeccCCCCccccccCCCCCC
Q 023458 79 GGPGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEGVMPKDLDIYVTTASNAQESSFGTYCPGMDP 158 (282)
Q Consensus 79 Gg~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~~lp~~~nV~~iTAS~~~EsSya~~~~~~~~ 158 (282)
||++||+||+.++|+.+||++++++|+++|||++++|+|||||+.+|+++... |||+|+++|.-++|||++|.+
T Consensus 149 Ggd~FlKFqdaeemtseDladai~ql~~~kRyNeIlfmiDTCQAnaly~k~ys--PNvLavgsSeig~ssyShhsd---- 222 (382)
T COG5206 149 GGDAFLKFQDAEEMTSEDLADAISQLAAKKRYNEILFMIDTCQANALYDKSYS--PNVLAVGSSEIGQSSYSHHSD---- 222 (382)
T ss_pred CCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccccchhhhhccC--CceEEEeccccCCccccccch----
Confidence 99999999999999999999999999999999999999999999999998754 799999999999999999987
Q ss_pred CCCCCccchhhhhhhhhhhhhhccc-cCchhcHHHHHHHHHhhhccCCCCCCCCccceec---CCccccccceeeccc
Q 023458 159 SPPPEYITCLGDLYSVAWMEDSETH-NLKRETISQQYQAVKERTSNFNNYNSGSHVMEYG---NTSVKSEKLYLYQGF 232 (282)
Q Consensus 159 ~~~~~~~t~lgD~fS~~wme~~~~~-~~~~~Tl~~~f~~vk~~t~~~~~~~~~Shv~~yG---d~~~~~~~l~~f~g~ 232 (282)
..+|+.++|+|++.+++..++. -.++.||++++.....+.. +|||-.-- |..-++-.+++|+|.
T Consensus 223 ---~~IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n~e~i-------hS~~gv~~~~fdr~p~d~litDFF~n 290 (382)
T COG5206 223 ---SLIGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLNKEPI-------HSHVGVRELVFDRRPSDFLITDFFAN 290 (382)
T ss_pred ---hhhhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcCcccc-------cCCCCcccccccCCccceeehHhhhh
Confidence 4899999999999888776653 3478899999998887654 58874321 334456668999975
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=98.66 E-value=3.8e-08 Score=87.22 Aligned_cols=142 Identities=19% Similarity=0.303 Sum_probs=95.3
Q ss_pred CCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCC--Cc-----cCCCCCCCCCHHH---HHHHHHHHH
Q 023458 36 GEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGP--GV-----LGMPNMPYVYAME---FIDVLKKKH 105 (282)
Q Consensus 36 g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~--g~-----l~fpd~~~L~a~d---L~~~l~~M~ 105 (282)
..++|.+++++.|+--.. ...++|.|+|||+|||.. +. ..+ ++..+..+. +.+.|..+.
T Consensus 43 ~~~~t~~~i~~~l~~l~~----------~~~~~D~~~~yfsGHG~~~~~~~~~~~~~~-d~~~~~~d~~~~~~~~l~~~~ 111 (248)
T PF00656_consen 43 IDNATRANILKALRELLQ----------RAQPGDSVVFYFSGHGIQVDGEGGDEDSGY-DGYLLPLDANLILDDELRDLL 111 (248)
T ss_dssp EESSSHHHHHHHHHHHHT----------SGGTCSEEEEEEESEEETETTCCSTEEEET-SSEEEEHHHHEEHHHHTSTTT
T ss_pred ccchHHHHHHHHHhhhhc----------cCCCCCeeEEEEeccccccCCccCcccccc-cceeeecchhhhHHHHHhhhh
Confidence 456899999998882211 123889999999999965 21 112 333344444 677777766
Q ss_pred HcCC-CC-eEEEEEecccccccccccC----------------------------CCCCCEEEEeccCCCCccccccCCC
Q 023458 106 AAKS-YK-GMVIYVEACESGSIFEGVM----------------------------PKDLDIYVTTASNAQESSFGTYCPG 155 (282)
Q Consensus 106 ~~~~-Yk-k~v~~iEAC~SGSmf~~~l----------------------------p~~~nV~~iTAS~~~EsSya~~~~~ 155 (282)
.+.. -+ + +|++|+|+||.+..... +...++++++|+.++|.||.. ++
T Consensus 112 ~~~~~~~~k-~~ilD~C~sg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~as~~~~~s~e~--~~ 188 (248)
T PF00656_consen 112 CKSLPKKPK-LFILDCCRSGGFIDGLSSSSGESSKREERKLSSSIPPEDPNRSDVPSPSGFIVLSASRPGQTSYED--SP 188 (248)
T ss_dssp TGGGTTS-E-EEEEESESSSBTBCEEEEEESSSTSS-EECHCCCCCCSSCCSEEEETTTSEEEEESSSTTBCEEEE--CT
T ss_pred hhhccCCcc-EEeeccccCCccCCccccccccccccccccccccccccccccccccCCCCcEEEEeccccceeecc--cC
Confidence 6522 22 4 99999999999865311 122489999999999999987 11
Q ss_pred CCCCCCCCccchhhhhhhhhhhhhhccc------cCchhcHHHHHHHHHhhhc
Q 023458 156 MDPSPPPEYITCLGDLYSVAWMEDSETH------NLKRETISQQYQAVKERTS 202 (282)
Q Consensus 156 ~~~~~~~~~~t~lgD~fS~~wme~~~~~------~~~~~Tl~~~f~~vk~~t~ 202 (282)
.-+-+|+..+++-.... .....+|.+++..+++++.
