Query psy17330
Match_columns 184
No_of_seqs 109 out of 1364
Neff 9.4
Searched_HMMs 46136
Date Fri Aug 16 19:31:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17330hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 100.0 1.5E-31 3.3E-36 206.5 17.4 162 7-184 88-255 (256)
2 cd00190 Tryp_SPc Trypsin-like 100.0 3.8E-31 8.1E-36 200.1 15.7 158 7-182 72-232 (232)
3 smart00020 Tryp_SPc Trypsin-li 99.9 4.8E-27 1E-31 177.8 14.4 155 6-179 71-229 (229)
4 PF00089 Trypsin: Trypsin; In 99.9 2.9E-25 6.4E-30 166.7 12.3 148 7-179 70-220 (220)
5 COG5640 Secreted trypsin-like 99.8 2.6E-17 5.6E-22 128.3 13.5 163 5-184 105-279 (413)
6 PF03761 DUF316: Domain of unk 98.7 2.7E-07 5.8E-12 72.4 12.0 118 18-179 158-275 (282)
7 PF09342 DUF1986: Domain of un 97.6 0.00038 8.2E-09 52.7 7.7 158 2-183 68-265 (267)
8 TIGR02037 degP_htrA_DO peripla 94.5 0.21 4.7E-06 41.6 7.8 48 131-181 176-224 (428)
9 TIGR02038 protease_degS peripl 94.4 0.27 5.8E-06 40.0 7.9 25 130-157 194-218 (351)
10 PRK10139 serine endoprotease; 94.1 0.37 8E-06 40.6 8.3 49 130-181 208-257 (455)
11 PRK10898 serine endoprotease; 94.1 0.54 1.2E-05 38.3 9.0 26 130-158 194-219 (353)
12 COG3591 V8-like Glu-specific e 92.9 0.24 5.3E-06 38.2 5.0 53 129-184 198-251 (251)
13 PF02395 Peptidase_S6: Immunog 92.3 0.16 3.5E-06 45.4 3.8 52 130-181 212-265 (769)
14 PRK10942 serine endoprotease; 91.5 1 2.2E-05 38.2 7.6 48 131-181 230-278 (473)
15 PF00947 Pico_P2A: Picornaviru 75.8 3 6.5E-05 28.7 2.6 34 133-175 89-122 (127)
16 PF05580 Peptidase_S55: SpoIVB 73.5 5.6 0.00012 30.0 3.7 39 116-158 158-200 (218)
17 PF13365 Trypsin_2: Trypsin-li 59.8 8.2 0.00018 25.2 2.2 19 132-153 102-120 (120)
18 PF00863 Peptidase_C4: Peptida 58.0 30 0.00066 26.6 5.1 35 134-173 151-185 (235)
19 PF02907 Peptidase_S29: Hepati 56.2 11 0.00023 26.4 2.2 22 132-156 106-127 (148)
20 PF05579 Peptidase_S32: Equine 52.7 15 0.00033 28.8 2.8 23 133-158 207-229 (297)
21 TIGR02860 spore_IV_B stage IV 42.2 27 0.00058 29.1 2.9 45 128-182 354-398 (402)
22 PF05416 Peptidase_C37: Southa 33.2 81 0.0018 26.6 4.3 31 128-158 497-527 (535)
23 PF00944 Peptidase_S3: Alphavi 25.1 23 0.0005 24.8 -0.1 24 132-158 104-127 (158)
24 PF00548 Peptidase_C3: 3C cyst 23.6 45 0.00097 24.2 1.2 26 133-158 146-171 (172)
25 PF08346 AntA: AntA/AntB antir 22.2 49 0.0011 20.3 1.0 11 173-183 14-24 (71)
26 PF10459 Peptidase_S46: Peptid 20.6 1.2E+02 0.0025 27.5 3.3 26 130-158 629-654 (698)
No 1
>KOG3627|consensus
Probab=100.00 E-value=1.5e-31 Score=206.46 Aligned_cols=162 Identities=33% Similarity=0.697 Sum_probs=136.0
Q ss_pred CCceEEEcCCCCC---C-CCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeecccC
Q psy17330 7 PDSSLHVIPSISD---D-SHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSVP 82 (184)
Q Consensus 7 ~~~~i~~Hp~y~~---~-~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~~ 82 (184)
.+.++++||+|+. . +|||||+|.+++. |+++|+||| ||..........+..|+++|||.+.
