Query psy6307
Match_columns 368
No_of_seqs 201 out of 437
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 23:01:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6307hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1349|consensus 100.0 4.4E-89 9.5E-94 638.3 22.5 281 21-351 25-306 (309)
2 KOG1348|consensus 100.0 1.6E-85 3.5E-90 638.4 20.2 260 23-340 44-320 (477)
3 PF01650 Peptidase_C13: Peptid 100.0 1E-78 2.2E-83 580.5 21.4 254 25-336 1-256 (256)
4 COG5206 GPI8 Glycosylphosphati 100.0 1.9E-77 4.1E-82 563.4 19.7 290 16-355 20-310 (382)
5 KOG1348|consensus 99.2 1.2E-11 2.7E-16 122.3 7.0 147 103-277 75-226 (477)
6 KOG1349|consensus 99.1 4.8E-11 1E-15 113.4 4.6 132 123-280 80-216 (309)
7 PF00656 Peptidase_C14: Caspas 99.1 5.7E-10 1.2E-14 103.4 8.9 193 25-316 1-237 (248)
8 PF01650 Peptidase_C13: Peptid 99.0 2.9E-10 6.2E-15 109.4 6.1 133 104-265 31-166 (256)
9 COG5206 GPI8 Glycosylphosphati 98.2 3.1E-06 6.8E-11 81.6 6.9 106 154-280 106-216 (382)
10 KOG1546|consensus 97.3 0.0025 5.4E-08 63.3 11.1 142 22-244 61-212 (362)
11 smart00115 CASc Caspase, inter 96.9 0.0081 1.8E-07 57.2 10.6 143 157-313 51-216 (241)
12 cd00032 CASc Caspase, interleu 96.8 0.0063 1.4E-07 57.8 9.3 143 156-313 52-220 (243)
13 PF14538 Raptor_N: Raptor N-te 77.4 5.7 0.00012 35.7 5.7 72 158-245 72-153 (154)
14 COG4249 Uncharacterized protei 74.3 3.8 8.3E-05 42.1 4.2 61 223-289 184-257 (380)
15 KOG1017|consensus 68.3 4.8 0.0001 38.2 3.0 23 43-65 203-225 (267)
16 PF00656 Peptidase_C14: Caspas 67.6 3.4 7.4E-05 38.0 1.9 13 187-199 121-133 (248)
17 PF12770 CHAT: CHAT domain 66.9 4.4 9.5E-05 38.3 2.6 46 187-239 144-201 (287)
18 smart00115 CASc Caspase, inter 50.7 37 0.00081 32.2 5.9 60 133-198 72-131 (241)
19 PF11181 YflT: Heat induced st 47.2 27 0.00058 28.9 3.8 31 39-69 6-36 (103)
20 PRK10834 vancomycin high tempe 43.9 24 0.00051 34.1 3.3 7 97-103 116-122 (239)
21 PRK10629 EnvZ/OmpR regulon mod 43.1 95 0.0021 27.1 6.7 38 22-63 32-70 (127)
22 TIGR00109 hemH ferrochelatase. 40.7 1.6E+02 0.0035 29.3 8.9 79 135-232 187-266 (322)
23 PF02698 DUF218: DUF218 domain 37.0 34 0.00075 29.5 3.1 35 28-64 41-75 (155)
24 cd06259 YdcF-like YdcF-like. Y 36.5 33 0.00071 29.4 2.8 37 26-64 36-72 (150)
25 PF10686 DUF2493: Protein of u 33.1 36 0.00079 26.6 2.3 22 27-48 5-26 (71)
26 PF07804 HipA_C: HipA-like C-t 29.2 50 0.0011 25.7 2.5 24 12-36 49-72 (79)
27 PRK10494 hypothetical protein; 27.9 56 0.0012 31.6 3.1 37 26-64 122-158 (259)
28 cd00419 Ferrochelatase_C Ferro 27.4 3.4E+02 0.0075 23.5 7.7 78 136-232 18-97 (135)
29 COG2949 SanA Uncharacterized m 26.5 78 0.0017 30.4 3.6 34 28-64 97-130 (235)
30 KOG1546|consensus 26.5 47 0.001 33.8 2.3 31 161-198 122-152 (362)
31 cd00032 CASc Caspase, interleu 25.8 91 0.002 29.5 4.1 122 23-199 8-133 (243)
32 PRK00035 hemH ferrochelatase; 24.3 3.8E+02 0.0083 26.4 8.4 80 136-232 189-268 (333)
33 KOG1552|consensus 24.2 72 0.0016 31.3 3.1 44 42-86 112-161 (258)
34 PF01364 Peptidase_C25: Peptid 23.7 45 0.00097 33.5 1.7 102 185-310 238-351 (378)
35 KOG1360|consensus 23.2 83 0.0018 33.2 3.4 31 40-70 431-465 (570)
36 TIGR01689 EcbF-BcbF capsule bi 22.4 1.5E+02 0.0032 25.7 4.4 41 24-64 39-85 (126)
No 1
>KOG1349|consensus
Probab=100.00 E-value=4.4e-89 Score=638.34 Aligned_cols=281 Identities=71% Similarity=1.184 Sum_probs=267.1
Q ss_pred CCCCcEEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCCCcccc
Q psy6307 21 KHSNNWAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGEDVEVD 100 (368)
Q Consensus 21 ~~~~~wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~~v~iD 100 (368)
.|++||||||++||+||||||.|||+.+|+.+||+||||+|||+|++||+|||+|||+||+||++.+++.|+||+.|++|
T Consensus 25 ~htnNwAVLv~tSRfwfNYRH~aNvl~~YrsvKrlGipDsqIilmladd~acn~RN~~pg~Vy~n~~~~~nlygd~vevd 104 (309)
T KOG1349|consen 25 GHTNNWAVLVCTSRFWFNYRHVANVLSVYRSVKRLGIPDSQIILMLADDMACNSRNPRPGTVYNNENHALNLYGDDVEVD 104 (309)
T ss_pred hccCceEEEEecchhhhhHHHHHHHHHHHHHHHHcCCCcccEEEEeccccccccCCCCCcceeccccccccccCCcceee
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhccccccc
Q psy6307 101 YRGYEVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELL 180 (368)
Q Consensus 101 Y~g~~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~ 180 (368)
|||++||+|||+++|||+.++.+|++|||++++++|||||+|||||+||+||||.+++|.+
T Consensus 105 yrgyevtvEnflr~LTgR~~~~tprSKrlltDe~SNIlIYmtGHGgd~FlKFqd~eelts~------------------- 165 (309)
T KOG1349|consen 105 YRGYEVTVENFLRVLTGRHPNNTPRSKRLLTDEGSNILIYLTGHGGDGFLKFQDAEELTSD------------------- 165 (309)
T ss_pred cccchhHHHHHHHHHcCCCCCCCchhhhhcccCCCcEEEEEccCCCccceecccHHHhhhH-------------------
Confidence 9999999999999999999999999999999999999999999999999999998776665
Q ss_pred cCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccCCCcEEEEEecCCCC
Q psy6307 181 TDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSPNILAMASSLVGE 260 (368)
Q Consensus 181 ~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~nV~~itAS~~~E 260 (368)
||++++++|++++||++++|++|+|||.||++++.+|||++++||..+|
T Consensus 166 -------------------------------dLadai~qm~e~~Ryneil~miDTCQaasly~~~~sPNVLav~SS~~ge 214 (309)
T KOG1349|consen 166 -------------------------------DLADAIQQMWEKKRYNEILFMIDTCQAASLYERFYSPNVLAVASSLVGE 214 (309)
T ss_pred -------------------------------HHHHHHHHHHHhhhhceEEEEeeccchHHHHHhhcCCCeEEEeecccCC
Confidence 9999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCcceeeccchHHHHHHHhcccCCChhhHHHHHhhccCcccccCceeeccCCCCCCCCccccccccCCcce
Q psy6307 261 DSLSHHVDPAIGVYIIDRYTYYALEFLEDVHLDSAKTMEDFLAVCPKRVCISTIGIRTDLFRRDPKHVPITDFFGSIRPV 340 (368)
Q Consensus 261 sSys~~~d~~ig~~l~D~FTy~~~~~le~~~~~~~~Tl~~lf~~v~~~~~~S~~~~~~~~~~~~~~~~~~~dF~g~~~~~ 340 (368)
+|||++.|+.||++++|+||||.++||++.......||+++|+.+.++.++||++.++|+|.+++++++++||||+++..
