Query psy17087
Match_columns 84
No_of_seqs 192 out of 1136
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 21:31:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17087hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 99.8 1.8E-19 3.8E-24 116.1 7.8 75 5-81 175-255 (256)
2 cd00190 Tryp_SPc Trypsin-like 99.7 1.2E-16 2.6E-21 100.3 6.2 66 11-79 163-232 (232)
3 COG5640 Secreted trypsin-like 99.7 6.3E-16 1.4E-20 104.0 7.8 63 17-81 215-279 (413)
4 smart00020 Tryp_SPc Trypsin-li 99.5 3.6E-14 7.8E-19 89.3 5.6 61 12-76 165-229 (229)
5 PF00089 Trypsin: Trypsin; In 99.5 1.3E-13 2.9E-18 85.9 5.9 60 11-76 158-220 (220)
6 PF03761 DUF316: Domain of unk 97.6 0.0002 4.3E-09 47.1 5.2 53 21-76 223-275 (282)
7 PF02395 Peptidase_S6: Immunog 96.7 0.0018 4E-08 48.4 3.1 30 27-56 214-243 (769)
8 PF00947 Pico_P2A: Picornaviru 94.6 0.051 1.1E-06 32.3 3.2 34 28-72 89-122 (127)
9 COG3591 V8-like Glu-specific e 92.2 0.4 8.6E-06 31.8 4.5 54 23-81 197-251 (251)
10 PF05580 Peptidase_S55: SpoIVB 86.5 0.83 1.8E-05 29.7 2.7 28 23-56 174-201 (218)
11 PF13365 Trypsin_2: Trypsin-li 86.0 0.49 1.1E-05 26.4 1.4 19 27-50 102-120 (120)
12 PRK10898 serine endoprotease; 85.8 1.4 3.1E-05 30.3 3.8 24 27-55 196-219 (353)
13 PF02907 Peptidase_S29: Hepati 82.9 0.82 1.8E-05 27.7 1.4 21 28-53 107-127 (148)
14 PF05579 Peptidase_S32: Equine 82.7 1.3 2.8E-05 29.9 2.4 23 28-55 207-229 (297)
15 TIGR02037 degP_htrA_DO peripla 80.5 3.5 7.5E-05 29.0 4.1 24 27-55 177-200 (428)
16 PRK10139 serine endoprotease; 80.2 3.9 8.5E-05 29.2 4.3 25 26-55 209-233 (455)
17 TIGR02038 protease_degS peripl 79.1 4.2 9E-05 28.0 4.0 25 26-55 195-219 (351)
18 TIGR02860 spore_IV_B stage IV 74.6 3 6.5E-05 29.5 2.4 46 23-80 354-399 (402)
19 PRK10942 serine endoprotease; 73.1 5.3 0.00012 28.7 3.4 24 27-55 231-254 (473)
20 PF00944 Peptidase_S3: Alphavi 64.5 4.7 0.0001 24.6 1.4 23 28-55 105-127 (158)
21 COG4888 Uncharacterized Zn rib 61.9 9.2 0.0002 22.0 2.2 20 63-82 61-80 (104)
22 PF10459 Peptidase_S46: Peptid 54.4 9.5 0.00021 29.0 1.8 61 15-81 619-687 (698)
23 PF00949 Peptidase_S7: Peptida 46.1 19 0.00041 21.6 1.9 27 24-55 92-118 (132)
24 PF00863 Peptidase_C4: Peptida 45.8 34 0.00074 22.6 3.2 37 28-71 150-186 (235)
25 PHA02560 FI major tail sheath 38.2 44 0.00096 23.5 3.1 35 49-83 265-299 (388)
26 PF11307 DUF3109: Protein of u 32.6 25 0.00054 22.4 1.0 23 14-36 15-40 (183)
27 KOG2007|consensus 32.1 25 0.00055 26.0 1.1 19 63-81 147-165 (586)
28 PF05129 Elf1: Transcription e 28.7 18 0.00039 19.7 -0.1 35 47-83 43-81 (81)
29 PF03091 CutA1: CutA1 divalent 28.7 30 0.00065 19.7 0.8 12 70-81 91-102 (102)
30 PF10411 DsbC_N: Disulfide bon 27.7 38 0.00082 17.0 1.0 26 24-50 23-49 (57)
31 PF08346 AntA: AntA/AntB antir 27.4 43 0.00093 17.8 1.2 13 70-82 14-26 (71)
32 PF05372 Delta_lysin: Delta ly 27.3 30 0.00064 14.5 0.5 14 69-82 9-22 (25)
33 COG0265 DegQ Trypsin-like seri 26.1 78 0.0017 21.5 2.6 28 24-56 189-216 (347)
34 PF01141 Gag_p12: Gag polyprot 25.0 29 0.00063 19.1 0.3 11 28-38 17-27 (85)
35 PF00548 Peptidase_C3: 3C cyst 24.0 54 0.0012 20.3 1.4 28 26-55 144-171 (172)
36 KOG3338|consensus 23.6 41 0.00088 20.5 0.8 13 70-82 135-147 (153)
