Query psy13815
Match_columns 388
No_of_seqs 321 out of 2776
Neff 9.6
Searched_HMMs 46136
Date Fri Aug 16 21:10:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13815.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13815hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 100.0 1.6E-43 3.6E-48 315.3 24.7 228 117-384 1-232 (232)
2 KOG3627|consensus 100.0 1.4E-41 3.1E-46 307.9 24.2 235 113-386 9-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 1.6E-40 3.6E-45 295.7 24.4 226 116-381 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 3.1E-38 6.8E-43 279.0 22.8 216 117-381 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 2E-31 4.4E-36 235.3 17.5 239 113-386 29-279 (413)
6 PF03761 DUF316: Domain of unk 99.7 1.2E-15 2.7E-20 139.9 18.1 220 103-386 29-280 (282)
7 PF09342 DUF1986: Domain of un 99.5 3E-13 6.6E-18 114.8 15.3 114 125-247 13-131 (267)
8 KOG3627|consensus 99.4 7.4E-13 1.6E-17 119.8 6.2 89 2-93 158-254 (256)
9 cd00190 Tryp_SPc Trypsin-like 99.1 7E-11 1.5E-15 104.8 6.9 87 2-91 138-231 (232)
10 COG3591 V8-like Glu-specific e 99.1 1.6E-09 3.5E-14 94.6 12.7 200 124-386 45-251 (251)
11 COG5640 Secreted trypsin-like 98.9 2.5E-09 5.5E-14 96.0 7.8 92 4-97 182-282 (413)
12 smart00020 Tryp_SPc Trypsin-li 98.9 7.4E-09 1.6E-13 91.7 8.8 83 3-89 140-229 (229)
13 PF00089 Trypsin: Trypsin; In 98.7 2.5E-08 5.5E-13 87.5 5.3 78 3-89 136-220 (220)
14 TIGR02037 degP_htrA_DO peripla 98.4 5.7E-06 1.2E-10 80.5 13.9 85 139-247 57-142 (428)
15 TIGR02038 protease_degS peripl 98.3 3.2E-05 7E-10 73.0 16.4 83 140-247 78-161 (351)
16 PRK10898 serine endoprotease; 98.2 5.7E-05 1.2E-09 71.3 16.1 83 140-247 78-161 (353)
17 PRK10139 serine endoprotease; 98.0 0.00022 4.9E-09 69.5 15.9 84 139-246 89-174 (455)
18 PRK10942 serine endoprotease; 97.9 0.00035 7.6E-09 68.5 15.6 84 139-246 110-195 (473)
19 PF13365 Trypsin_2: Trypsin-li 97.6 0.00027 5.8E-09 55.5 6.8 60 142-214 1-65 (120)
20 PF02395 Peptidase_S6: Immunog 96.2 0.01 2.2E-07 61.1 6.9 65 144-231 69-133 (769)
21 PF00863 Peptidase_C4: Peptida 96.1 0.13 2.8E-06 45.1 12.0 43 335-382 150-193 (235)
22 PF00947 Pico_P2A: Picornaviru 89.4 0.52 1.1E-05 36.8 3.7 38 335-382 89-126 (127)
23 PF00548 Peptidase_C3: 3C cyst 88.1 7.4 0.00016 32.7 10.2 72 137-227 22-93 (172)
24 PF03761 DUF316: Domain of unk 87.9 0.55 1.2E-05 42.9 3.6 31 45-75 225-255 (282)
25 COG0265 DegQ Trypsin-like seri 82.5 27 0.00059 32.9 12.4 82 140-245 72-154 (347)
26 PF05580 Peptidase_S55: SpoIVB 76.3 3.4 7.4E-05 35.6 3.6 23 335-361 179-201 (218)
27 PF02395 Peptidase_S6: Immunog 68.2 5.8 0.00013 41.4 3.9 31 47-77 212-244 (769)
28 PF02907 Peptidase_S29: Hepati 62.6 5.5 0.00012 31.5 1.9 21 335-358 107-127 (148)
29 TIGR02860 spore_IV_B stage IV 62.0 9.4 0.0002 36.6 3.7 43 335-387 359-401 (402)
30 PF13365 Trypsin_2: Trypsin-li 61.6 6.9 0.00015 29.9 2.4 18 335-355 103-120 (120)
31 PF05579 Peptidase_S32: Equine 56.6 12 0.00027 33.3 3.2 23 335-360 207-229 (297)
32 PF00944 Peptidase_S3: Alphavi 52.0 6 0.00013 31.2 0.5 24 335-361 105-128 (158)
33 PF10459 Peptidase_S46: Peptid 48.1 11 0.00024 39.0 1.9 21 141-161 48-69 (698)
34 PF00947 Pico_P2A: Picornaviru 47.5 15 0.00032 28.9 2.0 22 50-75 89-110 (127)
35 KOG1421|consensus 47.1 2.3E+02 0.005 29.3 10.5 82 142-244 86-170 (955)
36 KOG1320|consensus 43.5 2.6E+02 0.0056 27.6 10.2 38 204-244 222-259 (473)
37 PF05416 Peptidase_C37: Southa 39.9 53 0.0012 31.5 4.8 27 335-361 502-528 (535)
38 PF08192 Peptidase_S64: Peptid 30.6 1.6E+02 0.0035 30.2 6.7 51 335-387 638-691 (695)
39 PF05416 Peptidase_C37: Southa 24.3 1.8E+02 0.0039 28.1 5.4 49 34-82 484-534 (535)
40 COG3591 V8-like Glu-specific e 22.3 91 0.002 27.9 3.1 28 46-76 198-225 (251)
41 PF05580 Peptidase_S55: SpoIVB 21.9 97 0.0021 26.9 3.0 40 46-89 175-215 (218)
42 PF00949 Peptidase_S7: Peptida 21.9 73 0.0016 25.4 2.2 23 335-360 96-118 (132)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=100.00 E-value=1.6e-43 Score=315.29 Aligned_cols=228 Identities=44% Similarity=0.844 Sum_probs=198.6
Q ss_pred EecceecCCCCcceEEEEccC-CceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCC--ceeeeceEEE
Q psy13815 117 IVGGLAANPGEFPWIVSLKRH-GGHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRP--SISTVPVLRI 193 (388)
Q Consensus 117 i~~g~~~~~~~~Pw~v~i~~~-~~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~--~~~~~~v~~i 193 (388)
|+||.++..++|||+|.|... ..+.|+||||+++||||||||+.+. ....+.|++|....... ..+.+.|.++
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~----~~~~~~v~~g~~~~~~~~~~~~~~~v~~~ 76 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSS----APSNYTVRLGSHDLSSNEGGGQVIKVKKV 76 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCC----CCccEEEEeCcccccCCCCceEEEEEEEE
Confidence 579999999999999999877 7889999999999999999999762 25678899998776542 4567899999
Q ss_pred EECCCCCCCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCCC-CCCCCeEEEEEccccCCCCCCCCCCccceEEEEEeechh
Q psy13815 194 MFHPSHSCSSFNNDIALLELTRSIQWSDLIRPACLPSGSL-DYSEQSVTVAGWGWTNENPSQGRRSNILQKVALSVVSNQ 272 (388)
Q Consensus 194 ~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~-~~~~~~~~~~GwG~~~~~~~~~~~~~~l~~~~~~i~~~~ 272 (388)
+.||+|+.....+|||||+|++++.+++.++|||||.... ...+..+.++|||....... .+..++...+.+++..
T Consensus 77 ~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~---~~~~~~~~~~~~~~~~ 153 (232)
T cd00190 77 IVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGP---LPDVLQEVNVPIVSNA 153 (232)
T ss_pred EECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCC---CCceeeEEEeeeECHH
Confidence 9999999988899999999999999999999999998852 26678999999999776522 3678999999999999
Q ss_pred hhhhHhhcCCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCceEEecCCccEE
Q psy13815 273 VCQAWYQSEGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGPLMLLGAESTQV 352 (388)
Q Consensus 273 ~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgPL~~~~~~~~~l 352 (388)
+|...+.. ...+.++++|+.........| .|||||||++..+++++|
T Consensus 154 ~C~~~~~~---~~~~~~~~~C~~~~~~~~~~c------------------------------~gdsGgpl~~~~~~~~~l 200 (232)
T cd00190 154 ECKRAYSY---GGTITDNMLCAGGLEGGKDAC------------------------------QGDSGGPLVCNDNGRGVL 200 (232)
T ss_pred HhhhhccC---cccCCCceEeeCCCCCCCccc------------------------------cCCCCCcEEEEeCCEEEE
Confidence 99988762 235789999998765567788 999999999998899999
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCchhHHhhh
Q psy13815 353 IGLVSTGIGCARPRLPGLYTRLTRYIGWISDT 384 (388)
Q Consensus 353 ~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI~~~ 384 (388)
+||+|++..|...+.|.+||+|+.|.+||+++
T Consensus 201 vGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 201 VGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred EEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 99999999998777899999999999999874
No 2
>KOG3627|consensus
Probab=100.00 E-value=1.4e-41 Score=307.91 Aligned_cols=235 Identities=40% Similarity=0.800 Sum_probs=197.3
Q ss_pred CCCeEecceecCCCCcceEEEEccCC--ceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCC---c--e
Q psy13815 113 RTGKIVGGLAANPGEFPWIVSLKRHG--GHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRP---S--I 185 (388)
Q Consensus 113 ~~~~i~~g~~~~~~~~Pw~v~i~~~~--~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~---~--~ 185 (388)
...||++|.++.+++|||++++.... .+.|+|+||+++||||||||+.... .. .+.|++|.+..... . .
