Query psy3170
Match_columns 525
No_of_seqs 497 out of 3707
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 18:09:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3170.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3170hhsearch_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 4.8E-40 1.1E-44 311.2 22.4 204 279-487 24-232 (232)
2 KOG3627|consensus 100.0 3.9E-38 8.4E-43 302.9 22.3 234 188-489 9-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 3.3E-37 7.1E-42 291.4 23.0 224 191-484 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 1.3E-34 2.8E-39 271.8 19.2 216 192-484 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 4.8E-30 1E-34 238.1 15.6 240 189-495 30-285 (413)
6 cd00190 Tryp_SPc Trypsin-like 99.8 7.5E-18 1.6E-22 159.1 13.6 170 2-185 36-211 (232)
7 KOG3627|consensus 99.7 6.2E-17 1.3E-21 155.5 14.5 172 3-187 50-234 (256)
8 smart00020 Tryp_SPc Trypsin-li 99.7 5.3E-16 1.1E-20 146.3 14.5 170 2-185 37-211 (229)
9 PF03761 DUF316: Domain of unk 99.6 1.7E-14 3.7E-19 140.3 17.8 240 181-484 28-275 (282)
10 PF00089 Trypsin: Trypsin; In 99.6 1.3E-14 2.8E-19 135.8 12.1 165 2-186 36-203 (220)
11 PF09342 DUF1986: Domain of un 99.1 3.1E-10 6.8E-15 101.5 10.5 99 279-386 27-131 (267)
12 COG5640 Secreted trypsin-like 99.0 1.3E-09 2.7E-14 102.8 9.6 172 3-193 73-264 (413)
13 COG3591 V8-like Glu-specific e 98.9 1E-08 2.2E-13 94.5 10.7 182 279-488 63-250 (251)
14 TIGR02037 degP_htrA_DO peripla 97.9 0.00016 3.5E-09 74.6 13.4 142 278-462 56-199 (428)
15 PF13365 Trypsin_2: Trypsin-li 97.9 8.2E-05 1.8E-09 61.9 8.7 21 282-302 1-22 (120)
16 TIGR02038 protease_degS peripl 97.5 0.0014 3E-08 65.6 12.5 140 279-462 77-218 (351)
17 PRK10898 serine endoprotease; 97.4 0.0033 7.1E-08 63.0 13.5 139 279-462 77-218 (353)
18 PRK10139 serine endoprotease; 97.4 0.0016 3.5E-08 67.4 11.6 141 279-462 89-232 (455)
19 PF09342 DUF1986: Domain of un 97.2 0.0015 3.3E-08 59.3 7.9 86 3-97 40-131 (267)
20 PRK10942 serine endoprotease; 97.1 0.0048 1E-07 64.2 12.3 140 279-462 110-253 (473)
21 PF13365 Trypsin_2: Trypsin-li 92.8 0.21 4.6E-06 41.0 5.1 12 2-13 11-22 (120)
22 PF02395 Peptidase_S6: Immunog 88.6 0.22 4.8E-06 54.5 1.7 33 434-466 213-245 (769)
23 PF03761 DUF316: Domain of unk 88.5 0.23 5E-06 48.2 1.6 9 379-387 245-253 (282)
24 TIGR02037 degP_htrA_DO peripla 88.3 2.2 4.7E-05 44.2 8.7 71 2-96 70-141 (428)
25 PF00548 Peptidase_C3: 3C cyst 86.8 3.3 7.1E-05 36.8 7.8 71 278-367 23-93 (172)
26 PF00863 Peptidase_C4: Peptida 85.9 2.8 6E-05 39.0 7.0 155 286-486 37-194 (235)
27 PF00947 Pico_P2A: Picornaviru 82.5 1.3 2.7E-05 36.5 2.8 39 435-485 88-126 (127)
28 PRK10139 serine endoprotease; 80.3 6.7 0.00015 40.8 8.0 70 2-95 103-173 (455)
29 PRK10942 serine endoprotease; 78.6 9 0.0002 40.1 8.4 70 2-95 124-194 (473)
30 TIGR02038 protease_degS peripl 72.5 18 0.00039 36.2 8.5 70 2-96 90-160 (351)
31 COG3591 V8-like Glu-specific e 70.9 2.5 5.5E-05 39.6 1.8 47 198-249 44-90 (251)
32 PRK10898 serine endoprotease; 62.4 40 0.00087 33.8 8.6 70 2-96 90-160 (353)
33 COG0265 DegQ Trypsin-like seri 53.7 2.4E+02 0.0052 28.1 13.4 29 432-465 189-217 (347)
34 PF05579 Peptidase_S32: Equine 47.5 18 0.0004 34.0 3.0 22 436-462 207-228 (297)
35 PF10459 Peptidase_S46: Peptid 37.7 20 0.00043 39.3 2.0 21 281-301 48-69 (698)
36 KOG1421|consensus 32.8 3.2E+02 0.0069 29.8 9.5 84 280-383 84-170 (955)
37 PF05580 Peptidase_S55: SpoIVB 31.9 52 0.0011 30.1 3.3 25 433-463 176-200 (218)
38 PF00944 Peptidase_S3: Alphavi 24.7 29 0.00064 28.9 0.4 25 435-464 104-128 (158)
39 PF02907 Peptidase_S29: Hepati 23.6 50 0.0011 27.6 1.6 22 435-461 106-127 (148)
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=4.8e-40 Score=311.18 Aligned_cols=204 Identities=39% Similarity=0.672 Sum_probs=171.5
Q ss_pred eeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCCcc
Q psy3170 279 KWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVE 358 (525)
Q Consensus 279 ~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~~~ 358 (525)
.+.|+||||+++||||||||+.......+.|++|...............|.++++||.|+. ....+|||||||++|+.
T Consensus 24 ~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~--~~~~~DiAll~L~~~~~ 101 (232)
T cd00190 24 RHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHPNYNP--STYDNDIALLKLKRPVT 101 (232)
T ss_pred cEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECCCCCC--CCCcCCEEEEEECCccc
Confidence 5889999999999999999998755567888998773222212234445999999999988 56789999999999999
Q ss_pred cCCCccceecCCC--CCCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccC---CCCCCcEEEEeCCCCcC
Q psy3170 359 FSETLKPACLNRA--HNVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQET---TLISSQLCATVMAGGKD 433 (525)
Q Consensus 359 ~~~~v~picL~~~--~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~---~~~~~~~Ca~~~~~~~~ 433 (525)
++++++|||||.. ....+..+.++|||...... ..+..+++..+.+++...|...+. .+...++|+.......+
T Consensus 102 ~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~-~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~ 180 (232)
T cd00190 102 LSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGG-PLPDVLQEVNVPIVSNAECKRAYSYGGTITDNMLCAGGLEGGKD 180 (232)
T ss_pred CCCcccceECCCccccCCCCCEEEEEeCCcCCCCC-CCCceeeEEEeeeECHHHhhhhccCcccCCCceEeeCCCCCCCc
Confidence 9999999999988 45667899999999876542 466789999999999999998775 36788999987544778
Q ss_pred CCcCCCCCcceeecCCCceeEEEEEEeecCCCCCCCCceEEEEcCCchhhhccc
Q psy3170 434 TCQGDSGGPLQTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVSYYVPWIVHT 487 (525)
Q Consensus 434 ~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~~~~~WI~~~ 487 (525)
.|.|||||||++..++ +++|+||+|++..|.....|.+|++|+.|.+||+++
T Consensus 181 ~c~gdsGgpl~~~~~~--~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 181 ACQGDSGGPLVCNDNG--RGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred cccCCCCCcEEEEeCC--EEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 9999999999997664 899999999998898667899999999999999874
No 2
>KOG3627|consensus
Probab=100.00 E-value=3.9e-38 Score=302.86 Aligned_cols=234 Identities=36% Similarity=0.639 Sum_probs=191.5
Q ss_pred CCCeeecCccCCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccccccccchhheeeeeccee
Q psy3170 188 AMPMIIGGSRAKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGTMVKAPLRTLLFISMAEVG 267 (525)
Q Consensus 188 ~~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 (525)
...||+||.++..++|||++++.....
T Consensus 9 ~~~~i~~g~~~~~~~~Pw~~~l~~~~~----------------------------------------------------- 35 (256)
T KOG3627|consen 9 PEGRIVGGTEAEPGSFPWQVSLQYGGN----------------------------------------------------- 35 (256)
T ss_pred ccCCEeCCccCCCCCCCCEEEEEECCC-----------------------------------------------------
Confidence 357899999999999999999976431
Q ss_pred eeecCCccccceeEeEEEEEeCCEEEecCCCCCCC-CCCceEEEEEEEeeccccccc--ceEE-EEEEEeCCCCCCCCCC
Q psy3170 268 FLEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSP-LGKPRYVRFGLITKLSYSVTD--NIHR-VMQNILHPNYTTEGTS 343 (525)
Q Consensus 268 ~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~-~~~~~~v~~g~~~~~~~~~~~--~~~~-v~~i~~hp~y~~~~~~ 343 (525)
..++|+|+||+++||||||||+... .. .+.|++|.+......... .... +.++++||+|+. ..
T Consensus 36 ----------~~~~Cggsli~~~~vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i~H~~y~~--~~ 102 (256)
T KOG3627|consen 36 ----------GRHLCGGSLISPRWVLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVGDVEKIIVHPNYNP--RT 102 (256)
T ss_pred ----------cceeeeeEEeeCCEEEEChhhCCCCCCc-ceEEEECccccccccccCchhhhceeeEEEECCCCCC--CC
Confidence 1579999999999999999999873 22 788888876222221222 1333 778889999998 55
Q ss_pred cc-cceEEEEECCCcccCCCccceecCCCCC----CCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCC-
Q psy3170 344 QY-HDIALLKIAPPVEFSETLKPACLNRAHN----VKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETT- 417 (525)
Q Consensus 344 ~~-~DIAll~L~~~~~~~~~v~picL~~~~~----~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~- 417 (525)
.. ||||||+|++++.|++.|+|||||.... ..+..+.++|||.+.......+..|++..+.+++...|...+..
T Consensus 103 ~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v~i~~~~~C~~~~~~~ 182 (256)
T KOG3627|consen 103 LENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDVPIISNSECRRAYGGL 182 (256)
T ss_pred CCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEEeEcChhHhcccccCc
Confidence 55 9999999999999999999999985442 34478999999988765435678899999999999999988764
Q ss_pred --CCCCcEEEEeCCCCcCCCcCCCCCcceeecCCCceeEEEEEEeecCC-CCCCCCceEEEEcCCchhhhccccc
Q psy3170 418 --LISSQLCATVMAGGKDTCQGDSGGPLQTIMPDLCMYNIIGITSYGRQ-CGHANTPAIYTRVSYYVPWIVHTVW 489 (525)
Q Consensus 418 --~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~-c~~~~~p~v~t~v~~~~~WI~~~i~ 489 (525)
+...++|++....+.++|.|||||||++..++ +++++||+|||.. |+..+.|++||+|+.|.+||++.+.