37 PF05416 Peptidase_C37: Southa 22.9 98 0.0021 22.7 2.6 30 24-55 498-527 (535)
38 PHA02539 18 tail sheath protei 22.5 1.5E+02 0.0032 22.7 3.6 34 49-82 524-558 (648)
39 PRK10645 divalent-cation toler 21.8 44 0.00096 19.4 0.7 18 63-80 89-111 (112)
40 TIGR02841 spore_YyaC putative 21.6 44 0.00096 20.3 0.7 52 17-80 5-60 (140)
41 PF06866 DUF1256: Protein of u 21.3 47 0.001 20.7 0.8 19 16-37 28-47 (163)
No 1
>KOG3627|consensus
Probab=99.80 E-value=1.8e-19 Score=116.11 Aligned_cols=75 Identities=41% Similarity=0.821 Sum_probs=63.0
Q ss_pred CCCCCCC--CCCCCeec-C--CCCCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCC-CcEEEeccccHHHHHH
Q psy17087 5 NDHKGDI--SVTETKFL-V--FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIA 78 (84)
Q Consensus 5 ~~~~~~~--~i~~~~~C-~--~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~-p~v~t~v~~~~~WI~~ 78 (84)
|...+.. .+++.||| + ....++|+|||||||++.... +++++||+|||...|.... |++||+|+.|.+||++
T Consensus 175 C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~--~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~ 252 (256)
T KOG3627|consen 175 CRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG--RWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKE 252 (256)
T ss_pred hcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCC--cEEEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHH
Confidence 4444444 57778999 6 567788999999999998763 5999999999986699876 9999999999999999
Q ss_pred Hhh
Q psy17087 79 RMA 81 (84)
Q Consensus 79 ~~~ 81 (84)
.+.
T Consensus 253 ~~~ 255 (256)
T KOG3627|consen 253 NIG 255 (256)
T ss_pred Hhc
Confidence 875
No 2
>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=99.67 E-value=1.2e-16 Score=100.28 Aligned_cols=66 Identities=44% Similarity=0.928 Sum_probs=57.0
Q ss_pred CCCCCCeec-C-CC-CCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCC-CcEEEeccccHHHHHHH
Q psy17087 11 ISVTETKFL-V-FP-GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIAR 79 (84)
Q Consensus 11 ~~i~~~~~C-~-~~-~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~-p~v~t~v~~~~~WI~~~ 79 (84)
..+.+.+|| . .. ..+.|.||||+||++... + +++|+||+|++.. |.... |.+||+|+.|++||+++
T Consensus 163 ~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~-~-~~~lvGI~s~g~~-c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 163 GTITDNMLCAGGLEGGKDACQGDSGGPLVCNDN-G-RGVLVGIVSWGSG-CARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred ccCCCceEeeCCCCCCCccccCCCCCcEEEEeC-C-EEEEEEEEehhhc-cCCCCCCCEEEEcHHhhHHhhcC
Confidence 467899999 6 33 788999999999999875 4 4999999999998 98745 99999999999999863
No 3
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=6.3e-16 Score=103.99 Aligned_cols=63 Identities=41% Similarity=0.797 Sum_probs=55.9
Q ss_pred eec-CCCCCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCC-CcEEEeccccHHHHHHHhh
Q psy17087 17 KFL-VFPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWIIARMA 81 (84)
Q Consensus 17 ~~C-~~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~-p~v~t~v~~~~~WI~~~~~ 81 (84)
-+| +....++|+||||||++....++ +.++||+|||.+.|+.+. |+|||+|+.|.+||...+.