T Consensus 9 ~~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~---~~-~~~V~~G~~~~~~~~~~~~~~ 84 (256)
T KOG3627|consen 9 PEGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGAS---AS-LYTVRLGEHDINLSVSEGEEQ 84 (256)
T ss_pred ccCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCC---Cc-ceEEEECccccccccccCchh
Confidence 35799999999999999999999875 7899999999999999999998732 22 78888887644322 1 2
Q ss_pred eeeceEEEEECCCCCCCCCC-CcEEEEEeCCCCCCCCCeeeeeCCCCCC---CCCCCeEEEEEccccCCCCCCCCCCccc
Q psy13815 186 STVPVLRIMFHPSHSCSSFN-NDIALLELTRSIQWSDLIRPACLPSGSL---DYSEQSVTVAGWGWTNENPSQGRRSNIL 261 (388)
Q Consensus 186 ~~~~v~~i~~hp~y~~~~~~-~DIALl~L~~~v~~~~~v~picLp~~~~---~~~~~~~~~~GwG~~~~~~~~~~~~~~l 261 (388)
....|.+++.||+|+..... ||||||+|.+++.|++.|+|||||.... ......+.++|||.+..... ..+..|
T Consensus 85 ~~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~--~~~~~L 162 (256)
T KOG3627|consen 85 LVGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGG--PLPDTL 162 (256)
T ss_pred hhceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCC--CCCcee
Confidence 34557789999999998877 9999999999999999999999985543 25558899999999876511 237889
Q ss_pred eEEEEEeechhhhhhHhhcCCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCc
Q psy13815 262 QKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGP 341 (388)
Q Consensus 262 ~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgP 341 (388)
++..+++++..+|...+.... .+.+.|+||+...+..+.| +||||||
T Consensus 163 ~~~~v~i~~~~~C~~~~~~~~---~~~~~~~Ca~~~~~~~~~C------------------------------~GDSGGP 209 (256)
T KOG3627|consen 163 QEVDVPIISNSECRRAYGGLG---TITDTMLCAGGPEGGKDAC------------------------------QGDSGGP 209 (256)
T ss_pred EEEEEeEcChhHhcccccCcc---ccCCCEEeeCccCCCCccc------------------------------cCCCCCe
Confidence 999999999999998876321 3566789999866677889 9999999
Q ss_pred eEEecCCccEEEEEEEecCC-CCCCCCCeEEEeCCCchhHHhhhhc
Q psy13815 342 LMLLGAESTQVIGLVSTGIG-CARPRLPGLYTRLTRYIGWISDTLD 386 (388)
Q Consensus 342 L~~~~~~~~~l~Gi~s~g~~-c~~~~~p~v~t~V~~~~~WI~~~i~ 386 (388)
|++...++++++||+|||.. |...+.|++||+|+.|.+||++.+.
T Consensus 210 Lv~~~~~~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 210 LVCEDNGRWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred EEEeeCCcEEEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHHHhc
Confidence 99998778999999999998 9988899999999999999999875
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=100.00 E-value=1.6e-40 Score=295.73 Aligned_cols=226 Identities=45% Similarity=0.862 Sum_probs=194.1
Q ss_pred eEecceecCCCCcceEEEEccCC-ceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCCce-eeeceEEE
Q psy13815 116 KIVGGLAANPGEFPWIVSLKRHG-GHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSI-STVPVLRI 193 (388)
Q Consensus 116 ~i~~g~~~~~~~~Pw~v~i~~~~-~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~-~~~~v~~i 193 (388)
||+||.++.+++|||+|.++... .+.|+||||++++|||||||+.... ...+.|++|......... +.+.|.++
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~----~~~~~v~~g~~~~~~~~~~~~~~v~~~ 76 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSD----PSNIRVRLGSHDLSSGEEGQVIKVSKV 76 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCC----CcceEEEeCcccCCCCCCceEEeeEEE
Confidence 58899999999999999998776 8899999999999999999998722 467899999877654322 67899999
Q ss_pred EECCCCCCCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCCC-CCCCCeEEEEEccccCCCCCCCCCCccceEEEEEeechh
Q psy13815 194 MFHPSHSCSSFNNDIALLELTRSIQWSDLIRPACLPSGSL-DYSEQSVTVAGWGWTNENPSQGRRSNILQKVALSVVSNQ 272 (388)
Q Consensus 194 ~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~-~~~~~~~~~~GwG~~~~~~~~~~~~~~l~~~~~~i~~~~ 272 (388)
+.||+|+.....+|||||+|++|+.+++.++|+|||.... ...+..+.++|||...... ......++...+.+++.+
T Consensus 77 ~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~--~~~~~~~~~~~~~~~~~~ 154 (229)
T smart00020 77 IIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGA--GSLPDTLQEVNVPIVSNA 154 (229)
T ss_pred EECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCC--CcCCCEeeEEEEEEeCHH
Confidence 9999999888899999999999999999999999998732 2667899999999876521 123678999999999999
Q ss_pred hhhhHhhcCCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCceEEecCCccEE
Q psy13815 273 VCQAWYQSEGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGPLMLLGAESTQV 352 (388)
Q Consensus 273 ~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgPL~~~~~~~~~l 352 (388)
+|...+.. ...+..+++|++........| .|||||||++..+ +|+|
T Consensus 155 ~C~~~~~~---~~~~~~~~~C~~~~~~~~~~c------------------------------~gdsG~pl~~~~~-~~~l 200 (229)
T smart00020 155 TCRRAYSG---GGAITDNMLCAGGLEGGKDAC------------------------------QGDSGGPLVCNDG-RWVL 200 (229)
T ss_pred Hhhhhhcc---ccccCCCcEeecCCCCCCccc------------------------------CCCCCCeeEEECC-CEEE
Confidence 99987752 235788999998765567778 9999999999987 9999
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCchhHH
Q psy13815 353 IGLVSTGIGCARPRLPGLYTRLTRYIGWI 381 (388)
Q Consensus 353 ~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI 381 (388)
+||+|++..|...+.|.+|++|++|++||
T Consensus 201 ~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 201 VGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred EEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 99999999998778899999999999998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=100.00 E-value=3.1e-38 Score=279.02 Aligned_cols=216 Identities=45% Similarity=0.860 Sum_probs=188.0
Q ss_pred EecceecCCCCcceEEEEccCC-ceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCC--CCceeeeceEEE
Q psy13815 117 IVGGLAANPGEFPWIVSLKRHG-GHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLS--RPSISTVPVLRI 193 (388)
Q Consensus 117 i~~g~~~~~~~~Pw~v~i~~~~-~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~--~~~~~~~~v~~i 193 (388)
|+||.++.+++|||+|.+.... .++|+|+||+++||||||||+.. ...+.+.+|..... ....+.+.|.++
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~------~~~~~v~~g~~~~~~~~~~~~~~~v~~~ 74 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG------ASDIKVRLGTYSIRNSDGSEQTIKVSKI 74 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS------GGSEEEEESESBTTSTTTTSEEEEEEEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc------cccccccccccccccccccccccccccc
Confidence 6799999999999999999877 89999999999999999999966 56788888874333 333478999999
Q ss_pred EECCCCCCCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCCCC-CCCCeEEEEEccccCCCCCCCCCCccceEEEEEeechh
Q psy13815 194 MFHPSHSCSSFNNDIALLELTRSIQWSDLIRPACLPSGSLD-YSEQSVTVAGWGWTNENPSQGRRSNILQKVALSVVSNQ 272 (388)
Q Consensus 194 ~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~-~~~~~~~~~GwG~~~~~~~~~~~~~~l~~~~~~i~~~~ 272 (388)
+.||+|+.....+|||||+|++++.+.+.++|+||+..... ..+..+.++||+...... ....++...+.+++.+
T Consensus 75 ~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~----~~~~~~~~~~~~~~~~ 150 (220)
T PF00089_consen 75 IIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG----YSSNLQSVTVPVVSRK 150 (220)
T ss_dssp EEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS----BTSBEEEEEEEEEEHH
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc----cccccccccccccccc
Confidence 99999999888999999999999999999999999984432 677899999999976543 2567999999999999
Q ss_pred hhhhHhhcCCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCceEEecCCccEE
Q psy13815 273 VCQAWYQSEGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGPLMLLGAESTQV 352 (388)
Q Consensus 273 ~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgPL~~~~~~~~~l 352 (388)
.|...+.. .+.+.++|++.. +..+.| .|||||||++... +|
T Consensus 151 ~c~~~~~~-----~~~~~~~c~~~~-~~~~~~------------------------------~g~sG~pl~~~~~---~l 191 (220)
T PF00089_consen 151 TCRSSYND-----NLTPNMICAGSS-GSGDAC------------------------------QGDSGGPLICNNN---YL 191 (220)
T ss_dssp HHHHHTTT-----TSTTTEEEEETT-SSSBGG------------------------------TTTTTSEEEETTE---EE
T ss_pred cccccccc-----cccccccccccc-cccccc------------------------------cccccccccccee---ee
Confidence 99987541 378899999876 567888 9999999999886 89
Q ss_pred EEEEEecCCCCCCCCCeEEEeCCCchhHH
Q psy13815 353 IGLVSTGIGCARPRLPGLYTRLTRYIGWI 381 (388)
Q Consensus 353 ~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI 381 (388)
+||++++..|...+.|.+|++|+.|++||
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 99999999999888899999999999999
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=2e-31 Score=235.29 Aligned_cols=239 Identities=31% Similarity=0.508 Sum_probs=178.0
Q ss_pred CCCeEecceecCCCCcceEEEEccCC-----ceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCCceee
Q psy13815 113 RTGKIVGGLAANPGEFPWIVSLKRHG-----GHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSIST 187 (388)
Q Consensus 113 ~~~~i~~g~~~~~~~~Pw~v~i~~~~-----~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~ 187 (388)
.+.||+||..++.++||++|.+.... ..+|||+++..|||||||||+.... +......+|..+-.+... .+.
