Query psy17086
Match_columns 82
No_of_seqs 211 out of 1130
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 21:30:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17086.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17086hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 99.8 2.8E-20 6.1E-25 118.4 8.6 77 1-79 175-255 (256)
2 COG5640 Secreted trypsin-like 99.7 2.7E-17 6E-22 109.1 7.9 62 16-79 216-279 (413)
3 cd00190 Tryp_SPc Trypsin-like 99.7 1.8E-17 3.9E-22 102.8 6.5 66 9-77 163-232 (232)
4 smart00020 Tryp_SPc Trypsin-li 99.6 4.2E-15 9.1E-20 92.5 6.1 62 9-74 164-229 (229)
5 PF00089 Trypsin: Trypsin; In 99.5 8.9E-14 1.9E-18 85.7 6.1 59 10-74 159-220 (220)
6 PF03761 DUF316: Domain of unk 97.4 0.00036 7.9E-09 45.3 5.1 55 19-76 223-277 (282)
7 PF02395 Peptidase_S6: Immunog 96.3 0.0038 8.3E-08 46.2 2.7 29 25-54 214-243 (769)
8 COG3591 V8-like Glu-specific e 95.1 0.065 1.4E-06 35.0 4.9 54 21-79 197-251 (251)
9 PF00947 Pico_P2A: Picornaviru 93.7 0.086 1.9E-06 31.0 2.7 34 26-70 89-122 (127)
10 PF13365 Trypsin_2: Trypsin-li 88.6 0.47 1E-05 26.2 2.3 21 23-48 100-120 (120)
11 PF05579 Peptidase_S32: Equine 86.5 0.59 1.3E-05 31.1 2.0 23 26-53 207-229 (297)
12 PF02907 Peptidase_S29: Hepati 85.8 0.84 1.8E-05 27.4 2.3 21 26-51 107-127 (148)
13 PRK10898 serine endoprotease; 83.7 2.3 5E-05 29.0 4.0 24 25-53 196-219 (353)
14 PF05580 Peptidase_S55: SpoIVB 81.2 2.3 4.9E-05 27.4 3.0 27 22-54 175-201 (218)
15 PRK10139 serine endoprotease; 77.6 6 0.00013 28.0 4.5 24 24-52 209-232 (455)
16 TIGR02037 degP_htrA_DO peripla 77.6 4.8 0.0001 28.0 4.0 23 25-52 177-199 (428)
17 TIGR02038 protease_degS peripl 74.4 3.3 7.1E-05 28.1 2.5 24 24-52 195-218 (351)
18 COG4888 Uncharacterized Zn rib 68.1 5.8 0.00013 22.5 2.1 20 61-80 61-80 (104)
19 TIGR02860 spore_IV_B stage IV 67.4 6.3 0.00014 27.7 2.6 46 21-78 354-399 (402)
20 PRK10942 serine endoprotease; 66.2 8.4 0.00018 27.4 3.1 23 25-52 231-253 (473)
21 PF00949 Peptidase_S7: Peptida 57.8 9.5 0.00021 22.6 1.9 27 22-53 92-118 (132)
22 PF00944 Peptidase_S3: Alphavi 57.1 8 0.00017 23.3 1.5 21 26-51 105-125 (158)
23 PF10459 Peptidase_S46: Peptid 49.8 14 0.0003 27.9 2.0 32 14-50 620-651 (698)
24 PF05372 Delta_lysin: Delta ly 44.2 16 0.00034 15.2 1.0 13 68-80 10-22 (25)
25 PF00863 Peptidase_C4: Peptida 42.7 46 0.00099 21.8 3.4 37 26-69 150-186 (235)
26 KOG2007|consensus 37.8 17 0.00037 26.6 0.9 19 61-79 147-165 (586)
27 PF05129 Elf1: Transcription e 34.6 9.6 0.00021 20.6 -0.5 35 45-81 43-81 (81)
28 PF03091 CutA1: CutA1 divalent 33.8 24 0.00052 19.9 1.0 11 69-79 92-102 (102)
29 PF08346 AntA: AntA/AntB antir 33.7 28 0.0006 18.4 1.2 13 68-80 14-26 (71)
30 PF10411 DsbC_N: Disulfide bon 32.5 27 0.00059 17.3 1.0 26 21-47 22-48 (57)
31 PF00548 Peptidase_C3: 3C cyst 31.5 42 0.0009 20.6 1.9 28 24-53 144-171 (172)
32 PF08192 Peptidase_S64: Peptid 31.2 60 0.0013 24.6 2.8 54 22-79 634-690 (695)
33 PF01141 Gag_p12: Gag polyprot 26.8 25 0.00054 19.2 0.3 10 27-36 18-27 (85)
34 PRK14892 putative transcriptio 26.4 42 0.00091 18.9 1.1 21 61-81 57-77 (99)
35 PHA02560 FI major tail sheath 26.3 83 0.0018 21.9 2.8 34 47-80 265-298 (388)
36 KOG3338|consensus 25.4 38 0.00082 20.4 0.9 13 68-80 135-147 (153)
37 COG0265 DegQ Trypsin-like seri 23.6 97 0.0021 20.8 2.7 28 22-54 189-216 (347)
38 PRK10645 divalent-cation toler 22.9 45 0.00098 19.1 0.9 18 61-78 89-111 (112)
39 PF06866 DUF1256: Protein of u 21.0 47 0.001 20.5 0.7 19 14-35 28-47 (163)
40 TIGR02841 spore_YyaC putative 20.7 44 0.00096 20.1 0.5 18 15-35 5-23 (140)
41 PF05416 Peptidase_C37: Southa 20.5 1.5E+02 0.0032 21.6 3.1 30 22-53 498-527 (535)
No 1
>KOG3627|consensus
Probab=99.83 E-value=2.8e-20 Score=118.38 Aligned_cols=77 Identities=43% Similarity=0.821 Sum_probs=64.5
Q ss_pred CCCCCCCCCcCCCCeee-c--CCCCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCC-CcEEEEcCCcHHHHHH
Q psy17086 1 MNQNHKGDISVTETKFL-V--FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIA 76 (82)
Q Consensus 1 C~~~~~~~~~i~~~~~C-~--~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~-p~vyt~v~~~~~WI~~ 76 (82)
|++.+.....+++.||| + ....++|+|||||||++.... ++ +++||+|||...|.... |++||+|+.|.+||++
T Consensus 175 C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~-~~-~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~ 252 (256)
T KOG3627|consen 175 CRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG-RW-VLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKE 252 (256)
T ss_pred hcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCC-cE-EEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHH
Confidence 55555544467788999 6 567888999999999999854 56 99999999986688875 9999999999999999
Q ss_pred Hhh
Q psy17086 77 RMA 79 (82)
Q Consensus 77 ~~~ 79 (82)
.+.