T Consensus 215 ~~cag~~~~daCqGDSGGPi~~~g~~G--~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 215 GFCAGRPPKDACQGDSGGPIFHKGEEG--RVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred ceecCCCCcccccCCCCCceEEeCCCc--cEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhc
Confidence 399 86669999999999999986533 579999999998899988 9999999999999999765
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=99.51 E-value=3.6e-14 Score=89.32 Aligned_cols=61 Identities=46% Similarity=1.028 Sum_probs=53.1
Q ss_pred CCCCCeec-C-CC-CCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCC-CcEEEeccccHHHH
Q psy17087 12 SVTETKFL-V-FP-GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWI 76 (84)
Q Consensus 12 ~i~~~~~C-~-~~-~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~-p~v~t~v~~~~~WI 76 (84)
.+.+.++| + .. ....|.||||+||++... +|+|+||+|++.. |.... |.+|++|..|.+||
T Consensus 165 ~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~---~~~l~Gi~s~g~~-C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 165 AITDNMLCAGGLEGGKDACQGDSGGPLVCNDG---RWVLVGIVSWGSG-CARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred ccCCCcEeecCCCCCCcccCCCCCCeeEEECC---CEEEEEEEEECCC-CCCCCCCCEEEEeccccccC
Confidence 57889999 6 33 678999999999999853 5999999999996 98555 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=99.47 E-value=1.3e-13 Score=85.91 Aligned_cols=60 Identities=47% Similarity=0.987 Sum_probs=52.0
Q ss_pred CCCCCCeec-C-CCCCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCC-CcEEEeccccHHHH
Q psy17087 11 ISVTETKFL-V-FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGS-PGIYTRITAYLPWI 76 (84)
Q Consensus 11 ~~i~~~~~C-~-~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~-p~v~t~v~~~~~WI 76 (84)
..+.+.++| . ....+.|.||||+||++.. . +|+||++++.. |.... |.+|++|+.|++||
T Consensus 158 ~~~~~~~~c~~~~~~~~~~~g~sG~pl~~~~---~--~lvGI~s~~~~-c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 158 DNLTPNMICAGSSGSGDACQGDSGGPLICNN---N--YLVGIVSFGEN-CGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TTSTTTEEEEETTSSSBGGTTTTTSEEEETT---E--EEEEEEEEESS-SSBTTSEEEEEEGGGGHHHH
T ss_pred cccccccccccccccccccccccccccccce---e--eecceeeecCC-CCCCCcCEEEEEHHHhhccC
Confidence 347889999 6 4567899999999999873 2 69999999976 99887 99999999999998
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=97.57 E-value=0.0002 Score=47.11 Aligned_cols=53 Identities=36% Similarity=0.555 Sum_probs=40.0
Q ss_pred CCCCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCCCcEEEeccccHHHH
Q psy17087 21 FPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWI 76 (84)
Q Consensus 21 ~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~p~v~t~v~~~~~WI 76 (84)
......|.+|+||||+...+ ++ |+|+||.+.+...|... ...|.+|..|.+=|
T Consensus 223 ~~~~~~~~~d~Gg~lv~~~~-gr-~tlIGv~~~~~~~~~~~-~~~f~~v~~~~~~I 275 (282)
T PF03761_consen 223 CTKQYSCKGDRGGPLVKNIN-GR-WTLIGVGASGNYECNKN-NSYFFNVSWYQDEI 275 (282)
T ss_pred ecccccCCCCccCeEEEEEC-CC-EEEEEEEccCCCccccc-ccEEEEHHHhhhhh
Confidence 44567899999999998875 55 99999999776434432 67888888766533
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=96.65 E-value=0.0018 Score=48.44 Aligned_cols=30 Identities=37% Similarity=0.628 Sum_probs=23.8
Q ss_pred ccCCCCcccEEEeCCCCeEEEEEEEeecCC
Q psy17087 27 CNGDSGGPLVWKNNDTRKHYLIGLVSYGTP 56 (84)
Q Consensus 27 C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~ 56 (84)
=.||||+||+..+....+|.|+|+.+.+..
T Consensus 214 ~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~ 243 (769)
T PF02395_consen 214 SPGDSGSPLFAYDKEKKKWVLVGVLSGGNG 243 (769)
T ss_dssp -TT-TT-EEEEEETTTTEEEEEEEEEEECC
T ss_pred ccCcCCCceEEEEccCCeEEEEEEEccccc
Confidence 469999999998877778999999998765
No 8
>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=94.65 E-value=0.051 Score=32.34 Aligned_cols=34 Identities=32% Similarity=0.515 Sum_probs=26.4
Q ss_pred cCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCCCcEEEecccc
Q psy17087 28 NGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAY 72 (84)
Q Consensus 28 ~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~p~v~t~v~~~ 72 (84)
.||-||+|.|+. . ++||++.|.. +-..|++|..+
T Consensus 89 PGdCGg~L~C~H---G---ViGi~Tagg~-----g~VaF~dir~~ 122 (127)
T PF00947_consen 89 PGDCGGILRCKH---G---VIGIVTAGGE-----GHVAFADIRDL 122 (127)
T ss_dssp TT-TCSEEEETT---C---EEEEEEEEET-----TEEEEEECCCG
T ss_pred CCCCCceeEeCC---C---eEEEEEeCCC-----ceEEEEechhh
Confidence 378999999994 4 9999998765 35679998775
No 9
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=92.17 E-value=0.4 Score=31.77 Aligned_cols=54 Identities=22% Similarity=0.346 Sum_probs=35.8
Q ss_pred CCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCCCcEEEec-cccHHHHHHHhh
