Query psy12782
Match_columns 203
No_of_seqs 112 out of 1168
Neff 9.7
Searched_HMMs 46136
Date Fri Aug 16 19:31:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 100.0 1.7E-33 3.6E-38 220.3 19.3 186 9-199 64-255 (256)
2 cd00190 Tryp_SPc Trypsin-like 100.0 5.4E-33 1.2E-37 213.3 19.2 183 7-197 49-232 (232)
3 smart00020 Tryp_SPc Trypsin-li 100.0 8.8E-30 1.9E-34 195.5 18.5 179 7-194 50-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 4.7E-28 1E-32 184.5 16.6 173 7-194 47-220 (220)
5 COG5640 Secreted trypsin-like 99.8 3.2E-20 7E-25 145.4 14.7 185 9-200 87-280 (413)
6 PF03761 DUF316: Domain of unk 99.0 1.1E-08 2.3E-13 81.3 12.7 140 29-198 137-279 (282)
7 PF09342 DUF1986: Domain of un 97.1 0.0022 4.8E-08 49.1 6.6 76 8-92 55-131 (267)
8 TIGR02037 degP_htrA_DO peripla 96.7 0.034 7.4E-07 47.0 11.6 123 50-199 104-227 (428)
9 PRK10898 serine endoprotease; 96.2 0.17 3.7E-06 41.7 12.5 27 144-173 193-219 (353)
10 PRK10139 serine endoprotease; 96.0 0.17 3.7E-06 43.1 11.7 123 50-199 137-260 (455)
11 COG3591 V8-like Glu-specific e 95.8 0.12 2.7E-06 40.1 9.4 54 143-199 197-251 (251)
12 TIGR02038 protease_degS peripl 95.5 0.26 5.5E-06 40.6 10.8 37 50-91 124-160 (351)
13 PRK10942 serine endoprotease; 95.1 0.35 7.6E-06 41.5 10.6 37 50-90 158-194 (473)
14 PF02395 Peptidase_S6: Immunog 92.9 0.079 1.7E-06 47.8 2.7 32 144-175 211-244 (769)
15 PF00947 Pico_P2A: Picornaviru 90.6 0.34 7.3E-06 33.5 3.1 35 147-190 88-122 (127)
16 PF05580 Peptidase_S55: SpoIVB 78.1 2.3 4.9E-05 32.3 2.7 26 144-173 175-200 (218)
17 PF00863 Peptidase_C4: Peptida 77.2 9.7 0.00021 29.5 6.0 47 145-198 147-193 (235)
18 PF13365 Trypsin_2: Trypsin-li 69.7 4.3 9.3E-05 27.0 2.3 21 145-168 100-120 (120)
19 TIGR02860 spore_IV_B stage IV 64.8 5.7 0.00012 33.3 2.5 45 144-198 355-399 (402)
20 PF05579 Peptidase_S32: Equine 62.8 6 0.00013 31.2 2.1 22 148-172 207-228 (297)
21 PF02907 Peptidase_S29: Hepati 59.3 8.7 0.00019 27.0 2.2 25 145-172 104-128 (148)
22 PF00548 Peptidase_C3: 3C cyst 58.0 7.2 0.00016 28.6 1.8 28 145-172 143-170 (172)
23 PF14903 WG_beta_rep: WG conta 41.7 40 0.00087 16.8 2.7 25 35-60 9-33 (35)
24 KOG3939|consensus 40.7 77 0.0017 24.9 4.9 39 135-173 239-294 (312)
25 PF00944 Peptidase_S3: Alphavi 40.5 8.8 0.00019 27.0 -0.1 26 146-174 103-128 (158)
26 PF05416 Peptidase_C37: Southa 39.7 53 0.0012 27.9 4.2 31 145-175 499-529 (535)
27 PF10459 Peptidase_S46: Peptid 36.0 33 0.00072 31.2 2.7 63 132-201 619-689 (698)
28 PF00949 Peptidase_S7: Peptida 24.9 71 0.0015 22.4 2.3 27 145-174 93-119 (132)
29 KOG1421|consensus 20.4 4.3E+02 0.0093 24.4 6.5 48 144-194 211-258 (955)
30 PRK08572 rps17p 30S ribosomal 20.1 2.9E+02 0.0063 18.7 4.6 30 11-43 30-59 (108)
No 1
>KOG3627|consensus
Probab=100.00 E-value=1.7e-33 Score=220.25 Aligned_cols=186 Identities=45% Similarity=0.783 Sum_probs=152.8
Q ss_pred eeEEEeeeeeecccCCCCC-ceEEeeEEEEeCCCCCCCCCCCC-CCeEEEEECCCcCCCCCccceecCCCCC---CccCc
Q psy12782 9 QVQVTLGDYVINSAVEPLP-AYTFGVRKINVHPYFKFTPQADR-YDVAVLRLDRPVQYMPHIAPICLPEKGE---DFLGQ 83 (203)
Q Consensus 9 ~~~V~~G~~~~~~~~~~~~-~~~~~v~~i~~hp~y~~~~~~~~-~DiALl~L~~~~~~~~~i~picl~~~~~---~~~~~ 83 (203)
.+.|++|++......+... .+...|.++++||+|+ ..... ||||||+|.+++.|++.|+|+|||.... .....