T Consensus 88 ~v~~~i~H~~y~~~~~~~nDiall~l~~~v~--------------~~~~i~pic-lp~~~~~~~~~~~~~~~v~GWG~~~ 152 (256)
T KOG3627|consen 88 DVEKIIVHPNYNPRTLENNDIALLRLSEPVT--------------FSSHIQPIC-LPSSADPYFPPGGTTCLVSGWGRTE 152 (256)
T ss_pred eeeEEEECCCCCCCCCCCCCEEEEEECCCcc--------------cCCcccccC-CCCCcccCCCCCCCEEEEEeCCCcC
Confidence 4568889999966 3 8999999999988 999999999 7754433234555899999999987
Q ss_pred CC-CCCCcCceEEEEEeeCcccccccccccCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEEEEecCC-C
Q psy17330 83 GG-GPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKK-C 160 (184)
Q Consensus 83 ~~-~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~-c 160 (184)
.. ...+..|++.++++++.++|...+... ..+++.++|++......+.|+||+||||++..+++|+|+||+|||.. |
T Consensus 153 ~~~~~~~~~L~~~~v~i~~~~~C~~~~~~~-~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C 231 (256)
T KOG3627|consen 153 SGGGPLPDTLQEVDVPIISNSECRRAYGGL-GTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGC 231 (256)
T ss_pred CCCCCCCceeEEEEEeEcChhHhcccccCc-cccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCC
Confidence 65 245778999999999999999988621 14667789998556677789999999999998889999999999988 9
Q ss_pred CCCCCCeEEEeCcchHHHHHhhhC
Q psy17330 161 AEVGFPGVYTRVTNYIQWIADNIS 184 (184)
Q Consensus 161 ~~~~~p~vft~v~~~~~WI~~~i~ 184 (184)
.....|++||||+.|.+||++.+.
T Consensus 232 ~~~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 232 GQPNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred CCCCCCeEEeEhHHhHHHHHHHhc
Confidence 987799999999999999998763
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=99.97 E-value=3.8e-31 Score=200.13 Aligned_cols=158 Identities=38% Similarity=0.758 Sum_probs=136.3
Q ss_pred CCceEEEcCCCCC---CCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeecccCC
Q psy17330 7 PDSSLHVIPSISD---DSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSVPG 83 (184)
Q Consensus 7 ~~~~i~~Hp~y~~---~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~~~ 83 (184)
++.++++||.|+. .+|||||||++++. ++.++.||| ||... .....+..+.++|||....
T Consensus 72 ~v~~~~~hp~y~~~~~~~DiAll~L~~~~~--------------~~~~v~pic-l~~~~--~~~~~~~~~~~~G~g~~~~ 134 (232)
T cd00190 72 KVKKVIVHPNYNPSTYDNDIALLKLKRPVT--------------LSDNVRPIC-LPSSG--YNLPAGTTCTVSGWGRTSE 134 (232)
T ss_pred EEEEEEECCCCCCCCCcCCEEEEEECCccc--------------CCCcccceE-CCCcc--ccCCCCCEEEEEeCCcCCC
Confidence 5789999999976 57999999999998 889999999 77553 3456789999999998766
Q ss_pred CCCCCcCceEEEEEeeCcccccccccccCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCCCC
Q psy17330 84 GGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEV 163 (184)
Q Consensus 84 ~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~ 163 (184)
.......++...+.+++.++|.+.+.. ...+.++++|+.........|.||+||||++..+++|+|+||.|++..|...
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~C~~~~~~-~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~ 213 (232)
T cd00190 135 GGPLPDVLQEVNVPIVSNAECKRAYSY-GGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARP 213 (232)
T ss_pred CCCCCceeeEEEeeeECHHHhhhhccC-cccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCC
Confidence 545677899999999999999988763 3467899999985444778999999999999999999999999999888866
Q ss_pred CCCeEEEeCcchHHHHHhh
Q psy17330 164 GFPGVYTRVTNYIQWIADN 182 (184)
Q Consensus 164 ~~p~vft~v~~~~~WI~~~ 182 (184)
+.|.+||+|+.|.+||+++
T Consensus 214 ~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 214 NYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred CCCCEEEEcHHhhHHhhcC
Confidence 7799999999999999874
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.95 E-value=4.8e-27 Score=177.84 Aligned_cols=155 Identities=37% Similarity=0.749 Sum_probs=130.5
Q ss_pred CCCceEEEcCCCCC---CCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeecccC
Q psy17330 6 GPDSSLHVIPSISD---DSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSVP 82 (184)
Q Consensus 6 ~~~~~i~~Hp~y~~---~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~~ 82 (184)
-.+.++++||.|+. .+|||||+|++++. +++.++|+| ||..+ .....+..+.++|||...