T Consensus 189 -----------~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~~~v~~~~~ 230 (248)
T PF00656_consen 189 -----------GSGGLFTYALLEALKGNAADDPNQSWDELLEELLTEVNQKVA 230 (248)
T ss_dssp -----------TTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHHHHHHHHHH
T ss_pred -----------ccCHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHhHCC
Confidence 12346788888765322 2235789999999998874
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=97.08 E-value=0.0038 Score=57.05 Aligned_cols=123 Identities=11% Similarity=0.181 Sum_probs=75.0
Q ss_pred CCCCeEEEEEecCCCCCccCCCCCCCCCHHHHHHHHHHHH-HcCCCCeEEEEEecccccccccc----------------
Q 023458 66 KANDRIFIFYSDHGGPGVLGMPNMPYVYAMEFIDVLKKKH-AAKSYKGMVIYVEACESGSIFEG---------------- 128 (282)
Q Consensus 66 ~~~D~VFiY~tgHGg~g~l~fpd~~~L~a~dL~~~l~~M~-~~~~Ykk~v~~iEAC~SGSmf~~---------------- 128 (282)
...|-+++||.+||+.++|.-.|+..+.-++|.+.|..-. ..-+-|=-+|+|+||...-+-.+
T Consensus 71 ~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlffiqACRg~~~~~g~~~~~~~~~~~~~~~~ 150 (241)
T smart00115 71 SDSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLFFIQACRGDELDGGVPVEDDVDDPPTEFED 150 (241)
T ss_pred CCCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEEEEeCCCCCCCCCCeecccccccccccccc
Confidence 3567899999999999988877776677777777763211 01122346889999975422111
Q ss_pred ----cCCCCCCEEEEeccCCCCccccccCCCCCCCCCCCccchhhhhhhhhhhhhhccccCchhcHHHHHHHHHhhhcc
Q 023458 129 ----VMPKDLDIYVTTASNAQESSFGTYCPGMDPSPPPEYITCLGDLYSVAWMEDSETHNLKRETISQQYQAVKERTSN 203 (282)
Q Consensus 129 ----~lp~~~nV~~iTAS~~~EsSya~~~~~~~~~~~~~~~t~lgD~fS~~wme~~~~~~~~~~Tl~~~f~~vk~~t~~ 203 (282)
.+|...++++.=|+.++.-||-. +..|+ +|.-...+-...+ ...+.|.++|..|.+++..
T Consensus 151 ~~~~~~p~~~D~li~ysT~pG~va~r~----------~~~gS----~fi~~L~~~l~~~-~~~~~l~~ilt~V~~~V~~ 214 (241)
T smart00115 151 DAIYKIPVEADFLAAYSTTPGYVSWRN----------PTRGS----WFIQSLCQVLKEY-ARSLDLLDILTEVNRKVAV 214 (241)
T ss_pred cccccCCCcCcEEEEEeCCCCeEeecC----------CCCCc----hHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhh
Confidence 12333467777777777666543 12222 2333333322221 2567899999999999865
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=96.66 E-value=0.0097 Score=54.26 Aligned_cols=144 Identities=13% Similarity=0.154 Sum_probs=88.5
Q ss_pred CCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCCCccCCCCCCCCCHHHHHHHHHHHH-HcCCCCeEE
Q 023458 36 GEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGPGVLGMPNMPYVYAMEFIDVLKKKH-AAKSYKGMV 114 (282)
Q Consensus 36 g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~g~l~fpd~~~L~a~dL~~~l~~M~-~~~~Ykk~v 114 (282)
..++|.+.+.+.|.--. .+ +....|-+++||.+||..+.|.-.|...+.-++|.+.|..-. ..-+-|=-|
T Consensus 51 ~~nlt~~~~~~~l~~f~-------~~--~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl 121 (243)
T cd00032 51 KNNLTAEEILEELKEFA-------SP--DHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKL 121 (243)
T ss_pred eCCCCHHHHHHHHHHHH-------hc--cCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcE
Confidence 45777788877776321 11 235567789999999999988776756677777777765211 112234568
Q ss_pred EEEecccccccccc-----------------------cCCCCCCEEEEeccCCCCccccccCCCCCCCCCCCccchhhhh
Q 023458 115 IYVEACESGSIFEG-----------------------VMPKDLDIYVTTASNAQESSFGTYCPGMDPSPPPEYITCLGDL 171 (282)
Q Consensus 115 ~~iEAC~SGSmf~~-----------------------~lp~~~nV~~iTAS~~~EsSya~~~~~~~~~~~~~~~t~lgD~ 171 (282)
|+|+||...-+-.+ ..|...++++.=|+.++.-||-.- .-| -+
T Consensus 122 ~~iqACRg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~d~lv~ysT~pG~~a~r~~----------~~g----S~ 187 (243)
T cd00032 122 FFIQACRGDELDLGVEVDSGADEPPDVETEAEDDAVQTIPVEADFLVAYSTVPGYVSWRNT----------KKG----SW 187 (243)
T ss_pred EEEECCCCCcCCCceeccCccccccccccccccccccCCCCcccEEEEecCCCCeEeecCC----------CCC----CE
Confidence 99999997654221 123334677777777776666431 112 22
Q ss_pred hhhhhhhhhccccCchhcHHHHHHHHHhhhcc
Q 023458 172 YSVAWMEDSETHNLKRETISQQYQAVKERTSN 203 (282)
Q Consensus 172 fS~~wme~~~~~~~~~~Tl~~~f~~vk~~t~~ 203 (282)
|.-.+.+-.. +....+.|.+++..|.+++..