T Consensus 64 ~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i~H~~y~--~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~ 141 (256)
T KOG3627|consen 64 LYTVRLGEHDINLSVSEGEEQLVGDVEKIIVHPNYN--PRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGT 141 (256)
T ss_pred ceEEEECccccccccccCchhhhceeeEEEECCCCC--CCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCC
Confidence 7889999887666533211 2555588999999997 45555 9999999999999999999999986554 23458
Q ss_pred eeEEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcE
Q psy12782 84 FGWAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRW 163 (203)
Q Consensus 84 ~~~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~ 163 (203)
.|.++|||.........+..|+..++.+++.+.|...+.... .+.+.++|++......+.|+||+||||++..++++
T Consensus 142 ~~~v~GWG~~~~~~~~~~~~L~~~~v~i~~~~~C~~~~~~~~---~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~ 218 (256)
T KOG3627|consen 142 TCLVSGWGRTESGGGPLPDTLQEVDVPIISNSECRRAYGGLG---TITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRW 218 (256)
T ss_pred EEEEEeCCCcCCCCCCCCceeEEEEEeEcChhHhcccccCcc---ccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcE
Confidence 899999998876633347789999999999999998876421 25567899997555677899999999999987789
Q ss_pred EEEEEEEecCC-CCCCCCCeEEEeCCCCHHHHHHhhc
Q psy12782 164 FLIGIVSAGYS-CAQQGQPGIYHRVAYTVDWISYIMN 199 (203)
Q Consensus 164 ~lvGv~s~~~~-c~~~~~~~v~t~v~~~~~WI~~~i~ 199 (203)
+++||+||+.. |.....|++||+|+.|.+||++.+.
T Consensus 219 ~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 219 VLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred EEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHHHhc
Confidence 99999999988 9888899999999999999999875
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=100.00 E-value=5.4e-33 Score=213.25 Aligned_cols=183 Identities=40% Similarity=0.714 Sum_probs=155.2
Q ss_pred CceeEEEeeeeeecccCCCCCceEEeeEEEEeCCCCCCCCCCCCCCeEEEEECCCcCCCCCccceecCCCCC-CccCcee
Q psy12782 7 ARQVQVTLGDYVINSAVEPLPAYTFGVRKINVHPYFKFTPQADRYDVAVLRLDRPVQYMPHIAPICLPEKGE-DFLGQFG 85 (203)
Q Consensus 7 ~~~~~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DiALl~L~~~~~~~~~i~picl~~~~~-~~~~~~~ 85 (203)
+..+.|++|......... ..+.+.|.++++||+|+ .....+|||||+|++|+.++..++|+|||.... ...+..+
T Consensus 49 ~~~~~v~~g~~~~~~~~~--~~~~~~v~~~~~hp~y~--~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~ 124 (232)
T cd00190 49 PSNYTVRLGSHDLSSNEG--GGQVIKVKKVIVHPNYN--PSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTC 124 (232)
T ss_pred CccEEEEeCcccccCCCC--ceEEEEEEEEEECCCCC--CCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEE
Confidence 467999999988876443 37889999999999997 456889999999999999999999999998852 2357899
Q ss_pred EEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEE
Q psy12782 86 WAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFL 165 (203)
Q Consensus 86 ~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~l 165 (203)
.++|||....... ....++...+.+++...|...+.. ...+.+.++|+.........|.||+||||++..+++++|
T Consensus 125 ~~~G~g~~~~~~~-~~~~~~~~~~~~~~~~~C~~~~~~---~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~l 200 (232)
T cd00190 125 TVSGWGRTSEGGP-LPDVLQEVNVPIVSNAECKRAYSY---GGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVL 200 (232)
T ss_pred EEEeCCcCCCCCC-CCceeeEEEeeeECHHHhhhhccC---cccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEE
Confidence 9999998765522 367899999999999999987763 124789999998664457899999999999998899999
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCCHHHHHHh
Q psy12782 166 IGIVSAGYSCAQQGQPGIYHRVAYTVDWISYI 197 (203)
Q Consensus 166 vGv~s~~~~c~~~~~~~v~t~v~~~~~WI~~~ 197 (203)
+||+|++..|...+.|.+|++|+.|++||+++
T Consensus 201 vGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 201 VGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred EEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 99999998887667799999999999999864
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=99.97 E-value=8.8e-30 Score=195.51 Aligned_cols=179 Identities=41% Similarity=0.781 Sum_probs=150.3
Q ss_pred CceeEEEeeeeeecccCCCCCceEEeeEEEEeCCCCCCCCCCCCCCeEEEEECCCcCCCCCccceecCCCCCC-ccCcee
Q psy12782 7 ARQVQVTLGDYVINSAVEPLPAYTFGVRKINVHPYFKFTPQADRYDVAVLRLDRPVQYMPHIAPICLPEKGED-FLGQFG 85 (203)
Q Consensus 7 ~~~~~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DiALl~L~~~~~~~~~i~picl~~~~~~-~~~~~~ 85 (203)
+..+.|++|........+ .+.+.|.++++||+|+ .....+|||||+|++|+.++..++|+||+..... ..+..+
T Consensus 50 ~~~~~v~~g~~~~~~~~~---~~~~~v~~~~~~p~~~--~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~ 124 (229)
T smart00020 50 PSNIRVRLGSHDLSSGEE---GQVIKVSKVIIHPNYN--PSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTC 124 (229)
T ss_pred CcceEEEeCcccCCCCCC---ceEEeeEEEEECCCCC--CCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEE
Confidence 468999999988776432 3789999999999997 4678899999999999999999999999987322 357899
Q ss_pred EEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEE
Q psy12782 86 WAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFL 165 (203)
Q Consensus 86 ~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~l 165 (203)
.++|||............++...+.+++.+.|...+... ..+.+.++|++........|.+|+||||++..+ +|+|
T Consensus 125 ~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~---~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l 200 (229)