T Consensus 215 ~SySh~~d~~Igv~vIDrftyy~l~flek~~~~~~~~l~dl~~s~~~~~~~St~gvr~dl~~r~~~~v~itDFFg~vr~~ 294 (309)
T KOG1349|consen 215 PSYSHHSDSDIGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLFDSCPKRLLGSTPGVRTDLYQRDPKDVLITDFFGSVRIE 294 (309)
T ss_pred cccccCCCcccceeeeccchHHHHHHHHhcccchhhhHHHHHHhCChhhhcCCcCcccccccCCcccceeeeecccceeE
Confidence 99999999999999999999999999999644455599999999999999999999999999999999999999999955
Q ss_pred eecC-CccccCC
Q psy6307 341 ELSA-PINISDF 351 (368)
Q Consensus 341 ~~~~-~~~~~~~ 351 (368)
.++. ++++..+
T Consensus 295 ~~~~~~~~~~~~ 306 (309)
T KOG1349|consen 295 LHTSEEIKLDDE 306 (309)
T ss_pred eccchhhcccCc
Confidence 5544 5665553
No 2
>KOG1348|consensus
Probab=100.00 E-value=1.6e-85 Score=638.41 Aligned_cols=260 Identities=30% Similarity=0.511 Sum_probs=241.9
Q ss_pred CCcEEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCCCccccCC
Q psy6307 23 SNNWAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGEDVEVDYR 102 (368)
Q Consensus 23 ~~~wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~~v~iDY~ 102 (368)
..+||||||||+||||||||||||||||+||++|+|+||||+|||||||+||+||+||+|+|+|+ ++|||. ||++||+
T Consensus 44 gt~waVLVAGSngyyNYRHQADvcHAYqiLrkgGikeEnIvv~MYDDIA~~~~NPrpG~iiN~P~-G~DvY~-GvpkDYt 121 (477)
T KOG1348|consen 44 GTRWAVLVAGSNGYYNYRHQADVCHAYQILRKGGIKEENIVVMMYDDIANNEENPRPGVIINRPN-GKDVYQ-GVPKDYT 121 (477)
T ss_pred ceeEEEEEecCCcccchhhhhhHHHHHHHHHhcCCCchhEEEEEehhhhcCCCCCCCceeecCCC-chhhhc-CCCCccc
Confidence 37899999999999999999999999999999999999999999999999999999999999997 799995 9999999
Q ss_pred CCCCCHHHHHHHHcCCCCCCCC-CCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhcccccccc
Q psy6307 103 GYEVTVENFIRLLTGRLPPSTP-RSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLT 181 (368)
Q Consensus 103 g~~vt~enfl~vL~G~~~~~~p-~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~ 181 (368)
|++||++||++||.|+...+.+ ..|++.|+|||+||||||||||||+|.||+++.
T Consensus 122 g~~Vt~~Nf~aVllGd~savkGGsGKV~~SgpnDhiFiYytDHG~pGvl~mP~~~~------------------------ 177 (477)
T KOG1348|consen 122 GEDVTPQNFLAVLLGDASAVKGGSGKVLKSGPNDHIFIYYTDHGGPGVLGMPTSPD------------------------ 177 (477)
T ss_pred CCcCCHHHHHHHHhcccccccCCCceeeccCCCceEEEEEecCCCCceEecCCCcc------------------------
Confidence 9999999999999999998875 456688999999999999999999999998754
Q ss_pred CCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccCCC--cEEEEEecCCC
Q psy6307 182 DEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSP--NILAMASSLVG 259 (368)
Q Consensus 182 ~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~--nV~~itAS~~~ 259 (368)
|+++||.++|++||+.++|++||||+|||+|||||+.+++. ||||+|||++.
T Consensus 178 --------------------------l~akdlnevL~kmhk~k~Y~~mvfYlEACESGSmfegiLp~~lnIYatTAaNa~ 231 (477)
T KOG1348|consen 178 --------------------------LYAKDLNEVLKKMHKSKTYKKMVFYLEACESGSMFEGILPKNLNIYATTAANAR 231 (477)
T ss_pred --------------------------hhHHHHHHHHHHHHhccchheEEEEeeeccCcchhhhhccCCCcEEEeecCCcc
Confidence 55669999999999999999999999999999999998875 89999999999
Q ss_pred CcccCCCCC-C------CCcceeeccchHHHHHHHhcc--cCCChhhHHHHHhhccCccccc-----CceeeccCCCCCC
Q psy6307 260 EDSLSHHVD-P------AIGVYIIDRYTYYALEFLEDV--HLDSAKTMEDFLAVCPKRVCIS-----TIGIRTDLFRRDP 325 (368)
Q Consensus 260 EsSys~~~d-~------~ig~~l~D~FTy~~~~~le~~--~~~~~~Tl~~lf~~v~~~~~~S-----~~~~~~~~~~~~~ 325 (368)
||||+++|+ . +.++|++|.| +++|||++ ++..++||.+||+.||++|..| |++++|+ ..|
T Consensus 232 ESSwgtycp~~~psppse~~tcLGDly---SV~WmeDSd~hdL~kETL~qQYhlVK~rt~~s~s~gsHVmqyGd---~~i 305 (477)
T KOG1348|consen 232 ESSWGTYCPGEYPSPPSEYSTCLGDLY---SVNWMEDSDVHDLKKETLHQQYHLVKKRTNTSYSYGSHVMQYGD---KTI 305 (477)
T ss_pred ccccceeCCCCCCCChhhcccccccce---eeeeeccCccccchHHHHHHHHHHHHHhcCCCCCCcceeeecCc---chh
Confidence 999999986 2 7899999975 67999998 6789999999999999999988 9999998 599
Q ss_pred CCccccccccCCcce
Q psy6307 326 KHVPITDFFGSIRPV 340 (368)
Q Consensus 326 ~~~~~~dF~g~~~~~ 340 (368)
.+..|..|+|..+..
T Consensus 306 ske~l~lfqG~~pa~ 320 (477)
T KOG1348|consen 306 SKEKLMLFQGMKPAN 320 (477)
T ss_pred hHHHHHHHcCCCccc
Confidence 999999999998554
No 3
>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-78 Score=580.55 Aligned_cols=254 Identities=43% Similarity=0.772 Sum_probs=237.4
Q ss_pred cEEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCCCccccCCCC
Q psy6307 25 NWAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGEDVEVDYRGY 104 (368)
Q Consensus 25 ~wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~~v~iDY~g~ 104 (368)
|||||||||++|+|||||||+|+|||+||++|+|+||||||||||+|||||||+||+||++++ +.|+|. |++|||+|.
T Consensus 1 ~wAvlvagS~~~~NYRh~ad~~~~Y~~l~~~G~~~~~Iil~~~dd~a~~~~Np~~g~i~~~~~-~~n~y~-~~~iDY~g~ 78 (256)
T PF01650_consen 1 NWAVLVAGSNGWFNYRHQADVCHAYQLLKRNGIPDENIILMMYDDIACNPRNPFPGKIFNDPD-GTNVYK-GVEIDYRGE 78 (256)
T ss_pred CEEEEEeccCCceeeeEehHHHHHHHHHHHcCCCCceEEEEecCCccchhhCCCCceEEeCCC-cccccC-Ccccccccc
Confidence 799999999999999999999999999999999999999999999999999999999999997 789996 799999999
Q ss_pred CCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhccccccccCCC
Q psy6307 105 EVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLTDEG 184 (368)
Q Consensus 105 ~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~~~~ 184 (368)
+||+++|++||+|++. . +++|+|.++++|+|||||+|||++|+++||+++
T Consensus 79 ~v~~~~fl~vL~G~~~-~-~~~kvl~s~~~D~vfiy~~~HG~~~~l~~~~~~---------------------------- 128 (256)
T PF01650_consen 79 DVTPENFLNVLTGDKS-V-PSGKVLNSTENDNVFIYFTGHGGPGFLKFPDGE---------------------------- 128 (256)
T ss_pred ccCHHHHHHHhcCCCC-C-CccccccCCCCCeEEEEEeccCCCCcccCCCcc----------------------------
Confidence 9999999999999998 4 888999999999999999999999999998654
Q ss_pred ceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccc-cCCCcEEEEEecCCCCccc
Q psy6307 185 SNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEK-FYSPNILAMASSLVGEDSL 263 (368)
Q Consensus 185 d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~-l~~~nV~~itAS~~~EsSy 263 (368)
.|+++||+++|++|+++++|+++||++||||||||++. +..|||++||||+++|+||
T Consensus 129 ----------------------~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs~~~~L~~~~nv~~iTAa~~~e~Sy 186 (256)
T PF01650_consen 129 ----------------------ELTADDLADALDKMHEKKRYKKLVFVVEACYSGSFFEGLLKSPNVYVITAANADESSY 186 (256)
T ss_pred ----------------------cccHHHHHHHHHHHHhhCCcceEEEEEecccccchhhccCCCCCEEEEecCCcccccc
Confidence 45556999999999999999999999999999999999 5679999999999999999
Q ss_pred CCCC-CCCCcceeeccchHHHHHHHhcccCCChhhHHHHHhhccCcccccCceeeccCCCCCCCCccccccccC
Q psy6307 264 SHHV-DPAIGVYIIDRYTYYALEFLEDVHLDSAKTMEDFLAVCPKRVCISTIGIRTDLFRRDPKHVPITDFFGS 336 (368)
Q Consensus 264 s~~~-d~~ig~~l~D~FTy~~~~~le~~~~~~~~Tl~~lf~~v~~~~~~S~~~~~~~~~~~~~~~~~~~dF~g~ 336 (368)
+|++ |+.+++|++|+|++.|+..++. .+.+++||+++|+.++++|..||++++++. ++.++||++|+|.