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s-~is~d~~~vv~~l~d~Sq--~~r 105 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASS-PISSDVNRVVVDLNDSSQ--AER 105 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCC-CccccceEEEeccccccc--ccC
Confidence 46799999999999999999986542 4689999999999999999998754 455566666666655543 345
Q ss_pred eceEEEEECCCCCCCCCCCcEEEEEeCCCCCCCC-CeeeeeCCC--CCCCCCCCeEEEEEccccCCCCCCCCCC--ccce
Q psy13815 188 VPVLRIMFHPSHSCSSFNNDIALLELTRSIQWSD-LIRPACLPS--GSLDYSEQSVTVAGWGWTNENPSQGRRS--NILQ 262 (388)
Q Consensus 188 ~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~-~v~picLp~--~~~~~~~~~~~~~GwG~~~~~~~~~~~~--~~l~ 262 (388)
..|..++.|..|...++.||+|+++|+++..+.. .+.-.--+. .............+|+.+.........+ ..++
T Consensus 106 g~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~ 185 (413)
T COG5640 106 GHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILH 185 (413)
T ss_pred cceEEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccceee
Confidence 6799999999999999999999999998765321 111000011 0000233445667777766543322222 4799
Q ss_pred EEEEEeechhhhhhHhhc-CCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCc
Q psy13815 263 KVALSVVSNQVCQAWYQS-EGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGP 341 (388)
Q Consensus 263 ~~~~~i~~~~~C~~~~~~-~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgP 341 (388)
+..+..++...|...+.. ........-.-+|++.. ..+.| +||||||
T Consensus 186 e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~--~~daC------------------------------qGDSGGP 233 (413)
T COG5640 186 EVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP--PKDAC------------------------------QGDSGGP 233 (413)
T ss_pred eeeeeeechHHhhhhccccccCCCCCCccceecCCC--Ccccc------------------------------cCCCCCc
Confidence 999999999999987741 11112222334999865 38888 9999999
Q ss_pred eEEecCCccEEEEEEEecCC-CCCCCCCeEEEeCCCchhHHhhhhc
Q psy13815 342 LMLLGAESTQVIGLVSTGIG-CARPRLPGLYTRLTRYIGWISDTLD 386 (388)
Q Consensus 342 L~~~~~~~~~l~Gi~s~g~~-c~~~~~p~v~t~V~~~~~WI~~~i~ 386 (388)
++.+.+....++||+|||.+ |+.+..|.|||+|+.|-+||...++
T Consensus 234 i~~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 234 IFHKGEEGRVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred eEEeCCCccEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhc
Confidence 99999888899999999986 9999999999999999999998764
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.69 E-value=1.2e-15 Score=139.91 Aligned_cols=220 Identities=24% Similarity=0.424 Sum_probs=141.9
Q ss_pred CCCCCCccCCCCCeEecceecCCCCcceEEEEccCC----ceeEEEEEeeCCEEEecCcCCCCCCCCC----c-------
Q psy13815 103 VPCGRSLASRRTGKIVGGLAANPGEFPWIVSLKRHG----GHFCGGTIIHEQWIVTAAHCLCNGPSPL----S------- 167 (388)
Q Consensus 103 ~~cg~~~~~~~~~~i~~g~~~~~~~~Pw~v~i~~~~----~~~C~GtLI~~~~VLTAAhCv~~~~~~~----~------- 167 (388)
..||.... +...++.+|..+..++.||++.+...+ ...++|||||+||||||+||+.+....+ .
T Consensus 29 ~~CG~~~~-~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~ 107 (282)
T PF03761_consen 29 ETCGKKKL-PYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCE 107 (282)
T ss_pred HhcCCCCC-CCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceee
Confidence 47995432 234567899999999999999997654 3567999999999999999997532211 0
Q ss_pred c--ceEEEEe---ccccC------CCCceeeeceEEEEECCC----CCCCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCC
Q psy13815 168 A--SQINVTL---KEHDL------SRPSISTVPVLRIMFHPS----HSCSSFNNDIALLELTRSIQWSDLIRPACLPSGS 232 (388)
Q Consensus 168 ~--~~~~v~~---g~~~~------~~~~~~~~~v~~i~~hp~----y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~ 232 (388)
. ..+.|.- ..... ........++.++++--. ........+++||+|+++ +.....|+|||...
T Consensus 108 ~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~ 185 (282)
T PF03761_consen 108 GNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSS 185 (282)
T ss_pred CCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCc
Confidence 0 0111100 00000 011112345555555211 122344579999999999 67889999999876
Q ss_pred CC-CCCCeEEEEEccccCCCCCCCCCCccceEEEEEeechhhhhhHhhcCCCccccCCCeEEeccCCCCcCcccCCcccC
Q psy13815 233 LD-YSEQSVTVAGWGWTNENPSQGRRSNILQKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWVSRQWW 311 (388)
Q Consensus 233 ~~-~~~~~~~~~GwG~~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~ 311 (388)
.. ..++.+.+.|+ .. ...+...++.+.....| ...+| .....|
T Consensus 186 ~~~~~~~~~~~yg~----~~------~~~~~~~~~~i~~~~~~--------------~~~~~-----~~~~~~------- 229 (282)
T PF03761_consen 186 TNWEKGDEVDVYGF----NS------TGKLKHRKLKITNCTKC--------------AYSIC-----TKQYSC------- 229 (282)
T ss_pred cccccCceEEEeec----CC------CCeEEEEEEEEEEeecc--------------ceeEe-----cccccC-------
Confidence 64 45566666666 11 33466666665443221 11222 234556
Q ss_pred CcccccccccCCCCCCCCCCCCCCCcCCCceEEecCCccEEEEEEEecC-CCCCCCCCeEEEeCCCchhHHhhhhc
Q psy13815 312 TPHVARGRVYPSHRSGVHWDPPLQADSGGPLMLLGAESTQVIGLVSTGI-GCARPRLPGLYTRLTRYIGWISDTLD 386 (388)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~gdsGgPL~~~~~~~~~l~Gi~s~g~-~c~~~~~p~v~t~V~~~~~WI~~~i~ 386 (388)
.+|+||||+...+++++|+||.+.+. .|.. ....|.+|..|.+=|-+.++
T Consensus 230 -----------------------~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~--~~~~f~~v~~~~~~IC~ltG 280 (282)
T PF03761_consen 230 -----------------------KGDRGGPLVKNINGRWTLIGVGASGNYECNK--NNSYFFNVSWYQDEICELTG 280 (282)
T ss_pred -----------------------CCCccCeEEEEECCCEEEEEEEccCCCcccc--cccEEEEHHHhhhhhcccee
Confidence 99999999999999999999998775 4432 25789999999888776654
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.54 E-value=3e-13 Score=114.77 Aligned_cols=114 Identities=20% Similarity=0.417 Sum_probs=89.8
Q ss_pred CCCcceEEEEccCCceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccC----CCCceeeeceEEEEECCCCC
Q psy13815 125 PGEFPWIVSLKRHGGHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDL----SRPSISTVPVLRIMFHPSHS 200 (388)
Q Consensus 125 ~~~~Pw~v~i~~~~~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~----~~~~~~~~~v~~i~~hp~y~ 200 (388)
...|||.|.|+.++.+.|+|+||+++|||++..|+.+. ......+.+.+|.... ..+.+|.+.|..+..=|
T Consensus 13 ~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I--~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~--- 87 (267)
T PF09342_consen 13 DYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGI--SLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVP--- 87 (267)
T ss_pred cccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCc--ccccceEEEEecCcceecccCCChheEEEeeeeeecc---
Confidence 35699999999999999999999999999999999762 2445667888886653 25666766666554433
Q ss_pred CCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCCCC-CCCCeEEEEEccc
Q psy13815 201 CSSFNNDIALLELTRSIQWSDLIRPACLPSGSLD-YSEQSVTVAGWGW 247 (388)
Q Consensus 201 ~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~-~~~~~~~~~GwG~ 247 (388)
..+++||+|++|+.|+.+|+|..||..... .....|..+|-..