T Consensus 183 ~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~--~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 183 GTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG--RWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred cccCCCEEeeCccCCCCccccCCCCCeEEEeeCC--cEEEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHHHhc
Confidence 55678999976667889999999999997665 7999999999987 9977789999999999999998874
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=3.3e-37 Score=291.42 Aligned_cols=224 Identities=39% Similarity=0.701 Sum_probs=187.4
Q ss_pred eeecCccCCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccccccccchhheeeeecceeeee
Q psy3170 191 MIIGGSRAKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGTMVKAPLRTLLFISMAEVGFLE 270 (525)
Q Consensus 191 ~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 (525)
||+||.++..++|||+|.++...
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~--------------------------------------------------------- 23 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRG--------------------------------------------------------- 23 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcC---------------------------------------------------------
Confidence 57899999999999999997532
Q ss_pred cCCccccceeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEE
Q psy3170 271 EGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIAL 350 (525)
Q Consensus 271 ~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAl 350 (525)
..+.|+||||++++|||||||+.......+.|++|.. ............|..+++||.|+. ....+||||
T Consensus 24 -------~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~-~~~~~~~~~~~~v~~~~~~p~~~~--~~~~~DiAl 93 (229)
T smart00020 24 -------GRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSH-DLSSGEEGQVIKVSKVIIHPNYNP--STYDNDIAL 93 (229)
T ss_pred -------CCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcc-cCCCCCCceEEeeEEEEECCCCCC--CCCcCCEEE
Confidence 2588999999999999999999875446788999877 332222224455999999999987 677799999
Q ss_pred EEECCCcccCCCccceecCCC--CCCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCC---CCCCcEEE
Q psy3170 351 LKIAPPVEFSETLKPACLNRA--HNVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETT---LISSQLCA 425 (525)
Q Consensus 351 l~L~~~~~~~~~v~picL~~~--~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~---~~~~~~Ca 425 (525)
|+|++|+.+++.++|+||+.. ....+..+.++|||............++...+.+++...|...+.. +...++|+
T Consensus 94 l~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~ 173 (229)
T smart00020 94 LKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCA 173 (229)
T ss_pred EEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhhccccccCCCcEee
Confidence 999999999999999999986 4466789999999987653334567888999999999999987653 67889999
Q ss_pred EeCCCCcCCCcCCCCCcceeecCCCceeEEEEEEeecCCCCCCCCceEEEEcCCchhhh
Q psy3170 426 TVMAGGKDTCQGDSGGPLQTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVSYYVPWI 484 (525)
Q Consensus 426 ~~~~~~~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~~~~~WI 484 (525)
+......+.|.|||||||++..+ +|+|+||+|++..|...+.|.+|++|++|.+||
T Consensus 174 ~~~~~~~~~c~gdsG~pl~~~~~---~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 174 GGLEGGKDACQGDSGGPLVCNDG---RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred cCCCCCCcccCCCCCCeeEEECC---CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 87544678999999999998643 789999999999998677899999999999998
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=1.3e-34 Score=271.77 Aligned_cols=216 Identities=37% Similarity=0.718 Sum_probs=180.2
Q ss_pred eecCccCCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccccccccchhheeeeecceeeeec
Q psy3170 192 IIGGSRAKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGTMVKAPLRTLLFISMAEVGFLEE 271 (525)
Q Consensus 192 i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (525)
|.||..+..++|||+|.+....
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~---------------------------------------------------------- 22 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSN---------------------------------------------------------- 22 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETT----------------------------------------------------------
T ss_pred CCCCEECCCCCCCeEEEEeeCC----------------------------------------------------------
Confidence 6799999999999999997643
Q ss_pred CCccccceeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeeccccccc-ceEEEEEEEeCCCCCCCCCCcccceEE
Q psy3170 272 GGTMKDVKWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTD-NIHRVMQNILHPNYTTEGTSQYHDIAL 350 (525)
Q Consensus 272 ~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~-~~~~v~~i~~hp~y~~~~~~~~~DIAl 350 (525)
..++|+|+||+++||||||||+.. ...+.+++|.. ........ ....|.+++.||.|+. ....+||||
T Consensus 23 ------~~~~C~G~li~~~~vLTaahC~~~--~~~~~v~~g~~-~~~~~~~~~~~~~v~~~~~h~~~~~--~~~~~DiAl 91 (220)
T PF00089_consen 23 ------GRFFCTGTLISPRWVLTAAHCVDG--ASDIKVRLGTY-SIRNSDGSEQTIKVSKIIIHPKYDP--STYDNDIAL 91 (220)
T ss_dssp ------TEEEEEEEEEETTEEEEEGGGHTS--GGSEEEEESES-BTTSTTTTSEEEEEEEEEEETTSBT--TTTTTSEEE
T ss_pred ------CCeeEeEEeccccccccccccccc--ccccccccccc-ccccccccccccccccccccccccc--ccccccccc
Confidence 168999999999999999999976 45688888873 33333332 3445999999999998 556799999
Q ss_pred EEECCCcccCCCccceecCCCCC--CCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCC-CCCCcEEEEe
Q psy3170 351 LKIAPPVEFSETLKPACLNRAHN--VKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETT-LISSQLCATV 427 (525)
Q Consensus 351 l~L~~~~~~~~~v~picL~~~~~--~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~-~~~~~~Ca~~ 427 (525)
|+|++++.+.+.++|+||+.... ..+..+.+.||+...... ....++...+.+++.+.|...+.. +...++|+..
T Consensus 92 l~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~--~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~c~~~ 169 (220)
T PF00089_consen 92 LKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG--YSSNLQSVTVPVVSRKTCRSSYNDNLTPNMICAGS 169 (220)
T ss_dssp EEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS--BTSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEET
T ss_pred ccccccccccccccccccccccccccccccccccccccccccc--ccccccccccccccccccccccccccccccccccc
Confidence 99999999999999999998433 567899999999865433 456788899999999999986433 6788999987
Q ss_pred CCCCcCCCcCCCCCcceeecCCCceeEEEEEEeecCCCCCCCCceEEEEcCCchhhh
Q psy3170 428 MAGGKDTCQGDSGGPLQTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVSYYVPWI 484 (525)
Q Consensus 428 ~~~~~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~~~~~WI 484 (525)
. ...+.|.|||||||++.. . +|+||++++.+|...+.|.+|++|+.|++||
T Consensus 170 ~-~~~~~~~g~sG~pl~~~~----~-~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 170 S-GSGDACQGDSGGPLICNN----N-YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp T-SSSBGGTTTTTSEEEETT----E-EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred c-ccccccccccccccccce----e-eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 5 567899999999998842 2 7999999999999777899999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.8e-30 Score=238.11 Aligned_cols=240 Identities=27% Similarity=0.366 Sum_probs=174.7
Q ss_pred CCeeecCccCCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccccccccchhheeeeecceee
Q psy3170 189 MPMIIGGSRAKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGTMVKAPLRTLLFISMAEVGF 268 (525)
Q Consensus 189 ~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~ 268 (525)
.+||+||..|+.++||++|++.....+.
T Consensus 30 s~rIigGs~Anag~~P~~VaLv~~isd~---------------------------------------------------- 57 (413)
T COG5640 30 SSRIIGGSNANAGEYPSLVALVDRISDY---------------------------------------------------- 57 (413)
T ss_pred ceeEecCcccccccCchHHHHHhhcccc----------------------------------------------------
Confidence 5799999999999999999996543210
Q ss_pred eecCCccccceeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccce
Q psy3170 269 LEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDI 348 (525)
Q Consensus 269 ~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DI 348 (525)
-.-.+|+|+++..|||||||||+.....-...+..+.. ++......+...|..++.|..|.+ .++.||+
T Consensus 58 --------~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~-~l~d~Sq~~rg~vr~i~~~efY~~--~n~~ND~ 126 (413)
T COG5640 58 --------VSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVV-DLNDSSQAERGHVRTIYVHEFYSP--GNLGNDI 126 (413)
T ss_pred --------cceeEeccceecceEEeeehhhccCCCCccccceEEEe-cccccccccCcceEEEeeeccccc--ccccCcc
Confidence 02478999999999999999999875423333444444 555556666667999999999998 7889999
Q ss_pred EEEEECCCcccCC-CccceecCCC---CCCCCCcEEEEEeeeccCCCCc----ccccceEEEEEeeChhhhhcccCC---
Q psy3170 349 ALLKIAPPVEFSE-TLKPACLNRA---HNVKSPTAIASGFGKLNYFDTK----ESLRLMKVVLDIINNDTCSKQETT--- 417 (525)
Q Consensus 349 All~L~~~~~~~~-~v~picL~~~---~~~~~~~~~~~Gwg~~~~~~~~----~~~~l~~~~v~~~~~~~C~~~~~~--- 417 (525)
|+++|.++..... .+.-.--+.. ...........+|+.+.....+ ....+++..+..++...|.+.+..
T Consensus 127 Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e~~v~fv~~stc~~~~g~an~ 206 (413)
T COG5640 127 AVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKGCANA 206 (413)
T ss_pred eeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccceeeeeeeeeechHHhhhhcccccc
Confidence 9999998765321 1111000110 0012234456677766543321 124688999999999999987741
Q ss_pred ----CCCCcEEEEeCCCCcCCCcCCCCCcceeecCCCceeEEEEEEeecCC-CCCCCCceEEEEcCCchhhhcccccccc
Q psy3170 418 ----LISSQLCATVMAGGKDTCQGDSGGPLQTIMPDLCMYNIIGITSYGRQ-CGHANTPAIYTRVSYYVPWIVHTVWPDQ 492 (525)
Q Consensus 418 ----~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~-c~~~~~p~v~t~v~~~~~WI~~~i~~~~ 492 (525)
..-.-+|++.+ .+++|+||||||++...++ ...++||+|||.+ |+.+..|.|||+|+.|.+||..++..-.
T Consensus 207 ~dg~~~lT~~cag~~--~~daCqGDSGGPi~~~g~~--G~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~l~ 282 (413)
T COG5640 207 SDGATGLTGFCAGRP--PKDACQGDSGGPIFHKGEE--GRVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTNGLS 282 (413)
T ss_pred CCCCCCccceecCCC--CcccccCCCCCceEEeCCC--ccEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhcCCC
Confidence 11223999865 4899999999999987665 6789999999976 9999999999999999999999886544
Q ss_pred cCC
Q psy3170 493 FPN 495 (525)
Q Consensus 493 ~~~ 495 (525)
++.