Q psy17087 23 GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRI-TAYLPWIIARMA 81 (84)
Q Consensus 23 ~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~p~v~t~v-~~~~~WI~~~~~ 81 (84)
..+++.|+||+|++.... +++||..-+...-+...-.-.+++ ..+.+||++.++
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 357789999999997632 599999887752222223334444 446789888653
No 10
>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=86.46 E-value=0.83 Score=29.67 Aligned_cols=28 Identities=29% Similarity=0.374 Sum_probs=22.9
Q ss_pred CCCCccCCCCcccEEEeCCCCeEEEEEEEeecCC
Q psy17087 23 GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTP 56 (84)
Q Consensus 23 ~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~ 56 (84)
....-||.||+|++.. ++ |+|-+++..-
T Consensus 174 TGGIvqGMSGSPI~qd---GK---LiGAVthvf~ 201 (218)
T PF05580_consen 174 TGGIVQGMSGSPIIQD---GK---LIGAVTHVFV 201 (218)
T ss_pred hCCEEecccCCCEEEC---CE---EEEEEEEEEe
Confidence 3467899999999876 78 9999998764
No 11
>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=85.99 E-value=0.49 Score=26.40 Aligned_cols=19 Identities=42% Similarity=0.828 Sum_probs=14.1
Q ss_pred ccCCCCcccEEEeCCCCeEEEEEE
Q psy17087 27 CNGDSGGPLVWKNNDTRKHYLIGL 50 (84)
Q Consensus 27 C~gdsGgPl~~~~~~~~~~~l~Gi 50 (84)
=.|.|||||+- .++. ++||
T Consensus 102 ~~G~SGgpv~~--~~G~---vvGi 120 (120)
T PF13365_consen 102 RPGSSGGPVFD--SDGR---VVGI 120 (120)
T ss_dssp STTTTTSEEEE--TTSE---EEEE
T ss_pred CCCcEeHhEEC--CCCE---EEeC
Confidence 35899999975 2266 8886
No 12
>PRK10898 serine endoprotease; Provisional
Probab=85.79 E-value=1.4 Score=30.27 Aligned_cols=24 Identities=33% Similarity=0.522 Sum_probs=18.5
Q ss_pred ccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 27 CNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 27 C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
-.|.|||||+-.. |+ ++||.+...
T Consensus 196 ~~GnSGGPl~n~~--G~---vvGI~~~~~ 219 (353)
T PRK10898 196 NHGNSGGALVNSL--GE---LMGINTLSF 219 (353)
T ss_pred CCCCCcceEECCC--Ce---EEEEEEEEe
Confidence 4588999998542 77 999988654
No 13
>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=82.85 E-value=0.82 Score=27.74 Aligned_cols=21 Identities=29% Similarity=0.687 Sum_probs=14.7
Q ss_pred cCCCCcccEEEeCCCCeEEEEEEEee
Q psy17087 28 NGDSGGPLVWKNNDTRKHYLIGLVSY 53 (84)
Q Consensus 28 ~gdsGgPl~~~~~~~~~~~l~Gi~s~ 53 (84)
.|.||+|++|.. |. ++||.--
T Consensus 107 kGSSGgPiLC~~--GH---~vG~f~a 127 (148)
T PF02907_consen 107 KGSSGGPILCPS--GH---AVGMFRA 127 (148)
T ss_dssp TT-TT-EEEETT--SE---EEEEEEE
T ss_pred ecCCCCcccCCC--CC---EEEEEEE
Confidence 689999999985 55 8887643
No 14
>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=82.67 E-value=1.3 Score=29.86 Aligned_cols=23 Identities=39% Similarity=0.634 Sum_probs=16.6
Q ss_pred cCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 28 NGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 28 ~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
-||||+|++.++ +. |+||-+-.+
T Consensus 207 ~GDSGSPVVt~d--g~---liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTED--GD---LIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETT--C----EEEEEEEEE
T ss_pred CCCCCCccCcCC--CC---EEEEEecCC
Confidence 489999999764 66 999988654
No 15
>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=80.53 E-value=3.5 Score=28.97 Aligned_cols=24 Identities=38% Similarity=0.505 Sum_probs=18.1
Q ss_pred ccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 27 CNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 27 C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
-.|.|||||+-.. |. ++||.+...
T Consensus 177 ~~GnSGGpl~n~~--G~---viGI~~~~~ 200 (428)
T TIGR02037 177 NPGNSGGPLVNLR--GE---VIGINTAIY 200 (428)
T ss_pred CCCCCCCceECCC--Ce---EEEEEeEEE
Confidence 4588999998442 77 999987643
No 16
>PRK10139 serine endoprotease; Provisional
Probab=80.20 E-value=3.9 Score=29.21 Aligned_cols=25 Identities=36% Similarity=0.442 Sum_probs=19.2
Q ss_pred CccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 26 SCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 26 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
.-.|.|||||+-.. |+ ++||.+...
T Consensus 209 in~GnSGGpl~n~~--G~---vIGi~~~~~ 233 (455)
T PRK10139 209 INRGNSGGALLNLN--GE---LIGINTAIL 233 (455)
T ss_pred cCCCCCcceEECCC--Ce---EEEEEEEEE
Confidence 34689999999543 77 999998743
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=79.08 E-value=4.2 Score=27.97 Aligned_cols=25 Identities=32% Similarity=0.522 Sum_probs=18.7
Q ss_pred CccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 26 SCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 26 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
.-.|.|||||+-.. |+ ++||.+...