T smart00020 125 TVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAYSGG---GAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVL 200 (229)
T ss_pred EEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhhccc---cccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEE
Confidence 999999876432233567899999999999999876541 237889999986654578999999999999877 9999
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCCHHHH
Q psy12782 166 IGIVSAGYSCAQQGQPGIYHRVAYTVDWI 194 (203)
Q Consensus 166 vGv~s~~~~c~~~~~~~v~t~v~~~~~WI 194 (203)
+||++++..|...+.|.+|++|++|.+||
T Consensus 201 ~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 201 VGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred EEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 99999999898667899999999999998
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=99.96 E-value=4.7e-28 Score=184.49 Aligned_cols=173 Identities=39% Similarity=0.770 Sum_probs=144.4
Q ss_pred CceeEEEeeeeeecccCCCCCceEEeeEEEEeCCCCCCCCCCCCCCeEEEEECCCcCCCCCccceecCCCCCC-ccCcee
Q psy12782 7 ARQVQVTLGDYVINSAVEPLPAYTFGVRKINVHPYFKFTPQADRYDVAVLRLDRPVQYMPHIAPICLPEKGED-FLGQFG 85 (203)
Q Consensus 7 ~~~~~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DiALl~L~~~~~~~~~i~picl~~~~~~-~~~~~~ 85 (203)
.+++.|++|...+..... ..+.+.|++++.||+|+. ....+|||||+|++++.+.+.+.|+|++..... ..+..+
T Consensus 47 ~~~~~v~~g~~~~~~~~~--~~~~~~v~~~~~h~~~~~--~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 122 (220)
T PF00089_consen 47 ASDIKVRLGTYSIRNSDG--SEQTIKVSKIIIHPKYDP--STYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSC 122 (220)
T ss_dssp GGSEEEEESESBTTSTTT--TSEEEEEEEEEEETTSBT--TTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEE
T ss_pred cccccccccccccccccc--cccccccccccccccccc--cccccccccccccccccccccccccccccccccccccccc
Confidence 357889999844444333 268999999999999983 446899999999999999999999999995432 357899
Q ss_pred EEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEE
Q psy12782 86 WAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFL 165 (203)
Q Consensus 86 ~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~l 165 (203)
.+.||+...... ....++...+.+++.+.|...++. .+.+.++|++.. .....|.||+||||++.+. +|
T Consensus 123 ~~~G~~~~~~~~--~~~~~~~~~~~~~~~~~c~~~~~~-----~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~l 191 (220)
T PF00089_consen 123 IVVGWGRTSDNG--YSSNLQSVTVPVVSRKTCRSSYND-----NLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YL 191 (220)
T ss_dssp EEEESSBSSTTS--BTSBEEEEEEEEEEHHHHHHHTTT-----TSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EE
T ss_pred cccccccccccc--cccccccccccccccccccccccc-----cccccccccccc-cccccccccccccccccee---ee
Confidence 999999865554 256799999999999999987543 278999999865 4578999999999999865 89
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCCHHHH
Q psy12782 166 IGIVSAGYSCAQQGQPGIYHRVAYTVDWI 194 (203)
Q Consensus 166 vGv~s~~~~c~~~~~~~v~t~v~~~~~WI 194 (203)
+||.+++..|...+.|.+|++|+.|++||
T Consensus 192 vGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 192 VGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp EEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred cceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 99999998898877899999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=3.2e-20 Score=145.42 Aligned_cols=185 Identities=26% Similarity=0.356 Sum_probs=131.7
Q ss_pred eeEEEeeeeeecccCCCCCceEEeeEEEEeCCCCCCCCCCCCCCeEEEEECCCcCCCC-CccceecCC--CCCCccCcee
Q psy12782 9 QVQVTLGDYVINSAVEPLPAYTFGVRKINVHPYFKFTPQADRYDVAVLRLDRPVQYMP-HIAPICLPE--KGEDFLGQFG 85 (203)
Q Consensus 9 ~~~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DiALl~L~~~~~~~~-~i~picl~~--~~~~~~~~~~ 85 (203)
+..+..+...++.... .+-.+|++++.|..|. ..++.||||+++|+++..... .+....-+. ..........
T Consensus 87 s~d~~~vv~~l~d~Sq---~~rg~vr~i~~~efY~--~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~ 161 (413)
T COG5640 87 SSDVNRVVVDLNDSSQ---AERGHVRTIYVHEFYS--PGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPM 161 (413)
T ss_pred cccceEEEeccccccc---ccCcceEEEeeecccc--cccccCcceeeccccccccchhheeeccCcccceecccccccc
Confidence 3445555555555433 6778999999999996 789999999999999765431 122211111 1111124555
Q ss_pred EEeecccccCCCCC--Cc--cCceEEEEeeeChhhHhhHhhhC-CCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeC
Q psy12782 86 WAAGWGALQAGSRL--RP--KTLQAVDVPIIDNRQCERWHKSN-GINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERT 160 (203)
Q Consensus 86 ~~~Gwg~~~~~~~~--~~--~~l~~~~~~~~~~~~C~~~~~~~-~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~ 160 (203)
...+|+........ .+ ..+++..+...+...|..+.... .......-.-+|++... ++.|+||+|||++....
T Consensus 162 ~n~t~~~~~~~~v~~~~p~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~~~g~ 239 (413)
T COG5640 162 TNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIFHKGE 239 (413)
T ss_pred cceeeeeeeecCCCCCCCccceeeeeeeeeechHHhhhhccccccCCCCCCccceecCCCC--cccccCCCCCceEEeCC
Confidence 66677654422211 12 47899999999999999987511 11122333449998664 79999999999999987
Q ss_pred CcEEEEEEEEecCC-CCCCCCCeEEEeCCCCHHHHHHhhcc
Q psy12782 161 GRWFLIGIVSAGYS-CAQQGQPGIYHRVAYTVDWISYIMNT 200 (203)
Q Consensus 161 ~~~~lvGv~s~~~~-c~~~~~~~v~t~v~~~~~WI~~~i~~ 200 (203)
....++||+|||++ |+.+..|.|||+|+.|.+||...++.