T Consensus 283 ~~~ 285 (413)
T COG5640 283 YLQ 285 (413)
T ss_pred ccc
Confidence 443
No 6
>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=99.76 E-value=7.5e-18 Score=159.10 Aligned_cols=170 Identities=25% Similarity=0.356 Sum_probs=122.9
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.|||||||+.......+.|++|..+........+.+.|.++++||+|+.. ...||||||||++|+.++++++|||||.
T Consensus 36 ~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~--~~~~DiAll~L~~~~~~~~~v~picl~~ 113 (232)
T cd00190 36 WVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHPNYNPS--TYDNDIALLKLKRPVTLSDNVRPICLPS 113 (232)
T ss_pred EEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECCCCCCC--CCcCCEEEEEECCcccCCCcccceECCC
Confidence 58999999977545678999998877554445678899999999999875 5689999999999999999999999997
Q ss_pred C--CCCCCCCEEEEeccccccCCcccccccceeeeeeecCccccccccccccccccccceeeccCCcccCCchhhhchhh
Q psy3170 82 A--HNVKSPTAIASGFGKLNYFECTQYSKIQDESPIALAPALVGGVRYVKTQCDILAMPMIIGGSRAKYGEFPHQCTQYS 159 (525)
Q Consensus 82 ~--~~~~~~~~~v~GWG~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~C~~~~ 159 (525)
. ....+..+.++|||.+.... ..+..++...+.+.+...|...+.. .......++|.+... .....|..++
T Consensus 114 ~~~~~~~~~~~~~~G~g~~~~~~--~~~~~~~~~~~~~~~~~~C~~~~~~--~~~~~~~~~C~~~~~---~~~~~c~gds 186 (232)
T cd00190 114 SGYNLPAGTTCTVSGWGRTSEGG--PLPDVLQEVNVPIVSNAECKRAYSY--GGTITDNMLCAGGLE---GGKDACQGDS 186 (232)
T ss_pred ccccCCCCCEEEEEeCCcCCCCC--CCCceeeEEEeeeECHHHhhhhccC--cccCCCceEeeCCCC---CCCccccCCC
Confidence 7 45667889999999876542 3556788888888888888765542 112344566665432 1234566554
Q ss_pred hhcccCCcccc----cccccceeEeecccc
Q psy3170 160 KIQDESPIALA----PALVGGVRYVRTQCD 185 (525)
Q Consensus 160 ~~~~~~~l~~~----~~~~g~v~~~~~~Cg 185 (525)
++|+... ..++|.+++... |+
T Consensus 187 ----Ggpl~~~~~~~~~lvGI~s~g~~-c~ 211 (232)
T cd00190 187 ----GGPLVCNDNGRGVLVGIVSWGSG-CA 211 (232)
T ss_pred ----CCcEEEEeCCEEEEEEEEehhhc-cC
Confidence 5555544 334555555433 75
No 7
>KOG3627|consensus
Probab=99.72 E-value=6.2e-17 Score=155.51 Aligned_cols=172 Identities=24% Similarity=0.327 Sum_probs=125.2
Q ss_pred eeeeccCcccC-CCCCeEEEEceeecccC-CcC--cceEEEEEEEECCCCCCCCCCCc-CceEEEEeCCCccCCCceeee
Q psy3170 3 NNHAAHCITSP-LGKPRYVRFGLITKLSY-SVT--DNIHRVMQNILHPNYTTEGTSQY-HDIALLKIAPPVEFSETLKPA 77 (525)
Q Consensus 3 ~lTAAHC~~~~-~~~~~~v~~G~~~~~~~-~~~--~~~~~v~~i~~hp~y~~~~~~~~-nDIALl~L~~~v~~~~~v~pi 77 (525)
+||||||+... .. .+.|++|.++.... ... .....|.++++||+|+.. ... ||||||+|++++.|+++|+||
T Consensus 50 vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i~H~~y~~~--~~~~nDiall~l~~~v~~~~~i~pi 126 (256)
T KOG3627|consen 50 VLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVGDVEKIIVHPNYNPR--TLENNDIALLRLSEPVTFSSHIQPI 126 (256)
T ss_pred EEEChhhCCCCCCc-ceEEEECccccccccccCchhhhceeeEEEECCCCCCC--CCCCCCEEEEEECCCcccCCccccc
Confidence 79999999774 22 78899998755433 222 245668889999999875 445 999999999999999999999
Q ss_pred ecCCCC----CCCCCCEEEEeccccccCCcccccccceeeeeeecCccccccccccccccccccceeeccCCcccCCchh
Q psy3170 78 CLNRAH----NVKSPTAIASGFGKLNYFECTQYSKIQDESPIALAPALVGGVRYVKTQCDILAMPMIIGGSRAKYGEFPH 153 (525)
Q Consensus 78 cL~~~~----~~~~~~~~v~GWG~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 153 (525)
|||... ...+..|.++|||.+.... ...+..++.+.+.+.+...|...+.... ..+..++|++... ....
T Consensus 127 clp~~~~~~~~~~~~~~~v~GWG~~~~~~-~~~~~~L~~~~v~i~~~~~C~~~~~~~~--~~~~~~~Ca~~~~---~~~~ 200 (256)
T KOG3627|consen 127 CLPSSADPYFPPGGTTCLVSGWGRTESGG-GPLPDTLQEVDVPIISNSECRRAYGGLG--TITDTMLCAGGPE---GGKD 200 (256)
T ss_pred CCCCCcccCCCCCCCEEEEEeCCCcCCCC-CCCCceeEEEEEeEcChhHhcccccCcc--ccCCCEEeeCccC---CCCc
Confidence 998543 2334789999999987652 2456778888999999888988765421 2334578887531 1234
Q ss_pred hhchhhhhcccCCcccc----cccccceeEeeccccCC
Q psy3170 154 QCTQYSKIQDESPIALA----PALVGGVRYVRTQCDIL 187 (525)
Q Consensus 154 ~C~~~~~~~~~~~l~~~----~~~~g~v~~~~~~Cg~~ 187 (525)
.|++++ ++|+.+. ..++|.+++....|+..
T Consensus 201 ~C~GDS----GGPLv~~~~~~~~~~GivS~G~~~C~~~ 234 (256)
T KOG3627|consen 201 ACQGDS----GGPLVCEDNGRWVLVGIVSWGSGGCGQP 234 (256)
T ss_pred cccCCC----CCeEEEeeCCcEEEEEEEEecCCCCCCC
Confidence 688776 6788776 35678888876668754
No 8
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.68 E-value=5.3e-16 Score=146.31 Aligned_cols=170 Identities=25% Similarity=0.367 Sum_probs=119.2
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
+|||||||+.......+.|++|.++..... ..+.+.|..++.||+|+.. ...+|||||+|++|+.++++++|+||+.
T Consensus 37 ~VLTaahC~~~~~~~~~~v~~g~~~~~~~~-~~~~~~v~~~~~~p~~~~~--~~~~DiAll~L~~~i~~~~~~~pi~l~~ 113 (229)
T smart00020 37 WVLTAAHCVYGSDPSNIRVRLGSHDLSSGE-EGQVIKVSKVIIHPNYNPS--TYDNDIALLKLKSPVTLSDNVRPICLPS 113 (229)
T ss_pred EEEECHHHcCCCCCcceEEEeCcccCCCCC-CceEEeeEEEEECCCCCCC--CCcCCEEEEEECcccCCCCceeeccCCC
Confidence 589999999875456799999987654322 2377899999999999864 6689999999999999999999999997
Q ss_pred C--CCCCCCCEEEEeccccccCCcccccccceeeeeeecCccccccccccccccccccceeeccCCcccCCchhhhchhh
Q psy3170 82 A--HNVKSPTAIASGFGKLNYFECTQYSKIQDESPIALAPALVGGVRYVKTQCDILAMPMIIGGSRAKYGEFPHQCTQYS 159 (525)
Q Consensus 82 ~--~~~~~~~~~v~GWG~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~C~~~~ 159 (525)
. ....+..+.++|||.... ........++...+.+.+...|...+... ......++|.+... .....|..++
T Consensus 114 ~~~~~~~~~~~~~~g~g~~~~-~~~~~~~~~~~~~~~~~~~~~C~~~~~~~--~~~~~~~~C~~~~~---~~~~~c~gds 187 (229)
T smart00020 114 SNYNVPAGTTCTVSGWGRTSE-GAGSLPDTLQEVNVPIVSNATCRRAYSGG--GAITDNMLCAGGLE---GGKDACQGDS 187 (229)
T ss_pred cccccCCCCEEEEEeCCCCCC-CCCcCCCEeeEEEEEEeCHHHhhhhhccc--cccCCCcEeecCCC---CCCcccCCCC
Confidence 6 455678899999998754 21234556777788888877787644321 12344556665432 1234566554
Q ss_pred hhcccCCccccc---ccccceeEeecccc
Q psy3170 160 KIQDESPIALAP---ALVGGVRYVRTQCD 185 (525)
Q Consensus 160 ~~~~~~~l~~~~---~~~g~v~~~~~~Cg 185 (525)
++|+.... .++|.+.... .|+
T Consensus 188 ----G~pl~~~~~~~~l~Gi~s~g~-~C~ 211 (229)
T smart00020 188 ----GGPLVCNDGRWVLVGIVSWGS-GCA 211 (229)
T ss_pred ----CCeeEEECCCEEEEEEEEECC-CCC
Confidence 45555444 4566556654 775
No 9
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.62 E-value=1.7e-14 Score=140.34 Aligned_cols=240 Identities=21% Similarity=0.362 Sum_probs=139.8
Q ss_pred eccccCCC---CCeeecCccCCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccccccccchh
Q psy3170 181 RTQCDILA---MPMIIGGSRAKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGTMVKAPLRT 257 (525)
Q Consensus 181 ~~~Cg~~~---~~~i~~g~~~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~~~~~~~~~ 257 (525)
...||... ..++.+|..+...+.||.+.+...... ....+++||+||+||+||++||+......
T Consensus 28 l~~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~----~~~~~~~gtlIS~RHiLtss~~~~~~~~~--------- 94 (282)
T PF03761_consen 28 LETCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHN----EGNYFSTGTLISPRHILTSSHCVMNDKSK--------- 94 (282)
T ss_pred HHhcCCCCCCCcccccCCcccccCCCCCEEEEEeccCc----ccceecceEEeccCeEEEeeeEEEecccc---------
Confidence 35798443 345789999999999999999876532 24456699999999999999998542111
Q ss_pred heeeeecceeeeecCCccccceeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCC
Q psy3170 258 LLFISMAEVGFLEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNY 337 (525)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y 337 (525)
|++ ........|.+-. .+++|. .+-+ +.+.+ ...............+.++++--..