T Consensus 88 ----~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 88 ----ESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred ----ccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 368999999999999999999999974433 4556898888543
No 8
>KOG3627|consensus
Probab=99.36 E-value=7.4e-13 Score=119.81 Aligned_cols=89 Identities=34% Similarity=0.607 Sum_probs=73.9
Q ss_pred CCcCceEEEEeeeChhhhHhhhhcCCCccccCCCeeEecccCCCcCCCCCCCCCceEEeeCCcEEEEeeEEeecC-CC--
Q psy13815 2 RSNILQKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWADSGGPLMLLGAESTQVIGLVSTGIG-SP-- 78 (388)
Q Consensus 2 ~s~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~~~~Cag~~~~~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~-~~-- 78 (388)
.+..||++++++++..+|+..+.... .+++.||||+......++|+|||||||++..+.+|+++||+|||.+ |.
T Consensus 158 ~~~~L~~~~v~i~~~~~C~~~~~~~~---~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~ 234 (256)
T KOG3627|consen 158 LPDTLQEVDVPIISNSECRRAYGGLG---TITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQP 234 (256)
T ss_pred CCceeEEEEEeEcChhHhcccccCcc---ccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCC
Confidence 47789999999999999998876421 2566789999755667899999999999988778999999999988 83
Q ss_pred ---c--eeeEEEEeeccccc
Q psy13815 79 ---T--SVVQLLTRWTLDLE 93 (388)
Q Consensus 79 ---~--~~~~~~~~wi~~~~ 93 (388)
+ ++++.|.+||.+.+
T Consensus 235 ~~P~vyt~V~~y~~WI~~~~ 254 (256)
T KOG3627|consen 235 NYPGVYTRVSSYLDWIKENI 254 (256)
T ss_pred CCCeEEeEhHHhHHHHHHHh
Confidence 2 77788999998654
No 9
>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=99.15 E-value=7e-11 Score=104.76 Aligned_cols=87 Identities=34% Similarity=0.618 Sum_probs=72.9
Q ss_pred CCcCceEEEEeeeChhhhHhhhhcCCCccccCCCeeEecccCCCcCCCCCCCCCceEEeeCCcEEEEeeEEeecCCCc--
Q psy13815 2 RSNILQKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWADSGGPLMLLGAESTQVIGLVSTGIGSPT-- 79 (388)
Q Consensus 2 ~s~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~~~~Cag~~~~~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~~~~-- 79 (388)
.+..|++.++.+++..+|...+.. ...+.+.++|++......+.|.|||||||++..+++|+|+||+|++..|..
T Consensus 138 ~~~~~~~~~~~~~~~~~C~~~~~~---~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~ 214 (232)
T cd00190 138 LPDVLQEVNVPIVSNAECKRAYSY---GGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPN 214 (232)
T ss_pred CCceeeEEEeeeECHHHhhhhccC---cccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCC
Confidence 356799999999999999987753 115789999998654467899999999999988899999999999987841
Q ss_pred -----eeeEEEEeeccc
Q psy13815 80 -----SVVQLLTRWTLD 91 (388)
Q Consensus 80 -----~~~~~~~~wi~~ 91 (388)
+++..|.+||.+
T Consensus 215 ~~~~~t~v~~~~~WI~~ 231 (232)
T cd00190 215 YPGVYTRVSSYLDWIQK 231 (232)
T ss_pred CCCEEEEcHHhhHHhhc
Confidence 778889999975
No 10
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.09 E-value=1.6e-09 Score=94.62 Aligned_cols=200 Identities=19% Similarity=0.277 Sum_probs=111.4
Q ss_pred CCCCcceEEEEccC---CceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEe-ccccCCCCceeeeceEEEEECCC-
Q psy13815 124 NPGEFPWIVSLKRH---GGHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTL-KEHDLSRPSISTVPVLRIMFHPS- 198 (388)
Q Consensus 124 ~~~~~Pw~v~i~~~---~~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~-g~~~~~~~~~~~~~v~~i~~hp~- 198 (388)
+-..|||-+..... +..-|+++||+++.||||+||+.+... ....+.+.. |......+.. .+........|.
T Consensus 45 dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~--G~~~~~~~p~g~~~~~~~~~-~~~~~~~~~~~g~ 121 (251)
T COG3591 45 DTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDY--GEDDIAAAPPGVNSDGGPFY-GITKIEIRVYPGE 121 (251)
T ss_pred cCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCC--ChhhhhhcCCcccCCCCCCC-ceeeEEEEecCCc
Confidence 45679996665432 345577799999999999999987432 112222222 3322222111 122222222333
Q ss_pred -CCCCCCCCcEEEEEeCCCCCCCCCeeeeeCCCCCCCCCCCeEEEEEccccCCCCCCCCCCccceEEEEEeechhhhhhH
Q psy13815 199 -HSCSSFNNDIALLELTRSIQWSDLIRPACLPSGSLDYSEQSVTVAGWGWTNENPSQGRRSNILQKVALSVVSNQVCQAW 277 (388)
Q Consensus 199 -y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~GwG~~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~ 277 (388)
|.......|+..+.|+....+.+.+....++.......++...++||-...... ..+.+..-++.
T Consensus 122 ~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~~------~~~~e~t~~v~-------- 187 (251)
T COG3591 122 LYKEDGASYDVGEAALESGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPNI------GTMWESTGKVN-------- 187 (251)
T ss_pred eeccCCceeeccHHHhccCCCccccccccccccccccccCceeEEEeccCCCCcc------eeEeeecceeE--------
Confidence 344555567777777755566666665555544444455558888885433211 01111111110
Q ss_pred hhcCCCccccCCCeEEeccCCCCcCcccCCcccCCcccccccccCCCCCCCCCCCCCCCcCCCceEEecCCccEEEEEEE
Q psy13815 278 YQSEGKKINVKESQMCAGHEQGGKDACWVSRQWWTPHVARGRVYPSHRSGVHWDPPLQADSGGPLMLLGAESTQVIGLVS 357 (388)
Q Consensus 278 ~~~~~~~~~~~~~~~Ca~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdsGgPL~~~~~~~~~l~Gi~s 357 (388)
.+....+- -..+.+ .|+||+|++...+ +++||..
T Consensus 188 --------~~~~~~l~-----y~~dT~------------------------------pG~SGSpv~~~~~---~vigv~~ 221 (251)
T COG3591 188 --------SIKGNKLF-----YDADTL------------------------------PGSSGSPVLISKD---EVIGVHY 221 (251)
T ss_pred --------EEecceEE-----EEeccc------------------------------CCCCCCceEecCc---eEEEEEe
Confidence 01111110 123555 9999999998776 8999999
Q ss_pred ecCCCCCCCCCeEEEeCCC-chhHHhhhhc
Q psy13815 358 TGIGCARPRLPGLYTRLTR-YIGWISDTLD 386 (388)
Q Consensus 358 ~g~~c~~~~~p~v~t~V~~-~~~WI~~~i~ 386 (388)
-+..-.........+|+.. +++||++.++
T Consensus 222 ~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 222 NGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred cCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 8875332233445566654 7799998764
No 11
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=2.5e-09 Score=95.95 Aligned_cols=92 Identities=32% Similarity=0.483 Sum_probs=72.2
Q ss_pred cCceEEEEeeeChhhhHhhhh-cCCCccccCCCeeEecccCCCcCCCCCCCCCceEEeeCCcEEEEeeEEeecC-CCc--
Q psy13815 4 NILQKVALSVVSNQVCQAWYQ-SEGKKINVKESQMCAGHEQGGKDACWADSGGPLMLLGAESTQVIGLVSTGIG-SPT-- 79 (388)
Q Consensus 4 ~~L~~~~~~v~~~~~C~~~~~-~~~~~~~~~~~~~Cag~~~~~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~-~~~-- 79 (388)
..|++..+..++.++|+..++ .++......-.-+||+... +++|+||||||++...+...+++||+|||.+ |..
T Consensus 182 t~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~ 259 (413)
T COG5640 182 TILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGCGGTL 259 (413)
T ss_pred ceeeeeeeeeechHHhhhhccccccCCCCCCccceecCCCC--cccccCCCCCceEEeCCCccEEEeEEEecCCCCCCCC
Confidence 479999999999999998775 2222111222239999653 8999999999999998888899999999987 832
Q ss_pred -----eeeEEEEeeccccccCCC
Q psy13815 80 -----SVVQLLTRWTLDLEVGGS 97 (388)
Q Consensus 80 -----~~~~~~~~wi~~~~~~~~ 97 (388)
|+++.|.+||...+....