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 3333333221 122357899999999999865
No 8
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.0066 Score=58.34 Aligned_cols=60 Identities=20% Similarity=0.386 Sum_probs=39.8
Q ss_pred CCCCCeEEEEEecCCCC-------CccCCC------CC----CCCCHHHHHHHHHHHHHcCCCCeEEEEEeccccccccc
Q 023458 65 SKANDRIFIFYSDHGGP-------GVLGMP------NM----PYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFE 127 (282)
Q Consensus 65 S~~~D~VFiY~tgHGg~-------g~l~fp------d~----~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~ 127 (282)
..++|-+|+-|||||+. ..-+|. |- ..|..++.....+.+- ++ -+|-.++|+|+||++.+
T Consensus 135 aq~gD~LvfHYSGHGtr~~~~~gDe~dG~DE~I~P~D~~t~G~iIdDe~~r~lV~plp-~G--~~lt~I~DSCHSGgliD 211 (362)
T KOG1546|consen 135 AQPGDSLVFHYSGHGTRQPDTNGDEVDGYDETIVPCDHNTQGPIIDDEIFRILVRPLP-KG--CKLTAISDSCHSGGLID 211 (362)
T ss_pred CCCCCEEEEEecCCCCcCCCCCCCCCCCCcceeecccccccccccchHHHHHHHhccC-CC--ceEEEEeecccCCCccc
Confidence 36789999999999983 222221 11 1344555555555442 22 47899999999999987
No 9
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=92.58 E-value=0.17 Score=43.80 Aligned_cols=73 Identities=16% Similarity=0.270 Sum_probs=53.8
Q ss_pred CCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCCC------ccCCCCCC----CCCHHHHHHHHHHHHH
Q 023458 37 EHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGPG------VLGMPNMP----YVYAMEFIDVLKKKHA 106 (282)
Q Consensus 37 ~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~g------~l~fpd~~----~L~a~dL~~~l~~M~~ 106 (282)
-+.|++.+.+.+..-. ...+++.|.+.|.|||-|. +..|...- .|+-.||...+.
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 4677888887776321 1344588999999999984 55554432 378888888886
Q ss_pred cCCCCeEEEEEecccccccccc
Q 023458 107 AKSYKGMVIYVEACESGSIFEG 128 (282)
Q Consensus 107 ~~~Ykk~v~~iEAC~SGSmf~~ 128 (282)
.-.+|+.|+..||++++.
T Consensus 135 ----~Psi~V~DC~~AG~il~~ 152 (154)
T PF14538_consen 135 ----SPSIYVFDCSNAGSILNA 152 (154)
T ss_pred ----CCEEEEEECCcHHHHHHh
Confidence 468999999999998764
No 10
>PF12770 CHAT: CHAT domain
Probab=90.23 E-value=0.26 Score=44.72 Aligned_cols=67 Identities=21% Similarity=0.258 Sum_probs=44.0
Q ss_pred cCCCCCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCCC-------ccCCC-----CCCCCCHHHHHHH
Q 023458 33 DYTGEHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGPG-------VLGMP-----NMPYVYAMEFIDV 100 (282)
Q Consensus 33 DY~g~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~g-------~l~fp-----d~~~L~a~dL~~~ 100 (282)
-..+.+.|.++|+..|... .-=.|+|+|||... .|.+. +...|++.+|..
T Consensus 123 ~~~~~~at~~~l~~~l~~~-----------------~~~ilH~a~Hg~~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~- 184 (287)
T PF12770_consen 123 VLVGPEATKDALLEALERR-----------------GPDILHFAGHGTFDPDPPDQSGLVLSDESGQEDGLLSAEELAQ- 184 (287)
T ss_pred EeeccCCCHHHHHhhhccC-----------------CCCEEEEEcccccCCCCCCCCEEEEeccCCCCCcccCHHHHHh-
Confidence 3455666777766666211 11368999999876 66775 345699999988
Q ss_pred HHHHHHcCCCCeEEEEEeccccc
Q 023458 101 LKKKHAAKSYKGMVIYVEACESG 123 (282)
Q Consensus 101 l~~M~~~~~Ykk~v~~iEAC~SG 123 (282)
++ + .+ -+ ++++-||+||
T Consensus 185 l~-l--~~--~~-lVvLsaC~s~ 201 (287)
T PF12770_consen 185 LD-L--RG--PR-LVVLSACESA 201 (287)
T ss_pred hc-C--CC--CC-EEEecCcCCc
Confidence 32 1 11 33 5689999999
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=82.61 E-value=1.6 Score=42.01 Aligned_cols=104 Identities=18% Similarity=0.192 Sum_probs=48.6
Q ss_pred CeEEEEEecCCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEeccccccc-ccc--c-------CCCCCCEEE
Q 023458 69 DRIFIFYSDHGGPGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSI-FEG--V-------MPKDLDIYV 138 (282)
Q Consensus 69 D~VFiY~tgHGg~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSm-f~~--~-------lp~~~nV~~ 138 (282)
...||.|.|||++... ..+.|+..++. .|. ...|--|++.-||..|.+ ... . .|++--|-.
