Query psy7305
Match_columns 258
No_of_seqs 134 out of 1518
Neff 10.5
Searched_HMMs 46136
Date Fri Aug 16 23:25:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 100.0 8.2E-44 1.8E-48 280.6 17.3 227 18-256 1-232 (232)
2 KOG3627|consensus 100.0 2.7E-40 5.9E-45 264.6 19.6 234 15-257 10-254 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 9.5E-41 2.1E-45 262.9 16.6 223 17-253 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 2.2E-38 4.7E-43 247.8 13.7 215 18-253 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 8.9E-33 1.9E-37 216.9 15.1 237 14-258 29-279 (413)
6 PF03761 DUF316: Domain of unk 99.8 9.7E-19 2.1E-23 141.7 13.5 223 6-255 29-277 (282)
7 PF09342 DUF1986: Domain of un 99.3 3.5E-11 7.5E-16 91.2 8.5 118 25-157 12-131 (267)
8 COG3591 V8-like Glu-specific e 99.1 4.1E-09 8.9E-14 81.8 12.3 200 24-257 44-250 (251)
9 PF13365 Trypsin_2: Trypsin-li 98.2 3.4E-06 7.3E-11 59.0 5.2 22 47-68 1-23 (120)
10 TIGR02037 degP_htrA_DO peripla 97.8 0.00025 5.5E-09 61.1 10.6 58 44-123 57-115 (428)
11 TIGR02038 protease_degS peripl 97.8 0.00058 1.3E-08 57.2 11.9 73 29-123 55-135 (351)
12 PRK10898 serine endoprotease; 97.6 0.0013 2.8E-08 55.1 11.8 73 29-123 55-135 (353)
13 PRK10942 serine endoprotease; 97.1 0.0058 1.3E-07 53.3 10.3 58 44-123 110-169 (473)
14 PRK10139 serine endoprotease; 97.1 0.0065 1.4E-07 52.7 10.3 57 45-123 90-148 (455)
15 PF02395 Peptidase_S6: Immunog 96.9 0.0029 6.3E-08 57.8 7.1 30 205-234 213-244 (769)
16 PF00863 Peptidase_C4: Peptida 94.0 0.18 3.9E-06 39.4 5.8 42 207-253 150-192 (235)
17 PF00947 Pico_P2A: Picornaviru 93.2 0.14 2.9E-06 35.6 3.6 34 207-249 89-122 (127)
18 PF10459 Peptidase_S46: Peptid 77.5 1.5 3.3E-05 40.2 2.0 20 47-66 49-69 (698)
19 PF05579 Peptidase_S32: Equine 70.8 4.7 0.0001 32.1 2.9 23 207-232 207-229 (297)
20 PF02907 Peptidase_S29: Hepati 67.8 6 0.00013 28.0 2.6 22 206-230 106-127 (148)
21 PF05416 Peptidase_C37: Southa 63.6 9.8 0.00021 32.5 3.6 31 203-233 498-528 (535)
22 COG4844 Uncharacterized protei 51.2 1.8 3.9E-05 26.3 -1.9 24 2-25 34-57 (78)
23 PRK13669 hypothetical protein; 49.2 11 0.00025 23.9 1.4 25 2-26 34-58 (78)
24 COG3964 Predicted amidohydrola 38.1 32 0.0007 28.3 2.6 57 6-69 16-72 (386)
25 PF05580 Peptidase_S55: SpoIVB 37.4 31 0.00067 26.7 2.4 27 203-233 175-201 (218)
26 PF07293 DUF1450: Protein of u 36.8 26 0.00057 22.3 1.6 25 2-26 34-58 (78)
27 PF00944 Peptidase_S3: Alphavi 36.3 25 0.00054 25.0 1.6 23 207-232 105-127 (158)
28 PF00548 Peptidase_C3: 3C cyst 30.9 25 0.00054 26.2 1.0 27 205-231 144-170 (172)
29 COG2967 ApaG Uncharacterized p 30.5 1E+02 0.0022 21.5 3.7 32 27-62 26-57 (126)
30 COG0265 DegQ Trypsin-like seri 24.0 4.3E+02 0.0093 22.1 11.7 29 203-234 189-217 (347)
31 PF00949 Peptidase_S7: Peptida 22.3 75 0.0016 22.6 2.0 26 204-232 93-118 (132)
32 TIGR02860 spore_IV_B stage IV 20.1 76 0.0016 27.4 2.0 26 203-232 355-380 (402)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=100.00 E-value=8.2e-44 Score=280.64 Aligned_cols=227 Identities=37% Similarity=0.665 Sum_probs=183.4
Q ss_pred eecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCce
Q psy7305 18 VVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPET 97 (258)
Q Consensus 18 i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~ 97 (258)
|+||+.+..++|||+|.|+... ..+.|+||||+++||||||||+.... ...+.|++|...............
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~---~~~~C~GtlIs~~~VLTaAhC~~~~~-----~~~~~v~~g~~~~~~~~~~~~~~~ 72 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTG---GRHFCGGSLISPRWVLTAAHCVYSSA-----PSNYTVRLGSHDLSSNEGGGQVIK 72 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccC---CcEEEEEEEeeCCEEEECHHhcCCCC-----CccEEEEeCcccccCCCCceEEEE
Confidence 6899999999999999998642 57889999999999999999997642 457889999887765432222122
Q ss_pred eeeecCCCCCCC-CccccchhhhhcCC--CccCCCcceeeeecccccCCCCCCCCccccccceeEecCcccccceeeeec
Q psy7305 98 YRVEEGLNPCPS-DYYYQASVLTITSP--RYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWLSGKESTVQRQVDLP 174 (258)
Q Consensus 98 ~~v~~~~~~~~~-~~~~diall~L~~p--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~~ 174 (258)
+.....||.|+. ...+|||||+|++| +.....|+|++..... ...+.. +.++|||...........++...+.
T Consensus 73 v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~--~~~~~~--~~~~G~g~~~~~~~~~~~~~~~~~~ 148 (232)
T cd00190 73 VKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYN--LPAGTT--CTVSGWGRTSEGGPLPDVLQEVNVP 148 (232)
T ss_pred EEEEEECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCcccc--CCCCCE--EEEEeCCcCCCCCCCCceeeEEEee
Confidence 333348999998 68999999999999 4556799999877411 112223 8899999875444556788999999
Q ss_pred cccccccccccC--CCCCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCcccHHH
Q psy7305 175 VWENSECDKTYF--QPITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVTKYLDW 252 (258)
Q Consensus 175 ~~~~~~C~~~~~--~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~~~~~W 252 (258)
+++.+.|...+. ..+.++++|+.......+.|.||+||||++..+++++|+||+|++..|...+.|.+|++|..|.+|
T Consensus 149 ~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~W 228 (232)
T cd00190 149 IVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDW 228 (232)
T ss_pred eECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHH
Confidence 999999998886 467899999986544778999999999999988999999999999888766789999999999999
Q ss_pred Hhhh
Q psy7305 253 IEQN 256 (258)
Q Consensus 253 I~~~ 256 (258)
|+++
T Consensus 229 I~~~ 232 (232)
T cd00190 229 IQKT 232 (232)
T ss_pred hhcC
Confidence 9874
No 2
>KOG3627|consensus
Probab=100.00 E-value=2.7e-40 Score=264.55 Aligned_cols=234 Identities=38% Similarity=0.679 Sum_probs=183.4
Q ss_pred cCeeecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCC-
Q psy7305 15 KFRVVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPS- 93 (258)
Q Consensus 15 ~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~- 93 (258)
..||++|.++.++++||+++|..... ..++|+|+||+++||||||||+.... .. .+.|++|...........