T Consensus 240 ~G~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~ 280 (413)
T COG5640 240 EGRVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTNG 280 (413)
T ss_pred CccEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhcC
Confidence 77899999999997 99999999999999999999998764
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=98.99 E-value=1.1e-08 Score=81.32 Aligned_cols=140 Identities=23% Similarity=0.416 Sum_probs=93.6
Q ss_pred eEEeeEEEEeCCCC--CCCCCCCCCCeEEEEECCCcCCCCCccceecCCCCCCc-cCceeEEeecccccCCCCCCccCce
Q psy12782 29 YTFGVRKINVHPYF--KFTPQADRYDVAVLRLDRPVQYMPHIAPICLPEKGEDF-LGQFGWAAGWGALQAGSRLRPKTLQ 105 (203)
Q Consensus 29 ~~~~v~~i~~hp~y--~~~~~~~~~DiALl~L~~~~~~~~~i~picl~~~~~~~-~~~~~~~~Gwg~~~~~~~~~~~~l~ 105 (203)
...+|.++++--.- .........+++||+|+++ ++....|+|||+..... .++...+.|+. ....+.
T Consensus 137 ~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~~~~~~~~~~~yg~~--------~~~~~~ 206 (282)
T PF03761_consen 137 FSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSSTNWEKGDEVDVYGFN--------STGKLK 206 (282)
T ss_pred ccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCccccccCceEEEeecC--------CCCeEE
Confidence 34566666553222 1113455679999999999 77889999999887644 45666677761 133455
Q ss_pred EEEEeeeChhhHhhHhhhCCCcccccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEE
Q psy12782 106 AVDVPIIDNRQCERWHKSNGINVVIYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYH 185 (203)
Q Consensus 106 ~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t 185 (203)
...+.+..... |..........|.+|+||||+...+|+|+|+||.+.+...+..+ ...|.
T Consensus 207 ~~~~~i~~~~~-------------------~~~~~~~~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~-~~~f~ 266 (282)
T PF03761_consen 207 HRKLKITNCTK-------------------CAYSICTKQYSCKGDRGGPLVKNINGRWTLIGVGASGNYECNKN-NSYFF 266 (282)
T ss_pred EEEEEEEEeec-------------------cceeEecccccCCCCccCeEEEEECCCEEEEEEEccCCCccccc-ccEEE
Confidence 55555544322 22222233678999999999999999999999999876322212 57899
Q ss_pred eCCCCHHHHHHhh
Q psy12782 186 RVAYTVDWISYIM 198 (203)
Q Consensus 186 ~v~~~~~WI~~~i 198 (203)
+|..|.+=|.+.+
T Consensus 267 ~v~~~~~~IC~lt 279 (282)
T PF03761_consen 267 NVSWYQDEICELT 279 (282)
T ss_pred EHHHhhhhhccce
Confidence 9999888776554
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=97.08 E-value=0.0022 Score=49.06 Aligned_cols=76 Identities=21% Similarity=0.235 Sum_probs=53.7
Q ss_pred ceeEEEeeeeeecccCCCCCceEEeeEEEEeCCCCCCCCCCCCCCeEEEEECCCcCCCCCccceecCCCCCCc-cCceeE
Q psy12782 8 RQVQVTLGDYVINSAVEPLPAYTFGVRKINVHPYFKFTPQADRYDVAVLRLDRPVQYMPHIAPICLPEKGEDF-LGQFGW 86 (203)
Q Consensus 8 ~~~~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DiALl~L~~~~~~~~~i~picl~~~~~~~-~~~~~~ 86 (203)
.=+.|.+|..-.....+.+-+|.++|..+..=| +.+++||.|++|+.|+.+|+|..||....+. ....|.
T Consensus 55 ~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~---------~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CV 125 (267)
T PF09342_consen 55 HYVSALLGGGKTYLSVDGPHEQISRVDCFKDVP---------ESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECV 125 (267)
T ss_pred ceEEEEecCcceecccCCChheEEEeeeeeecc---------ccceeeeeecCcccceeeecccccccccCCCCCCCceE
Confidence 346677776553333344457777777763333 5589999999999999999999999743333 466899
Q ss_pred Eeeccc
Q psy12782 87 AAGWGA 92 (203)
Q Consensus 87 ~~Gwg~ 92 (203)
.+|-..
T Consensus 126 AVg~d~ 131 (267)
T PF09342_consen 126 AVGHDD 131 (267)
T ss_pred EEEccc
Confidence 998653
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=96.70 E-value=0.034 Score=46.95 Aligned_cols=123 Identities=24% Similarity=0.295 Sum_probs=61.9
Q ss_pred CCCeEEEEECCCcCCCCCccceecCCCCCCccCceeEEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCccc
Q psy12782 50 RYDVAVLRLDRPVQYMPHIAPICLPEKGEDFLGQFGWAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVV 129 (203)
Q Consensus 50 ~~DiALl~L~~~~~~~~~i~picl~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~ 129 (203)
..|||||+++.+ ..+.++.|........++.+.+.|+-.... ..+..-.+.-..+. . ....