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-NLN-----NKNKLPVVISAACYTGNFDDPDNPSLGEALVLNPNGGAIAF 308 (378)
T ss_dssp --SEEEEES-B-SSBB---TTT--BTTTGG-G--------TT---EEEEESSSTT-TTSSS---HHHHHHTTEE-S-SEE
T ss_pred CCeEEEEecCCchhhc---ccCcccHhHHH-Hhc-----CCCCceEEEEeECCCcCCCCCCCCcHHHHheECCCCcEEEE
Confidence 3468899999999855 22224444433 221 223556788889999998 333 1 122223445
Q ss_pred EeccCCCCccccccCCCCCCCCCCCccchhhhhhhhhhhhhhccccCchhcHHHHHHHHHhhhc
Q 023458 139 TTASNAQESSFGTYCPGMDPSPPPEYITCLGDLYSVAWMEDSETHNLKRETISQQYQAVKERTS 202 (282)
Q Consensus 139 iTAS~~~EsSya~~~~~~~~~~~~~~~t~lgD~fS~~wme~~~~~~~~~~Tl~~~f~~vk~~t~ 202 (282)
+++|. .+|... .+.|...|++..... ...+|.+.+...|....
T Consensus 309 ig~s~---~~~~~~----------------~~~~~~~~~~~l~~~--~~~~lG~a~~~a~~~~~ 351 (378)
T PF01364_consen 309 IGSSR---VSYASP----------------NDRLNRGFYEALFNS--NMDTLGEALRQAKNYYL 351 (378)
T ss_dssp EEESS-----SSHH----------------HHHHHHHHTT-STT------BHHHHHHHHHHHHH
T ss_pred Eecce---eEecch----------------HHHHHHHHHHHHhcc--CCCCHHHHHHHHHHHHH
Confidence 55543 444321 355666666544322 12288998888777554
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=73.61 E-value=2.9 Score=39.62 Aligned_cols=100 Identities=19% Similarity=0.399 Sum_probs=64.5
Q ss_pred CCeEeeCCCC--------CCccCCccccCCCCCCC----HHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCC
Q 023458 14 PGVIINHPQG--------ENLYDGVPKDYTGEHVT----AQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGP 81 (282)
Q Consensus 14 pG~i~n~~~g--------~nvY~gv~iDY~g~~Vt----~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~ 81 (282)
||+|.+- || .++|+-..|+-.|..|. |+.....|.-- .|+ | +.+|||-|
T Consensus 104 PGrVLHi-DGD~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~~~--------------~PD--I-lViTGHD~- 164 (283)
T TIGR02855 104 PGRVLHI-DGDPEYLRKCLKLYKKIGVPVVGIHCKEKEMPEKVLDLIEEV--------------RPD--I-LVITGHDA- 164 (283)
T ss_pred CCcEEee-cCCHHHHHHHHHHHHHhCCceEEEEecchhchHHHHHHHHHh--------------CCC--E-EEEeCchh-
Confidence 9998874 45 36676444444444443 55555555511 122 3 45799954
Q ss_pred CccC----CCC-CCCCCHHHHHHHHHHHHHcC-CCCeEEEEEecccccccccccCCCCCC
Q 023458 82 GVLG----MPN-MPYVYAMEFIDVLKKKHAAK-SYKGMVIYVEACESGSIFEGVMPKDLD 135 (282)
Q Consensus 82 g~l~----fpd-~~~L~a~dL~~~l~~M~~~~-~Ykk~v~~iEAC~SGSmf~~~lp~~~n 135 (282)
+++ |.| ..+-+++.+.++.+..-+-. -+-+|||+.-|||| -||.||..+-|
T Consensus 165 -~~K~~~d~~dl~~YrnSkyFVeaVk~aR~y~~~~D~LVIFAGACQS--~yEall~AGAN 221 (283)
T TIGR02855 165 -YSKNKGNYMDLNAYRHSKYFVETVREARKYVPSLDQLVIFAGACQS--HFESLIRAGAN 221 (283)
T ss_pred -hhcCCCChhhhhhhhhhHHHHHHHHHHHhcCCCcccEEEEcchhHH--HHHHHHHcCcc
Confidence 443 222 24678999999999876533 67799999999998 78888766655
No 13
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=70.62 E-value=3.2 Score=40.91 Aligned_cols=63 Identities=21% Similarity=0.425 Sum_probs=38.2
Q ss_pred CCCeEEEEEecCCCCC-------ccCCCCCC--C----CCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccccC
Q 023458 67 ANDRIFIFYSDHGGPG-------VLGMPNMP--Y----VYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEGVM 130 (282)
Q Consensus 67 ~~D~VFiY~tgHGg~g-------~l~fpd~~--~----L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~~l 130 (282)
+.|++++||+|||... |+.|-... . =+..-+-.....+|. ..-++-|.++++|.+|.+|....