T Consensus 95 ----------W~~---~~~~~~~~C~~~~--~~l~vP-~~~l-----~~~~v---~~~~~~~~~~~~~~~v~ka~il~~C 150 (282)
T PF03761_consen 95 ----------WLN---GEEFDNKKCEGNN--NHLIVP-EEVL-----SKIDV---RCCNCFSNGKCFSIKVKKAYILNGC 150 (282)
T ss_pred ----------ccc---CcccccceeeCCC--ceEEeC-HHHh-----ccEEE---EeecccccCCcccceeEEEEEEecC
Confidence 100 0111234566520 011111 1111 11222 1101111111122335555553222
Q ss_pred --CCCCCCcccceEEEEECCCcccCCCccceecCCCCCC--CCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhc
Q psy3170 338 --TTEGTSQYHDIALLKIAPPVEFSETLKPACLNRAHNV--KSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSK 413 (525)
Q Consensus 338 --~~~~~~~~~DIAll~L~~~~~~~~~v~picL~~~~~~--~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~ 413 (525)
........++++||+|+++ ++....|+||+..... .+....+.|+ .....+....+.+.....
T Consensus 151 ~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~~~~~~~~~~~yg~--------~~~~~~~~~~~~i~~~~~--- 217 (282)
T PF03761_consen 151 KKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSSTNWEKGDEVDVYGF--------NSTGKLKHRKLKITNCTK--- 217 (282)
T ss_pred CCcccccccccceEEEEEccc--ccccCCCEEeCCCccccccCceEEEeec--------CCCCeEEEEEEEEEEeec---
Confidence 1111344579999999999 6788999999987653 3455556666 122234444455443212
Q ss_pred ccCCCCCCcEEEEeCCCCcCCCcCCCCCcceeecCCCceeEEEEEEeecC-CCCCCCCceEEEEcCCchhhh
Q psy3170 414 QETTLISSQLCATVMAGGKDTCQGDSGGPLQTIMPDLCMYNIIGITSYGR-QCGHANTPAIYTRVSYYVPWI 484 (525)
Q Consensus 414 ~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~-~c~~~~~p~v~t~v~~~~~WI 484 (525)
|..........|.||+||||+...++ +++|+||.+.+. .|. .....|.+|..|.+=|
T Consensus 218 ----------~~~~~~~~~~~~~~d~Gg~lv~~~~g--r~tlIGv~~~~~~~~~--~~~~~f~~v~~~~~~I 275 (282)
T PF03761_consen 218 ----------CAYSICTKQYSCKGDRGGPLVKNING--RWTLIGVGASGNYECN--KNNSYFFNVSWYQDEI 275 (282)
T ss_pred ----------cceeEecccccCCCCccCeEEEEECC--CEEEEEEEccCCCccc--ccccEEEEHHHhhhhh
Confidence 22222234578999999999988776 899999998774 343 2267788888776644
No 10
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.58 E-value=1.3e-14 Score=135.76 Aligned_cols=165 Identities=26% Similarity=0.406 Sum_probs=117.6
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.|||||||+.. ...+.+++|...........+.+.|++++.||+|+.. ...+|||||+|++++.+.+.++|+||+.
T Consensus 36 ~vLTaahC~~~--~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~~~~--~~~~DiAll~L~~~~~~~~~~~~~~l~~ 111 (220)
T PF00089_consen 36 WVLTAAHCVDG--ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKYDPS--TYDNDIALLKLDRPITFGDNIQPICLPS 111 (220)
T ss_dssp EEEEEGGGHTS--GGSEEEEESESBTTSTTTTSEEEEEEEEEEETTSBTT--TTTTSEEEEEESSSSEHBSSBEESBBTS
T ss_pred ccccccccccc--ccccccccccccccccccccccccccccccccccccc--cccccccccccccccccccccccccccc
Confidence 58999999976 3578899998555444444678999999999999875 4579999999999999999999999997
Q ss_pred CC--CCCCCCEEEEeccccccCCcccccccceeeeeeecCccccccccccccccccccceeeccCCcccCCchhhhchhh
Q psy3170 82 AH--NVKSPTAIASGFGKLNYFECTQYSKIQDESPIALAPALVGGVRYVKTQCDILAMPMIIGGSRAKYGEFPHQCTQYS 159 (525)
Q Consensus 82 ~~--~~~~~~~~v~GWG~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~C~~~~ 159 (525)
.. ...+..+.+.|||.....+ ....++...+.+.+...|...+.. .....++|.+.. .....|..++
T Consensus 112 ~~~~~~~~~~~~~~G~~~~~~~~---~~~~~~~~~~~~~~~~~c~~~~~~----~~~~~~~c~~~~----~~~~~~~g~s 180 (220)
T PF00089_consen 112 AGSDPNVGTSCIVVGWGRTSDNG---YSSNLQSVTVPVVSRKTCRSSYND----NLTPNMICAGSS----GSGDACQGDS 180 (220)
T ss_dssp TTHTTTTTSEEEEEESSBSSTTS---BTSBEEEEEEEEEEHHHHHHHTTT----TSTTTEEEEETT----SSSBGGTTTT
T ss_pred ccccccccccccccccccccccc---cccccccccccccccccccccccc----cccccccccccc----cccccccccc
Confidence 43 3567889999999865433 345667777777777677664211 134455665542 1134666554
Q ss_pred hhcccCCcccccc-cccceeEeeccccC
Q psy3170 160 KIQDESPIALAPA-LVGGVRYVRTQCDI 186 (525)
Q Consensus 160 ~~~~~~~l~~~~~-~~g~v~~~~~~Cg~ 186 (525)
++|+..... ++|.+... ..|+.
T Consensus 181 ----G~pl~~~~~~lvGI~s~~-~~c~~ 203 (220)
T PF00089_consen 181 ----GGPLICNNNYLVGIVSFG-ENCGS 203 (220)
T ss_dssp ----TSEEEETTEEEEEEEEEE-SSSSB
T ss_pred ----ccccccceeeecceeeec-CCCCC
Confidence 566666555 66655554 66753
No 11
>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=99.14 E-value=3.1e-10 Score=101.52 Aligned_cols=99 Identities=17% Similarity=0.297 Sum_probs=70.3
Q ss_pred eeEeEEEEEeCCEEEecCCCCCCCCC--CceEEEEEEEeeccc-ccccce-EEEEEEEeCCCCCCCCCCcccceEEEEEC
Q psy3170 279 KWFCGGSLISPNYVMTAAHCITSPLG--KPRYVRFGLITKLSY-SVTDNI-HRVMQNILHPNYTTEGTSQYHDIALLKIA 354 (525)
Q Consensus 279 ~~~C~GtLIs~~~VLTAAhCv~~~~~--~~~~v~~g~~~~~~~-~~~~~~-~~v~~i~~hp~y~~~~~~~~~DIAll~L~ 354 (525)
.+.|+|+||.++|||++..|+.+... ....+.+|..-.... ....+| .+|..+..- ...+++||.|+
T Consensus 27 ~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V---------~~S~v~LLHL~ 97 (267)
T PF09342_consen 27 RYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDV---------PESNVLLLHLE 97 (267)
T ss_pred eEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeec---------cccceeeeeec
Confidence 78999999999999999999977533 456677776622221 222223 235543322 23599999999
Q ss_pred CCcccCCCccceecCC--CCCCCCCcEEEEEeee
Q psy3170 355 PPVEFSETLKPACLNR--AHNVKSPTAIASGFGK 386 (525)
Q Consensus 355 ~~~~~~~~v~picL~~--~~~~~~~~~~~~Gwg~ 386 (525)
+|+.|+.+|+|..||. .+......|..+|-..
T Consensus 98 ~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 98 QPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred CcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 9999999999999997 3345556888888643
No 12
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=1.3e-09 Score=102.81 Aligned_cols=172 Identities=17% Similarity=0.150 Sum_probs=106.2
Q ss_pred eeeeccCcccCCC---CCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeec
Q psy3170 3 NNHAAHCITSPLG---KPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACL 79 (525)
Q Consensus 3 ~lTAAHC~~~~~~---~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL 79 (525)
|||||||+....+ ....|.++..+. ...+...|..++.|..|.+. ++.||||+++|.++...- .+. +-+
T Consensus 73 vLTAAHC~~~~s~is~d~~~vv~~l~d~----Sq~~rg~vr~i~~~efY~~~--n~~ND~Av~~l~~~a~~p-r~k-i~~ 144 (413)
T COG5640 73 VLTAAHCADASSPISSDVNRVVVDLNDS----SQAERGHVRTIYVHEFYSPG--NLGNDIAVLELARAASLP-RVK-ITS 144 (413)
T ss_pred EeeehhhccCCCCccccceEEEeccccc----ccccCcceEEEeeecccccc--cccCcceeeccccccccc-hhh-eee
Confidence 7999999977543 334455554332 34456789999999999876 789999999999976531 111 111
Q ss_pred C--CC----CCCCCCCEEEEeccccccCCcccc-c--ccceeeeeeecCccccccccccccccccc----cceeeccCCc
Q psy3170 80 N--RA----HNVKSPTAIASGFGKLNYFECTQY-S--KIQDESPIALAPALVGGVRYVKTQCDILA----MPMIIGGSRA 146 (525)
Q Consensus 80 ~--~~----~~~~~~~~~v~GWG~~~~~~~~~~-~--~~~~~~~~~~~~~~~c~~~~~~~~~~~~~----~~~~~~~~~~ 146 (525)
. .. .........+.+||.+........ + ..++++.+.+.+-..|...+.. |.... -..+|.|..