T Consensus 104 ~~DlAllkv~~~----~~~~~~~l~~~~~~~~G~~v~aiG~p~g~~------~~~t~G~vs~~~~~---~-~~~~----- 164 (428)
T TIGR02037 104 RTDIAVLKIDAK----KNLPVIKLGDSDKLRVGDWVLAIGNPFGLG------QTVTSGIVSALGRS---G-LGIG----- 164 (428)
T ss_pred CCCEEEEEecCC----CCceEEEccCCCCCCCCCEEEEEECCCcCC------CcEEEEEEEecccC---c-cCCC-----
Confidence 359999999865 345577776554434789999999753211 11111111111110 0 0000
Q ss_pred ccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEEEEEEEecCC-CCCCCCCeEEEeCCCCHHHHHHhhc
Q psy12782 130 IYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFLIGIVSAGYS-CAQQGQPGIYHRVAYTVDWISYIMN 199 (203)
Q Consensus 130 ~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~-c~~~~~~~v~t~v~~~~~WI~~~i~ 199 (203)
....++= .......|.+||||+... |+ ++||.+.... ...........-+......+++.++
T Consensus 165 ~~~~~i~-----tda~i~~GnSGGpl~n~~-G~--viGI~~~~~~~~g~~~g~~faiP~~~~~~~~~~l~~ 227 (428)
T TIGR02037 165 DYENFIQ-----TDAAINPGNSGGPLVNLR-GE--VIGINTAIYSPSGGNVGIGFAIPSNMAKNVVDQLIE 227 (428)
T ss_pred CccceEE-----ECCCCCCCCCCCceECCC-Ce--EEEEEeEEEcCCCCccceEEEEEhHHHHHHHHHHHh
Confidence 0111111 123556789999998653 43 9999876432 1111112334444445555555443
No 9
>PRK10898 serine endoprotease; Provisional
Probab=96.20 E-value=0.17 Score=41.67 Aligned_cols=27 Identities=33% Similarity=0.634 Sum_probs=20.2
Q ss_pred CCCCcCCCCCeeEEeeCCcEEEEEEEEecC
Q psy12782 144 KDSCQGDSGGPLMMERTGRWFLIGIVSAGY 173 (203)
Q Consensus 144 ~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~ 173 (203)
.....|.+||||+..+ |+ ++||.+...
T Consensus 193 a~i~~GnSGGPl~n~~-G~--vvGI~~~~~ 219 (353)
T PRK10898 193 ASINHGNSGGALVNSL-GE--LMGINTLSF 219 (353)
T ss_pred cccCCCCCcceEECCC-Ce--EEEEEEEEe
Confidence 4567789999999753 32 999998653
No 10
>PRK10139 serine endoprotease; Provisional
Probab=95.95 E-value=0.17 Score=43.10 Aligned_cols=123 Identities=20% Similarity=0.228 Sum_probs=62.3
Q ss_pred CCCeEEEEECCCcCCCCCccceecCCCCCCccCceeEEeecccccCCCCCCccCceEEEEeeeChhhHhhHhhhCCCccc
Q psy12782 50 RYDVAVLRLDRPVQYMPHIAPICLPEKGEDFLGQFGWAAGWGALQAGSRLRPKTLQAVDVPIIDNRQCERWHKSNGINVV 129 (203)
Q Consensus 50 ~~DiALl~L~~~~~~~~~i~picl~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~ 129 (203)
..||||||++.+- ...++.|.+......++.+...|+-... ... +..-+++.. .+..... .
T Consensus 137 ~~DlAvlkv~~~~----~l~~~~lg~s~~~~~G~~V~aiG~P~g~------~~t---vt~GivS~~--~r~~~~~----~ 197 (455)
T PRK10139 137 QSDIALLQIQNPS----KLTQIAIADSDKLRVGDFAVAVGNPFGL------GQT---ATSGIISAL--GRSGLNL----E 197 (455)
T ss_pred CCCEEEEEecCCC----CCceeEecCccccCCCCEEEEEecCCCC------CCc---eEEEEEccc--cccccCC----C
Confidence 4699999998642 3446667655433468888888863211 111 112222221 0000000 0
Q ss_pred ccCCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEEEEEEEecCCC-CCCCCCeEEEeCCCCHHHHHHhhc
Q psy12782 130 IYDEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFLIGIVSAGYSC-AQQGQPGIYHRVAYTVDWISYIMN 199 (203)
Q Consensus 130 ~~~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c-~~~~~~~v~t~v~~~~~WI~~~i~ 199 (203)
-....+ ........|.+||||+... | .++||.+....- ......+...-+..-...+++.++
T Consensus 198 ~~~~~i-----qtda~in~GnSGGpl~n~~-G--~vIGi~~~~~~~~~~~~gigfaIP~~~~~~v~~~l~~ 260 (455)
T PRK10139 198 GLENFI-----QTDASINRGNSGGALLNLN-G--ELIGINTAILAPGGGSVGIGFAIPSNMARTLAQQLID 260 (455)
T ss_pred CcceEE-----EECCccCCCCCcceEECCC-C--eEEEEEEEEEcCCCCccceEEEEEhHHHHHHHHHHhh
Confidence 001112 1224567899999999754 2 299999874321 111123444555444555555554
No 11
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=95.82 E-value=0.12 Score=40.13 Aligned_cols=54 Identities=19% Similarity=0.335 Sum_probs=37.8
Q ss_pred CCCCCcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEEeCC-CCHHHHHHhhc
Q psy12782 143 AKDSCQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYHRVA-YTVDWISYIMN 199 (203)
Q Consensus 143 ~~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t~v~-~~~~WI~~~i~ 199 (203)
..+.+.|++|+|++...+ +++||..-+..-.......-.+|+. ..++||.+.++
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 357899999999999776 7999999887532222233344444 46799988763
No 12
>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=95.51 E-value=0.26 Score=40.59 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=24.3
Q ss_pred CCCeEEEEECCCcCCCCCccceecCCCCCCccCceeEEeecc
Q psy12782 50 RYDVAVLRLDRPVQYMPHIAPICLPEKGEDFLGQFGWAAGWG 91 (203)
Q Consensus 50 ~~DiALl~L~~~~~~~~~i~picl~~~~~~~~~~~~~~~Gwg 91 (203)
..||||||++.+- +.++.+........++.+.+.|+.