T Consensus 71 ~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~--------------~~~~~~pi~-l~~~~--~~~~~~~~~~~~g~g~~~ 133 (229)
T smart00020 71 IKVSKVIIHPNYNPSTYDNDIALLKLKSPVT--------------LSDNVRPIC-LPSSN--YNVPAGTTCTVSGWGRTS 133 (229)
T ss_pred EeeEEEEECCCCCCCCCcCCEEEEEECcccC--------------CCCceeecc-CCCcc--cccCCCCEEEEEeCCCCC
Confidence 35788999999974 66999999999998 888999999 77542 234568899999999876
Q ss_pred C-CCCCCcCceEEEEEeeCcccccccccccCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCC
Q psy17330 83 G-GGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCA 161 (184)
Q Consensus 83 ~-~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~ 161 (184)
. .+.....++...+++++.++|...+.. ...+.+.++|+++.......|.+|+|+||++..+ +|+|+||.|++..|.
T Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~C~~~~~~-~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~ 211 (229)
T smart00020 134 EGAGSLPDTLQEVNVPIVSNATCRRAYSG-GGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCA 211 (229)
T ss_pred CCCCcCCCEeeEEEEEEeCHHHhhhhhcc-ccccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCC
Confidence 4 234466888999999999999987762 2367899999985444678999999999999988 999999999999898
Q ss_pred CCCCCeEEEeCcchHHHH
Q psy17330 162 EVGFPGVYTRVTNYIQWI 179 (184)
Q Consensus 162 ~~~~p~vft~v~~~~~WI 179 (184)
..+.|.+|+||+.|.+||
T Consensus 212 ~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 212 RPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred CCCCCCEEEEeccccccC
Confidence 667899999999999998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.93 E-value=2.9e-25 Score=166.69 Aligned_cols=148 Identities=34% Similarity=0.695 Sum_probs=125.9
Q ss_pred CCceEEEcCCCCC---CCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeecccCC
Q psy17330 7 PDSSLHVIPSISD---DSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSVPG 83 (184)
Q Consensus 7 ~~~~i~~Hp~y~~---~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~~~ 83 (184)
.+++++.||+|+. .+|||||||++++. +.+.+.|+| ++... .....+..+.+.||+....
T Consensus 70 ~v~~~~~h~~~~~~~~~~DiAll~L~~~~~--------------~~~~~~~~~-l~~~~--~~~~~~~~~~~~G~~~~~~ 132 (220)
T PF00089_consen 70 KVSKIIIHPKYDPSTYDNDIALLKLDRPIT--------------FGDNIQPIC-LPSAG--SDPNVGTSCIVVGWGRTSD 132 (220)
T ss_dssp EEEEEEEETTSBTTTTTTSEEEEEESSSSE--------------HBSSBEESB-BTSTT--HTTTTTSEEEEEESSBSST
T ss_pred cccccccccccccccccccccccccccccc--------------ccccccccc-ccccc--ccccccccccccccccccc
Confidence 5678899999976 45999999999987 888999999 66422 2346789999999998765
Q ss_pred CCCCCcCceEEEEEeeCcccccccccccCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCCCC
Q psy17330 84 GGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEV 163 (184)
Q Consensus 84 ~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~ 163 (184)
.+ ....++...+.+++.+.|...+. ..+.+.++|+... .....|.||+||||++..+ +|+||.+++..|...
T Consensus 133 ~~-~~~~~~~~~~~~~~~~~c~~~~~---~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~ 204 (220)
T PF00089_consen 133 NG-YSSNLQSVTVPVVSRKTCRSSYN---DNLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSP 204 (220)
T ss_dssp TS-BTSBEEEEEEEEEEHHHHHHHTT---TTSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBT
T ss_pred cc-ccccccccccccccccccccccc---ccccccccccccc-cccccccccccccccccee---eecceeeecCCCCCC
Confidence 55 55688899999999999998754 4588999999844 5678999999999999975 799999999889887
Q ss_pred CCCeEEEeCcchHHHH
Q psy17330 164 GFPGVYTRVTNYIQWI 179 (184)
Q Consensus 164 ~~p~vft~v~~~~~WI 179 (184)
+.|.+|+||+.|.+||
T Consensus 205 ~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 205 NYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TSEEEEEEGGGGHHHH
T ss_pred CcCEEEEEHHHhhccC
Confidence 7799999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=2.6e-17 Score=128.34 Aligned_cols=163 Identities=26% Similarity=0.383 Sum_probs=113.7
Q ss_pred cCCCceEEEcCCCCC---CCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeeccc
Q psy17330 5 AGPDSSLHVIPSISD---DSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSV 81 (184)
Q Consensus 5 ~~~~~~i~~Hp~y~~---~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~ 81 (184)