T Consensus 187 ~~~~~~~~~~~~l~d~fs~~~m~~~~~-~~~~~~Tl~~~f~~v~~~~~~shv~~~gd~---s~~~~~v~~f~g~ 256 (256)
T PF01650_consen 187 GCYCSDDSIGTYLGDAFSYNWMEDSDS-HPLSEETLDDQFEYVKRKTTGSHVQQYGDP---SIPQLPVSEFQGT 256 (256)
T ss_pred cccccccccccEeHHHHHHHhhhhhcc-CCccccCHHHHHHHHHHhcccchHHhcCCC---CccccCHHHhcCC
Confidence 9988 9999999999998877766665 356679999999999999999999999994 8999999999984
No 4
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.9e-77 Score=563.40 Aligned_cols=290 Identities=56% Similarity=0.924 Sum_probs=279.1
Q ss_pred hhcccCCCCcEEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCC
Q psy6307 16 VLNEAKHSNNWAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGE 95 (368)
Q Consensus 16 ~~~~~~~~~~wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~ 95 (368)
++....+++|||||+++||+||||||.|||+.+|+.+||+||||++||+|.|||.|||.||-|||.||++.+...++|++
T Consensus 20 ga~~~t~tnNwAvLlstSRfwfNYRHmANVl~~Yr~vkrlGipDsQIilm~~dd~acnsRnlfpgsvf~N~Dra~dlyge 99 (382)
T COG5206 20 GAAARTNTNNWAVLLSTSRFWFNYRHMANVLVFYRVVKRLGIPDSQIILMSYDDQACNSRNLFPGSVFNNSDRAGDLYGE 99 (382)
T ss_pred hhhhcccCCceEEEEecccceeehhhhhhHHHHHHHHHHcCCCcceEEEEechhhhhhhcccCCcccccCcccccceeCc
Confidence 33444789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhcc
Q psy6307 96 DVEVDYRGYEVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRR 175 (368)
Q Consensus 96 ~v~iDY~g~~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~ 175 (368)
.++|||+|++||+|+|++.|+.+.++.+|.+||+.+++++|||||||||||++|+||+|-++++++
T Consensus 100 ~~eidY~gyevTve~firLLt~r~~en~p~sKrlltdE~SNIfIYmtGHGgd~FlKFqdaeemtse-------------- 165 (382)
T COG5206 100 DSEIDYSGYEVTVEVFIRLLTARSGENHPKSKRLLTDESSNIFIYMTGHGGDAFLKFQDAEEMTSE-------------- 165 (382)
T ss_pred ccccccccccchHHHHHHHHHhhccCCChhhhhhcccccCcEEEEEccCCCccceecccHHHhhhH--------------
Confidence 999999999999999999999999999999999999999999999999999999999997766665
Q ss_pred ccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccCCCcEEEEEe
Q psy6307 176 YHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSPNILAMAS 255 (368)
Q Consensus 176 yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~nV~~itA 255 (368)
||++++++|++++||++++|++|+|||.+|+++..+|||+++++
T Consensus 166 ------------------------------------Dladai~ql~~~kRyNeIlfmiDTCQAnaly~k~ysPNvLavgs 209 (382)
T COG5206 166 ------------------------------------DLADAISQLAAKKRYNEILFMIDTCQANALYDKSYSPNVLAVGS 209 (382)
T ss_pred ------------------------------------HHHHHHHHHHHhhhhceEEEEeeccccchhhhhccCCceEEEec
Confidence 99999999999999999999999999999999999999999999
Q ss_pred cCCCCcccCCCCCCCCcceeeccchHHHHHHHhcccCCChhhHHHHHhhccCcccccCceeeccCCCCCCCCcccccccc
Q psy6307 256 SLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLEDVHLDSAKTMEDFLAVCPKRVCISTIGIRTDLFRRDPKHVPITDFFG 335 (368)
Q Consensus 256 S~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~~~~~~~~Tl~~lf~~v~~~~~~S~~~~~~~~~~~~~~~~~~~dF~g 335 (368)
|.-+|||||++.|..||+.++|+||||.++|+|+++.+++.||++++....++..+||++.+...|.+++.++.++||||
T Consensus 210 Seig~ssyShhsd~~IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n~e~ihS~~gv~~~~fdr~p~d~litDFF~ 289 (382)
T COG5206 210 SEIGQSSYSHHSDSLIGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLNKEPIHSHVGVRELVFDRRPSDFLITDFFA 289 (382)
T ss_pred cccCCccccccchhhhhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcCcccccCCCCcccccccCCccceeehHhhh
Confidence 99999999999999999999999999999999999889999999999999999999999999999999999999999999
Q ss_pred CCcceeecC-CccccCCCCCc
Q psy6307 336 SIRPVELSA-PINISDFKKPT 355 (368)
Q Consensus 336 ~~~~~~~~~-~~~~~~~~~~~ 355 (368)
.++.+++.. +++|..|++-+
T Consensus 290 nVqn~~l~~~k~~~~~~~e~~ 310 (382)
T COG5206 290 NVQNSALELLKSHYHHFREAI 310 (382)
T ss_pred hhhhcchhhccccccchhhcc
Confidence 999999887 89999998764
No 5
>KOG1348|consensus
Probab=99.24 E-value=1.2e-11 Score=122.27 Aligned_cols=147 Identities=18% Similarity=0.274 Sum_probs=105.6
Q ss_pred CCCCCHHHHHHHHcCCCCC--CCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhh---cccc
Q psy6307 103 GYEVTVENFIRLLTGRLPP--STPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQK---RRYH 177 (368)
Q Consensus 103 g~~vt~enfl~vL~G~~~~--~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~---~~yk 177 (368)
..-+..||++-.|..|.+. .+|+++++.+.|+. -.|| . |+-+-.+|+.||++||++||+|+.++ +..|
T Consensus 75 kgGikeEnIvv~MYDDIA~~~~NPrpG~iiN~P~G-~DvY---~---GvpkDYtg~~Vt~~Nf~aVllGd~savkGGsGK 147 (477)
T KOG1348|consen 75 KGGIKEENIVVMMYDDIANNEENPRPGVIINRPNG-KDVY---Q---GVPKDYTGEDVTPQNFLAVLLGDASAVKGGSGK 147 (477)
T ss_pred hcCCCchhEEEEEehhhhcCCCCCCCceeecCCCc-hhhh---c---CCCCcccCCcCCHHHHHHHHhcccccccCCCce
Confidence 4457788988889988765 46888888876643 2344 3 45577889999999999999999877 4567
Q ss_pred ccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccCCCcEEEEEecC
Q psy6307 178 ELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSPNILAMASSL 257 (368)
Q Consensus 178 ~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~nV~~itAS~ 257 (368)
++.++|+|+|||||++|||+|.+.||+ ++.--+..|.+-. +++++. .+ +..-|+-+-| |
T Consensus 148 V~~SgpnDhiFiYytDHG~pGvl~mP~----~~~l~akdlnevL-~kmhk~-----------k~----Y~~mvfYlEA-C 206 (477)
T KOG1348|consen 148 VLKSGPNDHIFIYYTDHGGPGVLGMPT----SPDLYAKDLNEVL-KKMHKS-----------KT----YKKMVFYLEA-C 206 (477)
T ss_pred eeccCCCceEEEEEecCCCCceEecCC----CcchhHHHHHHHH-HHHHhc-----------cc----hheEEEEeee-c
Confidence 999999999999999999999999965 5555555565543 233322 11 2233555554 7
Q ss_pred CCCcccCCCCCCCCcceeec
Q psy6307 258 VGEDSLSHHVDPAIGVYIID 277 (368)
Q Consensus 258 ~~EsSys~~~d~~ig~~l~D 277 (368)
...|.|.......+.+|.+.
T Consensus 207 ESGSmfegiLp~~lnIYatT 226 (477)
T KOG1348|consen 207 ESGSMFEGILPKNLNIYATT 226 (477)
T ss_pred cCcchhhhhccCCCcEEEee
Confidence 77788876666666655543
No 6
>KOG1349|consensus
Probab=99.12 E-value=4.8e-11 Score=113.44 Aligned_cols=132 Identities=36% Similarity=0.539 Sum_probs=99.7
Q ss_pred CCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhh--ccccccccCCCceEEEEEeecCCCCcc
Q psy6307 123 TPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQK--RRYHELLTDEGSNILIYLTGHGGDGFL 200 (368)
Q Consensus 123 ~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~--~~yk~L~~~~~d~vFvY~s~HGg~~~~ 200 (368)
+|.++.+.++++-.+-+| |-.-.+. ..|.++|.|+|+++|.|.|++ .++|+|++++.+|||||++||||++|+
T Consensus 80 N~~pg~Vy~n~~~~~nly----gd~vevd-yrgyevtvEnflr~LTgR~~~~tprSKrlltDe~SNIlIYmtGHGgd~Fl 154 (309)
T KOG1349|consen 80 NPRPGTVYNNENHALNLY----GDDVEVD-YRGYEVTVENFLRVLTGRHPNNTPRSKRLLTDEGSNILIYLTGHGGDGFL 154 (309)
T ss_pred CCCCcceecccccccccc----CCcceee-cccchhHHHHHHHHHcCCCCCCCchhhhhcccCCCcEEEEEccCCCccce
Confidence 455666666676666666 2222222 347899999999999999998 599999999999999999999999999
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccCCCcEEEEEecCCCCcccCCCCCCCC---cceeec
Q psy6307 201 KFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSPNILAMASSLVGEDSLSHHVDPAI---GVYIID 277 (368)
Q Consensus 201 ~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~nV~~itAS~~~EsSys~~~d~~i---g~~l~D 277 (368)
+|++.++| -.+.|.+-. ..|+++.+..-++.|.-+|...+.|.-...|.+ +..+.+
T Consensus 155 KFqd~eel----ts~dLadai-----------------~qm~e~~Ryneil~miDTCQaasly~~~~sPNVLav~SS~~g 213 (309)
T KOG1349|consen 155 KFQDAEEL----TSDDLADAI-----------------QQMWEKKRYNEILFMIDTCQAASLYERFYSPNVLAVASSLVG 213 (309)
T ss_pred ecccHHHh----hhHHHHHHH-----------------HHHHHhhhhceEEEEeeccchHHHHHhhcCCCeEEEeecccC
Confidence 99997644 233343332 367888777889999999999999987777753 666666
Q ss_pred cch
Q psy6307 278 RYT 280 (368)
Q Consensus 278 ~FT 280 (368)
+=+
T Consensus 214 e~S 216 (309)
T KOG1349|consen 214 EPS 216 (309)
T ss_pred Ccc
Confidence 543
No 7
>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=99.05 E-value=5.7e-10 Score=103.36 Aligned_cols=193 Identities=19% Similarity=0.301 Sum_probs=123.1
Q ss_pred cEEEEEeCCCCCC-Ccchh--hhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCCCccccC
Q psy6307 25 NWAVLVDTSRFWF-NYRHV--ANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGEDVEVDY 101 (368)
Q Consensus 25 ~wAVlvagS~~w~-NYRHq--adv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~~v~iDY 101 (368)
+|||||+-+++=. +-++- .|+-.+.+.|++.|++.++| ++ ++
T Consensus 1 ~~AliIg~~~y~~~~~L~~~~~D~~~~~~~L~~~gf~~~~~-l~--~~-------------------------------- 45 (248)
T PF00656_consen 1 KRALIIGVNYYQNPPPLPGAVNDAEAMAEALEKLGFDVENI-LI--DN-------------------------------- 45 (248)
T ss_dssp EEEEEEEESSTSSTCHCTTHHHHHHHHHHHHHHTTEEEEEE-EE--ES--------------------------------
T ss_pred CEEEEEEeeCCCCCCCCCCHHHHHHHHHHHHHHcCCceeec-cc--cc--------------------------------
Confidence 4899999875322 33333 59999999999999988888 22 22
Q ss_pred CCCCCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhcccccccc
Q psy6307 102 RGYEVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLT 181 (368)
Q Consensus 102 ~g~~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~ 181 (368)
+|.+++.+.|+.-.. + ..++|.++|||+|||.. .++..