T Consensus 145 ~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e~~v~fv~~stc~~~~g~--an~~dg~~~lT~~cag~~- 221 (413)
T COG5640 145 FDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKGC--ANASDGATGLTGFCAGRP- 221 (413)
T ss_pred ccCcccceecccccccccceeeeeeeecCCCCCCCccceeeeeeeeeechHHhhhhccc--cccCCCCCCccceecCCC-
Confidence 1 11 011223456777776644332222 2 4788888888888777665431 11111 112444432
Q ss_pred ccCCchhhhchhhhhcccCCcccc----cccccceeEeeccccCCCCCeee
Q psy3170 147 KYGEFPHQCTQYSKIQDESPIALA----PALVGGVRYVRTQCDILAMPMII 193 (525)
Q Consensus 147 ~~g~~~~~C~~~~~~~~~~~l~~~----~~~~g~v~~~~~~Cg~~~~~~i~ 193 (525)
..+.|++++ ++|+... +.+.|.++|....||.+..+.|+
T Consensus 222 ----~~daCqGDS----GGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVy 264 (413)
T COG5640 222 ----PKDACQGDS----GGPIFHKGEEGRVQRGVVSWGDGGCGGTLIPGVY 264 (413)
T ss_pred ----CcccccCCC----CCceEEeCCCccEEEeEEEecCCCCCCCCcceeE
Confidence 267898887 5666433 45789999999999877666543
No 13
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.90 E-value=1e-08 Score=94.52 Aligned_cols=182 Identities=16% Similarity=0.157 Sum_probs=92.9
Q ss_pred eeEeEEEEEeCCEEEecCCCCCCCCCCc-eEEEEEEEeecccccccceEEEEEE--EeCCC-CCCCCCCcccceEEEEEC
Q psy3170 279 KWFCGGSLISPNYVMTAAHCITSPLGKP-RYVRFGLITKLSYSVTDNIHRVMQN--ILHPN-YTTEGTSQYHDIALLKIA 354 (525)
Q Consensus 279 ~~~C~GtLIs~~~VLTAAhCv~~~~~~~-~~v~~g~~~~~~~~~~~~~~~v~~i--~~hp~-y~~~~~~~~~DIAll~L~ 354 (525)
+.-|+++||+++.||||+||+....... ....+-.. ....+.....+..+ .+.|. +.. ......|+..+.|+
T Consensus 63 ~~~~~~~lI~pntvLTa~Hc~~s~~~G~~~~~~~p~g---~~~~~~~~~~~~~~~~~~~~g~~~~-~d~~~~~v~~~~~~ 138 (251)
T COG3591 63 RLCTAATLIGPNTVLTAGHCIYSPDYGEDDIAAAPPG---VNSDGGPFYGITKIEIRVYPGELYK-EDGASYDVGEAALE 138 (251)
T ss_pred cceeeEEEEcCceEEEeeeEEecCCCChhhhhhcCCc---ccCCCCCCCceeeEEEEecCCceec-cCCceeeccHHHhc
Confidence 4568889999999999999998753221 11111101 11111111112222 22343 222 14455677777777
Q ss_pred CCcccCCCccceecCCCCC-CCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCCCCcEEEEeCCCCcC
Q psy3170 355 PPVEFSETLKPACLNRAHN-VKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLISSQLCATVMAGGKD 433 (525)
Q Consensus 355 ~~~~~~~~v~picL~~~~~-~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~~~~~Ca~~~~~~~~ 433 (525)
....+.+......++.... ..+....+.||-..... .++.- +.|.+... + ...+- .-..+
T Consensus 139 ~g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~------~~~~~-------e~t~~v~~-~-~~~~l----~y~~d 199 (251)
T COG3591 139 SGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPN------IGTMW-------ESTGKVNS-I-KGNKL----FYDAD 199 (251)
T ss_pred cCCCccccccccccccccccccCceeEEEeccCCCCc------ceeEe-------eecceeEE-E-ecceE----EEEec
Confidence 4454455444333433322 34445788888543321 11110 11111100 0 11111 12458
Q ss_pred CCcCCCCCcceeecCCCceeEEEEEEeecCCCCCCCCceEEEEcC-Cchhhhcccc
Q psy3170 434 TCQGDSGGPLQTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVS-YYVPWIVHTV 488 (525)
Q Consensus 434 ~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~-~~~~WI~~~i 488 (525)
++.|+||+|++... .+++||.+-+..-.........+++. .+++||++.+
T Consensus 200 T~pG~SGSpv~~~~-----~~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~ 250 (251)
T COG3591 200 TLPGSSGSPVLISK-----DEVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNI 250 (251)
T ss_pred ccCCCCCCceEecC-----ceEEEEEecCCCcccccccCcceEecHHHHHHHHHhh
Confidence 99999999998642 27999999885432122333344443 4778888765
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=97.90 E-value=0.00016 Score=74.63 Aligned_cols=142 Identities=20% Similarity=0.192 Sum_probs=79.4
Q ss_pred ceeEeEEEEEeCC-EEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCC
Q psy3170 278 VKWFCGGSLISPN-YVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPP 356 (525)
Q Consensus 278 ~~~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~ 356 (525)
....++|.+|+++ +|||++|++.+ ...+.|.+... .....+-+..+| ..|||||+++.+
T Consensus 56 ~~~~GSGfii~~~G~IlTn~Hvv~~--~~~i~V~~~~~---------~~~~a~vv~~d~---------~~DlAllkv~~~ 115 (428)
T TIGR02037 56 VRGLGSGVIISADGYILTNNHVVDG--ADEITVTLSDG---------REFKAKLVGKDP---------RTDIAVLKIDAK 115 (428)
T ss_pred ccceeeEEEECCCCEEEEcHHHcCC--CCeEEEEeCCC---------CEEEEEEEEecC---------CCCEEEEEecCC
Confidence 3578999999976 99999999976 34444444211 122222222222 269999999864
Q ss_pred cccCCCccceecCCCC-CCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCCCCcEEEEeCCCCcCCC
Q psy3170 357 VEFSETLKPACLNRAH-NVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLISSQLCATVMAGGKDTC 435 (525)
Q Consensus 357 ~~~~~~v~picL~~~~-~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~~~~~Ca~~~~~~~~~C 435 (525)
..+.++.|.... ...+..+.+.|+.... ........+.-..... .........+- -+...-
T Consensus 116 ----~~~~~~~l~~~~~~~~G~~v~aiG~p~g~------~~~~t~G~vs~~~~~~---~~~~~~~~~i~-----tda~i~ 177 (428)
T TIGR02037 116 ----KNLPVIKLGDSDKLRVGDWVLAIGNPFGL------GQTVTSGIVSALGRSG---LGIGDYENFIQ-----TDAAIN 177 (428)
T ss_pred ----CCceEEEccCCCCCCCCCEEEEEECCCcC------CCcEEEEEEEecccCc---cCCCCccceEE-----ECCCCC
Confidence 245577776543 3678889998985321 1112222222111110 00000011111 122455
Q ss_pred cCCCCCcceeecCCCceeEEEEEEeec
Q psy3170 436 QGDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 436 ~gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
.|.|||||+.. ...++||.+..
T Consensus 178 ~GnSGGpl~n~-----~G~viGI~~~~ 199 (428)
T TIGR02037 178 PGNSGGPLVNL-----RGEVIGINTAI 199 (428)
T ss_pred CCCCCCceECC-----CCeEEEEEeEE
Confidence 78999999742 45799998764
No 15
>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=97.86 E-value=8.2e-05 Score=61.91 Aligned_cols=21 Identities=43% Similarity=0.705 Sum_probs=19.3
Q ss_pred eEEEEEeCC-EEEecCCCCCCC
Q psy3170 282 CGGSLISPN-YVMTAAHCITSP 302 (525)
Q Consensus 282 C~GtLIs~~-~VLTAAhCv~~~ 302 (525)
|+|.+|+++ +|||++||+...
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDW 22 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCC
T ss_pred CEEEEEcCCceEEEchhheecc
Confidence 789999999 999999999764
No 16
>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=97.49 E-value=0.0014 Score=65.64 Aligned_cols=140 Identities=17% Similarity=0.175 Sum_probs=75.5
Q ss_pred eeEeEEEEEeCC-EEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCCc
Q psy3170 279 KWFCGGSLISPN-YVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPV 357 (525)
Q Consensus 279 ~~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~~ 357 (525)
....+|.+|+++ +|||++|.+.. ...+.|.+.. +.....+-+..+| ..||||||++.+-
T Consensus 77 ~~~GSG~vi~~~G~IlTn~HVV~~--~~~i~V~~~d---------g~~~~a~vv~~d~---------~~DlAvlkv~~~~ 136 (351)
T TIGR02038 77 QGLGSGVIMSKEGYILTNYHVIKK--ADQIVVALQD---------GRKFEAELVGSDP---------LTDLAVLKIEGDN 136 (351)
T ss_pred cceEEEEEEeCCeEEEecccEeCC--CCEEEEEECC---------CCEEEEEEEEecC---------CCCEEEEEecCCC
Confidence 457999999976 99999999965 3344444321 1122222222222 2699999997542
Q ss_pred ccCCCccceecCCC-CCCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCCCCcEEEEeCCCCcCCCc
Q psy3170 358 EFSETLKPACLNRA-HNVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLISSQLCATVMAGGKDTCQ 436 (525)
Q Consensus 358 ~~~~~v~picL~~~-~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~~~~~Ca~~~~~~~~~C~ 436 (525)
..++.+... ....++.+...|+.... ........+....... ....-....+ .-+....+
T Consensus 137 -----~~~~~l~~s~~~~~G~~V~aiG~P~~~------~~s~t~GiIs~~~r~~---~~~~~~~~~i-----qtda~i~~ 197 (351)
T TIGR02038 137 -----LPTIPVNLDRPPHVGDVVLAIGNPYNL------GQTITQGIISATGRNG---LSSVGRQNFI-----QTDAAINA 197 (351)
T ss_pred -----CceEeccCcCccCCCCEEEEEeCCCCC------CCcEEEEEEEeccCcc---cCCCCcceEE-----EECCccCC
Confidence 334445332 34678888888885321 1112222222221110 0000001111 11234568
Q ss_pred CCCCCcceeecCCCceeEEEEEEeec
Q psy3170 437 GDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 437 gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
|.|||||+-. +..++||.+..