.+.+-+|+.|..|.. .||+|+++|+++...+....-..++...+ ..++.........+|+.+
T Consensus 105 rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~---------------l~sv~~~s~~~n~t~~~~ 169 (413)
T COG5640 105 RGHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTF---------------LNSVTTVSPMTNGTFGVT 169 (413)
T ss_pred CcceEEEeeecccccccccCcceeeccccccccchhheeeccCcccc---------------eecccccccccceeeeee
Confidence 456778999999965 55999999999776332221111111100 111222223344566544
Q ss_pred CCC---CCCC--cCceEEEEEeeCcccccccccc---cCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEE
Q psy17330 82 PGG---GPLS--PKLRHVQISVVDNPKCRQIFSN---YGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGV 153 (184)
Q Consensus 82 ~~~---~~~~--~~l~~~~~~~~~~~~C~~~~~~---~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi 153 (184)
... +..+ ..++...+..++...|..++.. -+....-.-+|++ ....+.|+||+|||++.+.+....++||
T Consensus 170 ~~~~v~~~~p~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag--~~~~daCqGDSGGPi~~~g~~G~vQ~GV 247 (413)
T COG5640 170 TPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAG--RPPKDACQGDSGGPIFHKGEEGRVQRGV 247 (413)
T ss_pred eecCCCCCCCccceeeeeeeeeechHHhhhhccccccCCCCCCccceecC--CCCcccccCCCCCceEEeCCCccEEEeE
Confidence 322 1112 4788999999999999988742 1112222239998 5558999999999999998888899999
Q ss_pred EEecCC-CCCCCCCeEEEeCcchHHHHHhhhC
Q psy17330 154 VSYGKK-CAEVGFPGVYTRVTNYIQWIADNIS 184 (184)
Q Consensus 154 ~s~~~~-c~~~~~p~vft~v~~~~~WI~~~i~ 184 (184)
+|||.+ |+.+..|+|||+|+.|.+||..+++
T Consensus 248 vSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 248 VSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred EEecCCCCCCCCcceeEEehhHHHHHHHHHhc
Confidence 999998 9999999999999999999998763
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=98.72 E-value=2.7e-07 Score=72.40 Aligned_cols=118 Identities=25% Similarity=0.387 Sum_probs=78.5
Q ss_pred CCCCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeecccCCCCCCCcCceEEEEE
Q psy17330 18 SDDSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLGSVPGGGPLSPKLRHVQIS 97 (184)
Q Consensus 18 ~~~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~ 97 (184)
....+++||+|+++ +.....|+| ||... .....+....+.|+ .....+....+.
T Consensus 158 ~~~~~~mIlEl~~~----------------~~~~~~~~C-l~~~~--~~~~~~~~~~~yg~-------~~~~~~~~~~~~ 211 (282)
T PF03761_consen 158 NRPYSPMILELEED----------------FSKNVSPPC-LADSS--TNWEKGDEVDVYGF-------NSTGKLKHRKLK 211 (282)
T ss_pred ccccceEEEEEccc----------------ccccCCCEE-eCCCc--cccccCceEEEeec-------CCCCeEEEEEEE
Confidence 34559999999988 235689999 77544 33455666666676 122334455555
Q ss_pred eeCcccccccccccCCCCCCCeEEeeecCCCCCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEeCcchHH
Q psy17330 98 VVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNYIQ 177 (184)
Q Consensus 98 ~~~~~~C~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vft~v~~~~~ 177 (184)
+..... |..........|.+|.||||+...+|+|+|+||.+.+...+..+ ...|.+|+.|.+
T Consensus 212 i~~~~~-----------------~~~~~~~~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~-~~~f~~v~~~~~ 273 (282)
T PF03761_consen 212 ITNCTK-----------------CAYSICTKQYSCKGDRGGPLVKNINGRWTLIGVGASGNYECNKN-NSYFFNVSWYQD 273 (282)
T ss_pred EEEeec-----------------cceeEecccccCCCCccCeEEEEECCCEEEEEEEccCCCccccc-ccEEEEHHHhhh
Confidence 554333 22222334577899999999999999999999998775422212 578889988876
Q ss_pred HH
Q psy17330 178 WI 179 (184)
Q Consensus 178 WI 179 (184)
=|
T Consensus 274 ~I 275 (282)
T PF03761_consen 274 EI 275 (282)
T ss_pred hh
Confidence 44
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=97.61 E-value=0.00038 Score=52.75 Aligned_cols=158 Identities=18% Similarity=0.222 Sum_probs=89.1
Q ss_pred ccccCCCceEEEcCCC--CCCCCeEEEEeceecccCcccccccCCcccCCCCCCCcccCCCCCceeccCCCCeeeeEeec
Q psy17330 2 FLAAGPDSSLHVIPSI--SDDSHYQILHLEQRKKSKACKPSQLGGVARLPGPAGPGCSLPWGEFRLDLSSGGLRGPGCLG 79 (184)
Q Consensus 2 ~~~~~~~~~i~~Hp~y--~~~~DiAllkL~~~~~~~~~~~~~l~~~~~~~~~v~piCllp~~~~~~~~~~~~~~~~~Gwg 79 (184)
+.++||=.+|.+=-.| -.+++++||+|++|+. |+.+|.|.+ +|... ........|..+|-.