T Consensus 253 ~~~ 255 (256)
T KOG3627|consen 253 NIG 255 (256)
T ss_pred Hhc
Confidence 875
No 2
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=2.7e-17 Score=109.13 Aligned_cols=62 Identities=44% Similarity=0.838 Sum_probs=57.0
Q ss_pred ee-cCCCCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCC-CcEEEEcCCcHHHHHHHhh
Q psy17086 16 FL-VFPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIARMA 79 (82)
Q Consensus 16 ~C-~~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~-p~vyt~v~~~~~WI~~~~~ 79 (82)
+| +....++|+||||||++.+..+|+ +++||+|||.+.|+... |.|||+|+.|.+||...|.
T Consensus 216 ~cag~~~~daCqGDSGGPi~~~g~~G~--vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 216 FCAGRPPKDACQGDSGGPIFHKGEEGR--VQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred eecCCCCcccccCCCCCceEEeCCCcc--EEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhc
Confidence 99 877799999999999999987776 79999999998899988 9999999999999999774
No 3
>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=99.72 E-value=1.8e-17 Score=102.83 Aligned_cols=66 Identities=45% Similarity=0.940 Sum_probs=57.1
Q ss_pred CcCCCCeee-c-CC-CCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCC-CcEEEEcCCcHHHHHHH
Q psy17086 9 ISVTETKFL-V-FP-GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIAR 77 (82)
Q Consensus 9 ~~i~~~~~C-~-~~-~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~-p~vyt~v~~~~~WI~~~ 77 (82)
..+.+.+|| . .. ..+.|.||+||||++... +++ +|+||+|++.. |.... |.+||+|+.|++||+++
T Consensus 163 ~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~-~~~-~lvGI~s~g~~-c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 163 GTITDNMLCAGGLEGGKDACQGDSGGPLVCNDN-GRG-VLVGIVSWGSG-CARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred ccCCCceEeeCCCCCCCccccCCCCCcEEEEeC-CEE-EEEEEEehhhc-cCCCCCCCEEEEcHHhhHHhhcC
Confidence 467899999 6 33 788999999999999875 677 99999999998 98744 99999999999999864
No 4
>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=99.58 E-value=4.2e-15 Score=92.50 Aligned_cols=62 Identities=47% Similarity=0.984 Sum_probs=53.6
Q ss_pred CcCCCCeee-c-CC-CCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCC-CcEEEEcCCcHHHH
Q psy17086 9 ISVTETKFL-V-FP-GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWI 74 (82)
Q Consensus 9 ~~i~~~~~C-~-~~-~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~-p~vyt~v~~~~~WI 74 (82)
..+.+.++| + .. ....|.||+|+||+.... +| +|+||+|++.. |.... |.+|+||+.|++||
T Consensus 164 ~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~--~~-~l~Gi~s~g~~-C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 164 GAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG--RW-VLVGIVSWGSG-CARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred cccCCCcEeecCCCCCCcccCCCCCCeeEEECC--CE-EEEEEEEECCC-CCCCCCCCEEEEeccccccC
Confidence 357889999 6 33 688999999999999874 66 99999999996 98554 99999999999998
No 5
>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=99.49 E-value=8.9e-14 Score=85.73 Aligned_cols=59 Identities=49% Similarity=1.045 Sum_probs=52.1
Q ss_pred cCCCCeee-c-CCCCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCC-CcEEEEcCCcHHHH
Q psy17086 10 SVTETKFL-V-FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWI 74 (82)
Q Consensus 10 ~i~~~~~C-~-~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~-p~vyt~v~~~~~WI 74 (82)
.+.+.++| . ....+.|.||+||||++... +|+||.+++.. |.... |.+|+||+.|++||
T Consensus 159 ~~~~~~~c~~~~~~~~~~~g~sG~pl~~~~~-----~lvGI~s~~~~-c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 159 NLTPNMICAGSSGSGDACQGDSGGPLICNNN-----YLVGIVSFGEN-CGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TSTTTEEEEETTSSSBGGTTTTTSEEEETTE-----EEEEEEEEESS-SSBTTSEEEEEEGGGGHHHH
T ss_pred cccccccccccccccccccccccccccccee-----eecceeeecCC-CCCCCcCEEEEEHHHhhccC
Confidence 37889999 6 36688999999999998873 59999999976 98886 99999999999998