T Consensus 195 i~~GnSGGpl~n~~--G~---vIGI~~~~~ 219 (351)
T TIGR02038 195 INAGNSGGALINTN--GE---LVGINTASF 219 (351)
T ss_pred cCCCCCcceEECCC--Ce---EEEEEeeee
Confidence 34688999998543 67 999987643
No 18
>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=74.60 E-value=3 Score=29.54 Aligned_cols=46 Identities=22% Similarity=0.445 Sum_probs=30.4
Q ss_pred CCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCCCcEEEeccccHHHHHHHh
Q psy17087 23 GKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWIIARM 80 (84)
Q Consensus 23 ~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~p~v~t~v~~~~~WI~~~~ 80 (84)
..+.-||.||+|++.. |+ |+|-++-..-+-.....++ |.+|..+..
T Consensus 354 tgGivqGMSGSPi~q~---gk---liGAvtHVfvndpt~GYGi------~ie~Ml~~~ 399 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQN---GK---VIGAVTHVFVNDPTSGYGV------YIEWMLKEA 399 (402)
T ss_pred hCCEEecccCCCEEEC---CE---EEEEEEEEEecCCCcceee------hHHHHHHHh
Confidence 3467899999999977 78 9998886543111112554 456776643
No 19
>PRK10942 serine endoprotease; Provisional
Probab=73.08 E-value=5.3 Score=28.68 Aligned_cols=24 Identities=42% Similarity=0.508 Sum_probs=18.1
Q ss_pred ccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 27 CNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 27 C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
-.|.|||||+-.. |. ++||.+...
T Consensus 231 ~~GnSGGpL~n~~--Ge---viGI~t~~~ 254 (473)
T PRK10942 231 NRGNSGGALVNLN--GE---LIGINTAIL 254 (473)
T ss_pred CCCCCcCccCCCC--Ce---EEEEEEEEE
Confidence 3578999998543 67 999987643
No 20
>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=64.46 E-value=4.7 Score=24.59 Aligned_cols=23 Identities=35% Similarity=0.596 Sum_probs=17.1
Q ss_pred cCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 28 NGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 28 ~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
.||||.|++-+ .|+ +|||+--|.
T Consensus 105 ~GDSGRpi~DN--sGr---VVaIVLGG~ 127 (158)
T PF00944_consen 105 PGDSGRPIFDN--SGR---VVAIVLGGA 127 (158)
T ss_dssp TTSTTEEEEST--TSB---EEEEEEEEE
T ss_pred CCCCCCccCcC--CCC---EEEEEecCC
Confidence 58999999843 367 888876554
No 21
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=61.92 E-value=9.2 Score=21.98 Aligned_cols=20 Identities=20% Similarity=0.481 Sum_probs=17.3
Q ss_pred CcEEEeccccHHHHHHHhhh
Q psy17087 63 PGIYTRITAYLPWIIARMAY 82 (84)
Q Consensus 63 p~v~t~v~~~~~WI~~~~~~ 82 (84)
|.+++.|-.|.+||+.....
T Consensus 61 ~~l~~~vDvYs~wvDay~eg 80 (104)
T COG4888 61 PELSEPVDVYSAWVDAYLEG 80 (104)
T ss_pred cccccchhHHHHHHHHHHhc
Confidence 88899999999999987654
No 22
>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=54.44 E-value=9.5 Score=28.98 Aligned_cols=61 Identities=23% Similarity=0.367 Sum_probs=35.0
Q ss_pred CCeecCCCCCCCccCCCCcccEEEeCCCCeEEEEEEEeecCCC-------CCCCC-CcEEEeccccHHHHHHHhh
Q psy17087 15 ETKFLVFPGKDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTPE-------CGIGS-PGIYTRITAYLPWIIARMA 81 (84)
Q Consensus 15 ~~~~C~~~~~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~-------C~~~~-p~v~t~v~~~~~WI~~~~~ 81 (84)
+.-+|--...+...|.||+|++-.. |. |||++-=|.-. -.... -.|.+++ .|+-|+-+.+.
T Consensus 619 ~~pv~FlstnDitGGNSGSPvlN~~--Ge---LVGl~FDgn~Esl~~D~~fdp~~~R~I~VDi-RyvL~~ldkv~ 687 (698)
T PF10459_consen 619 SVPVNFLSTNDITGGNSGSPVLNAK--GE---LVGLAFDGNWESLSGDIAFDPELNRTIHVDI-RYVLWALDKVY 687 (698)
T ss_pred CeeeEEEeccCcCCCCCCCccCCCC--ce---EEEEeecCchhhcccccccccccceeEEEEH-HHHHHHHHHHh
Confidence 3345522345667899999998543 67 99987533210 01111 2455553 47778876654
No 23
>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=46.08 E-value=19 Score=21.60 Aligned_cols=27 Identities=33% Similarity=0.572 Sum_probs=16.4
Q ss_pred CCCccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 24 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 24 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
.+.-.|.||+|++-.. ++ ++||...+.