T Consensus 124 ~~DlAvlkv~~~~-----~~~~~l~~s~~~~~G~~V~aiG~P 160 (351)
T TIGR02038 124 LTDLAVLKIEGDN-----LPTIPVNLDRPPHVGDVVLAIGNP 160 (351)
T ss_pred CCCEEEEEecCCC-----CceEeccCcCccCCCCEEEEEeCC
Confidence 4599999998642 334445333333368999999985
No 13
>PRK10942 serine endoprotease; Provisional
Probab=95.07 E-value=0.35 Score=41.47 Aligned_cols=37 Identities=24% Similarity=0.451 Sum_probs=24.5
Q ss_pred CCCeEEEEECCCcCCCCCccceecCCCCCCccCceeEEeec
Q psy12782 50 RYDVAVLRLDRPVQYMPHIAPICLPEKGEDFLGQFGWAAGW 90 (203)
Q Consensus 50 ~~DiALl~L~~~~~~~~~i~picl~~~~~~~~~~~~~~~Gw 90 (203)
..||||||++.+-. ..++.|.+......++.+.+.|.
T Consensus 158 ~~DlAvlki~~~~~----l~~~~lg~s~~l~~G~~V~aiG~ 194 (473)
T PRK10942 158 RSDIALIQLQNPKN----LTAIKMADSDALRVGDYTVAIGN 194 (473)
T ss_pred CCCEEEEEecCCCC----CceeEecCccccCCCCEEEEEcC
Confidence 46999999975322 34566655443346888888885
No 14
>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=92.90 E-value=0.079 Score=47.80 Aligned_cols=32 Identities=34% Similarity=0.737 Sum_probs=22.6
Q ss_pred CCCCcCCCCCeeEEee--CCcEEEEEEEEecCCC
Q psy12782 144 KDSCQGDSGGPLMMER--TGRWFLIGIVSAGYSC 175 (203)
Q Consensus 144 ~~~c~~d~G~pl~~~~--~~~~~lvGv~s~~~~c 175 (203)
...-.|||||||+.-+ +++|+|+||.+.+...
T Consensus 211 n~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~ 244 (769)
T PF02395_consen 211 NYGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGY 244 (769)
T ss_dssp EB--TT-TT-EEEEEETTTTEEEEEEEEEEECCC
T ss_pred cccccCcCCCceEEEEccCCeEEEEEEEcccccc
Confidence 3567899999998755 6789999999987554
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=90.58 E-value=0.34 Score=33.46 Aligned_cols=35 Identities=31% Similarity=0.416 Sum_probs=27.2
Q ss_pred CcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEEeCCCC
Q psy12782 147 CQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYHRVAYT 190 (203)
Q Consensus 147 c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t~v~~~ 190 (203)
-.||-||+|.|+.. ++||++.|-+ ....|++|+.+
T Consensus 88 ~PGdCGg~L~C~HG----ViGi~Tagg~-----g~VaF~dir~~ 122 (127)
T PF00947_consen 88 EPGDCGGILRCKHG----VIGIVTAGGE-----GHVAFADIRDL 122 (127)
T ss_dssp STT-TCSEEEETTC----EEEEEEEEET-----TEEEEEECCCG
T ss_pred CCCCCCceeEeCCC----eEEEEEeCCC-----ceEEEEechhh
Confidence 36799999999987 9999998732 24679999884
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=78.08 E-value=2.3 Score=32.34 Aligned_cols=26 Identities=35% Similarity=0.592 Sum_probs=22.9
Q ss_pred CCCCcCCCCCeeEEeeCCcEEEEEEEEecC
Q psy12782 144 KDSCQGDSGGPLMMERTGRWFLIGIVSAGY 173 (203)
Q Consensus 144 ~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~ 173 (203)
....+|.||||++.++. |+|-+++..
T Consensus 175 GGIvqGMSGSPI~qdGK----LiGAVthvf 200 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDGK----LIGAVTHVF 200 (218)
T ss_pred CCEEecccCCCEEECCE----EEEEEEEEE
Confidence 46789999999999877 999999875
No 17
>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=77.16 E-value=9.7 Score=29.51 Aligned_cols=47 Identities=21% Similarity=0.478 Sum_probs=25.1
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEEeCCCCHHHHHHhh
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYHRVAYTVDWISYIM 198 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t~v~~~~~WI~~~i 198 (203)
+.=.|+=|+||+...++. +|||-|.+..-... -.|+.+.. ++++..+
T Consensus 147 sTk~G~CG~PlVs~~Dg~--IVGiHsl~~~~~~~---N~F~~f~~--~f~~~~l 193 (235)
T PF00863_consen 147 STKDGDCGLPLVSTKDGK--IVGIHSLTSNTSSR---NYFTPFPD--DFEEFYL 193 (235)
T ss_dssp ---TT-TT-EEEETTT----EEEEEEEEETTTSS---EEEEE--T--THHHHHC
T ss_pred cCCCCccCCcEEEcCCCc--EEEEEcCccCCCCe---EEEEcCCH--HHHHHHh
Confidence 334567799999987765 99999987544333 35666554 4444443
No 18
>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=69.74 E-value=4.3 Score=26.96 Aligned_cols=21 Identities=48% Similarity=0.966 Sum_probs=15.0
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEE
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGI 168 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv 168 (203)
..-.|.|||||+. .+|+ ++||
T Consensus 100 ~~~~G~SGgpv~~-~~G~--vvGi 120 (120)
T PF13365_consen 100 DTRPGSSGGPVFD-SDGR--VVGI 120 (120)
T ss_dssp S-STTTTTSEEEE-TTSE--EEEE
T ss_pred ccCCCcEeHhEEC-CCCE--EEeC
Confidence 4456899999977 4454 8886
No 19
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=64.81 E-value=5.7 Score=33.34 Aligned_cols=45 Identities=22% Similarity=0.429 Sum_probs=31.4
Q ss_pred CCCCcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEEeCCCCHHHHHHhh
Q psy12782 144 KDSCQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYHRVAYTVDWISYIM 198 (203)
Q Consensus 144 ~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t~v~~~~~WI~~~i 198 (203)
....+|.||||++.++. |+|=+++..-......+++ |.+|..+..