T Consensus 46 ----~t~~~i~~~l~~l~~-------~--~~~~D~~~~yfsGHG~~----~~~~~------------------------- 83 (248)
T PF00656_consen 46 ----ATRANILKALRELLQ-------R--AQPGDSVVFYFSGHGIQ----VDGEG------------------------- 83 (248)
T ss_dssp ----SSHHHHHHHHHHHHT-------S--GGTCSEEEEEEESEEET----ETTCC-------------------------
T ss_pred ----hHHHHHHHHHhhhhc-------c--CCCCCeeEEEEeccccc----cCCcc-------------------------
Confidence 677777777753221 1 12677888888888853 11100
Q ss_pred CCCceEEEEEeecCCCCccccCCCCCCCHHH---HHHHHHHHHHhcc-cc-eEEEEeecccccccccccC----------
Q psy6307 182 DEGSNILIYLTGHGGDGFLKFQDSEEVTSQE---LGDALEQMWQKRR-YH-EVFFMIDTCQASSMYEKFY---------- 246 (368)
Q Consensus 182 ~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~d---L~~~L~~M~~k~~-y~-~lv~iidAC~SGSm~~~l~---------- 246 (368)
. ......+...+..+. +.+.|..+..+.. -+ + +||+|+|+||.+.....
T Consensus 84 --~-------------~~~~~~d~~~~~~d~~~~~~~~l~~~~~~~~~~~~k-~~ilD~C~sg~~~~~~~~~~~~~~~~~ 147 (248)
T PF00656_consen 84 --G-------------DEDSGYDGYLLPLDANLILDDELRDLLCKSLPKKPK-LFILDCCRSGGFIDGLSSSSGESSKRE 147 (248)
T ss_dssp --S-------------TEEEETSSEEEEHHHHEEHHHHTSTTTTGGGTTS-E-EEEEESESSSBTBCEEEEEESSSTSS-
T ss_pred --C-------------cccccccceeeecchhhhHHHHHhhhhhhhccCCcc-EEeeccccCCccCCccccccccccccc
Confidence 0 000001111233333 6666666654411 22 4 99999999999876421
Q ss_pred --------------------CCcEEEEEecCCCCcccCCCCCCCCcceeeccchHHHHHHHhcc-----cCCChhhHHHH
Q psy6307 247 --------------------SPNILAMASSLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLEDV-----HLDSAKTMEDF 301 (368)
Q Consensus 247 --------------------~~nV~~itAS~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~~-----~~~~~~Tl~~l 301 (368)
..++++++|+..+|.||.. +..-++.||+.+++-|+.. ......++.++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~as~~~~~s~e~------~~~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~ 221 (248)
T PF00656_consen 148 ERKLSSSIPPEDPNRSDVPSPSGFIVLSASRPGQTSYED------SPGSGGLFTYALLEALKGNAADDPNQSWDELLEEL 221 (248)
T ss_dssp EECHCCCCCCSSCCSEEEETTTSEEEEESSSTTBCEEEE------CTTTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHH
T ss_pred cccccccccccccccccccCCCCcEEEEeccccceeecc------cCccCHHHHHHHHHHHHhhcccccchhHHHHHHHH
Confidence 1378999999999999965 1123678999999999764 13456789999
Q ss_pred HhhccCccc-ccCcee
Q psy6307 302 LAVCPKRVC-ISTIGI 316 (368)
Q Consensus 302 f~~v~~~~~-~S~~~~ 316 (368)
+..+++++. ..+|+.
T Consensus 222 ~~~v~~~~~~~Q~P~~ 237 (248)
T PF00656_consen 222 LTEVNQKVAREQTPQF 237 (248)
T ss_dssp HHHHHHHHHSBEEEEE
T ss_pred HHHHHhHCCCceeCee
Confidence 999888763 334444
No 8
>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=99.03 E-value=2.9e-10 Score=109.37 Aligned_cols=133 Identities=26% Similarity=0.383 Sum_probs=91.7
Q ss_pred CCCCHHHHHHHHcCCCC--CCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhcccccccc
Q psy6307 104 YEVTVENFIRLLTGRLP--PSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLT 181 (368)
Q Consensus 104 ~~vt~enfl~vL~G~~~--~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~ 181 (368)
..+..+|++-++..+.+ +..|.+.++.+.++ ..-+| .|. .| -..|+.|++++|+++|+|+++....|+|.+
T Consensus 31 ~G~~~~~Iil~~~dd~a~~~~Np~~g~i~~~~~-~~n~y---~~~--~i-DY~g~~v~~~~fl~vL~G~~~~~~~kvl~s 103 (256)
T PF01650_consen 31 NGIPDENIILMMYDDIACNPRNPFPGKIFNDPD-GTNVY---KGV--EI-DYRGEDVTPENFLNVLTGDKSVPSGKVLNS 103 (256)
T ss_pred cCCCCceEEEEecCCccchhhCCCCceEEeCCC-ccccc---CCc--cc-cccccccCHHHHHHHhcCCCCCCccccccC
Confidence 44566666666666643 24676766665544 23344 332 23 344889999999999999998767789999
Q ss_pred CCCceEEEEEeecCCCCccccCCCCCCCHHHH-HHHHHHHHHhcccceEEEEeecccccccccccCCCcEEEEEecCCCC
Q psy6307 182 DEGSNILIYLTGHGGDGFLKFQDSEEVTSQEL-GDALEQMWQKRRYHEVFFMIDTCQASSMYEKFYSPNILAMASSLVGE 260 (368)
Q Consensus 182 ~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL-~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~~~nV~~itAS~~~E 260 (368)
+++|+||||++|||+++++++| ..++| .+.|+.+.+ .|.++.....++++..||...
T Consensus 104 ~~~D~vfiy~~~HG~~~~l~~~-----~~~~l~~~~L~~~L~-----------------~m~~~~~y~~lv~~veaC~SG 161 (256)
T PF01650_consen 104 TENDNVFIYFTGHGGPGFLKFP-----DGEELTADDLADALD-----------------KMHEKKRYKKLVFVVEACYSG 161 (256)
T ss_pred CCCCeEEEEEeccCCCCcccCC-----CcccccHHHHHHHHH-----------------HHHhhCCcceEEEEEeccccc
Confidence 9999999999999999999885 33333 344555432 333444445677777778888
Q ss_pred cccCC
Q psy6307 261 DSLSH 265 (368)
Q Consensus 261 sSys~ 265 (368)
+-+..
T Consensus 162 s~~~~ 166 (256)
T PF01650_consen 162 SFFEG 166 (256)
T ss_pred chhhc
Confidence 88765
No 9
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=3.1e-06 Score=81.55 Aligned_cols=106 Identities=35% Similarity=0.464 Sum_probs=78.5
Q ss_pred CCcccCHHHHHHHHHHHhhh--ccccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEE
Q psy6307 154 DSEEVTSQELGDALEQMWQK--RRYHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFF 231 (368)
Q Consensus 154 ~~~~vt~~~f~~~L~~~~~~--~~yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~ 231 (368)
.|=++|.+.|++.|...+.+ ...|+|.++++++||+|++||||++|++|.+-+++ -.+.|.+-.