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~--~~~~Cggsli~~~~vltaaHC~~~~~----~~-~~~V~~G~~~~~~~~~~~~ 82 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGN--GRHLCGGSLISPRWVLTAAHCVKGAS----AS-LYTVRLGEHDINLSVSEGE 82 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCC--cceeeeeEEeeCCEEEEChhhCCCCC----Cc-ceEEEECccccccccccCc
Confidence 57899999999999999999986432 36699999999999999999998753 12 678888877555442211
Q ss_pred --CCceeeeecCCCCCCC-Ccc-ccchhhhhcCC--CccCCCcceeeeecccccCCCCCCCCccccccceeEec-Ccccc
Q psy7305 94 --MPETYRVEEGLNPCPS-DYY-YQASVLTITSP--RYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWLS-GKEST 166 (258)
Q Consensus 94 --~~~~~~v~~~~~~~~~-~~~-~diall~L~~p--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~ 166 (258)
....+.....|+.|+. ... +|||||+|.+| ++..++|+|++............ .+.++|||..... ...+.
T Consensus 83 ~~~~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~--~~~v~GWG~~~~~~~~~~~ 160 (256)
T KOG3627|consen 83 EQLVGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGT--TCLVSGWGRTESGGGPLPD 160 (256)
T ss_pred hhhhceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCC--EEEEEeCCCcCCCCCCCCc
Confidence 1111222227999998 555 99999999998 78889999996444321111212 2778999987543 24578
Q ss_pred cceeeeeccccccccccccCC--CCCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCC-CCCCCCCeEE
Q psy7305 167 VQRQVDLPVWENSECDKTYFQ--PITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNK-CGEPGYPGVY 243 (258)
Q Consensus 167 ~l~~~~~~~~~~~~C~~~~~~--~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~-c~~~~~p~vf 243 (258)
.+++.++++++.++|...+.. .+.+.++|++......+.|.|||||||++..+++++|+||+|+|.. |...+.|++|
T Consensus 161 ~L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~~~P~vy 240 (256)
T KOG3627|consen 161 TLQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQPNYPGVY 240 (256)
T ss_pred eeEEEEEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCCCCCeEE
Confidence 888999999999999988865 4677789998656677799999999999998779999999999988 9887799999
Q ss_pred eeCcccHHHHhhhc
Q psy7305 244 TRVTKYLDWIEQNM 257 (258)
Q Consensus 244 ~~v~~~~~WI~~~i 257 (258)
++|..|.+||++.+
T Consensus 241 t~V~~y~~WI~~~~ 254 (256)
T KOG3627|consen 241 TRVSSYLDWIKENI 254 (256)
T ss_pred eEhHHhHHHHHHHh
Confidence 99999999999876
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=100.00 E-value=9.5e-41 Score=262.88 Aligned_cols=223 Identities=38% Similarity=0.677 Sum_probs=178.9
Q ss_pred eeecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCc
Q psy7305 17 RVVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPE 96 (258)
Q Consensus 17 ~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~ 96 (258)
||+||+.+.+++|||+|.+++.. ..+.|+||||++++|||||||+.... +..+.|++|........+. ...
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~---~~~~C~GtlIs~~~VLTaahC~~~~~-----~~~~~v~~g~~~~~~~~~~-~~~ 71 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRG---GRHFCGGSLISPRWVLTAAHCVYGSD-----PSNIRVRLGSHDLSSGEEG-QVI 71 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcC---CCcEEEEEEecCCEEEECHHHcCCCC-----CcceEEEeCcccCCCCCCc-eEE
Confidence 68999999999999999997632 57889999999999999999998743 3578899998876654322 112
Q ss_pred eeeeecCCCCCCC-CccccchhhhhcCC--CccCCCcceeeeecccccCCCCCCCCccccccceeEe-cCcccccceeee
Q psy7305 97 TYRVEEGLNPCPS-DYYYQASVLTITSP--RYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWL-SGKESTVQRQVD 172 (258)
Q Consensus 97 ~~~v~~~~~~~~~-~~~~diall~L~~p--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~-~~~~~~~l~~~~ 172 (258)
.+.-...||.|+. ...+|+|||+|++| +....+|+|++....... .... +.++|||.... .......++...
T Consensus 72 ~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~--~~~~--~~~~g~g~~~~~~~~~~~~~~~~~ 147 (229)
T smart00020 72 KVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVP--AGTT--CTVSGWGRTSEGAGSLPDTLQEVN 147 (229)
T ss_pred eeEEEEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccC--CCCE--EEEEeCCCCCCCCCcCCCEeeEEE
Confidence 2333337999986 88999999999999 566789999987632211 2223 88999997642 233456788899
Q ss_pred eccccccccccccCC--CCCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCcccH
Q psy7305 173 LPVWENSECDKTYFQ--PITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVTKYL 250 (258)
Q Consensus 173 ~~~~~~~~C~~~~~~--~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~~~~ 250 (258)
+.+++.+.|...+.. .+.++++|++......+.|.||+|+||++..+ +|+|+||++++..|...+.|.+|++|.+|.
T Consensus 148 ~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~ 226 (229)
T smart00020 148 VPIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCARPGKPGVYTRVSSYL 226 (229)
T ss_pred EEEeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCCCCCCCCEEEEecccc
Confidence 999999999988754 47889999986544678999999999999987 999999999999998667899999999999
Q ss_pred HHH
Q psy7305 251 DWI 253 (258)
Q Consensus 251 ~WI 253 (258)
+||
T Consensus 227 ~WI 229 (229)
T smart00020 227 DWI 229 (229)
T ss_pred ccC
Confidence 998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=100.00 E-value=2.2e-38 Score=247.82 Aligned_cols=215 Identities=39% Similarity=0.710 Sum_probs=173.5
Q ss_pred eecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCce
Q psy7305 18 VVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPET 97 (258)
Q Consensus 18 i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~ 97 (258)
|.||..+.+++|||+|.+++... .++|+|+||+++||||||||+.. ...+.+.+|........... ..