T Consensus 198 GnSGGpl~n~-----~G~vIGI~~~~ 218 (351)
T TIGR02038 198 GNSGGALINT-----NGELVGINTAS 218 (351)
T ss_pred CCCcceEECC-----CCeEEEEEeee
Confidence 9999999742 45799998764
No 17
>PRK10898 serine endoprotease; Provisional
Probab=97.37 E-value=0.0033 Score=62.95 Aligned_cols=139 Identities=17% Similarity=0.197 Sum_probs=74.1
Q ss_pred eeEeEEEEEeCC-EEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCCc
Q psy3170 279 KWFCGGSLISPN-YVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPV 357 (525)
Q Consensus 279 ~~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~~ 357 (525)
...-+|.+|+++ +|||++|=+.+ ...+.|.+.. +.....+-+..+| ..||||||++.+
T Consensus 77 ~~~GSGfvi~~~G~IlTn~HVv~~--a~~i~V~~~d---------g~~~~a~vv~~d~---------~~DlAvl~v~~~- 135 (353)
T PRK10898 77 RTLGSGVIMDQRGYILTNKHVIND--ADQIIVALQD---------GRVFEALLVGSDS---------LTDLAVLKINAT- 135 (353)
T ss_pred cceeeEEEEeCCeEEEecccEeCC--CCEEEEEeCC---------CCEEEEEEEEEcC---------CCCEEEEEEcCC-
Confidence 467999999976 99999998865 3444444421 1122222222222 269999999753
Q ss_pred ccCCCccceecCCCC-CCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCC-CCcEEEEeCCCCcCCC
Q psy3170 358 EFSETLKPACLNRAH-NVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLI-SSQLCATVMAGGKDTC 435 (525)
Q Consensus 358 ~~~~~v~picL~~~~-~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~-~~~~Ca~~~~~~~~~C 435 (525)
...++.|.... ...+..+...|+..... .......+.-..+. ...... ...+- .+...-
T Consensus 136 ----~l~~~~l~~~~~~~~G~~V~aiG~P~g~~------~~~t~Giis~~~r~----~~~~~~~~~~iq-----tda~i~ 196 (353)
T PRK10898 136 ----NLPVIPINPKRVPHIGDVVLAIGNPYNLG------QTITQGIISATGRI----GLSPTGRQNFLQ-----TDASIN 196 (353)
T ss_pred ----CCCeeeccCcCcCCCCCEEEEEeCCCCcC------CCcceeEEEecccc----ccCCccccceEE-----eccccC
Confidence 12344443332 35678888888753211 11111222111110 000000 11111 123456
Q ss_pred cCCCCCcceeecCCCceeEEEEEEeec
Q psy3170 436 QGDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 436 ~gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
+|.|||||+-. +..++||.+..
T Consensus 197 ~GnSGGPl~n~-----~G~vvGI~~~~ 218 (353)
T PRK10898 197 HGNSGGALVNS-----LGELMGINTLS 218 (353)
T ss_pred CCCCcceEECC-----CCeEEEEEEEE
Confidence 79999999742 55799998865
No 18
>PRK10139 serine endoprotease; Provisional
Probab=97.37 E-value=0.0016 Score=67.38 Aligned_cols=141 Identities=18% Similarity=0.187 Sum_probs=77.7
Q ss_pred eeEeEEEEEeC--CEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCC
Q psy3170 279 KWFCGGSLISP--NYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPP 356 (525)
Q Consensus 279 ~~~C~GtLIs~--~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~ 356 (525)
....+|.+|++ -+|||.+|.+.+ ...+.|.+... .....+-+... ...||||||++.+
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~--a~~i~V~~~dg---------~~~~a~vvg~D---------~~~DlAvlkv~~~ 148 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQ--AQKISIQLNDG---------REFDAKLIGSD---------DQSDIALLQIQNP 148 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCC--CCEEEEEECCC---------CEEEEEEEEEc---------CCCCEEEEEecCC
Confidence 45799999974 699999999976 45556655321 12222222222 2369999999854
Q ss_pred cccCCCccceecCCCC-CCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCCCCcEEEEeCCCCcCCC
Q psy3170 357 VEFSETLKPACLNRAH-NVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLISSQLCATVMAGGKDTC 435 (525)
Q Consensus 357 ~~~~~~v~picL~~~~-~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~~~~~Ca~~~~~~~~~C 435 (525)
- ...++.|.... ...+..+...|+.... ........+.-..+.. ..... ....+- .+...-
T Consensus 149 ~----~l~~~~lg~s~~~~~G~~V~aiG~P~g~------~~tvt~GivS~~~r~~--~~~~~-~~~~iq-----tda~in 210 (455)
T PRK10139 149 S----KLTQIAIADSDKLRVGDFAVAVGNPFGL------GQTATSGIISALGRSG--LNLEG-LENFIQ-----TDASIN 210 (455)
T ss_pred C----CCceeEecCccccCCCCEEEEEecCCCC------CCceEEEEEccccccc--cCCCC-cceEEE-----ECCccC
Confidence 2 34466665443 3568888888874211 1112222222111110 00000 011111 123456
Q ss_pred cCCCCCcceeecCCCceeEEEEEEeec
Q psy3170 436 QGDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 436 ~gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
+|.|||||+-. +..++||.+..
T Consensus 211 ~GnSGGpl~n~-----~G~vIGi~~~~ 232 (455)
T PRK10139 211 RGNSGGALLNL-----NGELIGINTAI 232 (455)
T ss_pred CCCCcceEECC-----CCeEEEEEEEE
Confidence 89999999742 45799999864
No 19
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=97.18 E-value=0.0015 Score=59.28 Aligned_cols=86 Identities=17% Similarity=0.156 Sum_probs=62.5
Q ss_pred eeeeccCcccCCC--CCeEEEEceee--cccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeee
Q psy3170 3 NNHAAHCITSPLG--KPRYVRFGLIT--KLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPAC 78 (525)
Q Consensus 3 ~lTAAHC~~~~~~--~~~~v~~G~~~--~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~pic 78 (525)
+|++-.|+...+. ..+.+.+|... +.-..+.+|+++|..+..-| ..+++||.|++|+.|+.+|+|+.
T Consensus 40 lLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~---------~S~v~LLHL~~~~~fTr~VlP~f 110 (267)
T PF09342_consen 40 LLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVP---------ESNVLLLHLEQPANFTRYVLPTF 110 (267)
T ss_pred EEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeecc---------ccceeeeeecCcccceeeecccc
Confidence 6889999976443 56778898653 22345677888887664332 34999999999999999999999
Q ss_pred cCC--CCCCCCCCEEEEeccc
Q psy3170 79 LNR--AHNVKSPTAIASGFGK 97 (525)
Q Consensus 79 L~~--~~~~~~~~~~v~GWG~ 97 (525)
||. .+......|...|=-.
T Consensus 111 lp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 111 LPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cccccCCCCCCCceEEEEccc
Confidence 996 3334455788877543
No 20
>PRK10942 serine endoprotease; Provisional
Probab=97.14 E-value=0.0048 Score=64.21 Aligned_cols=140 Identities=17% Similarity=0.175 Sum_probs=75.2
Q ss_pred eeEeEEEEEeC--CEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCC
Q psy3170 279 KWFCGGSLISP--NYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPP 356 (525)
Q Consensus 279 ~~~C~GtLIs~--~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~ 356 (525)
....+|.+|+. -+|||.+|.+.+ ...+.|.+... .....+-+..+| ..||||||++.+
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 46799999985 499999999876 34555554321 112222222222 269999999743
Q ss_pred cccCCCccceecCCCC-CCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCC-CCCCcEEEEeCCCCcCC
Q psy3170 357 VEFSETLKPACLNRAH-NVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETT-LISSQLCATVMAGGKDT 434 (525)
Q Consensus 357 ~~~~~~v~picL~~~~-~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~-~~~~~~Ca~~~~~~~~~ 434 (525)
- ...++.|...+ ...+..+...|+.... ........+.-+... .... -....+-. +...
T Consensus 170 ~----~l~~~~lg~s~~l~~G~~V~aiG~P~g~------~~tvt~GiVs~~~r~----~~~~~~~~~~iqt-----da~i 230 (473)
T PRK10942 170 K----NLTAIKMADSDALRVGDYTVAIGNPYGL------GETVTSGIVSALGRS----GLNVENYENFIQT-----DAAI 230 (473)
T ss_pred C----CCceeEecCccccCCCCEEEEEcCCCCC------CcceeEEEEEEeecc----cCCcccccceEEe-----cccc
Confidence 2 23456664433 3567888887763211 111112222211110 0000 00111111 2345
Q ss_pred CcCCCCCcceeecCCCceeEEEEEEeec
Q psy3170 435 CQGDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 435 C~gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
-.|.|||||+.. +..++||.+..
T Consensus 231 ~~GnSGGpL~n~-----~GeviGI~t~~ 253 (473)
T PRK10942 231 NRGNSGGALVNL-----NGELIGINTAI 253 (473)
T ss_pred CCCCCcCccCCC-----CCeEEEEEEEE
Confidence 578999999743 45799998764
No 21
>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=92.76 E-value=0.21 Score=40.99 Aligned_cols=12 Identities=25% Similarity=0.061 Sum_probs=10.2
Q ss_pred ceeeeccCcccC
Q psy3170 2 VNNHAAHCITSP 13 (525)
Q Consensus 2 ~~lTAAHC~~~~ 13 (525)
.+||||||+...
T Consensus 11 ~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 11 YILTAAHVVEDW 22 (120)
T ss_dssp EEEEEHHHHTCC
T ss_pred eEEEchhheecc
Confidence 589999999764
No 22
>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=88.63 E-value=0.22 Score=54.54 Aligned_cols=33 Identities=27% Similarity=0.417 Sum_probs=25.1
Q ss_pred CCcCCCCCcceeecCCCceeEEEEEEeecCCCC
Q psy3170 434 TCQGDSGGPLQTIMPDLCMYNIIGITSYGRQCG 466 (525)
Q Consensus 434 ~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~ 466 (525)
.-.||||+||+..+....+|+|+|+++.+....
T Consensus 213 ~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~ 245 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYN 245 (769)
T ss_dssp --TT-TT-EEEEEETTTTEEEEEEEEEEECCCC
T ss_pred cccCcCCCceEEEEccCCeEEEEEEEccccccC
Confidence 457999999999988777999999999886553
No 23
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=88.47 E-value=0.23 Score=48.19 Aligned_cols=9 Identities=22% Similarity=0.135 Sum_probs=4.2
Q ss_pred EEEEEeeec
Q psy3170 379 AIASGFGKL 387 (525)
Q Consensus 379 ~~~~Gwg~~ 387 (525)
.++.|.+..
T Consensus 245 ~tlIGv~~~ 253 (282)
T PF03761_consen 245 WTLIGVGAS 253 (282)
T ss_pred EEEEEEEcc
Confidence 345555543
No 24
>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=88.31 E-value=2.2 Score=44.19 Aligned_cols=71 Identities=18% Similarity=0.098 Sum_probs=46.0
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.+||++|++.+. ..+.|.+. .+..+..+-+..+| ..|+||||++.+ ..+.++.|..
T Consensus 70 ~IlTn~Hvv~~~--~~i~V~~~---------~~~~~~a~vv~~d~---------~~DlAllkv~~~----~~~~~~~l~~ 125 (428)
T TIGR02037 70 YILTNNHVVDGA--DEITVTLS---------DGREFKAKLVGKDP---------RTDIAVLKIDAK----KNLPVIKLGD 125 (428)
T ss_pred EEEEcHHHcCCC--CeEEEEeC---------CCCEEEEEEEEecC---------CCCEEEEEecCC----CCceEEEccC
Confidence 379999999763 44555543 12345555443433 249999999865 3456777754
Q ss_pred -CCCCCCCCEEEEecc
Q psy3170 82 -AHNVKSPTAIASGFG 96 (525)
Q Consensus 82 -~~~~~~~~~~v~GWG 96 (525)
.....|..+.+.|+.