T Consensus 106 ~gyevTve~firLLt~r~~en~p~sKrlltdE~SNIfIYmtGHGgd~FlKFqdaeem----tseDladai---------- 171 (382)
T COG5206 106 SGYEVTVEVFIRLLTARSGENHPKSKRLLTDESSNIFIYMTGHGGDAFLKFQDAEEM----TSEDLADAI---------- 171 (382)
T ss_pred ccccchHHHHHHHHHhhccCCChhhhhhcccccCcEEEEEccCCCccceecccHHHh----hhHHHHHHH----------
Confidence 36689999999999999887 47899999999999999999999999999886533 223333322
Q ss_pred EeecccccccccccCCCcEEEEEecCCCCcccCCCCCCCC---cceeeccch
Q psy6307 232 MIDTCQASSMYEKFYSPNILAMASSLVGEDSLSHHVDPAI---GVYIIDRYT 280 (368)
Q Consensus 232 iidAC~SGSm~~~l~~~nV~~itAS~~~EsSys~~~d~~i---g~~l~D~FT 280 (368)
..|.+..+...|+.|--+|...+-|...+.|++ |..-+|+=+
T Consensus 172 -------~ql~~~kRyNeIlfmiDTCQAnaly~k~ysPNvLavgsSeig~ss 216 (382)
T COG5206 172 -------SQLAAKKRYNEILFMIDTCQANALYDKSYSPNVLAVGSSEIGQSS 216 (382)
T ss_pred -------HHHHHhhhhceEEEEeeccccchhhhhccCCceEEEeccccCCcc
Confidence 133444455668888888888888887777743 555555433
No 10
>KOG1546|consensus
Probab=97.27 E-value=0.0025 Score=63.34 Aligned_cols=142 Identities=17% Similarity=0.278 Sum_probs=88.7
Q ss_pred CCCcEEEEEeCCCCCCCcch-----hhhHHHHHHHHH-hCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCC
Q psy6307 22 HSNNWAVLVDTSRFWFNYRH-----VANVLSIYRSVK-RLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGE 95 (368)
Q Consensus 22 ~~~~wAVlvagS~~w~NYRH-----qadv~~~Y~~L~-~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~ 95 (368)
+.++-||||.=+ |-|-++ ..||-+|.+.|. +.||+.|+|.+|.-+|- +| +
T Consensus 61 ~gkrrAvLiGIN--Y~gTk~ELrGCINDv~~M~~~Lv~rfGFs~ddI~~LtDt~~--s~------------------~-- 116 (362)
T KOG1546|consen 61 AGKRRAVLIGIN--YPGTKNELRGCINDVHRMRKLLVERFGFSEDDILMLTDTDE--SP------------------V-- 116 (362)
T ss_pred cccceEEEEeec--CCCcHHHHhhhHHHHHHHHHHHHHhhCCChhheEEEecCCC--cc------------------c--
Confidence 456679998752 233333 258999999988 58999999987653221 21 1
Q ss_pred CccccCCCCCCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhcc
Q psy6307 96 DVEVDYRGYEVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRR 175 (368)
Q Consensus 96 ~v~iDY~g~~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~ 175 (368)
..-|..|+.+.|.--+. ...++|-+|+-|||||+.- .-.+|++++
T Consensus 117 --------~~PT~~Nir~Al~wLV~---------~aq~gD~LvfHYSGHGtr~--~~~~gDe~d---------------- 161 (362)
T KOG1546|consen 117 --------RIPTGKNIRRALRWLVE---------SAQPGDSLVFHYSGHGTRQ--PDTNGDEVD---------------- 161 (362)
T ss_pred --------ccCcHHHHHHHHHHHHh---------cCCCCCEEEEEecCCCCcC--CCCCCCCCC----------------
Confidence 12355666666653221 1356788899999999952 223454442
Q ss_pred ccccccCCCceEEEEEeecCCCCccccCCCC----CCCHHHHHHHHHHHHHhcccceEEEEeecccccccccc
Q psy6307 176 YHELLTDEGSNILIYLTGHGGDGFLKFQDSE----EVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEK 244 (368)
Q Consensus 176 yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~----~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~ 244 (368)
|-++-+...|.+ -|+.++.....+.+- .=-++-.|+|+|+||+..+.
T Consensus 162 -------------------G~DE~I~P~D~~t~G~iIdDe~~r~lV~plp---~G~~lt~I~DSCHSGgliDl 212 (362)
T KOG1546|consen 162 -------------------GYDETIVPCDHNTQGPIIDDEIFRILVRPLP---KGCKLTAISDSCHSGGLIDL 212 (362)
T ss_pred -------------------CCcceeecccccccccccchHHHHHHHhccC---CCceEEEEeecccCCCcccc
Confidence 334445555554 566666666665542 22378899999999999873
No 11
>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=96.90 E-value=0.0081 Score=57.20 Aligned_cols=143 Identities=16% Similarity=0.235 Sum_probs=91.4
Q ss_pred ccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHH-HhcccceEEEEeec
Q psy6307 157 EVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMW-QKRRYHEVFFMIDT 235 (368)
Q Consensus 157 ~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~-~k~~y~~lv~iidA 235 (368)
.++..++.++|+.-.+. ..-...|.+.+|+.+||..+++...|+..+.-++|.+.|..-. ..-+-|=.||+++|
T Consensus 51 dlt~~em~~~l~~~~~~-----~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlffiqA 125 (241)
T smart00115 51 NLTAEEMLEELKEFAER-----PEHSDSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLFFIQA 125 (241)
T ss_pred CCCHHHHHHHHHHHHhc-----cccCCCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEEEEeC
Confidence 46777777777654331 1123568889999999999999988887887777776663100 01123446899999
Q ss_pred cccccccccc---------------------CC-CcEEEEEecCCCCcccCCCCCCCCcceeeccchHHHHHHHhcccCC
Q psy6307 236 CQASSMYEKF---------------------YS-PNILAMASSLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLEDVHLD 293 (368)
Q Consensus 236 C~SGSm~~~l---------------------~~-~nV~~itAS~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~~~~~ 293 (368)
|...-+-... .. .++++.-|+.++.-||.. +..| ..|.-.+++-|++ ..
T Consensus 126 CRg~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~D~li~ysT~pG~va~r~---~~~g----S~fi~~L~~~l~~--~~ 196 (241)
T smart00115 126 CRGDELDGGVPVEDDVDDPPTEFEDDAIYKIPVEADFLAAYSTTPGYVSWRN---PTRG----SWFIQSLCQVLKE--YA 196 (241)
T ss_pred CCCCCCCCCeecccccccccccccccccccCCCcCcEEEEEeCCCCeEeecC---CCCC----chHHHHHHHHHHH--cC
Confidence 9754221111 11 267777777777777732 2223 3455555555554 24
Q ss_pred ChhhHHHHHhhccCcccccC
Q psy6307 294 SAKTMEDFLAVCPKRVCIST 313 (368)
Q Consensus 294 ~~~Tl~~lf~~v~~~~~~S~ 313 (368)
+...|.++|..|+.++...+
T Consensus 197 ~~~~l~~ilt~V~~~V~~~~ 216 (241)
T smart00115 197 RSLDLLDILTEVNRKVAVKF 216 (241)
T ss_pred CCCCHHHHHHHHHHHHhhhh
Confidence 67789999999999887654
No 12
>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=96.84 E-value=0.0063 Score=57.84 Aligned_cols=143 Identities=14% Similarity=0.178 Sum_probs=93.5
Q ss_pred cccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHH-HhcccceEEEEee
Q psy6307 156 EEVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMW-QKRRYHEVFFMID 234 (368)
Q Consensus 156 ~~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~-~k~~y~~lv~iid 234 (368)
..++.+++.++|+.-.+ -.....|.+++|+++||..+++...|...+.-++|.+.|..-. ..-+-|=.||+++
T Consensus 52 ~nlt~~~~~~~l~~f~~------~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl~~iq 125 (243)
T cd00032 52 NNLTAEEILEELKEFAS------PDHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKLFFIQ 125 (243)
T ss_pred CCCCHHHHHHHHHHHHh------ccCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcEEEEE
Confidence 35677888888876533 1234678889999999999999888877887777766654110 1112355689999
Q ss_pred ccccccccccc---------------------C--C--CcEEEEEecCCCCcccCCCCCCCCcceeeccchHHHHHHHhc
Q psy6307 235 TCQASSMYEKF---------------------Y--S--PNILAMASSLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLED 289 (368)
Q Consensus 235 AC~SGSm~~~l---------------------~--~--~nV~~itAS~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~ 289 (368)
||...-.-... . + .++++.=|+.++..||-. +.. +..|+-.+++-|.+
T Consensus 126 ACRg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~d~lv~ysT~pG~~a~r~---~~~----gS~fi~~l~~~l~~ 198 (243)
T cd00032 126 ACRGDELDLGVEVDSGADEPPDVETEAEDDAVQTIPVEADFLVAYSTVPGYVSWRN---TKK----GSWFIQSLCQVLRK 198 (243)
T ss_pred CCCCCcCCCceeccCccccccccccccccccccCCCCcccEEEEecCCCCeEeecC---CCC----CCEeHHHHHHHHHH
Confidence 99976542211 0 1 267777777777777732 222 34566566666654
Q ss_pred ccCCChhhHHHHHhhccCcccccC
Q psy6307 290 VHLDSAKTMEDFLAVCPKRVCIST 313 (368)
Q Consensus 290 ~~~~~~~Tl~~lf~~v~~~~~~S~ 313 (368)
..+...|.+++..|+.++..-+
T Consensus 199 --~~~~~~l~~il~~V~~~V~~~~ 220 (243)
T cd00032 199 --YAHSLDLLDILTKVNRKVAEKF 220 (243)
T ss_pred --hCCCCcHHHHHHHHHHHHhhhh
Confidence 2356789999999988876543
No 13
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=77.39 E-value=5.7 Score=35.73 Aligned_cols=72 Identities=18% Similarity=0.319 Sum_probs=50.6
Q ss_pred cCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCC------ccccCCCC----CCCHHHHHHHHHHHHHhcccc
Q psy6307 158 VTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDG------FLKFQDSE----EVTSQELGDALEQMWQKRRYH 227 (368)
Q Consensus 158 vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~------~~~~~~~~----~l~~~dL~~~L~~M~~k~~y~ 227 (368)
-+.+++.+.+.+.-.+ .+++.|.+-|.|||-|. .+.|.+.- .++-.||.+.+. .