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~---~~~C~G~li~~~~vLTaahC~~~-------~~~~~v~~g~~~~~~~~~~~--~~ 68 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNG---RFFCTGTLISPRWVLTAAHCVDG-------ASDIKVRLGTYSIRNSDGSE--QT 68 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTT---EEEEEEEEEETTEEEEEGGGHTS-------GGSEEEEESESBTTSTTTTS--EE
T ss_pred CCCCEECCCCCCCeEEEEeeCCC---CeeEeEEeccccccccccccccc-------cccccccccccccccccccc--cc
Confidence 68999999999999999987432 88999999999999999999987 34677888884443333222 35
Q ss_pred eeeec--CCCCCCC-CccccchhhhhcCC--CccCCCcceeeeecccccCCCCCCCCccccccceeEecCcccccceeee
Q psy7305 98 YRVEE--GLNPCPS-DYYYQASVLTITSP--RYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWLSGKESTVQRQVD 172 (258)
Q Consensus 98 ~~v~~--~~~~~~~-~~~~diall~L~~p--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~ 172 (258)
+.+.. .||.|+. ...+|+|||+|++| +.....|++++...... ..+.. +.+.||+.....+ ....++...
T Consensus 69 ~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~--~~~~~--~~~~G~~~~~~~~-~~~~~~~~~ 143 (220)
T PF00089_consen 69 IKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDP--NVGTS--CIVVGWGRTSDNG-YSSNLQSVT 143 (220)
T ss_dssp EEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTT--TTTSE--EEEEESSBSSTTS-BTSBEEEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccc--ccccc--ccccccccccccc-ccccccccc
Confidence 55544 8899998 66999999999999 67777888888733211 12223 8999999854333 456788899
Q ss_pred eccccccccccccCCCCCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCcccHHH
Q psy7305 173 LPVWENSECDKTYFQPITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVTKYLDW 252 (258)
Q Consensus 173 ~~~~~~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~~~~~W 252 (258)
+.+++.+.|...+...+.+.++|++.. ...+.|.||+||||++.+. +|+||++++..|...+.|.+|++|+.|++|
T Consensus 144 ~~~~~~~~c~~~~~~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~~~~~v~~~v~~~~~W 219 (220)
T PF00089_consen 144 VPVVSRKTCRSSYNDNLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSPNYPGVYTRVSSYLDW 219 (220)
T ss_dssp EEEEEHHHHHHHTTTTSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBTTSEEEEEEGGGGHHH
T ss_pred ccccccccccccccccccccccccccc-cccccccccccccccccee---eecceeeecCCCCCCCcCEEEEEHHHhhcc
Confidence 999999999988666689999999865 5678999999999999876 899999999999887789999999999999
Q ss_pred H
Q psy7305 253 I 253 (258)
Q Consensus 253 I 253 (258)
|
T Consensus 220 I 220 (220)
T PF00089_consen 220 I 220 (220)
T ss_dssp H
T ss_pred C
Confidence 8
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.9e-33 Score=216.89 Aligned_cols=237 Identities=28% Similarity=0.404 Sum_probs=167.3
Q ss_pred CcCeeecCccCCCCCCceEEEEEEeCCC-CceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCC
Q psy7305 14 PKFRVVGGQESLPGRWPWMAAIFLHGTR-RTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEP 92 (258)
Q Consensus 14 ~~~~i~~g~~~~~~~~Pw~v~i~~~~~~-~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~ 92 (258)
-+.||+||..|+.++||++|++..+... -...+|+|+++..|||||||||+.... ++......|..+..+....+.
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s--~is~d~~~vv~~l~d~Sq~~r- 105 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASS--PISSDVNRVVVDLNDSSQAER- 105 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCC--CccccceEEEecccccccccC-
Confidence 4789999999999999999999544332 245579999999999999999998765 233444445544443333222
Q ss_pred CCCceeeeecCCCCCCC-CccccchhhhhcCCCccCCCcceeeeecccccCCCCCCCCccccccceeEecCc-----ccc
Q psy7305 93 SMPETYRVEEGLNPCPS-DYYYQASVLTITSPRYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWLSGK-----EST 166 (258)
Q Consensus 93 ~~~~~~~v~~~~~~~~~-~~~~diall~L~~p~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-----~~~ 166 (258)
..++....|..|.. ...||+|+++|.++.......+.................-....+|+...+... ...
T Consensus 106 ---g~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt 182 (413)
T COG5640 106 ---GHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGT 182 (413)
T ss_pred ---cceEEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccc
Confidence 13334447777777 999999999999985444333333333222222222232345556665443322 124
Q ss_pred cceeeeeccccccccccccCCC------CCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCC-CCCCCC
Q psy7305 167 VQRQVDLPVWENSECDKTYFQP------ITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNK-CGEPGY 239 (258)
Q Consensus 167 ~l~~~~~~~~~~~~C~~~~~~~------~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~-c~~~~~ 239 (258)
.+++..+...+...|.+.++.. ..-.-+|++.. ..+.|.||+|||++.+.++...++||+|||.. |..+..
T Consensus 183 ~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~--~~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~~ 260 (413)
T COG5640 183 ILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP--PKDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGCGGTLI 260 (413)
T ss_pred eeeeeeeeeechHHhhhhccccccCCCCCCccceecCCC--CcccccCCCCCceEEeCCCccEEEeEEEecCCCCCCCCc
Confidence 6778889999999998887411 12223999843 47899999999999999888999999999986 999999
Q ss_pred CeEEeeCcccHHHHhhhcC
Q psy7305 240 PGVYTRVTKYLDWIEQNMV 258 (258)
Q Consensus 240 p~vf~~v~~~~~WI~~~i~ 258 (258)
|.|||+|+.|.+||...|.
T Consensus 261 ~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 261 PGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred ceeEEehhHHHHHHHHHhc
Confidence 9999999999999998763
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.80 E-value=9.7e-19 Score=141.75 Aligned_cols=223 Identities=22% Similarity=0.394 Sum_probs=135.1
Q ss_pred CCCCCCC-CCcCeeecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCC-----Ccc-----
Q psy7305 6 HGCGRPD-VPKFRVVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRP-----FHA----- 74 (258)
Q Consensus 6 ~~cg~~~-~~~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~-----~~~----- 74 (258)
..||++. ..+.++.+|..+..++.||++.++..........++||+||+|||||++||+....... ...