T Consensus 260 ~~gVyT~vsny~~WI~a~~~~l~ 282 (413)
T COG5640 260 IPGVYTNVSNYQDWIAAMTNGLS 282 (413)
T ss_pred cceeEEehhHHHHHHHHHhcCCC
Confidence 889999999998776543
No 12
>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=98.88 E-value=7.4e-09 Score=91.71 Aligned_cols=83 Identities=36% Similarity=0.651 Sum_probs=69.4
Q ss_pred CcCceEEEEeeeChhhhHhhhhcCCCccccCCCeeEecccCCCcCCCCCCCCCceEEeeCCcEEEEeeEEeecCCC----
Q psy13815 3 SNILQKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWADSGGPLMLLGAESTQVIGLVSTGIGSP---- 78 (388)
Q Consensus 3 s~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~~~~Cag~~~~~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~~~---- 78 (388)
+..|+.+++.+++.++|...+... ..+.+.++|++........|.||||+||++..+ +|+++||+|++..|.
T Consensus 140 ~~~~~~~~~~~~~~~~C~~~~~~~---~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~~~~~ 215 (229)
T smart00020 140 PDTLQEVNVPIVSNATCRRAYSGG---GAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCARPGK 215 (229)
T ss_pred CCEeeEEEEEEeCHHHhhhhhccc---cccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCCCCCC
Confidence 457899999999999999876531 246889999986543678899999999999877 999999999999885
Q ss_pred ---ceeeEEEEeec
Q psy13815 79 ---TSVVQLLTRWT 89 (388)
Q Consensus 79 ---~~~~~~~~~wi 89 (388)
.+++..|.+||
T Consensus 216 ~~~~~~i~~~~~WI 229 (229)
T smart00020 216 PGVYTRVSSYLDWI 229 (229)
T ss_pred CCEEEEeccccccC
Confidence 17888899997
No 13
>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=98.67 E-value=2.5e-08 Score=87.53 Aligned_cols=78 Identities=37% Similarity=0.673 Sum_probs=64.4
Q ss_pred CcCceEEEEeeeChhhhHhhhhcCCCccccCCCeeEecccCCCcCCCCCCCCCceEEeeCCcEEEEeeEEeecCCCc---
Q psy13815 3 SNILQKVALSVVSNQVCQAWYQSEGKKINVKESQMCAGHEQGGKDACWADSGGPLMLLGAESTQVIGLVSTGIGSPT--- 79 (388)
Q Consensus 3 s~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~~~~Cag~~~~~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~~~~--- 79 (388)
++.++...+.+++...|...+.. .+.+.++|++.. ...+.|.||||+||++... +|+||++++..|..
T Consensus 136 ~~~~~~~~~~~~~~~~c~~~~~~-----~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~~~ 206 (220)
T PF00089_consen 136 SSNLQSVTVPVVSRKTCRSSYND-----NLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSPNY 206 (220)
T ss_dssp TSBEEEEEEEEEEHHHHHHHTTT-----TSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBTTS
T ss_pred ccccccccccccccccccccccc-----cccccccccccc-cccccccccccccccccee---eecceeeecCCCCCCCc
Confidence 35789999999999999987554 467899999864 5578999999999999874 79999999988832
Q ss_pred ----eeeEEEEeec
Q psy13815 80 ----SVVQLLTRWT 89 (388)
Q Consensus 80 ----~~~~~~~~wi 89 (388)
++++.|.+||
T Consensus 207 ~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 207 PGVYTRVSSYLDWI 220 (220)
T ss_dssp EEEEEEGGGGHHHH
T ss_pred CEEEEEHHHhhccC
Confidence 6677777886
No 14
>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=98.39 E-value=5.7e-06 Score=80.49 Aligned_cols=85 Identities=22% Similarity=0.249 Sum_probs=60.0
Q ss_pred ceeEEEEEeeCC-EEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCCC
Q psy13815 139 GHFCGGTIIHEQ-WIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRSI 217 (388)
Q Consensus 139 ~~~C~GtLI~~~-~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (388)
...++|.+|+++ +|||++|.+.+ ...+.|.+... ..+..+-+..++ ..|||||+++.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~------~~~i~V~~~~~-------~~~~a~vv~~d~-------~~DlAllkv~~~- 115 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDG------ADEITVTLSDG-------REFKAKLVGKDP-------RTDIAVLKIDAK- 115 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCC------CCeEEEEeCCC-------CEEEEEEEEecC-------CCCEEEEEecCC-
Confidence 457999999986 99999999976 45666665421 234444333444 369999999865
Q ss_pred CCCCCeeeeeCCCCCCCCCCCeEEEEEccc
Q psy13815 218 QWSDLIRPACLPSGSLDYSEQSVTVAGWGW 247 (388)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~GwG~ 247 (388)
..+.++.|........++.++++|+..
T Consensus 116 ---~~~~~~~l~~~~~~~~G~~v~aiG~p~ 142 (428)
T TIGR02037 116 ---KNLPVIKLGDSDKLRVGDWVLAIGNPF 142 (428)
T ss_pred ---CCceEEEccCCCCCCCCCEEEEEECCC
Confidence 345677787654447889999999854
No 15
>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=98.31 E-value=3.2e-05 Score=72.96 Aligned_cols=83 Identities=19% Similarity=0.241 Sum_probs=55.8
Q ss_pred eeEEEEEeeCC-EEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCCCC
Q psy13815 140 HFCGGTIIHEQ-WIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRSIQ 218 (388)
Q Consensus 140 ~~C~GtLI~~~-~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~ 218 (388)
...+|.+|+++ +|||++|.+.+ .+.+.|.+.+. ..++.+-+..+| ..||||||++.+-
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~------~~~i~V~~~dg-------~~~~a~vv~~d~-------~~DlAvlkv~~~~- 136 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKK------ADQIVVALQDG-------RKFEAELVGSDP-------LTDLAVLKIEGDN- 136 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCC------CCEEEEEECCC-------CEEEEEEEEecC-------CCCEEEEEecCCC-
Confidence 46999999977 99999999966 45566665421 234444444444 4699999998542
Q ss_pred CCCCeeeeeCCCCCCCCCCCeEEEEEccc
Q psy13815 219 WSDLIRPACLPSGSLDYSEQSVTVAGWGW 247 (388)
Q Consensus 219 ~~~~v~picLp~~~~~~~~~~~~~~GwG~ 247 (388)
+.++.|........++.+.++|+..
T Consensus 137 ----~~~~~l~~s~~~~~G~~V~aiG~P~ 161 (351)
T TIGR02038 137 ----LPTIPVNLDRPPHVGDVVLAIGNPY 161 (351)
T ss_pred ----CceEeccCcCccCCCCEEEEEeCCC
Confidence 3445554333337889999999854
No 16
>PRK10898 serine endoprotease; Provisional
Probab=98.23 E-value=5.7e-05 Score=71.31 Aligned_cols=83 Identities=19% Similarity=0.283 Sum_probs=55.3
Q ss_pred eeEEEEEeeCC-EEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCCCC
Q psy13815 140 HFCGGTIIHEQ-WIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRSIQ 218 (388)
Q Consensus 140 ~~C~GtLI~~~-~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~ 218 (388)
..-+|.+|+++ +|||++|=+.+ ...+.|.+.+. ..+..+-+..+| .+||||||++..
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~------a~~i~V~~~dg-------~~~~a~vv~~d~-------~~DlAvl~v~~~-- 135 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVIND------ADQIIVALQDG-------RVFEALLVGSDS-------LTDLAVLKINAT-- 135 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCC------CCEEEEEeCCC-------CEEEEEEEEEcC-------CCCEEEEEEcCC--
Confidence 57999999976 99999999965 45667766431 234443344444 379999999754
Q ss_pred CCCCeeeeeCCCCCCCCCCCeEEEEEccc
Q psy13815 219 WSDLIRPACLPSGSLDYSEQSVTVAGWGW 247 (388)
Q Consensus 219 ~~~~v~picLp~~~~~~~~~~~~~~GwG~ 247 (388)
...++.|........++.+.++|+..