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=97.45 E-value=0.00036 Score=45.32 Aligned_cols=55 Identities=33% Similarity=0.503 Sum_probs=42.3
Q ss_pred CCCCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCCCcEEEEcCCcHHHHHH
Q psy17086 19 FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWIIA 76 (82)
Q Consensus 19 ~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~p~vyt~v~~~~~WI~~ 76 (82)
......|.+|+||||+... +|++ +|+||.+.+...|... ...|.+|..|.+=|=+
T Consensus 223 ~~~~~~~~~d~Gg~lv~~~-~gr~-tlIGv~~~~~~~~~~~-~~~f~~v~~~~~~IC~ 277 (282)
T PF03761_consen 223 CTKQYSCKGDRGGPLVKNI-NGRW-TLIGVGASGNYECNKN-NSYFFNVSWYQDEICE 277 (282)
T ss_pred ecccccCCCCccCeEEEEE-CCCE-EEEEEEccCCCccccc-ccEEEEHHHhhhhhcc
Confidence 4456789999999999877 4888 9999999776434332 6788999888765543
No 7
>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=96.25 E-value=0.0038 Score=46.24 Aligned_cols=29 Identities=34% Similarity=0.582 Sum_probs=21.8
Q ss_pred CcCCCCceeEEEeCC-CceEEEEEEEeecCC
Q psy17086 25 CNGDSGGPLVWKNND-TRKHYLIGLVSYGTP 54 (82)
Q Consensus 25 C~gdsGgPl~~~~~~-~~~~~l~Gi~s~g~~ 54 (82)
=.||||+||+..+.. ..| +|+|+.+.+..
T Consensus 214 ~~GDSGSPlF~YD~~~kKW-vl~Gv~~~~~~ 243 (769)
T PF02395_consen 214 SPGDSGSPLFAYDKEKKKW-VLVGVLSGGNG 243 (769)
T ss_dssp -TT-TT-EEEEEETTTTEE-EEEEEEEEECC
T ss_pred ccCcCCCceEEEEccCCeE-EEEEEEccccc
Confidence 469999999988764 566 99999998765
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=95.15 E-value=0.065 Score=35.02 Aligned_cols=54 Identities=22% Similarity=0.346 Sum_probs=37.4
Q ss_pred CCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCCCcEEEEc-CCcHHHHHHHhh
Q psy17086 21 GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRI-TAYLPWIIARMA 79 (82)
Q Consensus 21 ~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~p~vyt~v-~~~~~WI~~~~~ 79 (82)
..+++.|+||+|+..... +++||.+-+...-+...-.-.+|+ ..+++||++.++
T Consensus 197 ~~dT~pG~SGSpv~~~~~-----~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 197 DADTLPGSSGSPVLISKD-----EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred EecccCCCCCCceEecCc-----eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 467889999999998774 899999987752222223334444 447799988753
No 9
>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=93.67 E-value=0.086 Score=31.04 Aligned_cols=34 Identities=32% Similarity=0.486 Sum_probs=26.7
Q ss_pred cCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCCCcEEEEcCCc
Q psy17086 26 NGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAY 70 (82)
Q Consensus 26 ~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~p~vyt~v~~~ 70 (82)
.||-||+|.|+. -++||++.|.. +-..|++|..+
T Consensus 89 PGdCGg~L~C~H------GViGi~Tagg~-----g~VaF~dir~~ 122 (127)
T PF00947_consen 89 PGDCGGILRCKH------GVIGIVTAGGE-----GHVAFADIRDL 122 (127)
T ss_dssp TT-TCSEEEETT------CEEEEEEEEET-----TEEEEEECCCG
T ss_pred CCCCCceeEeCC------CeEEEEEeCCC-----ceEEEEechhh
Confidence 478999999998 48999998754 35679998876
No 10
>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=88.59 E-value=0.47 Score=26.20 Aligned_cols=21 Identities=33% Similarity=0.692 Sum_probs=14.5
Q ss_pred CCCcCCCCceeEEEeCCCceEEEEEE
Q psy17086 23 DSCNGDSGGPLVWKNNDTRKHYLIGL 48 (82)
Q Consensus 23 ~~C~gdsGgPl~~~~~~~~~~~l~Gi 48 (82)
..=.|.|||||+-.+ | .++||
T Consensus 100 ~~~~G~SGgpv~~~~--G---~vvGi 120 (120)
T PF13365_consen 100 DTRPGSSGGPVFDSD--G---RVVGI 120 (120)
T ss_dssp S-STTTTTSEEEETT--S---EEEEE
T ss_pred ccCCCcEeHhEECCC--C---EEEeC
Confidence 334689999998644 3 67776
No 11
>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=86.45 E-value=0.59 Score=31.08 Aligned_cols=23 Identities=39% Similarity=0.619 Sum_probs=16.8
Q ss_pred cCCCCceeEEEeCCCceEEEEEEEeecC
Q psy17086 26 NGDSGGPLVWKNNDTRKHYLIGLVSYGT 53 (82)
Q Consensus 26 ~gdsGgPl~~~~~~~~~~~l~Gi~s~g~ 53 (82)
.||||+|++.++. .|+||-+-..