T Consensus 72 pt~e~~~~~~~~~R~~--------a~~~RvLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~dL~~~lg--------~ 135 (154)
T PF14538_consen 72 PTVEDLKRLCQSLRRN--------AKDERVLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIYDLQSWLG--------S 135 (154)
T ss_pred CCHHHHHHHHHHHHhh--------CCCceEEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHHHHHHhcC--------C
Confidence 3567777777766443 23477889999999986 45554432 377777776554 4
Q ss_pred eEEEEeeccccccccccc
Q psy6307 228 EVFFMIDTCQASSMYEKF 245 (368)
Q Consensus 228 ~lv~iidAC~SGSm~~~l 245 (368)
-.++|.|...||++++.+
T Consensus 136 Psi~V~DC~~AG~il~~f 153 (154)
T PF14538_consen 136 PSIYVFDCSNAGSILNAF 153 (154)
T ss_pred CEEEEEECCcHHHHHHhc
Confidence 679999999999987754
No 14
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=74.25 E-value=3.8 Score=42.06 Aligned_cols=61 Identities=15% Similarity=0.123 Sum_probs=41.1
Q ss_pred hcccceEEEEeecccccccccccCCC-------------cEEEEEecCCCCcccCCCCCCCCcceeeccchHHHHHHHhc
Q psy6307 223 KRRYHEVFFMIDTCQASSMYEKFYSP-------------NILAMASSLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLED 289 (368)
Q Consensus 223 k~~y~~lv~iidAC~SGSm~~~l~~~-------------nV~~itAS~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~ 289 (368)
...-++.|..+|+|++|.++...... ....+++..+.+.++.. |+ .-.+.||++.+.-+..
T Consensus 184 ~~~~~~ql~~~d~~~~~~~~~~~~~~~~p~l~~s~~~~~~~~~~~~~ap~~~~~e~---~~---~g~gv~t~al~~~l~~ 257 (380)
T COG4249 184 LSEPGNQLVDLDACVRGDVFKATAGQQRPWLAQSLAREFGFGILDSCAPDQQSAEA---PE---LGHGVFTDALLEGLRG 257 (380)
T ss_pred hccCCceeehhhhhcchhhhcccccccchHhhhhhhcceeeeeccCCCCCcccccc---cc---ccCceeehhhhhcccc
Confidence 34567788899999999999977521 23445555566665531 23 3367888888877766
No 15
>KOG1017|consensus
Probab=68.31 E-value=4.8 Score=38.17 Aligned_cols=23 Identities=39% Similarity=0.612 Sum_probs=21.1
Q ss_pred hhHHHHHHHHHhCCCCCCCEEEE
Q psy6307 43 ANVLSIYRSVKRLGIPDSHIILM 65 (368)
Q Consensus 43 adv~~~Y~~L~~~Gi~d~~Ii~m 65 (368)
..||.|-.+||++|+||++|||.
T Consensus 203 nTV~~Av~VL~EhgVp~s~IiL~ 225 (267)
T KOG1017|consen 203 NTVCKAVEVLKEHGVPDSNIILV 225 (267)
T ss_pred ccHHHHHHHHHHcCCCcccEEEE
Confidence 35999999999999999999976
No 16
>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=67.62 E-value=3.4 Score=37.98 Aligned_cols=13 Identities=15% Similarity=0.151 Sum_probs=10.9
Q ss_pred EEEEEeecCCCCc
Q psy6307 187 ILIYLTGHGGDGF 199 (368)
Q Consensus 187 vFvY~s~HGg~~~ 199 (368)
|||.=+||+|...
T Consensus 121 ~~ilD~C~sg~~~ 133 (248)
T PF00656_consen 121 LFILDCCRSGGFI 133 (248)
T ss_dssp EEEEESESSSBTB
T ss_pred EEeeccccCCccC
Confidence 8888899999764
No 17
>PF12770 CHAT: CHAT domain
Probab=66.89 E-value=4.4 Score=38.34 Aligned_cols=46 Identities=17% Similarity=0.447 Sum_probs=33.6
Q ss_pred EEEEEeecCCCC-------ccccC-----CCCCCCHHHHHHHHHHHHHhcccceEEEEeeccccc
Q psy6307 187 ILIYLTGHGGDG-------FLKFQ-----DSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQAS 239 (368)
Q Consensus 187 vFvY~s~HGg~~-------~~~~~-----~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SG 239 (368)
=.|.|+|||... .+.+. +...+++.++.. ++ + .+ --++++.||+||
T Consensus 144 ~ilH~a~Hg~~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~-l~-l--~~---~~lVvLsaC~s~ 201 (287)
T PF12770_consen 144 DILHFAGHGTFDPDPPDQSGLVLSDESGQEDGLLSAEELAQ-LD-L--RG---PRLVVLSACESA 201 (287)
T ss_pred CEEEEEcccccCCCCCCCCEEEEeccCCCCCcccCHHHHHh-hc-C--CC---CCEEEecCcCCc
Confidence 368999999988 57776 456788888887 21 0 11 446799999999
No 18
>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=50.66 E-value=37 Score=32.22 Aligned_cols=60 Identities=13% Similarity=0.169 Sum_probs=42.7
Q ss_pred CCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCC
Q psy6307 133 EGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDG 198 (368)
Q Consensus 133 ~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~ 198 (368)
..|-+.+|+.+||..+.|.-.|++.+.-+++.+.+.+.. -..|... -.||+.=+|-|.+.
T Consensus 72 ~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~----c~~L~~k--PKlffiqACRg~~~ 131 (241)
T smart00115 72 DSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDN----CPSLAGK--PKLFFIQACRGDEL 131 (241)
T ss_pred CCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhccccC----ChhhcCC--CcEEEEeCCCCCCC
Confidence 456788899999999999988988887777666554321 1222222 36899999998754
No 19
>PF11181 YflT: Heat induced stress protein YflT
Probab=47.20 E-value=27 Score=28.87 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=26.1
Q ss_pred cchhhhHHHHHHHHHhCCCCCCCEEEEecCC
Q psy6307 39 YRHVANVLSIYRSVKRLGIPDSHIILMIADD 69 (368)
Q Consensus 39 YRHqadv~~~Y~~L~~~Gi~d~~Ii~m~~DD 69 (368)
|+-+..+..+-+.|++.|+..++|.++..|+
T Consensus 6 ~~~~~E~~~~I~~L~~~Gy~~ddI~Vva~d~ 36 (103)
T PF11181_consen 6 YDNEEEALSAIEELKAQGYSEDDIYVVAKDK 36 (103)
T ss_pred ECCHHHHHHHHHHHHHcCCCcccEEEEEcCc
Confidence 4447789999999999999999999987543
No 20
>PRK10834 vancomycin high temperature exclusion protein; Provisional
Probab=43.87 E-value=24 Score=34.15 Aligned_cols=7 Identities=43% Similarity=1.023 Sum_probs=3.3
Q ss_pred ccccCCC
Q psy6307 97 VEVDYRG 103 (368)
Q Consensus 97 v~iDY~g 103 (368)
+.+|++|
T Consensus 116 Ii~e~~s 122 (239)
T PRK10834 116 IVLDYAG 122 (239)
T ss_pred EEecCCC
Confidence 3445554
No 21
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=43.11 E-value=95 Score=27.08 Aligned_cols=38 Identities=11% Similarity=0.079 Sum_probs=30.2
Q ss_pred CCCcEEEEEeCC-CCCCCcchhhhHHHHHHHHHhCCCCCCCEE
Q psy6307 22 HSNNWAVLVDTS-RFWFNYRHVANVLSIYRSVKRLGIPDSHII 63 (368)
Q Consensus 22 ~~~~wAVlvagS-~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii 63 (368)
..+.-||=|+++ +|--- .+...+|+.|.+.||+...|.
T Consensus 32 ygedpavQIs~~~~g~~~----~~~~~v~~~L~~~gI~~ksi~ 70 (127)
T PRK10629 32 RQQESTLAIRAVHQGASL----PDGFYVYQHLDANGIHIKSIT 70 (127)
T ss_pred cCCCceEEEecCCCCCcc----chHHHHHHHHHHCCCCcceEE
Confidence 467788999987 55322 799999999999999877765
No 22
>TIGR00109 hemH ferrochelatase. Human ferrochelatase, found at the mitochondrial inner membrane inner surface, was shown in an active recombinant form to be a homodimer. This contrasts to an earlier finding by gel filtration that overexpressed E. coli ferrochelatase runs as a monomer.
Probab=40.69 E-value=1.6e+02 Score=29.27 Aligned_cols=79 Identities=13% Similarity=0.171 Sum_probs=50.5
Q ss_pred ccEEEEecCCCCC-CccccCCCcccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHH
Q psy6307 135 SNILIYLTGHGGD-GFLKFQDSEEVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQEL 213 (368)
Q Consensus 135 d~vfiy~tgHG~~-g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL 213 (368)
+.+.+-||=||=| ..++- |+ .+..+..++-+...+.-+ ...+..+.|.|+.|...|+.. ++
T Consensus 187 ~~~~llfSaHglP~~~~~~--Gd-~Y~~~~~~ta~~l~~~l~------~~~~~~~~fQS~~g~~~Wl~P---------~~ 248 (322)
T TIGR00109 187 DNAVLLFSAHGLPQSYVDE--GD-PYPAECEATTRLIAEKLG------FPNEYRLTWQSRVGPEPWLGP---------YT 248 (322)
T ss_pred CCcEEEEeCCCCchhHhhC--CC-ChHHHHHHHHHHHHHHcC------CCCCeEEEEeCCCCCCCcCCC---------CH
Confidence 5566788889998 33332 32 244445444444433221 234678899999998888876 67
Q ss_pred HHHHHHHHHhcccceEEEE
Q psy6307 214 GDALEQMWQKRRYHEVFFM 232 (368)
Q Consensus 214 ~~~L~~M~~k~~y~~lv~i 232 (368)
.++|+++.++ .+++++++
T Consensus 249 ~~~l~~l~~~-G~k~V~vv 266 (322)
T TIGR00109 249 EELLEKLGEQ-GVQHIVVV 266 (322)
T ss_pred HHHHHHHHHc-CCceEEEE
Confidence 7888887655 66777754
No 23
>PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A.