T Consensus 92 ~d~~~GsSGSpi~n~~--g~---ivGlYg~g~ 118 (132)
T PF00949_consen 92 LDFPKGSSGSPIFNQN--GE---IVGLYGNGV 118 (132)
T ss_dssp --S-TTGTT-EEEETT--SC---EEEEEEEEE
T ss_pred cccCCCCCCCceEcCC--Cc---EEEEEccce
Confidence 3445689999998432 66 888876554
No 24
>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=45.76 E-value=34 Score=22.57 Aligned_cols=37 Identities=27% Similarity=0.501 Sum_probs=22.0
Q ss_pred cCCCCcccEEEeCCCCeEEEEEEEeecCCCCCCCCCcEEEeccc
Q psy17087 28 NGDSGGPLVWKNNDTRKHYLIGLVSYGTPECGIGSPGIYTRITA 71 (84)
Q Consensus 28 ~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~~C~~~~p~v~t~v~~ 71 (84)
.||=|.||+...+ +. +|||-|.+.. ...-..|+-+..
T Consensus 150 ~G~CG~PlVs~~D-g~---IVGiHsl~~~---~~~~N~F~~f~~ 186 (235)
T PF00863_consen 150 DGDCGLPLVSTKD-GK---IVGIHSLTSN---TSSRNYFTPFPD 186 (235)
T ss_dssp TT-TT-EEEETTT------EEEEEEEEET---TTSSEEEEE--T
T ss_pred CCccCCcEEEcCC-Cc---EEEEEcCccC---CCCeEEEEcCCH
Confidence 4788999997654 67 9999998765 112457777654
No 25
>PHA02560 FI major tail sheath protein; Provisional
Probab=38.21 E-value=44 Score=23.48 Aligned_cols=35 Identities=14% Similarity=0.167 Sum_probs=27.1
Q ss_pred EEEeecCCCCCCCCCcEEEeccccHHHHHHHhhhc
Q psy17087 49 GLVSYGTPECGIGSPGIYTRITAYLPWIIARMAYE 83 (84)
Q Consensus 49 Gi~s~~~~~C~~~~p~v~t~v~~~~~WI~~~~~~~ 83 (84)
|+..||...|.....--|..+.+..+||++.+...
T Consensus 265 G~r~WG~RT~s~d~~w~fi~vrR~~~~I~~si~~~ 299 (388)
T PHA02560 265 GFRFWGNRTCSDDPLFAFENYVRTAQVIADTIAEA 299 (388)
T ss_pred CEEEEccccCCCCCCeeEEeeHHHHHHHHHHHHHH
Confidence 88889988774322458999999999999987653
No 26
>PF11307 DUF3109: Protein of unknown function (DUF3109); InterPro: IPR021458 This bacterial family of proteins has no known function.
Probab=32.61 E-value=25 Score=22.36 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=13.3
Q ss_pred CCCeec-CCCCCCCc--cCCCCcccE
Q psy17087 14 TETKFL-VFPGKDSC--NGDSGGPLV 36 (84)
Q Consensus 14 ~~~~~C-~~~~~~~C--~gdsGgPl~ 36 (84)
+..+.| -..=++.| .||+|+||-
T Consensus 15 ~~~F~CdL~~CkG~CCvEGd~GAPl~ 40 (183)
T PF11307_consen 15 EEKFVCDLSACKGACCVEGDAGAPLE 40 (183)
T ss_pred hhcccCchhcCCCCCccCCCcCCCCC
Confidence 334444 33333344 689999984
No 27
>KOG2007|consensus
Probab=32.13 E-value=25 Score=26.03 Aligned_cols=19 Identities=37% Similarity=0.717 Sum_probs=14.9
Q ss_pred CcEEEeccccHHHHHHHhh
Q psy17087 63 PGIYTRITAYLPWIIARMA 81 (84)
Q Consensus 63 p~v~t~v~~~~~WI~~~~~ 81 (84)
|.|.|||+.|++=|-+.++
T Consensus 147 Ptv~tRVSeyvp~II~fIq 165 (586)
T KOG2007|consen 147 PTVQTRVSEYVPQIIKFIQ 165 (586)
T ss_pred CcccchhhhchHHHHHHHH
Confidence 8999999999866655554
No 28
>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=28.73 E-value=18 Score=19.73 Aligned_cols=35 Identities=29% Similarity=0.389 Sum_probs=17.9
Q ss_pred EEEEEeecCCCCCCCC----CcEEEeccccHHHHHHHhhhc
Q psy17087 47 LIGLVSYGTPECGIGS----PGIYTRITAYLPWIIARMAYE 83 (84)
Q Consensus 47 l~Gi~s~~~~~C~~~~----p~v~t~v~~~~~WI~~~~~~~ 83 (84)
-+|+++-+. |+... +.+..-|--|.+||+...+.|
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 456665442 65432 555666777999999876643
No 29
>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=28.67 E-value=30 Score=19.67 Aligned_cols=12 Identities=42% Similarity=0.794 Sum_probs=8.9
Q ss_pred cccHHHHHHHhh
Q psy17087 70 TAYLPWIIARMA 81 (84)
Q Consensus 70 ~~~~~WI~~~~~ 81 (84)
..|.+||.+.++