T Consensus 132 ~~d~~~~~fsG~g~~~~~d~~~~lia~~t~p~~~a~~~~~~~s~~~~~~~~~~-~~~~~ql~~~d~~~~~~~~~~~~ 207 (380)
T COG4249 132 PADTILFFFSGHGATPGADGRAYLIAFDTRPGAVAYDGEGGISPYSVAQALHL-SEPGNQLVDLDACVRGDVFKATA 207 (380)
T ss_pred hhhhhhheeeccccccCCCCceeEEeecCChhhhcccCCCcccHHHHHHHHHh-ccCCceeehhhhhcchhhhcccc
Confidence 3699999999999962 33332110 0 011112233333443 33456778999999999998764
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=68.56 E-value=4.5 Score=38.51 Aligned_cols=101 Identities=25% Similarity=0.502 Sum_probs=64.1
Q ss_pred CCCeEeeCCCC--------CCccCCccccCCCCCCC----HHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCC
Q 023458 13 RPGVIINHPQG--------ENLYDGVPKDYTGEHVT----AQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGG 80 (282)
Q Consensus 13 ~pG~i~n~~~g--------~nvY~gv~iDY~g~~Vt----~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg 80 (282)
.||+|.+- || .++|+-.-|+=.|..|. |+.+...|.--+ |+ | |.+|||=|
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 36676444444455454 455555554221 21 2 45799965
Q ss_pred CCccCC----CC-CCCCCHHHHHHHHHHHHH-cCCCCeEEEEEecccccccccccCCCCCC
Q 023458 81 PGVLGM----PN-MPYVYAMEFIDVLKKKHA-AKSYKGMVIYVEACESGSIFEGVMPKDLD 135 (282)
Q Consensus 81 ~g~l~f----pd-~~~L~a~dL~~~l~~M~~-~~~Ykk~v~~iEAC~SGSmf~~~lp~~~n 135 (282)
+++= .+ ..+=.++.+.++.+..-+ ..-+-+||++.-|||| -||.||..+-|
T Consensus 166 --~~K~~~d~~dl~~YrnSkyFVeaV~~aR~~ep~~D~LVIfAGACQS--~fEall~AGAN 222 (287)
T PF05582_consen 166 --YLKNKKDYSDLNNYRNSKYFVEAVKEARKYEPNLDDLVIFAGACQS--HFEALLEAGAN 222 (287)
T ss_pred --hhcCCCChhhhhhhhccHHHHHHHHHHHhcCCCcccEEEEcchhHH--HHHHHHHcCcc
Confidence 3332 22 235678889999987755 4456789999999998 78888766655
No 15
>PF07999 RHSP: Retrotransposon hot spot protein; InterPro: IPR006518 These sequences are full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position.
Probab=41.92 E-value=1.5e+02 Score=29.92 Aligned_cols=104 Identities=19% Similarity=0.320 Sum_probs=64.6
Q ss_pred CHHHHHHHHHHHHHcCCCCeEEEEEecccccc-cccccCCCCCCEEEEeccCCCCccccccCCCCCCCCCCCccchhhhh
Q 023458 93 YAMEFIDVLKKKHAAKSYKGMVIYVEACESGS-IFEGVMPKDLDIYVTTASNAQESSFGTYCPGMDPSPPPEYITCLGDL 171 (282)
Q Consensus 93 ~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGS-mf~~~lp~~~nV~~iTAS~~~EsSya~~~~~~~~~~~~~~~t~lgD~ 171 (282)
...+-..+++.|..+++ +=.||.|.|..+. ....++|....++++|| |+++.|........ ..+-+--|= |.
T Consensus 187 ~~~~a~~~i~~~~~~g~--~GyiI~Dv~~~~~~p~~~~~~~~Wg~ivlss--P~~~~~~~w~k~~~--~~~I~iNC~-d~ 259 (439)
T PF07999_consen 187 DQEAAVSVINEMSSRGV--KGYIIYDVAKKGHQPSPELPPRGWGMIVLSS--PNESNFEEWSKQRG--ALPIYINCY-DE 259 (439)
T ss_pred CchHHHHHHHHHHhhCc--eEEEEEecccccCccCCCcccCCCCEEEEcC--CChhhcccccccCC--ceeEEeeCC-cH
Confidence 35678889999977554 5678899999983 33346788889999987 56666766654311 111111221 11
Q ss_pred h----hhhhhhhhccc----cCchhcHHHHHHHHHhhhcc
Q 023458 172 Y----SVAWMEDSETH----NLKRETISQQYQAVKERTSN 203 (282)
Q Consensus 172 f----S~~wme~~~~~----~~~~~Tl~~~f~~vk~~t~~ 203 (282)
- -+.||+..... ...++.|.+-.+.|+++...