Probab=37.00 E-value=34 Score=29.46 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=21.6
Q ss_pred EEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEE
Q psy6307 28 VLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIIL 64 (368)
Q Consensus 28 VlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~ 64 (368)
||++|..+... ....+-.|-+.|.+.|+|+++|++
T Consensus 41 il~SGg~~~~~--~~~ea~~~~~~l~~~gvp~~~I~~ 75 (155)
T PF02698_consen 41 ILFSGGYGHGD--GRSEAEAMRDYLIELGVPEERIIL 75 (155)
T ss_dssp EEEE--SSTTH--TS-HHHHHHHHHHHT---GGGEEE
T ss_pred EEECCCCCCCC--CCCHHHHHHHHHHhcccchheeEc
Confidence 88888655544 445566777889999999999986
No 24
>cd06259 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.
Probab=36.52 E-value=33 Score=29.43 Aligned_cols=37 Identities=19% Similarity=0.174 Sum_probs=27.3
Q ss_pred EEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEE
Q psy6307 26 WAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIIL 64 (368)
Q Consensus 26 wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~ 64 (368)
--||++|..+.... .+.+-.|.+.|.+.|+|++.|++
T Consensus 36 ~~ii~sGg~~~~~~--~~ea~~m~~~l~~~gv~~~~I~~ 72 (150)
T cd06259 36 PKLIVSGGQGPGEG--YSEAEAMARYLIELGVPAEAILL 72 (150)
T ss_pred CEEEEcCCCCCCCC--CCHHHHHHHHHHHcCCCHHHeee
Confidence 34788887665533 34566778999999999999886
No 25
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=33.10 E-value=36 Score=26.58 Aligned_cols=22 Identities=23% Similarity=0.329 Sum_probs=17.8
Q ss_pred EEEEeCCCCCCCcchhhhHHHH
Q psy6307 27 AVLVDTSRFWFNYRHVANVLSI 48 (368)
Q Consensus 27 AVlvagS~~w~NYRHqadv~~~ 48 (368)
-|||+|||.|.++....+++..
T Consensus 5 rVli~GgR~~~D~~~i~~~Ld~ 26 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAALDK 26 (71)
T ss_pred EEEEEECCccccHHHHHHHHHH
Confidence 4899999999988886666554
No 26
>PF07804 HipA_C: HipA-like C-terminal domain; InterPro: IPR012893 The members of this entry are similar to a region close to the C terminus of the HipA protein expressed by various bacterial species (for example P23874 from SWISSPROT). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis []. When expressed alone, it is toxic to bacterial cells [], but it is usually tightly associated with HipB [], and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products []. ; PDB: 3AKL_D 3AKJ_B 3AKK_D 2WIU_C 3HZI_A 3DNT_B 3FBR_A 3DNU_A 3DNV_A.
Probab=29.20 E-value=50 Score=25.69 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=16.5
Q ss_pred HHHHhhcccCCCCcEEEEEeCCCCC
Q psy6307 12 STIFVLNEAKHSNNWAVLVDTSRFW 36 (368)
Q Consensus 12 ~~~~~~~~~~~~~~wAVlvagS~~w 36 (368)
.-++..+...|.+||++|.. +.+|
T Consensus 49 fn~ligN~D~H~kN~s~l~~-~~~~ 72 (79)
T PF07804_consen 49 FNYLIGNTDRHLKNFSFLYD-GGGW 72 (79)
T ss_dssp HHHHCTBS---CCCSEEEEE-CCEE
T ss_pred HHHHHcCCcCCcCCEEEEEc-CCeE
Confidence 45667788999999999999 5555
No 27
>PRK10494 hypothetical protein; Provisional
Probab=27.94 E-value=56 Score=31.63 Aligned_cols=37 Identities=22% Similarity=0.194 Sum_probs=26.5
Q ss_pred EEEEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEE
Q psy6307 26 WAVLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIIL 64 (368)
Q Consensus 26 wAVlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~ 64 (368)
--||++|..+..+. .+.+-.|-+.+++.|+|++.|++
T Consensus 122 ~~ii~SGg~~~~~~--~sEA~~~~~~l~~lGVp~~~Ii~ 158 (259)
T PRK10494 122 AKLIFTGGAAKTNT--VSTAEVGARVAQSLGVPREDIIT 158 (259)
T ss_pred CEEEEECCCCCCCC--CCHHHHHHHHHHHcCCCHHHeee
Confidence 45888887664442 34666777888899999998875
No 28
>cd00419 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=27.37 E-value=3.4e+02 Score=23.47 Aligned_cols=78 Identities=14% Similarity=0.160 Sum_probs=40.3
Q ss_pred cEEEEecCCCCC-CccccCCCcccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCC-ccccCCCCCCCHHHH
Q psy6307 136 NILIYLTGHGGD-GFLKFQDSEEVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDG-FLKFQDSEEVTSQEL 213 (368)
Q Consensus 136 ~vfiy~tgHG~~-g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~-~~~~~~~~~l~~~dL 213 (368)
...+-||-||-| ..++ .|+ -+.....++.+-.-+.-+ . +...+-+-|-+|.|++ |+.. ++
T Consensus 18 ~~~llfsaHgiP~~~~~--~gd-~Y~~~~~~~~~~v~~~l~-----~-~~~~~~~~fqS~~g~~~Wl~P---------~~ 79 (135)
T cd00419 18 KDRLLFSAHGLPVRDIK--KGD-PYPDQCEETARLVAERLG-----L-PFDEYELAYQSRFGPGEWLEP---------ST 79 (135)
T ss_pred CCEEEEEcCCCHHHHhh--CCC-CHHHHHHHHHHHHHHHhC-----C-CCCCEEEEecCCCCCCCCCCC---------CH
Confidence 345777889998 3332 232 344444444333332211 1 2223444455555444 5444 57
Q ss_pred HHHHHHHHHhcccceEEEE
Q psy6307 214 GDALEQMWQKRRYHEVFFM 232 (368)
Q Consensus 214 ~~~L~~M~~k~~y~~lv~i 232 (368)
.++|+.+.++ .+++++++
T Consensus 80 ~~~l~~l~~~-G~~~i~v~ 97 (135)
T cd00419 80 DDALEELAKE-GVKNVVVV 97 (135)
T ss_pred HHHHHHHHHc-CCCeEEEE
Confidence 7888887654 56776644
No 29
>COG2949 SanA Uncharacterized membrane protein [Function unknown]
Probab=26.49 E-value=78 Score=30.39 Aligned_cols=34 Identities=18% Similarity=0.380 Sum_probs=22.9
Q ss_pred EEEeCCCCCCCcchhhhHHHHHHHHHhCCCCCCCEEE
Q psy6307 28 VLVDTSRFWFNYRHVANVLSIYRSVKRLGIPDSHIIL 64 (368)
Q Consensus 28 VlvagS~~w~NYRHqadv~~~Y~~L~~~Gi~d~~Ii~ 64 (368)
+|++|-|+=-+|- .+-.|.+.|++.|+|.++|.+
T Consensus 97 LLlSGDN~~~sYn---Ep~tM~kdL~~~GVp~~~i~l 130 (235)
T COG2949 97 LLLSGDNATVSYN---EPRTMRKDLIAAGVPAKNIFL 130 (235)
T ss_pred EEEecCCCccccc---chHHHHHHHHHcCCCHHHeee
Confidence 5555555544432 346688888888888888875
No 30
>KOG1546|consensus
Probab=26.47 E-value=47 Score=33.75 Aligned_cols=31 Identities=19% Similarity=0.397 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCC
Q psy6307 161 QELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDG 198 (368)
Q Consensus 161 ~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~ 198 (368)
.|-.+||+ +-+.-..++|.+|+=|||||+.-
T Consensus 122 ~Nir~Al~-------wLV~~aq~gD~LvfHYSGHGtr~ 152 (362)
T KOG1546|consen 122 KNIRRALR-------WLVESAQPGDSLVFHYSGHGTRQ 152 (362)
T ss_pred HHHHHHHH-------HHHhcCCCCCEEEEEecCCCCcC
Confidence 45555555 44555778899999999999853
No 31
>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=25.85 E-value=91 Score=29.49 Aligned_cols=122 Identities=13% Similarity=0.184 Sum_probs=73.5
Q ss_pred CCcEEEEEeCCCCCC--Ccch--hhhHHHHHHHHHhCCCCCCCEEEEecCCCCCCCCCCCCCeeeeCCCCCCCccCCCcc
Q psy6307 23 SNNWAVLVDTSRFWF--NYRH--VANVLSIYRSVKRLGIPDSHIILMIADDMACNPRNPRPATVFNNANQHIDVYGEDVE 98 (368)
Q Consensus 23 ~~~wAVlvagS~~w~--NYRH--qadv~~~Y~~L~~~Gi~d~~Ii~m~~DDia~n~~Np~pG~i~n~~~~~~nvy~~~v~ 98 (368)
...+|+||.-+++-. .=|. ..|+-.+-++|++.|+ .+.+
T Consensus 8 ~~g~aLII~n~~f~~~~~~r~g~~~D~~~l~~~f~~lgF---~V~~---------------------------------- 50 (243)
T cd00032 8 RRGLALIINNENFDKGLKDRDGTDVDAENLTKLFESLGY---EVEV---------------------------------- 50 (243)
T ss_pred CCCEEEEEechhcCCCCCCCCChHHHHHHHHHHHHHCCC---EEEE----------------------------------
Confidence 456888887766532 1233 2478888888888888 2222
Q ss_pred ccCCCCCCCHHHHHHHHcCCCCCCCCCCcccccCCCccEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhccccc
Q psy6307 99 VDYRGYEVTVENFIRLLTGRLPPSTPRSKQLLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHE 178 (368)
Q Consensus 99 iDY~g~~vt~enfl~vL~G~~~~~~p~~k~l~s~~~d~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~ 178 (368)
..+++.+.+.+.|..=.. +. ....|-+++|+.+||..+.|.-.|++.+.-+++++.|.... -..