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 4899999998874 7999977543
No 12
>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=85.78 E-value=0.84 Score=27.37 Aligned_cols=21 Identities=29% Similarity=0.667 Sum_probs=15.5
Q ss_pred cCCCCceeEEEeCCCceEEEEEEEee
Q psy17086 26 NGDSGGPLVWKNNDTRKHYLIGLVSY 51 (82)
Q Consensus 26 ~gdsGgPl~~~~~~~~~~~l~Gi~s~ 51 (82)
.|.||||++|... ..+||.-.
T Consensus 107 kGSSGgPiLC~~G-----H~vG~f~a 127 (148)
T PF02907_consen 107 KGSSGGPILCPSG-----HAVGMFRA 127 (148)
T ss_dssp TT-TT-EEEETTS-----EEEEEEEE
T ss_pred ecCCCCcccCCCC-----CEEEEEEE
Confidence 6899999999884 78898654
No 13
>PRK10898 serine endoprotease; Provisional
Probab=83.69 E-value=2.3 Score=28.96 Aligned_cols=24 Identities=33% Similarity=0.479 Sum_probs=18.5
Q ss_pred CcCCCCceeEEEeCCCceEEEEEEEeecC
Q psy17086 25 CNGDSGGPLVWKNNDTRKHYLIGLVSYGT 53 (82)
Q Consensus 25 C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~ 53 (82)
-.|.|||||+... | .++||.+...
T Consensus 196 ~~GnSGGPl~n~~--G---~vvGI~~~~~ 219 (353)
T PRK10898 196 NHGNSGGALVNSL--G---ELMGINTLSF 219 (353)
T ss_pred CCCCCcceEECCC--C---eEEEEEEEEe
Confidence 4588999999665 3 7999987643
No 14
>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=81.25 E-value=2.3 Score=27.39 Aligned_cols=27 Identities=30% Similarity=0.361 Sum_probs=22.0
Q ss_pred CCCCcCCCCceeEEEeCCCceEEEEEEEeecCC
Q psy17086 22 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTP 54 (82)
Q Consensus 22 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~ 54 (82)
...-+|.||+|++... .|+|-+++...
T Consensus 175 GGIvqGMSGSPI~qdG------KLiGAVthvf~ 201 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG------KLIGAVTHVFV 201 (218)
T ss_pred CCEEecccCCCEEECC------EEEEEEEEEEe
Confidence 4578999999998766 89998887653
No 15
>PRK10139 serine endoprotease; Provisional
Probab=77.65 E-value=6 Score=27.99 Aligned_cols=24 Identities=38% Similarity=0.457 Sum_probs=18.9
Q ss_pred CCcCCCCceeEEEeCCCceEEEEEEEeec
Q psy17086 24 SCNGDSGGPLVWKNNDTRKHYLIGLVSYG 52 (82)
Q Consensus 24 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g 52 (82)
.-.|.|||||+-... .++||.+..
T Consensus 209 in~GnSGGpl~n~~G-----~vIGi~~~~ 232 (455)
T PRK10139 209 INRGNSGGALLNLNG-----ELIGINTAI 232 (455)
T ss_pred cCCCCCcceEECCCC-----eEEEEEEEE
Confidence 346899999997653 799998864
No 16
>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=77.63 E-value=4.8 Score=27.96 Aligned_cols=23 Identities=39% Similarity=0.510 Sum_probs=17.8
Q ss_pred CcCCCCceeEEEeCCCceEEEEEEEeec
Q psy17086 25 CNGDSGGPLVWKNNDTRKHYLIGLVSYG 52 (82)
Q Consensus 25 C~gdsGgPl~~~~~~~~~~~l~Gi~s~g 52 (82)
-.|.|||||+... | .++||.+..
T Consensus 177 ~~GnSGGpl~n~~--G---~viGI~~~~ 199 (428)
T TIGR02037 177 NPGNSGGPLVNLR--G---EVIGINTAI 199 (428)
T ss_pred CCCCCCCceECCC--C---eEEEEEeEE
Confidence 4588999999665 3 799998764
No 17
>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=74.41 E-value=3.3 Score=28.15 Aligned_cols=24 Identities=33% Similarity=0.552 Sum_probs=18.6
Q ss_pred CCcCCCCceeEEEeCCCceEEEEEEEeec
Q psy17086 24 SCNGDSGGPLVWKNNDTRKHYLIGLVSYG 52 (82)
Q Consensus 24 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g 52 (82)
.-.|.|||||+-.+. .++||.+..