T Consensus 260 ~e~KA~~aW~r~~~~~~~~~~~a~~~~e~~W~~Ve~RI~~ 299 (439)
T PF07999_consen 260 REVKAMCAWMRRSQLAEEQPEQAEVELENYWKEVEERIDE 299 (439)
T ss_pred HHHHHHHHHHHhchhhcccchhhhhHHHHHHHHHHHHHHH
Confidence 1 24699866441 11234677788888887654
No 16
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=36.17 E-value=37 Score=30.81 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=26.4
Q ss_pred EEEEEecCCC---------CCccCCCCCCCCCHHHHHHHHHHHHH
Q 023458 71 IFIFYSDHGG---------PGVLGMPNMPYVYAMEFIDVLKKKHA 106 (282)
Q Consensus 71 VFiY~tgHGg---------~g~l~fpd~~~L~a~dL~~~l~~M~~ 106 (282)
=-||+||||- .|-+-|=..+ +..++|.++++...+
T Consensus 78 PVIfiTGhgDIpmaV~AmK~GAvDFLeKP-~~~q~Lldav~~Al~ 121 (202)
T COG4566 78 PVIFLTGHGDIPMAVQAMKAGAVDFLEKP-FSEQDLLDAVERALA 121 (202)
T ss_pred CEEEEeCCCChHHHHHHHHcchhhHHhCC-CchHHHHHHHHHHHH
Confidence 3588999998 3555554444 889999999998865
No 17
>PF13709 DUF4159: Domain of unknown function (DUF4159)
Probab=34.88 E-value=84 Score=28.19 Aligned_cols=66 Identities=14% Similarity=0.146 Sum_probs=35.2
Q ss_pred HHHHHHHHcCCCCCccCC-CCceecCCC---CCeEEEEEecCCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEE
Q 023458 41 AQNLYAVLLGDRKAVKGG-SGKVVNSKA---NDRIFIFYSDHGGPGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIY 116 (282)
Q Consensus 41 ~~nfl~VL~G~~~~~~~~-s~kvl~S~~---~D~VFiY~tgHGg~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~ 116 (282)
..||+..|.-+-+...+. ....+.-+. -+.=||||+|||.-. ++.+++...=++|. ++- +++
T Consensus 21 l~~L~~~l~~~t~~~~~~~~~~~v~~~~~~L~~yP~ly~~g~~~~~---------~s~~e~~~Lr~Yl~-~GG----fl~ 86 (207)
T PF13709_consen 21 LRNLSRFLNQRTSLEVGPEEPQAVDLDDDELFFYPFLYWPGHGDFP---------LSDEEIANLRRYLE-NGG----FLL 86 (207)
T ss_pred HHHHHHHHHHHhCCCccCCCCcccCCCchhHHhCCEEEEeCCCCCC---------CCHHHHHHHHHHHH-cCC----EEE
Confidence 467777776443222211 113333222 245589999999652 45666655555553 343 456
Q ss_pred Eecc
Q 023458 117 VEAC 120 (282)
Q Consensus 117 iEAC 120 (282)
+|+|
T Consensus 87 ~D~~ 90 (207)
T PF13709_consen 87 FDDR 90 (207)
T ss_pred EECC
Confidence 6766
No 18
>PF03415 Peptidase_C11: Clostripain family This family belongs to family C11 of the peptidase classification.; InterPro: IPR005077 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 C11 (clostripain family, clan CD). ; PDB: 3UWS_A.
Probab=28.43 E-value=42 Score=33.12 Aligned_cols=73 Identities=23% Similarity=0.237 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCCC---------ccCCCC---CCCCCHHHHHHHHHHH
Q 023458 37 EHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGPG---------VLGMPN---MPYVYAMEFIDVLKKK 104 (282)
Q Consensus 37 ~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~g---------~l~fpd---~~~L~a~dL~~~l~~M 104 (282)
+..+|+.+-.+|. . +.+.=|-++-.+-|.+||+-- -+++.+ +..|+-.||+++|+
T Consensus 76 nm~dp~tL~~fi~-~----------~~~~yPA~~y~LIlw~HG~Gw~~~~~~~~rg~~~D~~~~~~~l~i~el~~aL~-- 142 (397)
T PF03415_consen 76 NMGDPDTLSDFIN-W----------AKENYPADRYGLILWDHGGGWLPASDSSTRGIGFDETSGGDYLSIPELAEALE-- 142 (397)
T ss_dssp -TTSHHHHHHHHH-H----------HHHHS-ECEEEEEEES-B-TT--TTGGG---EEEETTE---EE-HHHHHHHS---
T ss_pred CCCCHHHHHHHHH-H----------HHHhCCcccEEEEEEECCCCCCcCCCCCcceEecCCCChhhcccHHHHHHHHc--
Confidence 5677888888887 1 222346678888899999621 344433 24799999999999
Q ss_pred HHcCCCCeEEEEEeccccccc
Q 023458 105 HAAKSYKGMVIYVEACESGSI 125 (282)
Q Consensus 105 ~~~~~Ykk~v~~iEAC~SGSm 125 (282)
..-+==++..|||.=|++
T Consensus 143 ---~~~~~d~I~FDaClM~~v 160 (397)
T PF03415_consen 143 ---GGPKFDFIGFDACLMGSV 160 (397)
T ss_dssp ----TT-EEEEEEESTT--BH
T ss_pred ---CCCCCcEEEECcccchhH
Confidence 222234778999999886
No 19
>PRK10649 hypothetical protein; Provisional
Probab=27.52 E-value=36 Score=35.27 Aligned_cols=17 Identities=24% Similarity=0.700 Sum_probs=14.0
Q ss_pred CCCCCeEEEEEecCCCC
Q 023458 65 SKANDRIFIFYSDHGGP 81 (282)
Q Consensus 65 S~~~D~VFiY~tgHGg~ 81 (282)
...++.++||++|||..