T Consensus 126 ~~~~~~G~~v~aiG~p 141 (428)
T TIGR02037 126 SDKLRVGDWVLAIGNP 141 (428)
T ss_pred CCCCCCCCEEEEEECC
Confidence 344678888888875
No 25
>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=86.81 E-value=3.3 Score=36.77 Aligned_cols=71 Identities=13% Similarity=0.074 Sum_probs=39.2
Q ss_pred ceeEeEEEEEeCCEEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCCc
Q psy3170 278 VKWFCGGSLISPNYVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPV 357 (525)
Q Consensus 278 ~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~~ 357 (525)
..+.|.+..|..+|.|-..|.- ....+.++.. ...+.+.+.. .+. .....||++++|.+.-
T Consensus 23 g~~t~l~~gi~~~~~lvp~H~~-----~~~~i~i~g~----------~~~~~d~~~l--v~~--~~~~~Dl~~v~l~~~~ 83 (172)
T PF00548_consen 23 GEFTMLALGIYDRYFLVPTHEE-----PEDTIYIDGV----------EYKVDDSVVL--VDR--DGVDTDLTLVKLPRNP 83 (172)
T ss_dssp EEEEEEEEEEEBTEEEEEGGGG-----GCSEEEETTE----------EEEEEEEEEE--EET--TSSEEEEEEEEEESSS
T ss_pred ceEEEecceEeeeEEEEECcCC-----CcEEEEECCE----------EEEeeeeEEE--ecC--CCcceeEEEEEccCCc
Confidence 3567888899999999999921 2223333211 1111111111 111 2234699999999888
Q ss_pred ccCCCcccee
Q psy3170 358 EFSETLKPAC 367 (525)
Q Consensus 358 ~~~~~v~pic 367 (525)
.|.+-.+-++
T Consensus 84 kfrDIrk~~~ 93 (172)
T PF00548_consen 84 KFRDIRKFFP 93 (172)
T ss_dssp -B--GGGGSB
T ss_pred ccCchhhhhc
Confidence 8876666555
No 26
>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=85.85 E-value=2.8 Score=38.95 Aligned_cols=155 Identities=17% Similarity=0.177 Sum_probs=64.9
Q ss_pred EEeCCEEEecCCCCCCCCCCceEEEE--EEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCCcccCCCc
Q psy3170 286 LISPNYVMTAAHCITSPLGKPRYVRF--GLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETL 363 (525)
Q Consensus 286 LIs~~~VLTAAhCv~~~~~~~~~v~~--g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~~~~~~~v 363 (525)
+.-..|++|.+|-+.... ..+.++. |.+ .... ...+-+||-. ..||.||+|.++++ +.
T Consensus 37 igyG~~iItn~HLf~~nn-g~L~i~s~hG~f-~v~n--------t~~lkv~~i~-------~~DiviirmPkDfp--Pf- 96 (235)
T PF00863_consen 37 IGYGSYIITNAHLFKRNN-GELTIKSQHGEF-TVPN--------TTQLKVHPIE-------GRDIVIIRMPKDFP--PF- 96 (235)
T ss_dssp EEETTEEEEEGGGGSSTT-CEEEEEETTEEE-EECE--------GGGSEEEE-T-------CSSEEEEE--TTS------
T ss_pred EeECCEEEEChhhhccCC-CeEEEEeCceEE-EcCC--------ccccceEEeC-------CccEEEEeCCcccC--Cc-
Confidence 456889999999986643 2344432 222 1111 1112233322 25999999988764 22
Q ss_pred cceecCCCCCCCCCcEEEEEeeeccCCCCcccccceEEEEEeeChhhhhcccCCCCCCcEEEEeCCCCcCCCcCCCCCcc
Q psy3170 364 KPACLNRAHNVKSPTAIASGFGKLNYFDTKESLRLMKVVLDIINNDTCSKQETTLISSQLCATVMAGGKDTCQGDSGGPL 443 (525)
Q Consensus 364 ~picL~~~~~~~~~~~~~~Gwg~~~~~~~~~~~~l~~~~v~~~~~~~C~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL 443 (525)
|-.+--..+..+..+.++|--...... .....+... +.+ .. ...|=. ...++=.||=|.||
T Consensus 97 -~~kl~FR~P~~~e~v~mVg~~fq~k~~---~s~vSesS~-i~p-~~---------~~~fWk----HwIsTk~G~CG~Pl 157 (235)
T PF00863_consen 97 -PQKLKFRAPKEGERVCMVGSNFQEKSI---SSTVSESSW-IYP-EE---------NSHFWK----HWISTKDGDCGLPL 157 (235)
T ss_dssp --S---B----TT-EEEEEEEECSSCCC---EEEEEEEEE-EEE-ET---------TTTEEE----E-C---TT-TT-EE
T ss_pred -chhhhccCCCCCCEEEEEEEEEEcCCe---eEEECCceE-Eee-cC---------CCCeeE----EEecCCCCccCCcE
Confidence 222222233445666666764332211 111111111 111 00 111110 01233468889999
Q ss_pred eeecCCCceeEEEEEEeecCCCCCCCCceEEEEcCC-chhhhcc
Q psy3170 444 QTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVSY-YVPWIVH 486 (525)
Q Consensus 444 ~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~~-~~~WI~~ 486 (525)
|...+ ..++||.|.+..-. .-..|+.+.. +.+-+.+
T Consensus 158 Vs~~D----g~IVGiHsl~~~~~---~~N~F~~f~~~f~~~~l~ 194 (235)
T PF00863_consen 158 VSTKD----GKIVGIHSLTSNTS---SRNYFTPFPDDFEEFYLE 194 (235)
T ss_dssp EETTT------EEEEEEEEETTT---SSEEEEE--TTHHHHHCC
T ss_pred EEcCC----CcEEEEEcCccCCC---CeEEEEcCCHHHHHHHhc
Confidence 98553 47999999874422 3457777654 4444433
No 27
>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=82.51 E-value=1.3 Score=36.47 Aligned_cols=39 Identities=26% Similarity=0.511 Sum_probs=28.5
Q ss_pred CcCCCCCcceeecCCCceeEEEEEEeecCCCCCCCCceEEEEcCCchhhhc
Q psy3170 435 CQGDSGGPLQTIMPDLCMYNIIGITSYGRQCGHANTPAIYTRVSYYVPWIV 485 (525)
Q Consensus 435 C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c~~~~~p~v~t~v~~~~~WI~ 485 (525)
=+||-||+|.|+. -++||++.|- ..-..|++|+.+ .|++
T Consensus 88 ~PGdCGg~L~C~H------GViGi~Tagg-----~g~VaF~dir~~-~~~e 126 (127)
T PF00947_consen 88 EPGDCGGILRCKH------GVIGIVTAGG-----EGHVAFADIRDL-LWLE 126 (127)
T ss_dssp STT-TCSEEEETT------CEEEEEEEEE-----TTEEEEEECCCG-STTS
T ss_pred CCCCCCceeEeCC------CeEEEEEeCC-----CceEEEEechhh-heec
Confidence 3799999999842 2899999872 235779999986 4654
No 28
>PRK10139 serine endoprotease; Provisional
Probab=80.34 E-value=6.7 Score=40.82 Aligned_cols=70 Identities=19% Similarity=0.134 Sum_probs=43.1
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.+||+||.+.+. ..+.|.+. ++..+..+-+...| ..||||||++.+- ...++.|..
T Consensus 103 ~IlTn~HVv~~a--~~i~V~~~---------dg~~~~a~vvg~D~---------~~DlAvlkv~~~~----~l~~~~lg~ 158 (455)
T PRK10139 103 YVLTNNHVINQA--QKISIQLN---------DGREFDAKLIGSDD---------QSDIALLQIQNPS----KLTQIAIAD 158 (455)
T ss_pred EEEeChHHhCCC--CEEEEEEC---------CCCEEEEEEEEEcC---------CCCEEEEEecCCC----CCceeEecC
Confidence 379999999763 45667653 12345555444432 3599999998642 234666653
Q ss_pred -CCCCCCCCEEEEec
Q psy3170 82 -AHNVKSPTAIASGF 95 (525)
Q Consensus 82 -~~~~~~~~~~v~GW 95 (525)
.....|....+.|.
T Consensus 159 s~~~~~G~~V~aiG~ 173 (455)
T PRK10139 159 SDKLRVGDFAVAVGN 173 (455)
T ss_pred ccccCCCCEEEEEec
Confidence 33456777777665
No 29
>PRK10942 serine endoprotease; Provisional
Probab=78.56 E-value=9 Score=40.10 Aligned_cols=70 Identities=16% Similarity=0.113 Sum_probs=41.8
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.|||+||.+.+. ..+.|.+.. +..+..+-+..+| ..||||||++.+-. +.++.|..
T Consensus 124 ~IlTn~HVv~~a--~~i~V~~~d---------g~~~~a~vv~~D~---------~~DlAvlki~~~~~----l~~~~lg~ 179 (473)
T PRK10942 124 YVVTNNHVVDNA--TKIKVQLSD---------GRKFDAKVVGKDP---------RSDIALIQLQNPKN----LTAIKMAD 179 (473)
T ss_pred EEEeChhhcCCC--CEEEEEECC---------CCEEEEEEEEecC---------CCCEEEEEecCCCC----CceeEecC
Confidence 379999998653 456666531 2345554444433 24999999975332 33556643
Q ss_pred -CCCCCCCCEEEEec
Q psy3170 82 -AHNVKSPTAIASGF 95 (525)
Q Consensus 82 -~~~~~~~~~~v~GW 95 (525)
.....|..+.+.|.
T Consensus 180 s~~l~~G~~V~aiG~ 194 (473)
T PRK10942 180 SDALRVGDYTVAIGN 194 (473)
T ss_pred ccccCCCCEEEEEcC
Confidence 33456776666664
No 30
>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=72.51 E-value=18 Score=36.23 Aligned_cols=70 Identities=19% Similarity=0.077 Sum_probs=42.3
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.|||++|.+... ..+.|.+- .+..+..+-+..+| ..|+||||++.+- +.++.+..