T Consensus 195 i~~GnSGGpl~n~~G-----~vIGI~~~~ 218 (351)
T TIGR02038 195 INAGNSGGALINTNG-----ELVGINTAS 218 (351)
T ss_pred cCCCCCcceEECCCC-----eEEEEEeee
Confidence 346889999997653 799998754
No 18
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=68.08 E-value=5.8 Score=22.54 Aligned_cols=20 Identities=20% Similarity=0.481 Sum_probs=17.4
Q ss_pred CcEEEEcCCcHHHHHHHhhc
Q psy17086 61 PGIYTRITAYLPWIIARMAY 80 (82)
Q Consensus 61 p~vyt~v~~~~~WI~~~~~~ 80 (82)
|.+++.|-.|.+||+...+.
T Consensus 61 ~~l~~~vDvYs~wvDay~eg 80 (104)
T COG4888 61 PELSEPVDVYSAWVDAYLEG 80 (104)
T ss_pred cccccchhHHHHHHHHHHhc
Confidence 88999999999999987654
No 19
>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=67.45 E-value=6.3 Score=27.66 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=30.0
Q ss_pred CCCCCcCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCCCcEEEEcCCcHHHHHHHh
Q psy17086 21 GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWIIARM 78 (82)
Q Consensus 21 ~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~p~vyt~v~~~~~WI~~~~ 78 (82)
....-+|.||+|++..+ .|+|=++.-.-+-.....++ |.+|+.+..
T Consensus 354 tgGivqGMSGSPi~q~g------kliGAvtHVfvndpt~GYGi------~ie~Ml~~~ 399 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQNG------KVIGAVTHVFVNDPTSGYGV------YIEWMLKEA 399 (402)
T ss_pred hCCEEecccCCCEEECC------EEEEEEEEEEecCCCcceee------hHHHHHHHh
Confidence 35678999999999877 89997776443111111443 567876653
No 20
>PRK10942 serine endoprotease; Provisional
Probab=66.20 E-value=8.4 Score=27.41 Aligned_cols=23 Identities=43% Similarity=0.525 Sum_probs=17.8
Q ss_pred CcCCCCceeEEEeCCCceEEEEEEEeec
Q psy17086 25 CNGDSGGPLVWKNNDTRKHYLIGLVSYG 52 (82)
Q Consensus 25 C~gdsGgPl~~~~~~~~~~~l~Gi~s~g 52 (82)
=.|.|||||+.... .++||.+..
T Consensus 231 ~~GnSGGpL~n~~G-----eviGI~t~~ 253 (473)
T PRK10942 231 NRGNSGGALVNLNG-----ELIGINTAI 253 (473)
T ss_pred CCCCCcCccCCCCC-----eEEEEEEEE
Confidence 35789999997653 799998753
No 21
>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=57.85 E-value=9.5 Score=22.65 Aligned_cols=27 Identities=33% Similarity=0.553 Sum_probs=16.3
Q ss_pred CCCCcCCCCceeEEEeCCCceEEEEEEEeecC
Q psy17086 22 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 53 (82)
Q Consensus 22 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~ 53 (82)
.+.=.|.||+|++-.+. .++||.-.+.
T Consensus 92 ~d~~~GsSGSpi~n~~g-----~ivGlYg~g~ 118 (132)
T PF00949_consen 92 LDFPKGSSGSPIFNQNG-----EIVGLYGNGV 118 (132)
T ss_dssp --S-TTGTT-EEEETTS-----CEEEEEEEEE
T ss_pred cccCCCCCCCceEcCCC-----cEEEEEccce
Confidence 44557899999996553 5777766543
No 22
>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=57.11 E-value=8 Score=23.33 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=13.7
Q ss_pred cCCCCceeEEEeCCCceEEEEEEEee
Q psy17086 26 NGDSGGPLVWKNNDTRKHYLIGLVSY 51 (82)
Q Consensus 26 ~gdsGgPl~~~~~~~~~~~l~Gi~s~ 51 (82)
.||||.|++-.. | .++||+--
T Consensus 105 ~GDSGRpi~DNs--G---rVVaIVLG 125 (158)
T PF00944_consen 105 PGDSGRPIFDNS--G---RVVAIVLG 125 (158)
T ss_dssp TTSTTEEEESTT--S---BEEEEEEE
T ss_pred CCCCCCccCcCC--C---CEEEEEec
Confidence 589999998544 3 35555443
No 23
>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=49.80 E-value=14 Score=27.86 Aligned_cols=32 Identities=25% Similarity=0.420 Sum_probs=22.3
Q ss_pred CeeecCCCCCCCcCCCCceeEEEeCCCceEEEEEEEe
Q psy17086 14 TKFLVFPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVS 50 (82)
Q Consensus 14 ~~~C~~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s 50 (82)
.-+|--...++..|.||+|++-... .|||+.=
T Consensus 620 ~pv~FlstnDitGGNSGSPvlN~~G-----eLVGl~F 651 (698)
T PF10459_consen 620 VPVNFLSTNDITGGNSGSPVLNAKG-----ELVGLAF 651 (698)
T ss_pred eeeEEEeccCcCCCCCCCccCCCCc-----eEEEEee
Confidence 3455333456778999999996653 7999853
No 24
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=44.25 E-value=16 Score=15.22 Aligned_cols=13 Identities=15% Similarity=0.286 Sum_probs=9.6
Q ss_pred CCcHHHHHHHhhc
Q psy17086 68 TAYLPWIIARMAY 80 (82)
Q Consensus 68 ~~~~~WI~~~~~~ 80 (82)
..|..||.+++++
T Consensus 10 gdfvKlI~~TV~K 22 (25)
T PF05372_consen 10 GDFVKLIIETVKK 22 (25)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3578899888764
No 25
>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=42.66 E-value=46 Score=21.76 Aligned_cols=37 Identities=27% Similarity=0.458 Sum_probs=22.2
Q ss_pred cCCCCceeEEEeCCCceEEEEEEEeecCCCCCCCCCcEEEEcCC
Q psy17086 26 NGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITA 69 (82)
Q Consensus 26 ~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~~c~~~~p~vyt~v~~ 69 (82)
.||=|.|||.... | .++||-|.+.. ...-..|+-+..