T Consensus 449 ~~~~nt~iiy~SDHGe~ 465 (577)
T PRK10649 449 ATDPNGFLVYFSDHGEE 465 (577)
T ss_pred cCCCCeEEEEECCCCcc
Confidence 34578999999999975
No 20
>KOG1387 consensus Glycosyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=26.14 E-value=66 Score=32.16 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=26.1
Q ss_pred ccccCCCC-CCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEE
Q 023458 30 VPKDYTGE-HVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFY 75 (282)
Q Consensus 30 v~iDY~g~-~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~ 75 (282)
+.+=|+|+ +||++++|+=.+.+.+ ++-+++.-.|||+
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 9999999876664432 3445555677775
No 21
>KOG1654 consensus Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton]
Probab=23.84 E-value=70 Score=26.62 Aligned_cols=34 Identities=12% Similarity=0.369 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHcCCCCCccCCCCceecCCCCCeEEEEEecCCCC
Q 023458 37 EHVTAQNLYAVLLGDRKAVKGGSGKVVNSKANDRIFIFYSDHGGP 81 (282)
Q Consensus 37 ~~Vt~~nfl~VL~G~~~~~~~~s~kvl~S~~~D~VFiY~tgHGg~ 81 (282)
+++|+..|+.|++ + .|+-.|++-+|++..+|--+
T Consensus 53 ~dltvgqfi~iIR----------k-RiqL~~~kA~flfVn~~~p~ 86 (116)
T KOG1654|consen 53 DDLTVGQFIKIIR----------K-RIQLSPEKAFFLFVNNTSPP 86 (116)
T ss_pred ccccHHHHHHHHH----------H-HhccChhHeEEEEEcCcCCc
Confidence 6899999999999 2 37789999999999988543
No 22
>PF01972 SDH_sah: Serine dehydrogenase proteinase; InterPro: IPR002825 This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family belong to MEROPS peptidase family S49; they are mostly unassigned peptidases but include the archaean signal peptide peptidase 1 []. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan []. ; GO: 0016021 integral to membrane
Probab=23.47 E-value=2e+02 Score=27.53 Aligned_cols=55 Identities=18% Similarity=0.240 Sum_probs=43.5
Q ss_pred CCCCCeEEEEEecCCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEec
Q 023458 65 SKANDRIFIFYSDHGGPGVLGMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEA 119 (282)
Q Consensus 65 S~~~D~VFiY~tgHGg~g~l~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEA 119 (282)
-.-+++|..|+.+-...+++++|-..++.-.|....++.......-+.+.++++|
T Consensus 45 ~kr~srvI~~Ihrqe~~~~~giPi~~~I~i~dse~v~raI~~~~~~~~IdLii~T 99 (285)
T PF01972_consen 45 EKRGSRVITLIHRQERVSFLGIPIYRYIDIDDSEFVLRAIREAPKDKPIDLIIHT 99 (285)
T ss_pred HHhCCEEEEEEEeccccceeccccceeEcHhhHHHHHHHHHhcCCCCceEEEEEC
Confidence 3457889999988877889999987778877777777777776667778888876
No 23
>COG2194 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]
Probab=23.23 E-value=46 Score=34.58 Aligned_cols=16 Identities=38% Similarity=0.845 Sum_probs=12.8
Q ss_pred CCCCCeEEEEEecCCC
Q 023458 65 SKANDRIFIFYSDHGG 80 (282)
Q Consensus 65 S~~~D~VFiY~tgHGg 80 (282)
....+-++||+||||-
T Consensus 441 ~~~~~~~liY~SDHGE 456 (555)
T COG2194 441 DKKDNTSLIYFSDHGE 456 (555)
T ss_pred hCCCCeEEEEEcCccH
Confidence 3334889999999996
No 24
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=23.05 E-value=1.2e+02 Score=26.78 Aligned_cols=31 Identities=19% Similarity=0.366 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHcCCCCeEEEEEecccc
Q 023458 91 YVYAMEFIDVLKKKHAAKSYKGMVIYVEACES 122 (282)
Q Consensus 91 ~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~S 122 (282)
.++|.-|.++|++.+++.. +..++-||||-+
T Consensus 67 PVHA~NL~e~l~~I~~~~~-~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHP-NPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCC-CCeEEEEECCCC
Confidence 5999999999999876333 668899999976
No 25
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=22.38 E-value=1.2e+02 Score=25.03 Aligned_cols=38 Identities=24% Similarity=0.235 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccc
Q 023458 91 YVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEG 128 (282)
Q Consensus 91 ~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~ 128 (282)
.-.+.+|++.|.+...++.|.++|++.+.=.=|-|-+.