T Consensus 29 ~~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~~ 108 (282)
T PF03761_consen 29 ETCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCEG 108 (282)
T ss_pred HhcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceeeC
Confidence 3599553 34566899999999999999999887666667778999999999999999997433211 000
Q ss_pred c--eEEEE---eCcccC--CCCCCCCCCceeeeec--CCCCC-----CCCccccchhhhhcCCCccCCCcceeeeecccc
Q psy7305 75 Q--QFTVR---LGDIDL--RREDEPSMPETYRVEE--GLNPC-----PSDYYYQASVLTITSPRYLTGIPAMVLFVEATS 140 (258)
Q Consensus 75 ~--~~~v~---~g~~~~--~~~~~~~~~~~~~v~~--~~~~~-----~~~~~~diall~L~~p~~~~~~~i~~~~~~~~~ 140 (258)
. .+.|. +..... .............+.+ +.... ......+.+||+|++++.....|+|++......
T Consensus 109 ~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~~~~~~~~~Cl~~~~~~~ 188 (282)
T PF03761_consen 109 NNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEEDFSKNVSPPCLADSSTNW 188 (282)
T ss_pred CCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEcccccccCCCEEeCCCcccc
Confidence 0 11110 000011 0000000001111211 11111 226677899999999988999999998655331
Q ss_pred cCCCCCCCCccccccceeEecCcccccceeeeeccccccccccccCCCCCCCeEeeccCCCCCCCCCCCCCCeeEEecCC
Q psy7305 141 LDFKRPSGLNNAVDFKNVWLSGKESTVQRQVDLPVWENSECDKTYFQPITDNFICAGLREGGKDACQGDSGGPLMMKKDG 220 (258)
Q Consensus 141 ~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~ 220 (258)
..... +.+.|+ .....+....+.+..... |..........|.+|+||||+...++
T Consensus 189 --~~~~~--~~~yg~-------~~~~~~~~~~~~i~~~~~--------------~~~~~~~~~~~~~~d~Gg~lv~~~~g 243 (282)
T PF03761_consen 189 --EKGDE--VDVYGF-------NSTGKLKHRKLKITNCTK--------------CAYSICTKQYSCKGDRGGPLVKNING 243 (282)
T ss_pred --ccCce--EEEeec-------CCCCeEEEEEEEEEEeec--------------cceeEecccccCCCCccCeEEEEECC
Confidence 11111 344444 112223333333332211 22111234577999999999999999
Q ss_pred eEEEEEEeeeCCC-CCCCCCCeEEeeCcccHHHHhh
Q psy7305 221 YWMQVGIVSFGNK-CGEPGYPGVYTRVTKYLDWIEQ 255 (258)
Q Consensus 221 ~~~L~Gi~s~~~~-c~~~~~p~vf~~v~~~~~WI~~ 255 (258)
+|+|+||.+.+.. |.. + ...|.+|..|.+=|.+
T Consensus 244 r~tlIGv~~~~~~~~~~-~-~~~f~~v~~~~~~IC~ 277 (282)
T PF03761_consen 244 RWTLIGVGASGNYECNK-N-NSYFFNVSWYQDEICE 277 (282)
T ss_pred CEEEEEEEccCCCcccc-c-ccEEEEHHHhhhhhcc
Confidence 9999999988763 332 2 5789999999887754
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.25 E-value=3.5e-11 Score=91.19 Aligned_cols=118 Identities=17% Similarity=0.320 Sum_probs=83.9
Q ss_pred CCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeeeecCC
Q psy7305 25 LPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRVEEGL 104 (258)
Q Consensus 25 ~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~~~ 104 (258)
+..-|||+|.||. ++.+.|+|+||.++|+|++.+|+..-. +...-+.+.+|.......-+.-..+...|..++
T Consensus 12 e~y~WPWlA~IYv----dG~~~CsgvLlD~~WlLvsssCl~~I~---L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~ 84 (267)
T PF09342_consen 12 EDYHWPWLADIYV----DGRYWCSGVLLDPHWLLVSSSCLRGIS---LSHHYVSALLGGGKTYLSVDGPHEQISRVDCFK 84 (267)
T ss_pred ccccCcceeeEEE----cCeEEEEEEEeccceEEEeccccCCcc---cccceEEEEecCcceecccCCChheEEEeeeee
Confidence 3456999999997 568899999999999999999997633 233457788887765544344444566666655
Q ss_pred CCCCCCccccchhhhhcCC--CccCCCcceeeeecccccCCCCCCCCccccccce
Q psy7305 105 NPCPSDYYYQASVLTITSP--RYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKN 157 (258)
Q Consensus 105 ~~~~~~~~~diall~L~~p--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~ 157 (258)
.- ...+++||.|+.| |+..+.|..++.... ....... |...|-..
T Consensus 85 ~V----~~S~v~LLHL~~~~~fTr~VlP~flp~~~~--~~~~~~~--CVAVg~d~ 131 (267)
T PF09342_consen 85 DV----PESNVLLLHLEQPANFTRYVLPTFLPETSN--ENESDDE--CVAVGHDD 131 (267)
T ss_pred ec----cccceeeeeecCcccceeeecccccccccC--CCCCCCc--eEEEEccc
Confidence 44 3458999999999 899999999985222 2222233 76666543
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.06 E-value=4.1e-09 Score=81.81 Aligned_cols=200 Identities=16% Similarity=0.110 Sum_probs=97.5
Q ss_pred CCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCCCCCccceEEEEe-CcccCCCCCCCCCCceeeeec
Q psy7305 24 SLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQRPFHAQQFTVRL-GDIDLRREDEPSMPETYRVEE 102 (258)
Q Consensus 24 ~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~~~~~~~~~~v~~-g~~~~~~~~~~~~~~~~~v~~ 102 (258)
....+|||-+-..+... ..++-|+++||+|+.||||+||+...... ...+.+.. |...-....... ......
T Consensus 44 ~dt~~~Py~av~~~~~~-tG~~~~~~~lI~pntvLTa~Hc~~s~~~G---~~~~~~~p~g~~~~~~~~~~~---~~~~~~ 116 (251)
T COG3591 44 TDTTQFPYSAVVQFEAA-TGRLCTAATLIGPNTVLTAGHCIYSPDYG---EDDIAAAPPGVNSDGGPFYGI---TKIEIR 116 (251)
T ss_pred ccCCCCCcceeEEeecC-CCcceeeEEEEcCceEEEeeeEEecCCCC---hhhhhhcCCcccCCCCCCCce---eeEEEE
Confidence 34588999777655544 44556777999999999999999875431 01222222 221111111111 111111
Q ss_pred CCCC-C-CC-Cccccchhhhhc--CCCccCCCcceeeeecccccCCCCCCCCccccccceeEecCcccccceeeeecccc
Q psy7305 103 GLNP-C-PS-DYYYQASVLTIT--SPRYLTGIPAMVLFVEATSLDFKRPSGLNNAVDFKNVWLSGKESTVQRQVDLPVWE 177 (258)
Q Consensus 103 ~~~~-~-~~-~~~~diall~L~--~p~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~ 177 (258)
..+. + .. ....|+..+.|+ .++............. ....+.. ..+.||-... .+..+ .