T Consensus 150 ~G~CG~PlVs~~D-g---~IVGiHsl~~~---~~~~N~F~~f~~ 186 (235)
T PF00863_consen 150 DGDCGLPLVSTKD-G---KIVGIHSLTSN---TSSRNYFTPFPD 186 (235)
T ss_dssp TT-TT-EEEETTT------EEEEEEEEET---TTSSEEEEE--T
T ss_pred CCccCCcEEEcCC-C---cEEEEEcCccC---CCCeEEEEcCCH
Confidence 4788999998763 3 89999998764 112557777754
No 26
>KOG2007|consensus
Probab=37.76 E-value=17 Score=26.59 Aligned_cols=19 Identities=37% Similarity=0.717 Sum_probs=14.7
Q ss_pred CcEEEEcCCcHHHHHHHhh
Q psy17086 61 PGIYTRITAYLPWIIARMA 79 (82)
Q Consensus 61 p~vyt~v~~~~~WI~~~~~ 79 (82)
|.|.|||+.|++=|-+.++
T Consensus 147 Ptv~tRVSeyvp~II~fIq 165 (586)
T KOG2007|consen 147 PTVQTRVSEYVPQIIKFIQ 165 (586)
T ss_pred CcccchhhhchHHHHHHHH
Confidence 9999999999866655543
No 27
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=34.56 E-value=9.6 Score=20.61 Aligned_cols=35 Identities=29% Similarity=0.389 Sum_probs=17.5
Q ss_pred EEEEEeecCCCCCCCC----CcEEEEcCCcHHHHHHHhhcc
Q psy17086 45 LIGLVSYGTPECGIGS----PGIYTRITAYLPWIIARMAYE 81 (82)
Q Consensus 45 l~Gi~s~g~~~c~~~~----p~vyt~v~~~~~WI~~~~~~~ 81 (82)
-+|+++=+. |+... +.+...|--|.+||+...+.|
T Consensus 43 ~~~~~~C~~--Cg~~~~~~i~~L~epiDVY~~wiD~~~~~n 81 (81)
T PF05129_consen 43 GIGILSCRV--CGESFQTKINPLSEPIDVYSEWIDACEEGN 81 (81)
T ss_dssp TEEEEEESS--S--EEEEE--SS--TTHHHHHHHHHHH---
T ss_pred CEEEEEecC--CCCeEEEccCccCcccchhHHHHHHHHhcC
Confidence 345555432 55432 556666777999999876543
No 28
>PF03091 CutA1: CutA1 divalent ion tolerance protein; InterPro: IPR004323 The CutA family of proteins which exhibit ion tolerance are found in a large variety of species []. In E.Coli, two operons on the cutA locus contain genes that encode three proteins, CutA1, CutA2 and CutA3. CutA1 proteins are found in the cytoplasm while CutA2 (50kDa) and CutA3 (24kDa) are located in the inner membrane. Although the role of E. Coli CutA1 is not clear, studies on E. coli cutA locus describe some mutations that lead to an increase in copper sensitivity, thus suggesting a role in ion tolerance []. To date, the structure of CutA proteins from several species have been solved [, ]. The crystal structures of the E.Coli and rat CutA1 proteins show both these proteins to be trimeric in the crystal as well as in solution[].Trimerisation seems to supported by the formation of beta sheets between the subunit. This trimeric structure suggests the protein may be involved in signal transduction due to architectural similarities with PII signal transducer proteins []. Recent studies propose that mammalian CutA1 in the neuronal cell membrane acts as an anchor for acetylcholinesterase (AChE)1 [].; GO: 0010038 response to metal ion; PDB: 1O5J_A 1KR4_A 1VHF_A 3GSD_H 1OSC_A 3OPK_A 4E98_C 1V9B_F 1UKU_A 2E66_C ....
Probab=33.79 E-value=24 Score=19.87 Aligned_cols=11 Identities=45% Similarity=0.863 Sum_probs=8.5
Q ss_pred CcHHHHHHHhh
Q psy17086 69 AYLPWIIARMA 79 (82)
Q Consensus 69 ~~~~WI~~~~~ 79 (82)
.|.+||.+.++
T Consensus 92 ~Yl~Wi~~~~~ 102 (102)
T PF03091_consen 92 AYLEWINEETK 102 (102)
T ss_dssp HHHHHHHHHT-
T ss_pred HHHHHHHHhcC
Confidence 49999998764
No 29
>PF08346 AntA: AntA/AntB antirepressor; InterPro: IPR013557 In Escherichia coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB. The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the Bacteriophage 933W.