T Consensus 90 ~IlTn~HVV~~~--~~i~V~~~---------dg~~~~a~vv~~d~---------~~DlAvlkv~~~~-----~~~~~l~~ 144 (351)
T TIGR02038 90 YILTNYHVIKKA--DQIVVALQ---------DGRKFEAELVGSDP---------LTDLAVLKIEGDN-----LPTIPVNL 144 (351)
T ss_pred EEEecccEeCCC--CEEEEEEC---------CCCEEEEEEEEecC---------CCCEEEEEecCCC-----CceEeccC
Confidence 479999998653 44555542 12344554443333 3599999998642 33455532
Q ss_pred -CCCCCCCCEEEEecc
Q psy3170 82 -AHNVKSPTAIASGFG 96 (525)
Q Consensus 82 -~~~~~~~~~~v~GWG 96 (525)
.....|....+.|+.
T Consensus 145 s~~~~~G~~V~aiG~P 160 (351)
T TIGR02038 145 DRPPHVGDVVLAIGNP 160 (351)
T ss_pred cCccCCCCEEEEEeCC
Confidence 334668888888875
No 31
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=70.89 E-value=2.5 Score=39.60 Aligned_cols=47 Identities=40% Similarity=0.634 Sum_probs=34.5
Q ss_pred CCCCCCCceeeeeeeecCCcceeeeeeecceeeccceeeeccccccCCcccc
Q psy3170 198 AKYGEFPHQAEVGFVEEGGTMKDVKWFCGGSLISPNYVMTAAHCITSPLVGT 249 (525)
Q Consensus 198 ~~~~~~Pw~v~i~~~~~~~~~~~~~~~cggtli~~~~~~t~~~c~~~~~~~~ 249 (525)
.+...|||-+...+....+ .+-|+++||+++-++||+||...+..++
T Consensus 44 ~dt~~~Py~av~~~~~~tG-----~~~~~~~lI~pntvLTa~Hc~~s~~~G~ 90 (251)
T COG3591 44 TDTTQFPYSAVVQFEAATG-----RLCTAATLIGPNTVLTAGHCIYSPDYGE 90 (251)
T ss_pred ccCCCCCcceeEEeecCCC-----cceeeEEEEcCceEEEeeeEEecCCCCh
Confidence 4567899977665544322 3356679999999999999998866553
No 32
>PRK10898 serine endoprotease; Provisional
Probab=62.44 E-value=40 Score=33.78 Aligned_cols=70 Identities=17% Similarity=0.126 Sum_probs=39.9
Q ss_pred ceeeeccCcccCCCCCeEEEEceeecccCCcCcceEEEEEEEECCCCCCCCCCCcCceEEEEeCCCccCCCceeeeecCC
Q psy3170 2 VNNHAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPPVEFSETLKPACLNR 81 (525)
Q Consensus 2 ~~lTAAHC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~nDIALl~L~~~v~~~~~v~picL~~ 81 (525)
.+||+||=+.+. ..+.|.+. .+..+..+-+...| ..||||||++.+ . ..++.|..
T Consensus 90 ~IlTn~HVv~~a--~~i~V~~~---------dg~~~~a~vv~~d~---------~~DlAvl~v~~~-~----l~~~~l~~ 144 (353)
T PRK10898 90 YILTNKHVINDA--DQIIVALQ---------DGRVFEALLVGSDS---------LTDLAVLKINAT-N----LPVIPINP 144 (353)
T ss_pred EEEecccEeCCC--CEEEEEeC---------CCCEEEEEEEEEcC---------CCCEEEEEEcCC-C----CCeeeccC
Confidence 378889877542 44555543 12334444343332 359999999864 1 23444533
Q ss_pred -CCCCCCCCEEEEecc
Q psy3170 82 -AHNVKSPTAIASGFG 96 (525)
Q Consensus 82 -~~~~~~~~~~v~GWG 96 (525)
.....|....+.|+.
T Consensus 145 ~~~~~~G~~V~aiG~P 160 (353)
T PRK10898 145 KRVPHIGDVVLAIGNP 160 (353)
T ss_pred cCcCCCCCEEEEEeCC
Confidence 234567777777764
No 33
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=53.73 E-value=2.4e+02 Score=28.07 Aligned_cols=29 Identities=31% Similarity=0.413 Sum_probs=21.6
Q ss_pred cCCCcCCCCCcceeecCCCceeEEEEEEeecCCC
Q psy3170 432 KDTCQGDSGGPLQTIMPDLCMYNIIGITSYGRQC 465 (525)
Q Consensus 432 ~~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~c 465 (525)
...++|.||||++.. ...++||.+.....
T Consensus 189 Aain~gnsGgpl~n~-----~g~~iGint~~~~~ 217 (347)
T COG0265 189 AAINPGNSGGPLVNI-----DGEVVGINTAIIAP 217 (347)
T ss_pred cccCCCCCCCceEcC-----CCcEEEEEEEEecC
Confidence 357899999999753 45699998876443
No 34
>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=47.53 E-value=18 Score=33.97 Aligned_cols=22 Identities=36% Similarity=0.602 Sum_probs=16.0
Q ss_pred cCCCCCcceeecCCCceeEEEEEEeec
Q psy3170 436 QGDSGGPLQTIMPDLCMYNIIGITSYG 462 (525)
Q Consensus 436 ~gDsGgPL~~~~~~~~~~~l~GI~S~g 462 (525)
.||||+|++..+. .|+||.+-.
T Consensus 207 ~GDSGSPVVt~dg-----~liGVHTGS 228 (297)
T PF05579_consen 207 PGDSGSPVVTEDG-----DLIGVHTGS 228 (297)
T ss_dssp GGCTT-EEEETTC------EEEEEEEE
T ss_pred CCCCCCccCcCCC-----CEEEEEecC
Confidence 6899999987543 499999865
No 35
>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=37.71 E-value=20 Score=39.32 Aligned_cols=21 Identities=43% Similarity=0.820 Sum_probs=18.9
Q ss_pred EeEEEEEeCC-EEEecCCCCCC
Q psy3170 281 FCGGSLISPN-YVMTAAHCITS 301 (525)
Q Consensus 281 ~C~GtLIs~~-~VLTAAhCv~~ 301 (525)
.|+|++||++ .|||--||..+
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 4999999987 99999999855
No 36
>KOG1421|consensus
Probab=32.77 E-value=3.2e+02 Score=29.76 Aligned_cols=84 Identities=17% Similarity=0.292 Sum_probs=44.0
Q ss_pred eEeEEEEEeCC--EEEecCCCCCCCCCCceEEEEEEEeecccccccceEEEEEEEeCCCCCCCCCCcccceEEEEECCC-
Q psy3170 280 WFCGGSLISPN--YVMTAAHCITSPLGKPRYVRFGLITKLSYSVTDNIHRVMQNILHPNYTTEGTSQYHDIALLKIAPP- 356 (525)
Q Consensus 280 ~~C~GtLIs~~--~VLTAAhCv~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~~DIAll~L~~~- 356 (525)
.--+|.++++. ++||+.|-+.- .+....+-.. . -+.+-+.|.|.. .-+|+++++.+..
T Consensus 84 ~~atgfvvd~~~gyiLtnrhvv~p---gP~va~avf~----n--------~ee~ei~pvyrD----pVhdfGf~r~dps~ 144 (955)
T KOG1421|consen 84 SEATGFVVDKKLGYILTNRHVVAP---GPFVASAVFD----N--------HEEIEIYPVYRD----PVHDFGFFRYDPST 144 (955)
T ss_pred cceeEEEEecccceEEEeccccCC---CCceeEEEec----c--------cccCCcccccCC----chhhcceeecChhh
Confidence 34567777664 89999997643 2222211110 0 011224555543 3378888887543
Q ss_pred cccCCCccceecCCCCCCCCCcEEEEE
Q psy3170 357 VEFSETLKPACLNRAHNVKSPTAIASG 383 (525)
Q Consensus 357 ~~~~~~v~picL~~~~~~~~~~~~~~G 383 (525)
+.| ..+.-+||...-...+....++|
T Consensus 145 ir~-s~vt~i~lap~~akvgseirvvg 170 (955)
T KOG1421|consen 145 IRF-SIVTEICLAPELAKVGSEIRVVG 170 (955)
T ss_pred cce-eeeeccccCccccccCCceEEec
Confidence 333 35677888655444444444433
No 37
>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=31.92 E-value=52 Score=30.11 Aligned_cols=25 Identities=28% Similarity=0.304 Sum_probs=20.8
Q ss_pred CCCcCCCCCcceeecCCCceeEEEEEEeecC
Q psy3170 433 DTCQGDSGGPLQTIMPDLCMYNIIGITSYGR 463 (525)
Q Consensus 433 ~~C~gDsGgPL~~~~~~~~~~~l~GI~S~g~ 463 (525)
+..+|-||+|++. ..+|+|-+++..
T Consensus 176 GIvqGMSGSPI~q------dGKLiGAVthvf 200 (218)
T PF05580_consen 176 GIVQGMSGSPIIQ------DGKLIGAVTHVF 200 (218)
T ss_pred CEEecccCCCEEE------CCEEEEEEEEEE
Confidence 5789999999975 457999999874
No 38
>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=24.66 E-value=29 Score=28.89 Aligned_cols=25 Identities=28% Similarity=0.391 Sum_probs=18.2
Q ss_pred CcCCCCCcceeecCCCceeEEEEEEeecCC
Q psy3170 435 CQGDSGGPLQTIMPDLCMYNIIGITSYGRQ 464 (525)
Q Consensus 435 C~gDsGgPL~~~~~~~~~~~l~GI~S~g~~ 464 (525)
-+||||-|++- + ...++||+--|.+
T Consensus 104 ~~GDSGRpi~D--N---sGrVVaIVLGG~n 128 (158)
T PF00944_consen 104 KPGDSGRPIFD--N---SGRVVAIVLGGAN 128 (158)
T ss_dssp STTSTTEEEES--T---TSBEEEEEEEEEE
T ss_pred CCCCCCCccCc--C---CCCEEEEEecCCC
Confidence 37899999952 2 4568999877643
No 39
>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=23.61 E-value=50 Score=27.63 Aligned_cols=22 Identities=27% Similarity=0.468 Sum_probs=15.0
Q ss_pred CcCCCCCcceeecCCCceeEEEEEEee
Q psy3170 435 CQGDSGGPLQTIMPDLCMYNIIGITSY 461 (525)
Q Consensus 435 C~gDsGgPL~~~~~~~~~~~l~GI~S~ 461 (525)
-.|.||||++|. ...++||...
T Consensus 106 lkGSSGgPiLC~-----~GH~vG~f~a 127 (148)
T PF02907_consen 106 LKGSSGGPILCP-----SGHAVGMFRA 127 (148)
T ss_dssp HTT-TT-EEEET-----TSEEEEEEEE
T ss_pred EecCCCCcccCC-----CCCEEEEEEE
Confidence 368999999995 3468888754
Done!