T Consensus 117 ~~~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~---~~~~~d~--i~v~GYP~dk-----~~~~~-------~ 179 (251)
T COG3591 117 VYPGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTAS---EAKANDR--ITVIGYPGDK-----PNIGT-------M 179 (251)
T ss_pred ecCCceeccCCceeeccHHHhccCCCcccccccccccccc---ccccCce--eEEEeccCCC-----Cccee-------E
Confidence 2332 1 22 566677777777 2222221111111111 1111111 3444442210 00000 0
Q ss_pred ccccccccCCCCCCCeEeeccCCCCCCCCCCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCc-ccHHHHhhh
Q psy7305 178 NSECDKTYFQPITDNFICAGLREGGKDACQGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVT-KYLDWIEQN 256 (258)
Q Consensus 178 ~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~-~~~~WI~~~ 256 (258)
.+.|.+... +.... ..-..+++.|+||+|++...+ +++||..-++.-.......-.+++. ..++||++.
T Consensus 180 ~e~t~~v~~--~~~~~-----l~y~~dT~pG~SGSpv~~~~~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~ 249 (251)
T COG3591 180 WESTGKVNS--IKGNK-----LFYDADTLPGSSGSPVLISKD---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQN 249 (251)
T ss_pred eeecceeEE--Eecce-----EEEEecccCCCCCCceEecCc---eEEEEEecCCCcccccccCcceEecHHHHHHHHHh
Confidence 111111110 11111 122457899999999999876 8999999987533222234455555 589999987
Q ss_pred c
Q psy7305 257 M 257 (258)
Q Consensus 257 i 257 (258)
+
T Consensus 250 ~ 250 (251)
T COG3591 250 I 250 (251)
T ss_pred h
Confidence 6
No 9
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=98.18 E-value=3.4e-06 Score=59.02 Aligned_cols=22 Identities=50% Similarity=0.697 Sum_probs=19.8
Q ss_pred eeEEEEeCC-EEEecccCcccCC
Q psy7305 47 CGGSLIGTR-YVLTAAHCTKDTR 68 (258)
Q Consensus 47 C~GtlIs~~-~VLTaa~C~~~~~ 68 (258)
|+|.+|.++ +|||++||+....
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~~ 23 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDWN 23 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCCT
T ss_pred CEEEEEcCCceEEEchhheeccc
Confidence 789999999 9999999998643
No 10
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=97.80 E-value=0.00025 Score=61.08 Aligned_cols=58 Identities=22% Similarity=0.239 Sum_probs=37.6
Q ss_pred eeEeeEEEEeCC-EEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeeeecCCCCCCCCccccchhhhhcC
Q psy7305 44 EFWCGGSLIGTR-YVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRVEEGLNPCPSDYYYQASVLTITS 122 (258)
Q Consensus 44 ~~~C~GtlIs~~-~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~diall~L~~ 122 (258)
...++|.+|+++ +|||++|.+... ..+.|.+.... .. ...+...+ ...|+||||++.
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~-------~~i~V~~~~~~------~~---~a~vv~~d------~~~DlAllkv~~ 114 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGA-------DEITVTLSDGR------EF---KAKLVGKD------PRTDIAVLKIDA 114 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCC-------CeEEEEeCCCC------EE---EEEEEEec------CCCCEEEEEecC
Confidence 457999999986 999999999763 34555543211 00 11222222 246999999986
Q ss_pred C
Q psy7305 123 P 123 (258)
Q Consensus 123 p 123 (258)
+
T Consensus 115 ~ 115 (428)
T TIGR02037 115 K 115 (428)
T ss_pred C
Confidence 5
No 11
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=97.76 E-value=0.00058 Score=57.18 Aligned_cols=73 Identities=22% Similarity=0.243 Sum_probs=44.8
Q ss_pred CceEEEEEEeCCC-------CceeEeeEEEEeCC-EEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeee
Q psy7305 29 WPWMAAIFLHGTR-------RTEFWCGGSLIGTR-YVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRV 100 (258)
Q Consensus 29 ~Pw~v~i~~~~~~-------~~~~~C~GtlIs~~-~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v 100 (258)
-|-+|.|+-.... ......+|.+|+++ +|||++|.+... ..+.|.+.+-. . ....+
T Consensus 55 ~psVV~I~~~~~~~~~~~~~~~~~~GSG~vi~~~G~IlTn~HVV~~~-------~~i~V~~~dg~------~---~~a~v 118 (351)
T TIGR02038 55 APAVVNIYNRSISQNSLNQLSIQGLGSGVIMSKEGYILTNYHVIKKA-------DQIVVALQDGR------K---FEAEL 118 (351)
T ss_pred CCcEEEEEeEeccccccccccccceEEEEEEeCCeEEEecccEeCCC-------CEEEEEECCCC------E---EEEEE
Confidence 5889988643211 11346999999977 999999999763 34555543210 0 01122
Q ss_pred ecCCCCCCCCccccchhhhhcCC
Q psy7305 101 EEGLNPCPSDYYYQASVLTITSP 123 (258)
Q Consensus 101 ~~~~~~~~~~~~~diall~L~~p 123 (258)
... +...|+||||++.+
T Consensus 119 v~~------d~~~DlAvlkv~~~ 135 (351)
T TIGR02038 119 VGS------DPLTDLAVLKIEGD 135 (351)
T ss_pred EEe------cCCCCEEEEEecCC
Confidence 221 23579999999875
No 12
>PRK10898 serine endoprotease; Provisional
Probab=97.61 E-value=0.0013 Score=55.13 Aligned_cols=73 Identities=22% Similarity=0.278 Sum_probs=44.5
Q ss_pred CceEEEEEEeCCC-------CceeEeeEEEEeCC-EEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeee
Q psy7305 29 WPWMAAIFLHGTR-------RTEFWCGGSLIGTR-YVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRV 100 (258)
Q Consensus 29 ~Pw~v~i~~~~~~-------~~~~~C~GtlIs~~-~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v 100 (258)
-|-+|.|.-.... ......+|.+|+++ +|||++|=+... ..+.|.+.+-. . ....+
T Consensus 55 ~psvV~v~~~~~~~~~~~~~~~~~~GSGfvi~~~G~IlTn~HVv~~a-------~~i~V~~~dg~------~---~~a~v 118 (353)
T PRK10898 55 APAVVNVYNRSLNSTSHNQLEIRTLGSGVIMDQRGYILTNKHVINDA-------DQIIVALQDGR------V---FEALL 118 (353)
T ss_pred CCcEEEEEeEeccccCcccccccceeeEEEEeCCeEEEecccEeCCC-------CEEEEEeCCCC------E---EEEEE
Confidence 4888888653211 11357999999976 999999988752 34555553211 0 01112
Q ss_pred ecCCCCCCCCccccchhhhhcCC
Q psy7305 101 EEGLNPCPSDYYYQASVLTITSP 123 (258)
Q Consensus 101 ~~~~~~~~~~~~~diall~L~~p 123 (258)
... +...|+||||++.+
T Consensus 119 v~~------d~~~DlAvl~v~~~ 135 (353)