T Consensus 68 ~~v~Gp~EQI~rVD~~~~V~~S~v~LLHL~~~~~--------------fTr~VlP~f-lp~~~--~~~~~~~~CVAVg~d 130 (267)
T PF09342_consen 68 LSVDGPHEQISRVDCFKDVPESNVLLLHLEQPAN--------------FTRYVLPTF-LPETS--NENESDDECVAVGHD 130 (267)
T ss_pred cccCCChheEEEeeeeeeccccceeeeeecCccc--------------ceeeecccc-ccccc--CCCCCCCceEEEEcc
Confidence 3467888888776666 3477999999999999 999999999 78533 233344599999975
Q ss_pred ccCCCCCCCcCceEEEEEeeCc-ccccc------cccccC------------CCCCCCeEEeeecC--------------
Q psy17330 80 SVPGGGPLSPKLRHVQISVVDN-PKCRQ------IFSNYG------------ATINENILCAGVLS-------------- 126 (184)
Q Consensus 80 ~~~~~~~~~~~l~~~~~~~~~~-~~C~~------~~~~~~------------~~~~~~~~C~~~~~-------------- 126 (184)
.+ +. .+...+.++.+ +.|.. .....+ ..-.+...|.....
T Consensus 131 ~~--g~-----~kt~si~l~~n~~nC~s~~~Cy~~~~~~p~~~~n~e~~~s~s~w~g~i~c~~~~~~~~~a~F~~c~~~~ 203 (267)
T PF09342_consen 131 DT--GR-----IKTVSIFLIPNLENCDSCNRCYKLQSKQPYALLNAEDMASISEWVGLISCVSEKGWYPAAKFTSCDQFG 203 (267)
T ss_pred cC--Cc-----eeeeEEEeeccccCCCchhhhhhhcccCCcccccccccccccccceeEEeecCCCCcceEEEEeccccc
Confidence 41 11 12222222211 22332 211100 12234456654100
Q ss_pred --CCC-CCCCCCCCCeeEEEe-CCeEEEEEEEEecCC-CCCCCCCeEEEeCcchHHHHHhhh
Q psy17330 127 --GGK-DSCGGDSGGPLMYPL-DTKYYIIGVVSYGKK-CAEVGFPGVYTRVTNYIQWIADNI 183 (184)
Q Consensus 127 --~~~-~~c~~d~G~pl~~~~-~~~~~L~Gi~s~~~~-c~~~~~p~vft~v~~~~~WI~~~i 183 (184)
+.. ..-...-+|-++|+. ...|+-+|+.++..+ |..-..|.--+.+-...+=|++++
T Consensus 204 ~kn~~~~~~~~s~~gv~vC~~~~~gw~p~~~~~~~~~~C~~f~~~~~i~~le~~y~~~q~~~ 265 (267)
T PF09342_consen 204 LKNFSDKQHSPSDQGVLVCRDSHSGWYPTAFFNYNNGDCQGFNDPFGIRTLEEAYKSLQDSI 265 (267)
T ss_pred ccccccCCCCcccCceEEEcCCCCCccchhhhccCCCccccccCeeeEeEHHHhHHHHHHHh
Confidence 000 011223466778884 447999999998765 644444443344444555555544
No 8
>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=94.48 E-value=0.21 Score=41.61 Aligned_cols=48 Identities=19% Similarity=0.109 Sum_probs=26.9
Q ss_pred CCCCCCCCeeEEEeCCeEEEEEEEEecCC-CCCCCCCeEEEeCcchHHHHHh
Q psy17330 131 SCGGDSGGPLMYPLDTKYYIIGVVSYGKK-CAEVGFPGVYTRVTNYIQWIAD 181 (184)
Q Consensus 131 ~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~-c~~~~~p~vft~v~~~~~WI~~ 181 (184)
.-.|.+||||+...+ .++||.+.... .+.......+..+......+++
T Consensus 176 i~~GnSGGpl~n~~G---~viGI~~~~~~~~g~~~g~~faiP~~~~~~~~~~ 224 (428)
T TIGR02037 176 INPGNSGGPLVNLRG---EVIGINTAIYSPSGGNVGIGFAIPSNMAKNVVDQ 224 (428)
T ss_pred CCCCCCCCceECCCC---eEEEEEeEEEcCCCCccceEEEEEhHHHHHHHHH
Confidence 345789999987643 89999876422 1111112344555444444443
No 9
>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=94.35 E-value=0.27 Score=40.01 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=19.1
Q ss_pred CCCCCCCCCeeEEEeCCeEEEEEEEEec
Q psy17330 130 DSCGGDSGGPLMYPLDTKYYIIGVVSYG 157 (184)
Q Consensus 130 ~~c~~d~G~pl~~~~~~~~~L~Gi~s~~ 157 (184)
..-.|.+||||+...+ .++||.+..