T Consensus 136 ---~l~~~~l~~~~~~~~G~~V~aiG~P~ 161 (353)
T PRK10898 136 ---NLPVIPINPKRVPHIGDVVLAIGNPY 161 (353)
T ss_pred ---CCCeeeccCcCcCCCCCEEEEEeCCC
Confidence 13444454433336788889888753
No 17
>PRK10139 serine endoprotease; Provisional
Probab=98.02 E-value=0.00022 Score=69.53 Aligned_cols=84 Identities=18% Similarity=0.240 Sum_probs=58.3
Q ss_pred ceeEEEEEeeC--CEEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCC
Q psy13815 139 GHFCGGTIIHE--QWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRS 216 (388)
Q Consensus 139 ~~~C~GtLI~~--~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~ 216 (388)
....+|.+|++ -+|||.+|.+.+ ...+.|.+.+. ..++.+-+...| ..||||||++.+
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~------a~~i~V~~~dg-------~~~~a~vvg~D~-------~~DlAvlkv~~~ 148 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQ------AQKISIQLNDG-------REFDAKLIGSDD-------QSDIALLQIQNP 148 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCC------CCEEEEEECCC-------CEEEEEEEEEcC-------CCCEEEEEecCC
Confidence 35799999974 599999999976 46677776432 234444444444 479999999854
Q ss_pred CCCCCCeeeeeCCCCCCCCCCCeEEEEEcc
Q psy13815 217 IQWSDLIRPACLPSGSLDYSEQSVTVAGWG 246 (388)
Q Consensus 217 v~~~~~v~picLp~~~~~~~~~~~~~~GwG 246 (388)
- ...++.|........++.+.++|+.
T Consensus 149 ~----~l~~~~lg~s~~~~~G~~V~aiG~P 174 (455)
T PRK10139 149 S----KLTQIAIADSDKLRVGDFAVAVGNP 174 (455)
T ss_pred C----CCceeEecCccccCCCCEEEEEecC
Confidence 2 3456777655444678999999874
No 18
>PRK10942 serine endoprotease; Provisional
Probab=97.93 E-value=0.00035 Score=68.55 Aligned_cols=84 Identities=21% Similarity=0.258 Sum_probs=56.9
Q ss_pred ceeEEEEEeeC--CEEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCC
Q psy13815 139 GHFCGGTIIHE--QWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRS 216 (388)
Q Consensus 139 ~~~C~GtLI~~--~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~ 216 (388)
....+|.+|+. -+|||.+|.+.+ ...+.|.+.+. ..+..+-+..+| ..||||||++.+
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~------a~~i~V~~~dg-------~~~~a~vv~~D~-------~~DlAvlki~~~ 169 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDN------ATKIKVQLSDG-------RKFDAKVVGKDP-------RSDIALIQLQNP 169 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCC------CCEEEEEECCC-------CEEEEEEEEecC-------CCCEEEEEecCC
Confidence 34799999985 499999999976 45677776432 234444344444 479999999743
Q ss_pred CCCCCCeeeeeCCCCCCCCCCCeEEEEEcc
Q psy13815 217 IQWSDLIRPACLPSGSLDYSEQSVTVAGWG 246 (388)
Q Consensus 217 v~~~~~v~picLp~~~~~~~~~~~~~~GwG 246 (388)
- ...++.|........++.++++|+-
T Consensus 170 ~----~l~~~~lg~s~~l~~G~~V~aiG~P 195 (473)
T PRK10942 170 K----NLTAIKMADSDALRVGDYTVAIGNP 195 (473)
T ss_pred C----CCceeEecCccccCCCCEEEEEcCC
Confidence 2 2456666654444678888888864
No 19
>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=97.55 E-value=0.00027 Score=55.46 Aligned_cols=60 Identities=28% Similarity=0.455 Sum_probs=35.3
Q ss_pred EEEEEeeCC-EEEecCcCCCCCCCCC--ccceEEEEeccccCCCCceeeec--eEEEEECCCCCCCCCCCcEEEEEeC
Q psy13815 142 CGGTIIHEQ-WIVTAAHCLCNGPSPL--SASQINVTLKEHDLSRPSISTVP--VLRIMFHPSHSCSSFNNDIALLELT 214 (388)
Q Consensus 142 C~GtLI~~~-~VLTAAhCv~~~~~~~--~~~~~~v~~g~~~~~~~~~~~~~--v~~i~~hp~y~~~~~~~DIALl~L~ 214 (388)
|+|.+|.++ +|||++||+.+..... ....+.+...... ... ..-+...+. ..|+|||+++
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~------~~D~All~v~ 65 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDWNDGKQPDNSSVEVVFPDGR-------RVPPVAEVVYFDPD------DYDLALLKVD 65 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCCTT--G-TCSEEEEEETTSC-------EEETEEEEEEEETT-------TTEEEEEES
T ss_pred CEEEEEcCCceEEEchhheecccccccCCCCEEEEEecCCC-------EEeeeEEEEEECCc------cccEEEEEEe
Confidence 789999999 9999999998633221 2333333332211 111 222223322 4799999999
No 20
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=96.25 E-value=0.01 Score=61.11 Aligned_cols=65 Identities=22% Similarity=0.280 Sum_probs=37.8
Q ss_pred EEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCCCCCCCCe
Q psy13815 144 GTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRSIQWSDLI 223 (388)
Q Consensus 144 GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~v 223 (388)
.|||+|++|+|++|=... .-.|.+|.... ..+.+..--.|+. .|..+-||.+=|. .+
T Consensus 69 aTLigpqYiVSV~HN~~g--------y~~v~FG~~g~-----~~Y~iV~RNn~~~-------~Df~~pRLnK~VT---Ev 125 (769)
T PF02395_consen 69 ATLIGPQYIVSVKHNGKG--------YNSVSFGNEGQ-----NTYKIVDRNNYPS-------GDFHMPRLNKFVT---EV 125 (769)
T ss_dssp -EEEETTEEEBETTG-TS--------CCEECESCSST-----CEEEEEEEEBETT-------STEBEEEESS------SS
T ss_pred EEEecCCeEEEEEccCCC--------cCceeecccCC-----ceEEEEEccCCCC-------cccceeecCceEE---EE
Confidence 899999999999998722 12456665322 3455555555543 5999999998665 46
Q ss_pred eeeeCCCC
Q psy13815 224 RPACLPSG 231 (388)
Q Consensus 224 ~picLp~~ 231 (388)
.|+.....
T Consensus 126 aP~~~t~~ 133 (769)
T PF02395_consen 126 APAEMTTA 133 (769)
T ss_dssp ----BBSS
T ss_pred eccccccc
Confidence 77666544
No 21
>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=96.11 E-value=0.13 Score=45.11 Aligned_cols=43 Identities=16% Similarity=0.299 Sum_probs=25.8
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCCCCCCCCCeEEEeCCC-chhHHh
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIGCARPRLPGLYTRLTR-YIGWIS 382 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~c~~~~~p~v~t~V~~-~~~WI~ 382 (388)
.||=|.||+...++ .+|||.|-+..-. .-.+|+.+.. +.+-+.
T Consensus 150 ~G~CG~PlVs~~Dg--~IVGiHsl~~~~~---~~N~F~~f~~~f~~~~l 193 (235)
T PF00863_consen 150 DGDCGLPLVSTKDG--KIVGIHSLTSNTS---SRNYFTPFPDDFEEFYL 193 (235)
T ss_dssp TT-TT-EEEETTT----EEEEEEEEETTT---SSEEEEE--TTHHHHHC
T ss_pred CCccCCcEEEcCCC--cEEEEEcCccCCC---CeEEEEcCCHHHHHHHh
Confidence 67779999998776 4999999765332 2358888765 444443
No 22
>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=89.41 E-value=0.52 Score=36.76 Aligned_cols=38 Identities=26% Similarity=0.482 Sum_probs=29.0
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCCCCCCCCCeEEEeCCCchhHHh
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIGCARPRLPGLYTRLTRYIGWIS 382 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI~ 382 (388)
+||-||+|.|+.+ ++||++.|-. .-.-|++|+.+. |++
T Consensus 89 PGdCGg~L~C~HG----ViGi~Tagg~-----g~VaF~dir~~~-~~e 126 (127)
T PF00947_consen 89 PGDCGGILRCKHG----VIGIVTAGGE-----GHVAFADIRDLL-WLE 126 (127)
T ss_dssp TT-TCSEEEETTC----EEEEEEEEET-----TEEEEEECCCGS-TTS
T ss_pred CCCCCceeEeCCC----eEEEEEeCCC-----ceEEEEechhhh-eec
Confidence 8999999999998 9999998732 235799998763 443
No 23
>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=88.12 E-value=7.4 Score=32.67 Aligned_cols=72 Identities=13% Similarity=0.137 Sum_probs=40.3
Q ss_pred CCceeEEEEEeeCCEEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCC
Q psy13815 137 HGGHFCGGTIIHEQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRS 216 (388)
Q Consensus 137 ~~~~~C~GtLI~~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~ 216 (388)
.+.+.|.+..|..+|.|-..|.-. .. .+.++. ..+++...+.. .+......||++++|.+.