T Consensus 91 ~~Yl~Wi~~~~~ 102 (102)
T PF03091_consen 91 PAYLEWINEETK 102 (102)
T ss_dssp HHHHHHHHHHT-
T ss_pred HHHHHHHHHhcC
Confidence 349999998764
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=27.71 E-value=38 Score=16.95 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=18.1
Q ss_pred CCCccCCC-CcccEEEeCCCCeEEEEEE
Q psy17087 24 KDSCNGDS-GGPLVWKNNDTRKHYLIGL 50 (84)
Q Consensus 24 ~~~C~gds-GgPl~~~~~~~~~~~l~Gi 50 (84)
.+.|+-.. |++++.-..+++ |.++|=
T Consensus 23 ~GlyeV~~~~~~i~Y~~~dg~-yli~G~ 49 (57)
T PF10411_consen 23 PGLYEVVLKGGGILYVDEDGR-YLIQGQ 49 (57)
T ss_dssp TTEEEEEE-TTEEEEEETTSS-EEEES-
T ss_pred CCeEEEEECCCeEEEEcCCCC-EEEEeE
Confidence 45666666 788887777666 888873
No 31
>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=27.43 E-value=43 Score=17.82 Aligned_cols=13 Identities=23% Similarity=0.580 Sum_probs=9.5
Q ss_pred cccHHHHHHHhhh
Q psy17087 70 TAYLPWIIARMAY 82 (84)
Q Consensus 70 ~~~~~WI~~~~~~ 82 (84)
..|.+||++.+.+
T Consensus 14 ~~Fs~Wik~ri~~ 26 (71)
T PF08346_consen 14 KRFSTWIKRRIEE 26 (71)
T ss_pred CcHHHHHHHHhhh
Confidence 4588999976653
No 32
>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=27.26 E-value=30 Score=14.53 Aligned_cols=14 Identities=21% Similarity=0.361 Sum_probs=10.0
Q ss_pred ccccHHHHHHHhhh
Q psy17087 69 ITAYLPWIIARMAY 82 (84)
Q Consensus 69 v~~~~~WI~~~~~~ 82 (84)
+..|..||.++++.
T Consensus 9 IgdfvKlI~~TV~K 22 (25)
T PF05372_consen 9 IGDFVKLIIETVKK 22 (25)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 34578899888764
No 33
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.08 E-value=78 Score=21.50 Aligned_cols=28 Identities=29% Similarity=0.434 Sum_probs=21.5
Q ss_pred CCCccCCCCcccEEEeCCCCeEEEEEEEeecCC
Q psy17087 24 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGTP 56 (84)
Q Consensus 24 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~~ 56 (84)
.....|.|||||+-.. +. ++||.+....
T Consensus 189 Aain~gnsGgpl~n~~--g~---~iGint~~~~ 216 (347)
T COG0265 189 AAINPGNSGGPLVNID--GE---VVGINTAIIA 216 (347)
T ss_pred cccCCCCCCCceEcCC--Cc---EEEEEEEEec
Confidence 4567899999998643 66 9998887655
No 34
>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=24.99 E-value=29 Score=19.12 Aligned_cols=11 Identities=55% Similarity=0.694 Sum_probs=8.4
Q ss_pred cCCCCcccEEE
Q psy17087 28 NGDSGGPLVWK 38 (84)
Q Consensus 28 ~gdsGgPl~~~ 38 (84)
.-|+||||+-.
T Consensus 17 Lpd~ggPLIDL 27 (85)
T PF01141_consen 17 LPDSGGPLIDL 27 (85)
T ss_pred ccCCCCchhhh
Confidence 34999999754
No 35
>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=23.98 E-value=54 Score=20.29 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=19.6
Q ss_pred CccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 26 SCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 26 ~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
+-.|+=|+||+.... +. ..++||-.-|.
T Consensus 144 t~~G~CG~~l~~~~~-~~-~~i~GiHvaG~ 171 (172)
T PF00548_consen 144 TKPGMCGSPLVSRIG-GQ-GKIIGIHVAGN 171 (172)
T ss_dssp EETTGTTEEEEESCG-GT-TEEEEEEEEEE
T ss_pred CCCCccCCeEEEeec-cC-ccEEEEEeccC
Confidence 346888999998654 33 55999877654
No 36
>KOG3338|consensus
Probab=23.57 E-value=41 Score=20.47 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=9.9
Q ss_pred cccHHHHHHHhhh
Q psy17087 70 TAYLPWIIARMAY 82 (84)
Q Consensus 70 ~~~~~WI~~~~~~ 82 (84)
..|++|+++.+..