T Consensus 72 ~~Fa~~vA~~L~~~~~~~~~~~LvlvA~p~~LG~LR~~ 109 (138)
T PF10116_consen 72 ERFAREVADRLEKARRAGKFDRLVLVAPPRFLGLLREH 109 (138)
T ss_pred HHHHHHHHHHHHHHHHhCCCCeEEEEECHHHHHHHHHH
Confidence 35678999999999999999999999877555555443
No 26
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=21.37 E-value=53 Score=33.71 Aligned_cols=15 Identities=33% Similarity=0.702 Sum_probs=12.5
Q ss_pred CCCeEEEEEecCCCC
Q 023458 67 ANDRIFIFYSDHGGP 81 (282)
Q Consensus 67 ~~D~VFiY~tgHGg~ 81 (282)
+.+.++||++|||..
T Consensus 428 ~~~t~iIy~SDHGe~ 442 (522)
T PRK09598 428 KQPALMIYLSDHGES 442 (522)
T ss_pred CCCeEEEEEccCccc
Confidence 348999999999953
No 27
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=21.30 E-value=1.1e+02 Score=26.32 Aligned_cols=31 Identities=23% Similarity=0.293 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHHcCCCCeEEEEEecccc
Q 023458 91 YVYAMEFIDVLKKKHAAKSYKGMVIYVEACES 122 (282)
Q Consensus 91 ~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~S 122 (282)
.++|.-|.++|++.+++.. +-.++-||||=.
T Consensus 43 PVHA~NL~e~l~~I~~~~~-~~~iIAIDAcLG 73 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHP-NPFIIAIDACLG 73 (140)
T ss_pred CcccccHHHHHHHHHHhCC-CCeEEEEECccC
Confidence 4999999999999876443 567889999976
No 28
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=20.05 E-value=2e+02 Score=24.77 Aligned_cols=35 Identities=26% Similarity=0.346 Sum_probs=26.8
Q ss_pred CCeEeeCCCCCCccCCccccCCCC--CCCHHHHHHHH
Q 023458 14 PGVIINHPQGENLYDGVPKDYTGE--HVTAQNLYAVL 48 (282)
Q Consensus 14 pG~i~n~~~g~nvY~gv~iDY~g~--~Vt~~nfl~VL 48 (282)
+|.+|..++|.-+..|--+|=++. ++|.+....+.
T Consensus 21 ~~~~y~~~dg~~~i~G~l~d~~~~~~~~t~~~~~~~~ 57 (197)
T cd03020 21 GGVLYTDDDGRYLIQGNLYDAKGRKDDLTEARLAQLN 57 (197)
T ss_pred CEEEEEcCCCCEEEEeEEEEccCCCCChhHHHHHHhh
Confidence 578899999988888888887776 57776655543
No 29
>cd01906 proteasome_protease_HslV proteasome_protease_HslV. This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleo
Probab=20.01 E-value=2.2e+02 Score=23.74 Aligned_cols=116 Identities=12% Similarity=0.082 Sum_probs=61.2
Q ss_pred ceecCCCCCeEEEEEecCCCCCcc------------CCCCCCCCCHHHHHHHHHHHHHcCCCCeEEEEEecccccccccc
Q 023458 61 KVVNSKANDRIFIFYSDHGGPGVL------------GMPNMPYVYAMEFIDVLKKKHAAKSYKGMVIYVEACESGSIFEG 128 (282)
Q Consensus 61 kvl~S~~~D~VFiY~tgHGg~g~l------------~fpd~~~L~a~dL~~~l~~M~~~~~Ykk~v~~iEAC~SGSmf~~ 128 (282)
|+..- ++++++-++|+.++... .+..+..++.+.+.+.|..+..+.+.+.--|.+.. ++-+
T Consensus 33 Ki~~i--~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~p~~~~~-----lv~G 105 (182)
T cd01906 33 KIFKI--DDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSL-----LVAG 105 (182)
T ss_pred eEEEE--CCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCCccChheEE-----EEEE
Confidence 55433 45799999999987411 11224569999999999887665554211112222 2222
Q ss_pred cCC-CCCCEEEEeccCCCCccccccCCCCCCCCCCCccchhhhhhhhhhhhhhccccCchhcHHHHHHHHHh
Q 023458 129 VMP-KDLDIYVTTASNAQESSFGTYCPGMDPSPPPEYITCLGDLYSVAWMEDSETHNLKRETISQQYQAVKE 199 (282)
Q Consensus 129 ~lp-~~~nV~~iTAS~~~EsSya~~~~~~~~~~~~~~~t~lgD~fS~~wme~~~~~~~~~~Tl~~~f~~vk~ 199 (282)
+-. ..+.+|.+..+........+ ..| -|-.+-..||+.....++ |+.+..+.+++
T Consensus 106 ~d~~~~~~Ly~id~~G~~~~~~~~-----------a~G--~g~~~~~~~L~~~~~~~~---s~~ea~~l~~~ 161 (182)
T cd01906 106 VDEEGGPQLYSVDPSGSYIEYKAT-----------AIG--SGSQYALGILEKLYKPDM---TLEEAIELALK 161 (182)
T ss_pred EeCCCCcEEEEECCCCCEeeccEE-----------EEC--CCcHHHHHHHHHHccCCC---CHHHHHHHHHH
Confidence 111 23567777665543332111 122 123455678876544333 55555555544
Done!