T PRK10898 119 VGS------DSLTDLAVLKINAT 135 (353)
T ss_pred EEE------cCCCCEEEEEEcCC
Confidence 211 23479999999865
No 13
>PRK10942 serine endoprotease; Provisional
Probab=97.09 E-value=0.0058 Score=53.27 Aligned_cols=58 Identities=19% Similarity=0.251 Sum_probs=37.3
Q ss_pred eeEeeEEEEeC--CEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeeeecCCCCCCCCccccchhhhhc
Q psy7305 44 EFWCGGSLIGT--RYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRVEEGLNPCPSDYYYQASVLTIT 121 (258)
Q Consensus 44 ~~~C~GtlIs~--~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~diall~L~ 121 (258)
....+|.+|++ -+|||.+|.+.+. ..+.|.+.+-. . ....+...+ ...|+||||++
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~a-------~~i~V~~~dg~------~---~~a~vv~~D------~~~DlAvlki~ 167 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDNA-------TKIKVQLSDGR------K---FDAKVVGKD------PRSDIALIQLQ 167 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCCC-------CEEEEEECCCC------E---EEEEEEEec------CCCCEEEEEec
Confidence 34799999985 4999999998763 45666654311 0 122222222 35799999997
Q ss_pred CC
Q psy7305 122 SP 123 (258)
Q Consensus 122 ~p 123 (258)
.+
T Consensus 168 ~~ 169 (473)
T PRK10942 168 NP 169 (473)
T ss_pred CC
Confidence 54
No 14
>PRK10139 serine endoprotease; Provisional
Probab=97.07 E-value=0.0065 Score=52.72 Aligned_cols=57 Identities=25% Similarity=0.338 Sum_probs=37.0
Q ss_pred eEeeEEEEeC--CEEEecccCcccCCCCCCccceEEEEeCcccCCCCCCCCCCceeeeecCCCCCCCCccccchhhhhcC
Q psy7305 45 FWCGGSLIGT--RYVLTAAHCTKDTRQRPFHAQQFTVRLGDIDLRREDEPSMPETYRVEEGLNPCPSDYYYQASVLTITS 122 (258)
Q Consensus 45 ~~C~GtlIs~--~~VLTaa~C~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~diall~L~~ 122 (258)
...+|.+|++ -+|||.+|.+.+. ..+.|.+.+-. . ....+... +...||||||++.
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~a-------~~i~V~~~dg~------~---~~a~vvg~------D~~~DlAvlkv~~ 147 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQA-------QKISIQLNDGR------E---FDAKLIGS------DDQSDIALLQIQN 147 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCCC-------CEEEEEECCCC------E---EEEEEEEE------cCCCCEEEEEecC
Confidence 4699999974 5999999999763 45666653221 0 11222211 2357999999986
Q ss_pred C
Q psy7305 123 P 123 (258)
Q Consensus 123 p 123 (258)
+
T Consensus 148 ~ 148 (455)
T PRK10139 148 P 148 (455)
T ss_pred C
Confidence 5
No 15
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=96.91 E-value=0.0029 Score=57.80 Aligned_cols=30 Identities=40% Similarity=0.719 Sum_probs=22.0
Q ss_pred CCCCCCCCeeEEe--cCCeEEEEEEeeeCCCC
Q psy7305 205 ACQGDSGGPLMMK--KDGYWMQVGIVSFGNKC 234 (258)
Q Consensus 205 ~c~gdsG~Pl~~~--~~~~~~L~Gi~s~~~~c 234 (258)
.-.||||+||+.. .+++|+|+|+++.+...
T Consensus 213 ~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~ 244 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGY 244 (769)
T ss_dssp --TT-TT-EEEEEETTTTEEEEEEEEEEECCC
T ss_pred cccCcCCCceEEEEccCCeEEEEEEEcccccc
Confidence 4579999999877 46899999999987554
No 16
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 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 []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=93.95 E-value=0.18 Score=39.43 Aligned_cols=42 Identities=31% Similarity=0.536 Sum_probs=25.2
Q ss_pred CCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCcc-cHHHH
Q psy7305 207 QGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVTK-YLDWI 253 (258)
Q Consensus 207 ~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~~-~~~WI 253 (258)
.||-|.||+...++. ++||.|.+..-.. -..|+.+.. +.+.+
T Consensus 150 ~G~CG~PlVs~~Dg~--IVGiHsl~~~~~~---~N~F~~f~~~f~~~~ 192 (235)
T PF00863_consen 150 DGDCGLPLVSTKDGK--IVGIHSLTSNTSS---RNYFTPFPDDFEEFY 192 (235)
T ss_dssp TT-TT-EEEETTT----EEEEEEEEETTTS---SEEEEE--TTHHHHH
T ss_pred CCccCCcEEEcCCCc--EEEEEcCccCCCC---eEEEEcCCHHHHHHH
Confidence 589999999986655 9999998854333 257777754 44433
No 17
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 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 domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=93.24 E-value=0.14 Score=35.64 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=27.5
Q ss_pred CCCCCCeeEEecCCeEEEEEEeeeCCCCCCCCCCeEEeeCccc
Q psy7305 207 QGDSGGPLMMKKDGYWMQVGIVSFGNKCGEPGYPGVYTRVTKY 249 (258)
Q Consensus 207 ~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vf~~v~~~ 249 (258)
+||-||+|.|+.+ ++||++-|-+ ...-|++|+.+
T Consensus 89 PGdCGg~L~C~HG----ViGi~Tagg~-----g~VaF~dir~~ 122 (127)
T PF00947_consen 89 PGDCGGILRCKHG----VIGIVTAGGE-----GHVAFADIRDL 122 (127)
T ss_dssp TT-TCSEEEETTC----EEEEEEEEET-----TEEEEEECCCG
T ss_pred CCCCCceeEeCCC----eEEEEEeCCC-----ceEEEEechhh
Confidence 6899999999998 9999998733 23789999885
No 18
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=77.52 E-value=1.5 Score=40.24 Aligned_cols=20 Identities=40% Similarity=0.820 Sum_probs=18.4
Q ss_pred eeEEEEeCC-EEEecccCccc
Q psy7305 47 CGGSLIGTR-YVLTAAHCTKD 66 (258)
Q Consensus 47 C~GtlIs~~-~VLTaa~C~~~ 66 (258)
|+|++||++ .|||-.||..+
T Consensus 49 CSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 49 CSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred eeEEEEcCCceEEecchhhhh
Confidence 999999998 99999999754
No 19
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=70.85 E-value=4.7 Score=32.11 Aligned_cols=23 Identities=30% Similarity=0.569 Sum_probs=17.6
Q ss_pred CCCCCCeeEEecCCeEEEEEEeeeCC
Q psy7305 207 QGDSGGPLMMKKDGYWMQVGIVSFGN 232 (258)
Q Consensus 207 ~gdsG~Pl~~~~~~~~~L~Gi~s~~~ 232 (258)
.||||+|++...+ .|+||.+...