T Consensus 135 ~~YLeW~~q~v~~ 147 (153)
T KOG3338|consen 135 RPYLEWMNQCVDD 147 (153)
T ss_pred cHHHHHHHHhccc
Confidence 4589999987753
No 37
>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=22.85 E-value=98 Score=22.68 Aligned_cols=30 Identities=30% Similarity=0.500 Sum_probs=20.7
Q ss_pred CCCccCCCCcccEEEeCCCCeEEEEEEEeecC
Q psy17087 24 KDSCNGDSGGPLVWKNNDTRKHYLIGLVSYGT 55 (84)
Q Consensus 24 ~~~C~gdsGgPl~~~~~~~~~~~l~Gi~s~~~ 55 (84)
.++-.||-|.|-+.+.. +. |+++||-.-..
T Consensus 498 LGT~PGDCGcPYvyKrg-Nd-~VV~GVH~AAt 527 (535)
T PF05416_consen 498 LGTIPGDCGCPYVYKRG-ND-WVVIGVHAAAT 527 (535)
T ss_dssp TS--TTGTT-EEEEEET-TE-EEEEEEEEEE-
T ss_pred cCCCCCCCCCceeeecC-Cc-EEEEEEEehhc
Confidence 34567899999998875 45 99999987543
No 38
>PHA02539 18 tail sheath protein; Provisional
Probab=22.46 E-value=1.5e+02 Score=22.75 Aligned_cols=34 Identities=12% Similarity=0.132 Sum_probs=25.6
Q ss_pred EEEeecCCCCCC-CCCcEEEeccccHHHHHHHhhh
Q psy17087 49 GLVSYGTPECGI-GSPGIYTRITAYLPWIIARMAY 82 (84)
Q Consensus 49 Gi~s~~~~~C~~-~~p~v~t~v~~~~~WI~~~~~~ 82 (84)
|+..||...+.. +.+--|..|.+...||++.+..
T Consensus 524 G~rLWGaRTls~~ps~wryInVRRLf~~Ie~SI~~ 558 (648)
T PHA02539 524 GIVLFGDKTATAVPSAFDRINVRRLFNMLKKNIGD 558 (648)
T ss_pred EEEEEccccCCCCCCcceeeehhhHHHHHHHHHHH
Confidence 788898875442 2234499999999999998764
No 39
>PRK10645 divalent-cation tolerance protein CutA; Provisional
Probab=21.84 E-value=44 Score=19.39 Aligned_cols=18 Identities=33% Similarity=0.816 Sum_probs=12.0
Q ss_pred CcEE-Eec----cccHHHHHHHh
Q psy17087 63 PGIY-TRI----TAYLPWIIARM 80 (84)
Q Consensus 63 p~v~-t~v----~~~~~WI~~~~ 80 (84)
|.+. ..+ ..|.+||.+.+
T Consensus 89 PeIi~~~i~~g~~~Yl~Wi~~~~ 111 (112)
T PRK10645 89 PELLVLPVTHGDTDYLSWLNASL 111 (112)
T ss_pred CEEEEEEcccCCHHHHHHHHHhc
Confidence 6654 333 34999999875
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=21.61 E-value=44 Score=20.35 Aligned_cols=52 Identities=23% Similarity=0.218 Sum_probs=28.1
Q ss_pred eec-CCCCCCCccCCCCcccEEEeCCC---CeEEEEEEEeecCCCCCCCCCcEEEeccccHHHHHHHh
Q psy17087 17 KFL-VFPGKDSCNGDSGGPLVWKNNDT---RKHYLIGLVSYGTPECGIGSPGIYTRITAYLPWIIARM 80 (84)
Q Consensus 17 ~~C-~~~~~~~C~gdsGgPl~~~~~~~---~~~~l~Gi~s~~~~~C~~~~p~v~t~v~~~~~WI~~~~ 80 (84)
.+| | .+-|.||+=|||+-..=.. ..+.++| .- + .|---.++...++.|++.-
T Consensus 5 ~lCIG---TDRstGDsLGPLVGt~L~~~~~~~~~VyG-----TL--~--~PVHA~NL~e~l~~I~~~~ 60 (140)
T TIGR02841 5 LLCIG---TDRSTGDALGPLVGMKLKFLLLNNFHVFG-----TL--E--EPVHAKNLEEKLKIIKKKH 60 (140)
T ss_pred EEEEC---CCCCcccccchhhHHHHHhccCCCCeEEE-----CC--C--CCcccccHHHHHHHHHHhC
Confidence 467 5 3568899999997321000 0123433 11 1 1544567777777776643
No 41
>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=21.30 E-value=47 Score=20.72 Aligned_cols=19 Identities=42% Similarity=0.454 Sum_probs=14.1
Q ss_pred Ceec-CCCCCCCccCCCCcccEE
Q psy17087 16 TKFL-VFPGKDSCNGDSGGPLVW 37 (84)
Q Consensus 16 ~~~C-~~~~~~~C~gdsGgPl~~ 37 (84)
-.+| | .+-|.|||=|||+-
T Consensus 28 v~lCIG---TDRstGDsLGPLVG 47 (163)
T PF06866_consen 28 VFLCIG---TDRSTGDSLGPLVG 47 (163)
T ss_pred EEEEEC---CCCCccccccchhh
Confidence 3578 6 35688999999973
Done!