T Consensus 194 ~i~~GnSGGpl~n~~G---~vIGI~~~~ 218 (351)
T TIGR02038 194 AINAGNSGGALINTNG---ELVGINTAS 218 (351)
T ss_pred ccCCCCCcceEECCCC---eEEEEEeee
Confidence 3456789999997744 899998754
No 10
>PRK10139 serine endoprotease; Provisional
Probab=94.07 E-value=0.37 Score=40.64 Aligned_cols=49 Identities=16% Similarity=0.029 Sum_probs=28.3
Q ss_pred CCCCCCCCCeeEEEeCCeEEEEEEEEecCCCC-CCCCCeEEEeCcchHHHHHh
Q psy17330 130 DSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCA-EVGFPGVYTRVTNYIQWIAD 181 (184)
Q Consensus 130 ~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~-~~~~p~vft~v~~~~~WI~~ 181 (184)
..-.|.+||||+...+ .++||.+....-. .....++...+......+++
T Consensus 208 ~in~GnSGGpl~n~~G---~vIGi~~~~~~~~~~~~gigfaIP~~~~~~v~~~ 257 (455)
T PRK10139 208 SINRGNSGGALLNLNG---ELIGINTAILAPGGGSVGIGFAIPSNMARTLAQQ 257 (455)
T ss_pred ccCCCCCcceEECCCC---eEEEEEEEEEcCCCCccceEEEEEhHHHHHHHHH
Confidence 3456789999998744 8999998643211 11112445555444444444
No 11
>PRK10898 serine endoprotease; Provisional
Probab=94.05 E-value=0.54 Score=38.29 Aligned_cols=26 Identities=27% Similarity=0.480 Sum_probs=19.4
Q ss_pred CCCCCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 130 DSCGGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 130 ~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
..-.|++||||+...+ .++||.+...
T Consensus 194 ~i~~GnSGGPl~n~~G---~vvGI~~~~~ 219 (353)
T PRK10898 194 SINHGNSGGALVNSLG---ELMGINTLSF 219 (353)
T ss_pred ccCCCCCcceEECCCC---eEEEEEEEEe
Confidence 3455789999987633 8999988643
No 12
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=92.90 E-value=0.24 Score=38.19 Aligned_cols=53 Identities=26% Similarity=0.434 Sum_probs=39.0
Q ss_pred CCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEeC-cchHHHHHhhhC
Q psy17330 129 KDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRV-TNYIQWIADNIS 184 (184)
Q Consensus 129 ~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vft~v-~~~~~WI~~~i~ 184 (184)
.+.+.|++|+|++...+ +++|+..-+..-.........+|+ ..+.+||++.++
T Consensus 198 ~dT~pG~SGSpv~~~~~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 198 ADTLPGSSGSPVLISKD---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred ecccCCCCCCceEecCc---eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 46788999999999865 899999887763322333455666 446799998875
No 13
>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=92.34 E-value=0.16 Score=45.39 Aligned_cols=52 Identities=25% Similarity=0.191 Sum_probs=29.9
Q ss_pred CCCCCCCCCeeEEE--eCCeEEEEEEEEecCCCCCCCCCeEEEeCcchHHHHHh
Q psy17330 130 DSCGGDSGGPLMYP--LDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNYIQWIAD 181 (184)
Q Consensus 130 ~~c~~d~G~pl~~~--~~~~~~L~Gi~s~~~~c~~~~~p~vft~v~~~~~WI~~ 181 (184)
..-.||||+||+.- .+..|.|+|+.+.+.+.......-..++...+.+|+++
T Consensus 212 ~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~g~~~~~~~~~~~f~~~~~~~ 265 (769)
T PF02395_consen 212 YGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYNGKGNWWNVIPPDFINQIKQN 265 (769)
T ss_dssp B--TT-TT-EEEEEETTTTEEEEEEEEEEECCCCHSEEEEEEECHHHHHHHHHH
T ss_pred ccccCcCCCceEEEEccCCeEEEEEEEccccccCCccceeEEecHHHHHHHHhh
Confidence 34679999999865 66799999999987654332211222333334455543
No 14
>PRK10942 serine endoprotease; Provisional
Probab=91.53 E-value=1 Score=38.17 Aligned_cols=48 Identities=17% Similarity=0.026 Sum_probs=27.1
Q ss_pred CCCCCCCCeeEEEeCCeEEEEEEEEecCCC-CCCCCCeEEEeCcchHHHHHh