T Consensus 22 ~g~~t~l~~gi~~~~~lvp~H~~~-------~~--~i~i~g--------~~~~~~d~~~l--v~~~~~~~Dl~~v~l~~~ 82 (172)
T PF00548_consen 22 KGEFTMLALGIYDRYFLVPTHEEP-------ED--TIYIDG--------VEYKVDDSVVL--VDRDGVDTDLTLVKLPRN 82 (172)
T ss_dssp TEEEEEEEEEEEBTEEEEEGGGGG-------CS--EEEETT--------EEEEEEEEEEE--EETTSSEEEEEEEEEESS
T ss_pred CceEEEecceEeeeEEEEECcCCC-------cE--EEEECC--------EEEEeeeeEEE--ecCCCcceeEEEEEccCC
Confidence 346678888999999999999221 12 222221 12333332211 111222459999999888
Q ss_pred CCCCCCeeeee
Q psy13815 217 IQWSDLIRPAC 227 (388)
Q Consensus 217 v~~~~~v~pic 227 (388)
-.|.+..+-++
T Consensus 83 ~kfrDIrk~~~ 93 (172)
T PF00548_consen 83 PKFRDIRKFFP 93 (172)
T ss_dssp S-B--GGGGSB
T ss_pred cccCchhhhhc
Confidence 77766666555
No 24
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=87.88 E-value=0.55 Score=42.89 Aligned_cols=31 Identities=29% Similarity=0.442 Sum_probs=27.6
Q ss_pred CcCCCCCCCCCceEEeeCCcEEEEeeEEeec
Q psy13815 45 GKDACWADSGGPLMLLGAESTQVIGLVSTGI 75 (388)
Q Consensus 45 ~~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~ 75 (388)
.+..|.||+||||+...+++|.++||.+.+.
T Consensus 225 ~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~ 255 (282)
T PF03761_consen 225 KQYSCKGDRGGPLVKNINGRWTLIGVGASGN 255 (282)
T ss_pred ccccCCCCccCeEEEEECCCEEEEEEEccCC
Confidence 4678999999999999999999999998655
No 25
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=82.51 E-value=27 Score=32.86 Aligned_cols=82 Identities=26% Similarity=0.307 Sum_probs=46.6
Q ss_pred eeEEEEEee-CCEEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCCCC
Q psy13815 140 HFCGGTIIH-EQWIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRSIQ 218 (388)
Q Consensus 140 ~~C~GtLI~-~~~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~ 218 (388)
...+|.+++ ..+|+|..|=+.. ...+.+.+.. ...+...-+-..+ ..|+|+||.+..-.
T Consensus 72 ~~gSg~i~~~~g~ivTn~hVi~~------a~~i~v~l~d-------g~~~~a~~vg~d~-------~~dlavlki~~~~~ 131 (347)
T COG0265 72 GLGSGFIISSDGYIVTNNHVIAG------AEEITVTLAD-------GREVPAKLVGKDP-------ISDLAVLKIDGAGG 131 (347)
T ss_pred ccccEEEEcCCeEEEecceecCC------cceEEEEeCC-------CCEEEEEEEecCC-------ccCEEEEEeccCCC
Confidence 567888888 6799999998855 5556665511 1233333333222 46999999986532
Q ss_pred CCCCeeeeeCCCCCCCCCCCeEEEEEc
Q psy13815 219 WSDLIRPACLPSGSLDYSEQSVTVAGW 245 (388)
Q Consensus 219 ~~~~v~picLp~~~~~~~~~~~~~~Gw 245 (388)
...+.+........++....+|-
T Consensus 132 ----~~~~~~~~s~~l~vg~~v~aiGn 154 (347)
T COG0265 132 ----LPVIALGDSDKLRVGDVVVAIGN 154 (347)
T ss_pred ----CceeeccCCCCcccCCEEEEecC
Confidence 22233333333234555555553
No 26
>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=76.25 E-value=3.4 Score=35.63 Aligned_cols=23 Identities=35% Similarity=0.508 Sum_probs=20.2
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCC
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIG 361 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~ 361 (388)
+|-||+|++.++ .|+|-+++.+-
T Consensus 179 qGMSGSPI~qdG----KLiGAVthvf~ 201 (218)
T PF05580_consen 179 QGMSGSPIIQDG----KLIGAVTHVFV 201 (218)
T ss_pred ecccCCCEEECC----EEEEEEEEEEe
Confidence 999999999877 49999999863
No 27
>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=68.16 E-value=5.8 Score=41.43 Aligned_cols=31 Identities=29% Similarity=0.430 Sum_probs=22.3
Q ss_pred CCCCCCCCCceEEee--CCcEEEEeeEEeecCC
Q psy13815 47 DACWADSGGPLMLLG--AESTQVIGLVSTGIGS 77 (388)
Q Consensus 47 ~~C~gdsGgpl~~~~--~~~~~~~Gi~s~~~~~ 77 (388)
..=.||||+||+..+ ...|+|+|+.+.+.+.
T Consensus 212 ~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~ 244 (769)
T PF02395_consen 212 YGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGY 244 (769)
T ss_dssp B--TT-TT-EEEEEETTTTEEEEEEEEEEECCC
T ss_pred ccccCcCCCceEEEEccCCeEEEEEEEcccccc
Confidence 356899999999765 4689999999987654
No 28
>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=62.59 E-value=5.5 Score=31.49 Aligned_cols=21 Identities=24% Similarity=0.675 Sum_probs=16.4
Q ss_pred CCcCCCceEEecCCccEEEEEEEe
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVST 358 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~ 358 (388)
.|.||||++|..+ .++||.-.
T Consensus 107 kGSSGgPiLC~~G---H~vG~f~a 127 (148)
T PF02907_consen 107 KGSSGGPILCPSG---HAVGMFRA 127 (148)
T ss_dssp TT-TT-EEEETTS---EEEEEEEE
T ss_pred ecCCCCcccCCCC---CEEEEEEE
Confidence 7999999999887 79999854
No 29
>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=62.01 E-value=9.4 Score=36.55 Aligned_cols=43 Identities=33% Similarity=0.485 Sum_probs=30.4
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCCCCCCCCCeEEEeCCCchhHHhhhhcc
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIGCARPRLPGLYTRLTRYIGWISDTLDI 387 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI~~~i~~ 387 (388)
+|-||+|++.++. |+|-++.-+--+....+++ |++|+.+..++
T Consensus 359 qGMSGSPi~q~gk----liGAvtHVfvndpt~GYGi------~ie~Ml~~~~~ 401 (402)
T TIGR02860 359 QGMSGSPIIQNGK----VIGAVTHVFVNDPTSGYGV------YIEWMLKEAGI 401 (402)
T ss_pred ecccCCCEEECCE----EEEEEEEEEecCCCcceee------hHHHHHHHhcc
Confidence 9999999999884 9999987652222222333 68888876654
No 30
>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=61.61 E-value=6.9 Score=29.88 Aligned_cols=18 Identities=33% Similarity=0.700 Sum_probs=14.2
Q ss_pred CCcCCCceEEecCCccEEEEE
Q psy13815 335 QADSGGPLMLLGAESTQVIGL 355 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi 355 (388)
.|.|||||+... + .++||
T Consensus 103 ~G~SGgpv~~~~-G--~vvGi 120 (120)
T PF13365_consen 103 PGSSGGPVFDSD-G--RVVGI 120 (120)
T ss_dssp TTTTTSEEEETT-S--EEEEE
T ss_pred CCcEeHhEECCC-C--EEEeC
Confidence 899999998743 3 48886
No 31
>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=56.59 E-value=12 Score=33.33 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=17.8
Q ss_pred CCcCCCceEEecCCccEEEEEEEecC
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGI 360 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~ 360 (388)
.||||+|++..++ .|+||.+.+.
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 6999999998775 4999998653
No 32
>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=51.96 E-value=6 Score=31.21 Aligned_cols=24 Identities=29% Similarity=0.506 Sum_probs=19.1
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCC
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIG 361 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~ 361 (388)
.||||-|++.+.+ .+|||+-.|..
T Consensus 105 ~GDSGRpi~DNsG---rVVaIVLGG~n 128 (158)
T PF00944_consen 105 PGDSGRPIFDNSG---RVVAIVLGGAN 128 (158)
T ss_dssp TTSTTEEEESTTS---BEEEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCCC
Confidence 8999999986654 59999877653
No 33
>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=48.09 E-value=11 Score=38.99 Aligned_cols=21 Identities=24% Similarity=0.599 Sum_probs=19.2
Q ss_pred eEEEEEeeCC-EEEecCcCCCC
Q psy13815 141 FCGGTIIHEQ-WIVTAAHCLCN 161 (388)
Q Consensus 141 ~C~GtLI~~~-~VLTAAhCv~~ 161 (388)
-|+|++||++ .|||--||..+
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 3999999998 99999999865
No 34
>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=47.52 E-value=15 Score=28.87 Aligned_cols=22 Identities=41% Similarity=0.480 Sum_probs=18.0
Q ss_pred CCCCCCceEEeeCCcEEEEeeEEeec
Q psy13815 50 WADSGGPLMLLGAESTQVIGLVSTGI 75 (388)
Q Consensus 50 ~gdsGgpl~~~~~~~~~~~Gi~s~~~ 75 (388)
.||-||+|.|+. -++||++.|-
T Consensus 89 PGdCGg~L~C~H----GViGi~Tagg 110 (127)
T PF00947_consen 89 PGDCGGILRCKH----GVIGIVTAGG 110 (127)
T ss_dssp TT-TCSEEEETT----CEEEEEEEEE
T ss_pred CCCCCceeEeCC----CeEEEEEeCC
Confidence 589999999987 6899998764
No 35
>KOG1421|consensus
Probab=47.15 E-value=2.3e+02 Score=29.29 Aligned_cols=82 Identities=17% Similarity=0.421 Sum_probs=42.9
Q ss_pred EEEEEeeCC--EEEecCcCCCCCCCCCccceEEEEeccccCCCCceeeeceEEEEECCCCCCCCCCCcEEEEEeCCC-CC
Q psy13815 142 CGGTIIHEQ--WIVTAAHCLCNGPSPLSASQINVTLKEHDLSRPSISTVPVLRIMFHPSHSCSSFNNDIALLELTRS-IQ 218 (388)
Q Consensus 142 C~GtLI~~~--~VLTAAhCv~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~-v~ 218 (388)
-.|.++++. ++||+.|-+.-. +-.-.+.+-.+ ....+.-++..| -||+.+++-... +.