Probab=33.70 E-value=28 Score=18.35 Aligned_cols=13 Identities=23% Similarity=0.580 Sum_probs=9.6
Q ss_pred CCcHHHHHHHhhc
Q psy17086 68 TAYLPWIIARMAY 80 (82)
Q Consensus 68 ~~~~~WI~~~~~~ 80 (82)
..|.+||++.+.+
T Consensus 14 ~~Fs~Wik~ri~~ 26 (71)
T PF08346_consen 14 KRFSTWIKRRIEE 26 (71)
T ss_pred CcHHHHHHHHhhh
Confidence 4588999976653
No 30
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=32.47 E-value=27 Score=17.29 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=19.2
Q ss_pred CCCCCcCCC-CceeEEEeCCCceEEEEE
Q psy17086 21 GKDSCNGDS-GGPLVWKNNDTRKHYLIG 47 (82)
Q Consensus 21 ~~~~C~gds-GgPl~~~~~~~~~~~l~G 47 (82)
-.+.++... |++++.-..+|++ .+.|
T Consensus 22 i~GlyeV~~~~~~i~Y~~~dg~y-li~G 48 (57)
T PF10411_consen 22 IPGLYEVVLKGGGILYVDEDGRY-LIQG 48 (57)
T ss_dssp STTEEEEEE-TTEEEEEETTSSE-EEES
T ss_pred CCCeEEEEECCCeEEEEcCCCCE-EEEe
Confidence 345566666 8888888888888 7776
No 31
>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=31.53 E-value=42 Score=20.55 Aligned_cols=28 Identities=29% Similarity=0.427 Sum_probs=19.9
Q ss_pred CCcCCCCceeEEEeCCCceEEEEEEEeecC
Q psy17086 24 SCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 53 (82)
Q Consensus 24 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~ 53 (82)
+-.|+=||||+.... +.. .++||-..|.
T Consensus 144 t~~G~CG~~l~~~~~-~~~-~i~GiHvaG~ 171 (172)
T PF00548_consen 144 TKPGMCGSPLVSRIG-GQG-KIIGIHVAGN 171 (172)
T ss_dssp EETTGTTEEEEESCG-GTT-EEEEEEEEEE
T ss_pred CCCCccCCeEEEeec-cCc-cEEEEEeccC
Confidence 346888999998654 333 8999877653
No 32
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 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 family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=31.18 E-value=60 Score=24.59 Aligned_cols=54 Identities=20% Similarity=0.193 Sum_probs=35.6
Q ss_pred CCCCcCCCCceeEEEeCC---CceEEEEEEEeecCCCCCCCCCcEEEEcCCcHHHHHHHhh
Q psy17086 22 KDSCNGDSGGPLVWKNND---TRKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWIIARMA 79 (82)
Q Consensus 22 ~~~C~gdsGgPl~~~~~~---~~~~~l~Gi~s~g~~~c~~~~p~vyt~v~~~~~WI~~~~~ 79 (82)
.-.=.||||+-++....+ |- -++|++.--. +....-++||-+...++=++.+++
T Consensus 634 ~Fa~~GDSGS~VLtk~~d~~~gL--gvvGMlhsyd--ge~kqfglftPi~~il~rl~~vT~ 690 (695)
T PF08192_consen 634 AFASGGDSGSWVLTKLEDNNKGL--GVVGMLHSYD--GEQKQFGLFTPINEILDRLEEVTG 690 (695)
T ss_pred cccCCCCcccEEEecccccccCc--eeeEEeeecC--CccceeeccCcHHHHHHHHHHhhc
Confidence 334568999999886432 22 4677665332 333347889998888888877764
No 33
>PF01141 Gag_p12: Gag polyprotein, inner coat protein p12; InterPro: IPR002079 The retroviral p12 protein is a proline rich virion structural protein found in the inner coat. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus [].; GO: 0019028 viral capsid
Probab=26.78 E-value=25 Score=19.17 Aligned_cols=10 Identities=60% Similarity=0.863 Sum_probs=8.1
Q ss_pred CCCCceeEEE
Q psy17086 27 GDSGGPLVWK 36 (82)
Q Consensus 27 gdsGgPl~~~ 36 (82)
-|+||||+-.
T Consensus 18 pd~ggPLIDL 27 (85)
T PF01141_consen 18 PDSGGPLIDL 27 (85)
T ss_pred cCCCCchhhh
Confidence 4999999864
No 34
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.39 E-value=42 Score=18.92 Aligned_cols=21 Identities=19% Similarity=0.437 Sum_probs=16.3
Q ss_pred CcEEEEcCCcHHHHHHHhhcc
Q psy17086 61 PGIYTRITAYLPWIIARMAYE 81 (82)
Q Consensus 61 p~vyt~v~~~~~WI~~~~~~~ 81 (82)
+.+...|.-|.+||+......
T Consensus 57 ~~l~epIDVY~~wiD~~~eg~ 77 (99)
T PRK14892 57 PSVYDEVDVYNKFIDLYLEGK 77 (99)
T ss_pred CccccchhhHHHHHHHHHhcC
Confidence 566777888999999876654
No 35
>PHA02560 FI major tail sheath protein; Provisional
Probab=26.32 E-value=83 Score=21.93 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=25.9
Q ss_pred EEEeecCCCCCCCCCcEEEEcCCcHHHHHHHhhc
Q psy17086 47 GLVSYGTPECGIGSPGIYTRITAYLPWIIARMAY 80 (82)
Q Consensus 47 Gi~s~g~~~c~~~~p~vyt~v~~~~~WI~~~~~~ 80 (82)
|+..||..-|.....-.|..+....+||++.+..