T Consensus 207 ~GDSGSPVVt~dg---~liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTEDG---DLIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETTC----EEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCC
Confidence 4899999999865 5999988753
No 20
>PF02907 Peptidase_S29: Hepatitis C virus NS3 protease; InterPro: IPR004109 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies the Hepatitis C virus NS3 protein as a serine protease which belongs to MEROPS peptidase family S29 (hepacivirin family, clan PA(S)), which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. The NS2 proteinase (IPR002518 from INTERPRO), a zinc-dependent enzyme, performs a single proteolytic cut to release the N terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4. It has been suggested that the NS3 serine protease of hepatitus C is involved in cell transformation and that the ability to transform requires an active enzyme [].; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0019087 transformation of host cell by virus; PDB: 2QV1_B 3LOX_C 2OBQ_C 2OC1_C 2OC0_A 3LON_A 3KNX_A 2O8M_A 2OBO_A 2OC8_A ....
Probab=67.79 E-value=6 Score=27.99 Aligned_cols=22 Identities=32% Similarity=0.652 Sum_probs=16.2
Q ss_pred CCCCCCCeeEEecCCeEEEEEEeee
Q psy7305 206 CQGDSGGPLMMKKDGYWMQVGIVSF 230 (258)
Q Consensus 206 c~gdsG~Pl~~~~~~~~~L~Gi~s~ 230 (258)
-.|.||+|++|... .++||+--
T Consensus 106 lkGSSGgPiLC~~G---H~vG~f~a 127 (148)
T PF02907_consen 106 LKGSSGGPILCPSG---HAVGMFRA 127 (148)
T ss_dssp HTT-TT-EEEETTS---EEEEEEEE
T ss_pred EecCCCCcccCCCC---CEEEEEEE
Confidence 46899999999976 69998754
No 21
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 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 C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=63.57 E-value=9.8 Score=32.48 Aligned_cols=31 Identities=23% Similarity=0.576 Sum_probs=23.3
Q ss_pred CCCCCCCCCCeeEEecCCeEEEEEEeeeCCC
Q psy7305 203 KDACQGDSGGPLMMKKDGYWMQVGIVSFGNK 233 (258)
Q Consensus 203 ~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~ 233 (258)
-++-+||-|.|.+.+.+|.|+++||..-.-+
T Consensus 498 LGT~PGDCGcPYvyKrgNd~VV~GVH~AAtr 528 (535)
T PF05416_consen 498 LGTIPGDCGCPYVYKRGNDWVVIGVHAAATR 528 (535)
T ss_dssp TS--TTGTT-EEEEEETTEEEEEEEEEEE-S
T ss_pred cCCCCCCCCCceeeecCCcEEEEEEEehhcc
Confidence 3456899999999999999999999866433
No 22
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.18 E-value=1.8 Score=26.26 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCCcCeeecCccCC
Q psy7305 2 FSCLHGCGRPDVPKFRVVGGQESL 25 (258)
Q Consensus 2 ~~~~~~cg~~~~~~~~i~~g~~~~ 25 (258)
|.|+++||.-+......+||+.+.
T Consensus 34 YgCLt~Cg~Ca~~lfALVnGevV~ 57 (78)
T COG4844 34 YGCLTHCGICAASLFALVNGEVVE 57 (78)
T ss_pred hhhHhhhhhHHHhHHHHhcCceec
Confidence 579999997766677788887655
No 23
>PRK13669 hypothetical protein; Provisional
Probab=49.24 E-value=11 Score=23.91 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCcCeeecCccCCC
Q psy7305 2 FSCLHGCGRPDVPKFRVVGGQESLP 26 (258)
Q Consensus 2 ~~~~~~cg~~~~~~~~i~~g~~~~~ 26 (258)
+.|+..||.=..+.+.++||+.+..
T Consensus 34 ~gCls~CG~C~~~~FAlVng~~V~a 58 (78)
T PRK13669 34 YGCLGYCGICSEGLFALVNGEVVEG 58 (78)
T ss_pred cchhhhCcCcccCceEEECCeEeec
Confidence 5799999977777889999987654
No 24
>COG3964 Predicted amidohydrolase [General function prediction only]
Probab=38.13 E-value=32 Score=28.29 Aligned_cols=57 Identities=11% Similarity=0.222 Sum_probs=43.5
Q ss_pred CCCCCCCCCcCeeecCccCCCCCCceEEEEEEeCCCCceeEeeEEEEeCCEEEecccCcccCCC
Q psy7305 6 HGCGRPDVPKFRVVGGQESLPGRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAHCTKDTRQ 69 (258)
Q Consensus 6 ~~cg~~~~~~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~C~~~~~~ 69 (258)
|+-|.....+.+|.||..+..+.+|--...+... -.|.+|+|-||=-=+||......
T Consensus 16 pa~g~d~~tniai~ngkIaa~~d~~apa~tq~Id-------a~Gc~VspG~iDlHvHvy~ggt~ 72 (386)
T COG3964 16 PARGIDEITNIAIINGKIAAADDYPAPAETQIID-------ADGCIVSPGLIDLHVHVYYGGTE 72 (386)
T ss_pred cccccCccceeeeecCeEEeccCcCCChhheEEc-------cCccEeccCeeeeeeEEecCCCc
Confidence 4456555567899999999999988766554332 56789999999999999876543
No 25
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=37.37 E-value=31 Score=26.74 Aligned_cols=27 Identities=26% Similarity=0.366 Sum_probs=22.4
Q ss_pred CCCCCCCCCCeeEEecCCeEEEEEEeeeCCC
Q psy7305 203 KDACQGDSGGPLMMKKDGYWMQVGIVSFGNK 233 (258)
Q Consensus 203 ~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~ 233 (258)
...-.|=||+|++.+.+ |+|-+++..-
T Consensus 175 GGIvqGMSGSPI~qdGK----LiGAVthvf~ 201 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDGK----LIGAVTHVFV 201 (218)
T ss_pred CCEEecccCCCEEECCE----EEEEEEEEEe
Confidence 35677899999999886 9999998753
No 26
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=36.84 E-value=26 Score=22.33 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCCcCeeecCccCCC
Q psy7305 2 FSCLHGCGRPDVPKFRVVGGQESLP 26 (258)
Q Consensus 2 ~~~~~~cg~~~~~~~~i~~g~~~~~ 26 (258)
+.|+..||.=....+.++||+.+.+
T Consensus 34 ~gCl~~Cg~C~~~pFAlVnG~~V~A 58 (78)
T PF07293_consen 34 YGCLSYCGPCAKKPFALVNGEIVAA 58 (78)
T ss_pred cChhhhCcCCCCCccEEECCEEEec
Confidence 5799999977777888999987654
No 27
>PF00944 Peptidase_S3: Alphavirus core protein ; InterPro: IPR000930 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. Togavirin, also known as Sindbis virus core endopeptidase, is a serine protease resident at the N terminus of the p130 polyprotein of togaviruses []. The endopeptidase signature identifies the peptidase as belonging to the MEROPS peptidase family S3 (togavirin family, clan PA(S)). The polyprotein also includes structural proteins for the nucleocapsid core and for the glycoprotein spikes []. Togavirin is only active while part of the polyprotein, cleavage at a Trp-Ser bond resulting in total lack of activity []. Mutagenesis studies have identified the location of the His-Asp-Ser catalytic triad, and X-ray studies have revealed the protein fold to be similar to that of chymotrypsin [, ].; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YEW_D 1EP5_A 3J0C_F 1EP6_C 1WYK_D 1DYL_A 1VCQ_B 1VCP_B 1LD4_D 1KXA_A ....