T Consensus 355 gGivqGMSGSPi~q~gk----liGAvtHVfvndpt~GYGi------~ie~Ml~~~ 399 (402)
T TIGR02860 355 GGIVQGMSGSPIIQNGK----VIGAVTHVFVNDPTSGYGV------YIEWMLKEA 399 (402)
T ss_pred CCEEecccCCCEEECCE----EEEEEEEEEecCCCcceee------hHHHHHHHh
Confidence 47789999999999987 9998887642211122345 467877643
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=62.83 E-value=6 Score=31.17 Aligned_cols=22 Identities=41% Similarity=0.774 Sum_probs=16.8
Q ss_pred cCCCCCeeEEeeCCcEEEEEEEEec
Q psy12782 148 QGDSGGPLMMERTGRWFLIGIVSAG 172 (203)
Q Consensus 148 ~~d~G~pl~~~~~~~~~lvGv~s~~ 172 (203)
.||||+|++..+.. |+||-+..
T Consensus 207 ~GDSGSPVVt~dg~---liGVHTGS 228 (297)
T PF05579_consen 207 PGDSGSPVVTEDGD---LIGVHTGS 228 (297)
T ss_dssp GGCTT-EEEETTC----EEEEEEEE
T ss_pred CCCCCCccCcCCCC---EEEEEecC
Confidence 57999999997652 99998864
No 21
>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=59.35 E-value=8.7 Score=26.97 Aligned_cols=25 Identities=28% Similarity=0.646 Sum_probs=17.3
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEEEEec
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGIVSAG 172 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv~s~~ 172 (203)
+.-+|-+|||++|... + ++|++...
T Consensus 104 s~lkGSSGgPiLC~~G-H--~vG~f~aa 128 (148)
T PF02907_consen 104 SDLKGSSGGPILCPSG-H--AVGMFRAA 128 (148)
T ss_dssp HHHTT-TT-EEEETTS-E--EEEEEEEE
T ss_pred EEEecCCCCcccCCCC-C--EEEEEEEE
Confidence 4467889999999753 2 99988764
No 22
>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=57.98 E-value=7.2 Score=28.63 Aligned_cols=28 Identities=36% Similarity=0.494 Sum_probs=22.0
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEEEEec
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGIVSAG 172 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv~s~~ 172 (203)
....|+=||||+.+..+...++||-..|
T Consensus 143 ~t~~G~CG~~l~~~~~~~~~i~GiHvaG 170 (172)
T PF00548_consen 143 PTKPGMCGSPLVSRIGGQGKIIGIHVAG 170 (172)
T ss_dssp EEETTGTTEEEEESCGGTTEEEEEEEEE
T ss_pred CCCCCccCCeEEEeeccCccEEEEEecc
Confidence 4457888999999766666799997765
No 23
>PF14903 WG_beta_rep: WG containing repeat
Probab=41.74 E-value=40 Score=16.81 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=17.3
Q ss_pred EEEeCCCCCCCCCCCCCCeEEEEECC
Q psy12782 35 KINVHPYFKFTPQADRYDVAVLRLDR 60 (203)
Q Consensus 35 ~i~~hp~y~~~~~~~~~DiALl~L~~ 60 (203)
++++.|.|+. -..+.+++|+++...
T Consensus 9 ~~vi~~~yd~-i~~~~~g~~~v~~~~ 33 (35)
T PF14903_consen 9 KIVIPPKYDE-IYPFSNGYAIVKKDG 33 (35)
T ss_pred CEEEEccccC-ccccCCCEEEEEECC
Confidence 3566788873 345678899988753
No 24
>KOG3939|consensus
Probab=40.68 E-value=77 Score=24.94 Aligned_cols=39 Identities=28% Similarity=0.455 Sum_probs=27.6
Q ss_pred EEeeeeCCCCCCCcCCCCCeeEEe-----------------eCCcEEEEEEEEecC
Q psy12782 135 MCAGYRGGAKDSCQGDSGGPLMME-----------------RTGRWFLIGIVSAGY 173 (203)
Q Consensus 135 ~C~~~~~~~~~~c~~d~G~pl~~~-----------------~~~~~~lvGv~s~~~ 173 (203)
.|......-+..|...+||+|+|. +.+..+++|++..+.
T Consensus 239 a~G~~f~l~qGts~ETsGGlLIclP~eqaakfcaei~s~k~gegqAWIIGiVekgn 294 (312)
T KOG3939|consen 239 ACGNMFKLRQGTSAETSGGLLICLPREQAAKFCAEIKSPKNGEGQAWIIGIVEKGN 294 (312)
T ss_pred hccccceeccCCCccCCCceEEEccHHHHHHHHHHhcCCccCCCceEEEEEEecCC
Confidence 444333344678888999999982 234688999999864
No 25
>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=40.49 E-value=8.8 Score=26.96 Aligned_cols=26 Identities=38% Similarity=0.693 Sum_probs=18.9
Q ss_pred CCcCCCCCeeEEeeCCcEEEEEEEEecCC
Q psy12782 146 SCQGDSGGPLMMERTGRWFLIGIVSAGYS 174 (203)
Q Consensus 146 ~c~~d~G~pl~~~~~~~~~lvGv~s~~~~ 174 (203)
--.||||-|++.+. |+ +|||+-.|.+
T Consensus 103 g~~GDSGRpi~DNs-Gr--VVaIVLGG~n 128 (158)
T PF00944_consen 103 GKPGDSGRPIFDNS-GR--VVAIVLGGAN 128 (158)
T ss_dssp -STTSTTEEEESTT-SB--EEEEEEEEEE
T ss_pred CCCCCCCCccCcCC-CC--EEEEEecCCC
Confidence 35789999998764 44 8888877643
No 26
>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=39.75 E-value=53 Score=27.90 Aligned_cols=31 Identities=29% Similarity=0.646 Sum_probs=23.4
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEEEEecCCC
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGIVSAGYSC 175 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c 175 (203)
..-.||-|.|-++...+.|+++||-+.....