T Consensus 51 ----~~nlt~~~~~~~l~~f~~------~~--~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~----~~s 114 (243)
T cd00032 51 ----KNNLTAEEILEELKEFAS------PD--HSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGDN----CPS 114 (243)
T ss_pred ----eCCCCHHHHHHHHHHHHh------cc--CCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccCC----Ccc
Confidence 112334444444432110 01 13456688899999999999888888887777666554321 111
Q ss_pred cccCCCceEEEEEeecCCCCc
Q psy6307 179 LLTDEGSNILIYLTGHGGDGF 199 (368)
Q Consensus 179 L~~~~~d~vFvY~s~HGg~~~ 199 (368)
|. ..-.||+.=+|-|.+--
T Consensus 115 l~--~kPKl~~iqACRg~~~~ 133 (243)
T cd00032 115 LA--GKPKLFFIQACRGDELD 133 (243)
T ss_pred cc--CCCcEEEEECCCCCcCC
Confidence 21 23368999999998764
No 32
>PRK00035 hemH ferrochelatase; Reviewed
Probab=24.31 E-value=3.8e+02 Score=26.43 Aligned_cols=80 Identities=14% Similarity=0.184 Sum_probs=44.2
Q ss_pred cEEEEecCCCCCCccccCCCcccCHHHHHHHHHHHhhhccccccccCCCceEEEEEeecCCCCccccCCCCCCCHHHHHH
Q psy6307 136 NILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHELLTDEGSNILIYLTGHGGDGFLKFQDSEEVTSQELGD 215 (368)
Q Consensus 136 ~vfiy~tgHG~~g~i~~~~~~~vt~~~f~~~L~~~~~~~~yk~L~~~~~d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~ 215 (368)
..-+-|++||-|--. ...|+. +.....++.+-..+.-.. ...+..+.|.|==|...|+.. ++.+
T Consensus 189 ~~~llfs~HG~P~~~-~~~gd~-Y~~~~~~t~~~l~~~l~~-----~~~~~~~~fqs~~g~~~Wl~P---------~~~~ 252 (333)
T PRK00035 189 PDRLLFSAHGLPQRY-IDKGDP-YQQQCEETARLLAEALGL-----PDEDYDLTYQSRFGPEPWLEP---------YTDD 252 (333)
T ss_pred CcEEEEecCCCchHH-hhcCCC-hHHHHHHHHHHHHHHhCC-----CCCCeEEEeeCCCCCCccCCC---------CHHH
Confidence 345778999988322 123443 455555555555443221 223444455542233355554 6788
Q ss_pred HHHHHHHhcccceEEEE
Q psy6307 216 ALEQMWQKRRYHEVFFM 232 (368)
Q Consensus 216 ~L~~M~~k~~y~~lv~i 232 (368)
+|+++.+ ..+++++++
T Consensus 253 ~l~~l~~-~g~k~V~v~ 268 (333)
T PRK00035 253 TLEELAE-KGVKKVVVV 268 (333)
T ss_pred HHHHHHH-cCCCeEEEE
Confidence 8888765 467888754
No 33
>KOG1552|consensus
Probab=24.18 E-value=72 Score=31.29 Aligned_cols=44 Identities=23% Similarity=0.397 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHh-CCCCCCCEEEEecC-----CCCCCCCCCCCCeeeeCC
Q psy6307 42 VANVLSIYRSVKR-LGIPDSHIILMIAD-----DMACNPRNPRPATVFNNA 86 (368)
Q Consensus 42 qadv~~~Y~~L~~-~Gi~d~~Ii~m~~D-----Dia~n~~Np~pG~i~n~~ 86 (368)
.+|+-++|+.||+ .| ++++||++-.= .+---.|+|..|.|-..|
T Consensus 112 y~Di~avye~Lr~~~g-~~~~Iil~G~SiGt~~tv~Lasr~~~~alVL~SP 161 (258)
T KOG1552|consen 112 YADIKAVYEWLRNRYG-SPERIILYGQSIGTVPTVDLASRYPLAAVVLHSP 161 (258)
T ss_pred hhhHHHHHHHHHhhcC-CCceEEEEEecCCchhhhhHhhcCCcceEEEecc
Confidence 5899999999995 68 99999997541 111224566667777765
No 34
>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=23.73 E-value=45 Score=33.53 Aligned_cols=102 Identities=18% Similarity=0.196 Sum_probs=46.0
Q ss_pred ceEEEEEeecCCCCccccCCCCCCCHHHHHHHHHHHHHhcccceEEEEeecccccccccccC---------CC--c-EEE
Q psy6307 185 SNILIYLTGHGGDGFLKFQDSEEVTSQELGDALEQMWQKRRYHEVFFMIDTCQASSMYEKFY---------SP--N-ILA 252 (368)
Q Consensus 185 d~vFvY~s~HGg~~~~~~~~~~~l~~~dL~~~L~~M~~k~~y~~lv~iidAC~SGSm~~~l~---------~~--n-V~~ 252 (368)
...++.+.|||++.-+.- +.++.+++. .+. ...|--+++.-||..|.+-.... .| + |-+
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 GAGFVNYFGHGSPTSWAD---EDFTSSDIS----NLN--NKNKLPVVISAACYTGNFDDPDNPSLGEALVLNPNGGAIAF 308 (378)
T ss_dssp --SEEEEES-B-SSBBTT---T--BTTTGG----G-----TT---EEEEESSSTT-TTSSS---HHHHHHTTEE-S-SEE
T ss_pred CCeEEEEecCCchhhccc---CcccHhHHH----Hhc--CCCCceEEEEeECCCcCCCCCCCCcHHHHheECCCCcEEEE
Confidence 467889999999987621 222333333 221 22255688889999999833321 22 2 444
Q ss_pred EEecCCCCcccCCCCCCCCcceeeccchHHHHHHHhcccCCChhhHHHHHhhccCccc
Q psy6307 253 MASSLVGEDSLSHHVDPAIGVYIIDRYTYYALEFLEDVHLDSAKTMEDFLAVCPKRVC 310 (368)
Q Consensus 253 itAS~~~EsSys~~~d~~ig~~l~D~FTy~~~~~le~~~~~~~~Tl~~lf~~v~~~~~ 310 (368)
+++|. .+|... .+. +...|++..-.....+|.+++...+....
T Consensus 309 ig~s~---~~~~~~---------~~~---~~~~~~~~l~~~~~~~lG~a~~~a~~~~~ 351 (378)
T PF01364_consen 309 IGSSR---VSYASP---------NDR---LNRGFYEALFNSNMDTLGEALRQAKNYYL 351 (378)
T ss_dssp EEESS-----SSHH---------HHH---HHHHHTT-STT----BHHHHHHHHHHHHH
T ss_pred Eecce---eEecch---------HHH---HHHHHHHHHhccCCCCHHHHHHHHHHHHH
Confidence 55543 233211 222 33345555422233388998888776554
No 35
>KOG1360|consensus
Probab=23.24 E-value=83 Score=33.17 Aligned_cols=31 Identities=39% Similarity=0.523 Sum_probs=25.0
Q ss_pred chhhhHHHHHHHHHhCCCC----CCCEEEEecCCC
Q psy6307 40 RHVANVLSIYRSVKRLGIP----DSHIILMIADDM 70 (368)
Q Consensus 40 RHqadv~~~Y~~L~~~Gi~----d~~Ii~m~~DDi 70 (368)
-||.+|-++-|.|.+.||| ++|||=.+--|.
T Consensus 431 ~hqrnv~~~kq~l~~~GiPVi~~pSHIiPv~vgda 465 (570)
T KOG1360|consen 431 QHQRNVKYVKQLLMELGIPVIPNPSHIIPVRVGDA 465 (570)
T ss_pred HHHHHHHHHHHHHHHcCCcccCCCcceeeeeccCH
Confidence 4899999999999999996 788885444343
No 36
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=22.40 E-value=1.5e+02 Score=25.74 Aligned_cols=41 Identities=15% Similarity=0.288 Sum_probs=30.1
Q ss_pred CcEEEEEeCCCCCCCcc------hhhhHHHHHHHHHhCCCCCCCEEE
Q psy6307 24 NNWAVLVDTSRFWFNYR------HVANVLSIYRSVKRLGIPDSHIIL 64 (368)
Q Consensus 24 ~~wAVlvagS~~w~NYR------Hqadv~~~Y~~L~~~Gi~d~~Ii~ 64 (368)
..+.|+++|+|....+. ++...-...+.|.++|+|-++|++
T Consensus 39 ~G~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~l~~ 85 (126)
T TIGR01689 39 LGFEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDEIYV 85 (126)
T ss_pred CCCEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCceEEe
Confidence 44668999988877665 222234567889999999999986
Done!