Q psy17330 131 SCGGDSGGPLMYPLDTKYYIIGVVSYGKKC-AEVGFPGVYTRVTNYIQWIAD 181 (184)
Q Consensus 131 ~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c-~~~~~p~vft~v~~~~~WI~~ 181 (184)
.-.|.+||||+...+ .++||.+....- +.....+++.-+.....++++
T Consensus 230 i~~GnSGGpL~n~~G---eviGI~t~~~~~~g~~~g~gfaIP~~~~~~v~~~ 278 (473)
T PRK10942 230 INRGNSGGALVNLNG---ELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQ 278 (473)
T ss_pred cCCCCCcCccCCCCC---eEEEEEEEEEcCCCCcccEEEEEEHHHHHHHHHH
Confidence 345789999997743 899998763221 111112344454444444444
No 15
>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=75.81 E-value=3 Score=28.69 Aligned_cols=34 Identities=26% Similarity=0.422 Sum_probs=26.0
Q ss_pred CCCCCCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEeCcch
Q psy17330 133 GGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNY 175 (184)
Q Consensus 133 ~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vft~v~~~ 175 (184)
.||-||+|.|+. =++||++.|.. ....|++|+.+
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 378899999997 49999988632 24779999885
No 16
>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=73.50 E-value=5.6 Score=30.04 Aligned_cols=39 Identities=18% Similarity=0.153 Sum_probs=28.0
Q ss_pred CCCeEEeeec-C---CCCCCCCCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 116 NENILCAGVL-S---GGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 116 ~~~~~C~~~~-~---~~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
..+++..... + ...+.-+|.||+|++.++ .|+|-+++..
T Consensus 158 ~k~~vi~vtd~~Ll~~TGGIvqGMSGSPI~qdG----KLiGAVthvf 200 (218)
T PF05580_consen 158 GKGMVIKVTDPRLLEKTGGIVQGMSGSPIIQDG----KLIGAVTHVF 200 (218)
T ss_pred CCcEEEEECCcchhhhhCCEEecccCCCEEECC----EEEEEEEEEE
Confidence 4555654321 1 234678999999999988 9999998864
No 17
>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=59.81 E-value=8.2 Score=25.21 Aligned_cols=19 Identities=37% Similarity=0.789 Sum_probs=14.0
Q ss_pred CCCCCCCeeEEEeCCeEEEEEE
Q psy17330 132 CGGDSGGPLMYPLDTKYYIIGV 153 (184)
Q Consensus 132 c~~d~G~pl~~~~~~~~~L~Gi 153 (184)
-.|.+||||+.. +| .++||
T Consensus 102 ~~G~SGgpv~~~-~G--~vvGi 120 (120)
T PF13365_consen 102 RPGSSGGPVFDS-DG--RVVGI 120 (120)
T ss_dssp STTTTTSEEEET-TS--EEEEE
T ss_pred CCCcEeHhEECC-CC--EEEeC
Confidence 357899999774 44 68886
No 18
>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=58.02 E-value=30 Score=26.58 Aligned_cols=35 Identities=29% Similarity=0.441 Sum_probs=21.2
Q ss_pred CCCCCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEeCc
Q psy17330 134 GDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVT 173 (184)
Q Consensus 134 ~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vft~v~ 173 (184)
|+=|.||+...+| .++||.|.+..-... -.|+.+.
T Consensus 151 G~CG~PlVs~~Dg--~IVGiHsl~~~~~~~---N~F~~f~ 185 (235)
T PF00863_consen 151 GDCGLPLVSTKDG--KIVGIHSLTSNTSSR---NYFTPFP 185 (235)
T ss_dssp T-TT-EEEETTT----EEEEEEEEETTTSS---EEEEE--
T ss_pred CccCCcEEEcCCC--cEEEEEcCccCCCCe---EEEEcCC
Confidence 4569999999777 999999987554332 4666653
No 19
>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=56.20 E-value=11 Score=26.39 Aligned_cols=22 Identities=32% Similarity=0.670 Sum_probs=16.5
Q ss_pred CCCCCCCeeEEEeCCeEEEEEEEEe
Q psy17330 132 CGGDSGGPLMYPLDTKYYIIGVVSY 156 (184)
Q Consensus 132 c~~d~G~pl~~~~~~~~~L~Gi~s~ 156 (184)
-+|.+|||+.|..+ ..+||...