T Consensus 265 G~r~WG~RT~s~d~~w~fi~vrR~~~~I~~si~~ 298 (388)
T PHA02560 265 GFRFWGNRTCSDDPLFAFENYVRTAQVIADTIAE 298 (388)
T ss_pred CEEEEccccCCCCCCeeEEeeHHHHHHHHHHHHH
Confidence 7788887756432245899999999999988764
No 36
>KOG3338|consensus
Probab=25.40 E-value=38 Score=20.36 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=9.9
Q ss_pred CCcHHHHHHHhhc
Q psy17086 68 TAYLPWIIARMAY 80 (82)
Q Consensus 68 ~~~~~WI~~~~~~ 80 (82)
..|++|+++.+..
T Consensus 135 ~~YLeW~~q~v~~ 147 (153)
T KOG3338|consen 135 RPYLEWMNQCVDD 147 (153)
T ss_pred cHHHHHHHHhccc
Confidence 3599999988753
No 37
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.60 E-value=97 Score=20.83 Aligned_cols=28 Identities=29% Similarity=0.415 Sum_probs=21.3
Q ss_pred CCCCcCCCCceeEEEeCCCceEEEEEEEeecCC
Q psy17086 22 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTP 54 (82)
Q Consensus 22 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~~ 54 (82)
.....|.+||||+.... .++||.+....
T Consensus 189 Aain~gnsGgpl~n~~g-----~~iGint~~~~ 216 (347)
T COG0265 189 AAINPGNSGGPLVNIDG-----EVVGINTAIIA 216 (347)
T ss_pred cccCCCCCCCceEcCCC-----cEEEEEEEEec
Confidence 45678999999997653 68888776554
No 38
>PRK10645 divalent-cation tolerance protein CutA; Provisional
Probab=22.93 E-value=45 Score=19.14 Aligned_cols=18 Identities=33% Similarity=0.816 Sum_probs=12.1
Q ss_pred CcEE-EEc----CCcHHHHHHHh
Q psy17086 61 PGIY-TRI----TAYLPWIIARM 78 (82)
Q Consensus 61 p~vy-t~v----~~~~~WI~~~~ 78 (82)
|.+. ..+ ..|.+||.+.+
T Consensus 89 PeIi~~~i~~g~~~Yl~Wi~~~~ 111 (112)
T PRK10645 89 PELLVLPVTHGDTDYLSWLNASL 111 (112)
T ss_pred CEEEEEEcccCCHHHHHHHHHhc
Confidence 6654 444 33999998875
No 39
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=20.99 E-value=47 Score=20.51 Aligned_cols=19 Identities=42% Similarity=0.454 Sum_probs=14.3
Q ss_pred Ceee-cCCCCCCCcCCCCceeEE
Q psy17086 14 TKFL-VFPGKDSCNGDSGGPLVW 35 (82)
Q Consensus 14 ~~~C-~~~~~~~C~gdsGgPl~~ 35 (82)
-.+| | .|-|.||+=|||+-
T Consensus 28 v~lCIG---TDRstGDsLGPLVG 47 (163)
T PF06866_consen 28 VFLCIG---TDRSTGDSLGPLVG 47 (163)
T ss_pred EEEEEC---CCCCccccccchhh
Confidence 3578 5 35688999999974
No 40
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=20.72 E-value=44 Score=20.12 Aligned_cols=18 Identities=39% Similarity=0.480 Sum_probs=13.6
Q ss_pred eee-cCCCCCCCcCCCCceeEE
Q psy17086 15 KFL-VFPGKDSCNGDSGGPLVW 35 (82)
Q Consensus 15 ~~C-~~~~~~~C~gdsGgPl~~ 35 (82)
.+| | .|-|.||+=|||+-
T Consensus 5 ~lCIG---TDRstGDsLGPLVG 23 (140)
T TIGR02841 5 LLCIG---TDRSTGDALGPLVG 23 (140)
T ss_pred EEEEC---CCCCcccccchhhH
Confidence 467 5 35688999999974
No 41
>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=20.49 E-value=1.5e+02 Score=21.60 Aligned_cols=30 Identities=30% Similarity=0.470 Sum_probs=20.5
Q ss_pred CCCCcCCCCceeEEEeCCCceEEEEEEEeecC
Q psy17086 22 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 53 (82)
Q Consensus 22 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~g~ 53 (82)
-++-.||-|.|.+.+.. ..| +++||-....
T Consensus 498 LGT~PGDCGcPYvyKrg-Nd~-VV~GVH~AAt 527 (535)
T PF05416_consen 498 LGTIPGDCGCPYVYKRG-NDW-VVIGVHAAAT 527 (535)
T ss_dssp TS--TTGTT-EEEEEET-TEE-EEEEEEEEE-
T ss_pred cCCCCCCCCCceeeecC-CcE-EEEEEEehhc
Confidence 34467999999999884 677 9999976543
Done!