T Consensus 86 atgfvvd~~~gyiLtnrhvv~pg-----P~va~avf~n~-------ee~ei~pvyrDp-------VhdfGf~r~dps~ir 146 (955)
T KOG1421|consen 86 ATGFVVDKKLGYILTNRHVVAPG-----PFVASAVFDNH-------EEIEIYPVYRDP-------VHDFGFFRYDPSTIR 146 (955)
T ss_pred eeEEEEecccceEEEeccccCCC-----CceeEEEeccc-------ccCCcccccCCc-------hhhcceeecChhhcc
Confidence 457788775 899999988642 11112222211 122233233333 357777776543 33
Q ss_pred CCCCeeeeeCCCCCCCCCCCeEEEEE
Q psy13815 219 WSDLIRPACLPSGSLDYSEQSVTVAG 244 (388)
Q Consensus 219 ~~~~v~picLp~~~~~~~~~~~~~~G 244 (388)
| ..+..+||..... ..+....++|
T Consensus 147 ~-s~vt~i~lap~~a-kvgseirvvg 170 (955)
T KOG1421|consen 147 F-SIVTEICLAPELA-KVGSEIRVVG 170 (955)
T ss_pred e-eeeeccccCcccc-ccCCceEEec
Confidence 3 3567778865444 3444444444
No 36
>KOG1320|consensus
Probab=43.54 E-value=2.6e+02 Score=27.63 Aligned_cols=38 Identities=16% Similarity=0.122 Sum_probs=22.1
Q ss_pred CCCcEEEEEeCCCCCCCCCeeeeeCCCCCCCCCCCeEEEEE
Q psy13815 204 FNNDIALLELTRSIQWSDLIRPACLPSGSLDYSEQSVTVAG 244 (388)
Q Consensus 204 ~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~G 244 (388)
...|||+++++.+- ....+|.++.......+..+...|
T Consensus 222 ~~~gvA~l~ik~~~---~i~~~i~~~~~~~~~~G~~~~a~~ 259 (473)
T KOG1320|consen 222 KVAGVAFLKIKTPE---NILYVIPLGVSSHFRTGVEVSAIG 259 (473)
T ss_pred cccceEEEEEecCC---cccceeecceeeeecccceeeccc
Confidence 45799999997553 223556666544434555544433
No 37
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=39.94 E-value=53 Score=31.48 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=23.1
Q ss_pred CCcCCCceEEecCCccEEEEEEEecCC
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGIG 361 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~~ 361 (388)
+||-|-|-++..++.|+++||......
T Consensus 502 PGDCGcPYvyKrgNd~VV~GVH~AAtr 528 (535)
T PF05416_consen 502 PGDCGCPYVYKRGNDWVVIGVHAAATR 528 (535)
T ss_dssp TTGTT-EEEEEETTEEEEEEEEEEE-S
T ss_pred CCCCCCceeeecCCcEEEEEEEehhcc
Confidence 899999999999999999999987544
No 38
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=30.57 E-value=1.6e+02 Score=30.18 Aligned_cols=51 Identities=18% Similarity=0.326 Sum_probs=35.4
Q ss_pred CCcCCCceEEecCC---ccEEEEEEEecCCCCCCCCCeEEEeCCCchhHHhhhhcc
Q psy13815 335 QADSGGPLMLLGAE---STQVIGLVSTGIGCARPRLPGLYTRLTRYIGWISDTLDI 387 (388)
Q Consensus 335 ~gdsGgPL~~~~~~---~~~l~Gi~s~g~~c~~~~~p~v~t~V~~~~~WI~~~i~~ 387 (388)
.||||+=++...++ ..-++|++.. .++. ...-++||-+..-++=+++++++
T Consensus 638 ~GDSGS~VLtk~~d~~~gLgvvGMlhs-ydge-~kqfglftPi~~il~rl~~vT~I 691 (695)
T PF08192_consen 638 GGDSGSWVLTKLEDNNKGLGVVGMLHS-YDGE-QKQFGLFTPINEILDRLEEVTGI 691 (695)
T ss_pred CCCcccEEEecccccccCceeeEEeee-cCCc-cceeeccCcHHHHHHHHHHhhcc
Confidence 89999988886433 3347787743 2332 34567899998888888888765
No 39
>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=24.31 E-value=1.8e+02 Score=28.10 Aligned_cols=49 Identities=22% Similarity=0.311 Sum_probs=31.9
Q ss_pred CCeeEecccCCCcC--CCCCCCCCceEEeeCCcEEEEeeEEeecCCCceee
Q psy13815 34 ESQMCAGHEQGGKD--ACWADSGGPLMLLGAESTQVIGLVSTGIGSPTSVV 82 (388)
Q Consensus 34 ~~~~Cag~~~~~~~--~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~~~~~~~ 82 (388)
..|+=+|.+..++| +-.||-|.|-++.....|+++|+-.....-..|++
T Consensus 484 ~GMLLTGaNAK~mDLGT~PGDCGcPYvyKrgNd~VV~GVH~AAtr~GNTVi 534 (535)
T PF05416_consen 484 MGMLLTGANAKGMDLGTIPGDCGCPYVYKRGNDWVVIGVHAAATRSGNTVI 534 (535)
T ss_dssp EEEETTSTT-SSTTTS--TTGTT-EEEEEETTEEEEEEEEEEE-SSSSEEE
T ss_pred eeeeeecCCccccccCCCCCCCCCceeeecCCcEEEEEEEehhccCCCeee
Confidence 34666665444444 47899999999998899999999876554444543
No 40
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=22.30 E-value=91 Score=27.89 Aligned_cols=28 Identities=32% Similarity=0.534 Sum_probs=22.8
Q ss_pred cCCCCCCCCCceEEeeCCcEEEEeeEEeecC
Q psy13815 46 KDACWADSGGPLMLLGAESTQVIGLVSTGIG 76 (388)
Q Consensus 46 ~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~ 76 (388)
.+++.|+||+|+..... +++|+..-+..
T Consensus 198 ~dT~pG~SGSpv~~~~~---~vigv~~~g~~ 225 (251)
T COG3591 198 ADTLPGSSGSPVLISKD---EVIGVHYNGPG 225 (251)
T ss_pred ecccCCCCCCceEecCc---eEEEEEecCCC
Confidence 58899999999997654 89998876554
No 41
>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=21.91 E-value=97 Score=26.94 Aligned_cols=40 Identities=25% Similarity=0.432 Sum_probs=27.7
Q ss_pred cCCCCCCCCCceEEeeCCcEEEEeeEEeecCC-CceeeEEEEeec
Q psy13815 46 KDACWADSGGPLMLLGAESTQVIGLVSTGIGS-PTSVVQLLTRWT 89 (388)
Q Consensus 46 ~~~C~gdsGgpl~~~~~~~~~~~Gi~s~~~~~-~~~~~~~~~~wi 89 (388)
...-+|-||+|+...+ .|+|-+++...- |..-...|..|.
T Consensus 175 GGIvqGMSGSPI~qdG----KLiGAVthvf~~dp~~Gygi~ie~M 215 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG----KLIGAVTHVFVNDPTKGYGIFIEWM 215 (218)
T ss_pred CCEEecccCCCEEECC----EEEEEEEEEEecCCCceeeecHHHH
Confidence 4678999999999877 999999887533 223333344443
No 42
>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=21.90 E-value=73 Score=25.39 Aligned_cols=23 Identities=26% Similarity=0.696 Sum_probs=17.0
Q ss_pred CCcCCCceEEecCCccEEEEEEEecC
Q psy13815 335 QADSGGPLMLLGAESTQVIGLVSTGI 360 (388)
Q Consensus 335 ~gdsGgPL~~~~~~~~~l~Gi~s~g~ 360 (388)
.|.||+|++...+ .++||.-.+.
T Consensus 96 ~GsSGSpi~n~~g---~ivGlYg~g~ 118 (132)
T PF00949_consen 96 KGSSGSPIFNQNG---EIVGLYGNGV 118 (132)
T ss_dssp TTGTT-EEEETTS---CEEEEEEEEE
T ss_pred CCCCCCceEcCCC---cEEEEEccce
Confidence 8999999996544 4999987664
Done!