T Consensus 106 lkGSSGgPiLC~~G---H~vG~f~a 127 (148)
T PF02907_consen 106 LKGSSGGPILCPSG---HAVGMFRA 127 (148)
T ss_dssp HTT-TT-EEEETTS---EEEEEEEE
T ss_pred EecCCCCcccCCCC---CEEEEEEE
Confidence 46889999999965 89999765
No 20
>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=52.74 E-value=15 Score=28.79 Aligned_cols=23 Identities=35% Similarity=0.498 Sum_probs=17.3
Q ss_pred CCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 133 GGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 133 ~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
.||+|+|++.+++ .|+||.+-+.
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 4799999999865 6999997643
No 21
>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=42.15 E-value=27 Score=29.15 Aligned_cols=45 Identities=27% Similarity=0.370 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEeCcchHHHHHhh
Q psy17330 128 GKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNYIQWIADN 182 (184)
Q Consensus 128 ~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~~c~~~~~p~vft~v~~~~~WI~~~ 182 (184)
..+.-+|.||+|++.++ .|+|-++.-.--.-...+++ |.+|+.+.
T Consensus 354 tgGivqGMSGSPi~q~g----kliGAvtHVfvndpt~GYGi------~ie~Ml~~ 398 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQNG----KVIGAVTHVFVNDPTSGYGV------YIEWMLKE 398 (402)
T ss_pred hCCEEecccCCCEEECC----EEEEEEEEEEecCCCcceee------hHHHHHHH
Confidence 34678999999999999 99998775322111112344 57787654
No 22
>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=33.16 E-value=81 Score=26.62 Aligned_cols=31 Identities=26% Similarity=0.493 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 128 GKDSCGGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 128 ~~~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
+.+.-.||-|.|.+++.++.|.++||.....
T Consensus 497 DLGT~PGDCGcPYvyKrgNd~VV~GVH~AAt 527 (535)
T PF05416_consen 497 DLGTIPGDCGCPYVYKRGNDWVVIGVHAAAT 527 (535)
T ss_dssp TTS--TTGTT-EEEEEETTEEEEEEEEEEE-
T ss_pred ccCCCCCCCCCceeeecCCcEEEEEEEehhc
Confidence 3355688999999999999999999987643
No 23
>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=25.10 E-value=23 Score=24.79 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=17.2
Q ss_pred CCCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 132 CGGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 132 c~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
-.||+|.|++.+.+ .++||+--|.
T Consensus 104 ~~GDSGRpi~DNsG---rVVaIVLGG~ 127 (158)
T PF00944_consen 104 KPGDSGRPIFDNSG---RVVAIVLGGA 127 (158)
T ss_dssp STTSTTEEEESTTS---BEEEEEEEEE
T ss_pred CCCCCCCccCcCCC---CEEEEEecCC
Confidence 35899999987744 6777776553
No 24
>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=23.58 E-value=45 Score=24.18 Aligned_cols=26 Identities=31% Similarity=0.470 Sum_probs=21.3
Q ss_pred CCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 133 GGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 133 ~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
.|+=||+|+.+.++...++||...|.
T Consensus 146 ~G~CG~~l~~~~~~~~~i~GiHvaG~ 171 (172)
T PF00548_consen 146 PGMCGSPLVSRIGGQGKIIGIHVAGN 171 (172)
T ss_dssp TTGTTEEEEESCGGTTEEEEEEEEEE
T ss_pred CCccCCeEEEeeccCccEEEEEeccC
Confidence 46779999998777789999987653
No 25
>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=22.19 E-value=49 Score=20.29 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=8.7
Q ss_pred cchHHHHHhhh
Q psy17330 173 TNYIQWIADNI 183 (184)
Q Consensus 173 ~~~~~WI~~~i 183 (184)
..|.+||.+.|
T Consensus 14 ~~Fs~Wik~ri 24 (71)
T PF08346_consen 14 KRFSTWIKRRI 24 (71)
T ss_pred CcHHHHHHHHh
Confidence 56899999765
No 26
>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=20.60 E-value=1.2e+02 Score=27.49 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=20.7
Q ss_pred CCCCCCCCCeeEEEeCCeEEEEEEEEecC
Q psy17330 130 DSCGGDSGGPLMYPLDTKYYIIGVVSYGK 158 (184)
Q Consensus 130 ~~c~~d~G~pl~~~~~~~~~L~Gi~s~~~ 158 (184)
++..|.||||++-..+ .|+|+.--+.
T Consensus 629 DitGGNSGSPvlN~~G---eLVGl~FDgn 654 (698)
T PF10459_consen 629 DITGGNSGSPVLNAKG---ELVGLAFDGN 654 (698)
T ss_pred CcCCCCCCCccCCCCc---eEEEEeecCc
Confidence 5677899999998744 8999986554
Done!