Probab=36.29 E-value=25 Score=24.96 Aligned_cols=23 Identities=39% Similarity=0.523 Sum_probs=17.5
Q ss_pred CCCCCCeeEEecCCeEEEEEEeeeCC
Q psy7305 207 QGDSGGPLMMKKDGYWMQVGIVSFGN 232 (258)
Q Consensus 207 ~gdsG~Pl~~~~~~~~~L~Gi~s~~~ 232 (258)
.||||-|++-+.+ .++||+..|.
T Consensus 105 ~GDSGRpi~DNsG---rVVaIVLGG~ 127 (158)
T PF00944_consen 105 PGDSGRPIFDNSG---RVVAIVLGGA 127 (158)
T ss_dssp TTSTTEEEESTTS---BEEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCC
Confidence 6899999987644 4888877663
No 28
>PF00548 Peptidase_C3: 3C cysteine protease (picornain 3C); InterPro: IPR000199 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 signature defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral C3 cysteine protease. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SJO_E 2H6M_A 1QA7_C 1HAV_B 2HAL_A 2H9H_A 3QZQ_B 3QZR_A 3R0F_B 3SJ9_A ....
Probab=30.86 E-value=25 Score=26.24 Aligned_cols=27 Identities=30% Similarity=0.413 Sum_probs=22.2
Q ss_pred CCCCCCCCeeEEecCCeEEEEEEeeeC
Q psy7305 205 ACQGDSGGPLMMKKDGYWMQVGIVSFG 231 (258)
Q Consensus 205 ~c~gdsG~Pl~~~~~~~~~L~Gi~s~~ 231 (258)
+..|+-||||+.+.++...++||..-|
T Consensus 144 t~~G~CG~~l~~~~~~~~~i~GiHvaG 170 (172)
T PF00548_consen 144 TKPGMCGSPLVSRIGGQGKIIGIHVAG 170 (172)
T ss_dssp EETTGTTEEEEESCGGTTEEEEEEEEE
T ss_pred CCCCccCCeEEEeeccCccEEEEEecc
Confidence 346899999999877777899998765
No 29
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=30.54 E-value=1e+02 Score=21.47 Aligned_cols=32 Identities=9% Similarity=0.245 Sum_probs=23.2
Q ss_pred CCCceEEEEEEeCCCCceeEeeEEEEeCCEEEeccc
Q psy7305 27 GRWPWMAAIFLHGTRRTEFWCGGSLIGTRYVLTAAH 62 (258)
Q Consensus 27 ~~~Pw~v~i~~~~~~~~~~~C~GtlIs~~~VLTaa~ 62 (258)
++|=|.-.|.+.+.+.. .--|++.+|.||-|.
T Consensus 26 ~RyvfaYtitI~N~g~~----~vqLlsR~W~ITd~~ 57 (126)
T COG2967 26 ERYVFAYTVTIRNLGEV----PVQLLSRYWLITDGN 57 (126)
T ss_pred ceEEEEEEEEEecCCCc----cceeeeeEEEEecCC
Confidence 46777777766655443 347999999999875
No 30
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.99 E-value=4.3e+02 Score=22.08 Aligned_cols=29 Identities=31% Similarity=0.311 Sum_probs=22.0
Q ss_pred CCCCCCCCCCeeEEecCCeEEEEEEeeeCCCC
Q psy7305 203 KDACQGDSGGPLMMKKDGYWMQVGIVSFGNKC 234 (258)
Q Consensus 203 ~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~~c 234 (258)
.....|.+|+|++-... .++||.+.....
T Consensus 189 Aain~gnsGgpl~n~~g---~~iGint~~~~~ 217 (347)
T COG0265 189 AAINPGNSGGPLVNIDG---EVVGINTAIIAP 217 (347)
T ss_pred cccCCCCCCCceEcCCC---cEEEEEEEEecC
Confidence 45678999999998754 599988876543
No 31
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=22.31 E-value=75 Score=22.62 Aligned_cols=26 Identities=31% Similarity=0.498 Sum_probs=16.4
Q ss_pred CCCCCCCCCeeEEecCCeEEEEEEeeeCC
Q psy7305 204 DACQGDSGGPLMMKKDGYWMQVGIVSFGN 232 (258)
Q Consensus 204 ~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~ 232 (258)
+.-.|.||+|++-.++ .++||.-.+.
T Consensus 93 d~~~GsSGSpi~n~~g---~ivGlYg~g~ 118 (132)
T PF00949_consen 93 DFPKGSSGSPIFNQNG---EIVGLYGNGV 118 (132)
T ss_dssp -S-TTGTT-EEEETTS---CEEEEEEEEE
T ss_pred ccCCCCCCCceEcCCC---cEEEEEccce
Confidence 4456899999996644 3888876653
No 32
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=20.14 E-value=76 Score=27.37 Aligned_cols=26 Identities=27% Similarity=0.406 Sum_probs=21.8
Q ss_pred CCCCCCCCCCeeEEecCCeEEEEEEeeeCC
Q psy7305 203 KDACQGDSGGPLMMKKDGYWMQVGIVSFGN 232 (258)
Q Consensus 203 ~~~c~gdsG~Pl~~~~~~~~~L~Gi~s~~~ 232 (258)
...-.|=||+|++.+.+ |+|-+++-.
T Consensus 355 gGivqGMSGSPi~q~gk----liGAvtHVf 380 (402)
T TIGR02860 355 GGIVQGMSGSPIIQNGK----VIGAVTHVF 380 (402)
T ss_pred CCEEecccCCCEEECCE----EEEEEEEEE
Confidence 45667899999999987 999988864
Done!