T Consensus 499 GT~PGDCGcPYvyKrgNd~VV~GVH~AAtr~ 529 (535)
T PF05416_consen 499 GTIPGDCGCPYVYKRGNDWVVIGVHAAATRS 529 (535)
T ss_dssp S--TTGTT-EEEEEETTEEEEEEEEEEE-SS
T ss_pred CCCCCCCCCceeeecCCcEEEEEEEehhccC
Confidence 4577899999999999999999998876443
No 27
>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=35.99 E-value=33 Score=31.16 Aligned_cols=63 Identities=19% Similarity=0.169 Sum_probs=36.4
Q ss_pred CCeEEeeeeCCCCCCCcCCCCCeeEEeeCCcEEEEEEEEecC-C---CCCCCC----CeEEEeCCCCHHHHHHhhccc
Q psy12782 132 DEMMCAGYRGGAKDSCQGDSGGPLMMERTGRWFLIGIVSAGY-S---CAQQGQ----PGIYHRVAYTVDWISYIMNTA 201 (203)
Q Consensus 132 ~~~~C~~~~~~~~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~-~---c~~~~~----~~v~t~v~~~~~WI~~~i~~~ 201 (203)
+.-+|.-+ +.+...|.||||++.... .|||++==+. . ..-.-. =.|-+++. |.-|+.+.+..+
T Consensus 619 ~~pv~Fls---tnDitGGNSGSPvlN~~G---eLVGl~FDgn~Esl~~D~~fdp~~~R~I~VDiR-yvL~~ldkv~gA 689 (698)
T PF10459_consen 619 SVPVNFLS---TNDITGGNSGSPVLNAKG---ELVGLAFDGNWESLSGDIAFDPELNRTIHVDIR-YVLWALDKVYGA 689 (698)
T ss_pred CeeeEEEe---ccCcCCCCCCCccCCCCc---eEEEEeecCchhhcccccccccccceeEEEEHH-HHHHHHHHHhCh
Confidence 34477653 357889999999998543 3999864221 0 000001 14455554 477877666544
No 28
>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=24.95 E-value=71 Score=22.42 Aligned_cols=27 Identities=26% Similarity=0.589 Sum_probs=17.2
Q ss_pred CCCcCCCCCeeEEeeCCcEEEEEEEEecCC
Q psy12782 145 DSCQGDSGGPLMMERTGRWFLIGIVSAGYS 174 (203)
Q Consensus 145 ~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~ 174 (203)
+.-.|.||+|++..+. + ++||.-.+..
T Consensus 93 d~~~GsSGSpi~n~~g-~--ivGlYg~g~~ 119 (132)
T PF00949_consen 93 DFPKGSSGSPIFNQNG-E--IVGLYGNGVE 119 (132)
T ss_dssp -S-TTGTT-EEEETTS-C--EEEEEEEEEE
T ss_pred ccCCCCCCCceEcCCC-c--EEEEEcccee
Confidence 4567899999996542 2 8998776543
No 29
>KOG1421|consensus
Probab=20.41 E-value=4.3e+02 Score=24.41 Aligned_cols=48 Identities=15% Similarity=0.224 Sum_probs=26.0
Q ss_pred CCCCcCCCCCeeEEeeCCcEEEEEEEEecCCCCCCCCCeEEEeCCCCHHHH
Q psy12782 144 KDSCQGDSGGPLMMERTGRWFLIGIVSAGYSCAQQGQPGIYHRVAYTVDWI 194 (203)
Q Consensus 144 ~~~c~~d~G~pl~~~~~~~~~lvGv~s~~~~c~~~~~~~v~t~v~~~~~WI 194 (203)
.+.-.|.+|+|++--.. +.|.+.+.+...+..+......||-.-+..|
T Consensus 211 sstsggssgspVv~i~g---yAVAl~agg~~ssas~ffLpLdrV~RaL~cl 258 (955)
T KOG1421|consen 211 SSTSGGSSGSPVVDIPG---YAVALNAGGSISSASDFFLPLDRVVRALRCL 258 (955)
T ss_pred hcCCCCCCCCceecccc---eEEeeecCCcccccccceeeccchhhhhhhh
Confidence 46677899999986432 3666666554333323223334444434433
No 30
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=20.06 E-value=2.9e+02 Score=18.66 Aligned_cols=30 Identities=17% Similarity=0.199 Sum_probs=22.2
Q ss_pred EEEeeeeeecccCCCCCceEEeeEEEEeCCCCC
Q psy12782 11 QVTLGDYVINSAVEPLPAYTFGVRKINVHPYFK 43 (203)
Q Consensus 11 ~V~~G~~~~~~~~~~~~~~~~~v~~i~~hp~y~ 43 (203)
.+..|..--+.++. .-.+.|.+.+.||.|.
T Consensus 30 k~l~G~VvS~Km~K---TvvV~v~r~~~hpkY~ 59 (108)
T PRK08572 30 QVLEGTVVSDKMHK---TVVVEREYLHYVPKYE 59 (108)
T ss_pred EEEEEEEEecCCCc---eEEEEEEEEEecCCcc
Confidence 35667666666655 5678899999999996
Done!