Query psy285
Match_columns 842
No_of_seqs 768 out of 4592
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 18:28:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy285.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/285hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 100.0 2.4E-30 5.1E-35 273.8 23.7 223 425-664 10-255 (256)
2 cd00190 Tryp_SPc Trypsin-like 100.0 7.2E-30 1.6E-34 265.4 22.7 214 428-662 1-232 (232)
3 smart00020 Tryp_SPc Trypsin-li 99.9 1E-26 2.3E-31 241.5 21.9 210 427-659 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 99.9 1.1E-25 2.4E-30 231.9 21.4 208 428-659 1-220 (220)
5 cd00190 Tryp_SPc Trypsin-like 99.9 1.1E-25 2.3E-30 234.0 16.3 173 211-401 1-232 (232)
6 KOG3627|consensus 99.9 8.6E-25 1.9E-29 231.3 16.6 182 207-403 9-255 (256)
7 smart00020 Tryp_SPc Trypsin-li 99.9 1.9E-23 4E-28 217.0 15.2 169 210-398 1-229 (229)
8 PF00089 Trypsin: Trypsin; In 99.9 5.2E-22 1.1E-26 204.6 14.9 166 211-398 1-220 (220)
9 COG5640 Secreted trypsin-like 99.8 2.4E-21 5.3E-26 197.8 10.9 179 207-404 29-280 (413)
10 COG5640 Secreted trypsin-like 99.8 1.6E-20 3.4E-25 191.9 15.3 217 424-665 29-280 (413)
11 PF03761 DUF316: Domain of unk 98.5 2.4E-06 5.3E-11 91.6 16.6 207 418-660 29-276 (282)
12 PF03761 DUF316: Domain of unk 98.4 1.8E-06 3.8E-11 92.7 12.2 182 202-398 30-275 (282)
13 PF09342 DUF1986: Domain of un 98.0 2.8E-05 6.1E-10 77.2 9.6 102 437-557 14-130 (267)
14 PF09342 DUF1986: Domain of un 97.4 0.00032 6.9E-09 69.9 6.4 82 219-316 13-113 (267)
15 COG3591 V8-like Glu-specific e 91.7 0.69 1.5E-05 47.7 8.1 54 340-403 197-251 (251)
16 PF13365 Trypsin_2: Trypsin-li 89.2 1.2 2.5E-05 40.3 6.8 21 342-371 100-120 (120)
17 COG3591 V8-like Glu-specific e 88.4 5.9 0.00013 41.0 11.7 126 508-663 124-250 (251)
18 PF02395 Peptidase_S6: Immunog 86.4 0.25 5.5E-06 59.4 0.6 55 781-840 214-268 (769)
19 TIGR02037 degP_htrA_DO peripla 84.6 10 0.00022 43.2 12.6 25 343-376 176-200 (428)
20 PRK10139 serine endoprotease; 84.1 11 0.00024 43.1 12.5 25 342-375 208-232 (455)
21 PF02395 Peptidase_S6: Immunog 80.7 1.3 2.8E-05 53.5 3.3 57 604-665 213-269 (769)
22 TIGR02037 degP_htrA_DO peripla 77.6 18 0.0004 41.1 11.4 38 513-557 104-141 (428)
23 PRK10942 serine endoprotease; 71.4 41 0.00088 38.8 12.2 23 344-375 231-253 (473)
24 PRK10898 serine endoprotease; 67.4 74 0.0016 35.2 12.7 25 343-376 195-219 (353)
25 TIGR02038 protease_degS peripl 65.5 89 0.0019 34.5 12.9 25 342-375 194-218 (351)
26 PF00947 Pico_P2A: Picornaviru 64.2 6.2 0.00013 36.0 2.8 35 782-832 89-123 (127)
27 PRK10139 serine endoprotease; 60.5 1.1E+02 0.0025 35.0 13.0 37 513-556 137-173 (455)
28 PRK10898 serine endoprotease; 59.5 1.2E+02 0.0025 33.6 12.5 37 513-557 124-160 (353)
29 PF00947 Pico_P2A: Picornaviru 57.1 12 0.00026 34.1 3.4 102 27-160 16-122 (127)
30 TIGR02038 protease_degS peripl 56.6 1E+02 0.0023 33.9 11.5 37 513-557 124-160 (351)
31 PRK10942 serine endoprotease; 49.9 1.5E+02 0.0033 34.2 11.8 37 513-556 158-194 (473)
32 PF00548 Peptidase_C3: 3C cyst 25.0 1.3E+02 0.0028 29.5 5.1 28 342-375 143-170 (172)
33 PF13365 Trypsin_2: Trypsin-li 23.2 54 0.0012 29.1 2.0 18 111-137 103-120 (120)
34 PF02907 Peptidase_S29: Hepati 21.8 74 0.0016 29.4 2.4 24 108-140 104-127 (148)
No 1
>KOG3627|consensus
Probab=99.97 E-value=2.4e-30 Score=273.84 Aligned_cols=223 Identities=31% Similarity=0.562 Sum_probs=185.3
Q ss_pred CCceeCCCcccccccceEEEEeecC--ccce----EE---EE----eecCCC--CeEEEECcccccCCccccccCCcccc
Q psy285 425 GHKVCAPPVQDIKVIQFLTHENYTG--TKND----IA---LL----RLEKSP--DHIVRLGEQNVITDPDCQNINGHEVC 489 (842)
Q Consensus 425 ~~ri~gG~~a~~~~~~w~V~l~~~~--~~~C----Is---VL----C~~~~~--~~~V~lG~~~~~~~~dc~~~~~~~~~ 489 (842)
..||+||.++.+.+.||+|+|+... .|.| |+ || |+.... .+.|++|++......+
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~~~~V~~G~~~~~~~~~---------- 79 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASASLYTVRLGEHDINLSVS---------- 79 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCcceEEEECccccccccc----------
Confidence 4799999999889999999999875 7899 55 77 998874 4899999987766211
Q ss_pred CC-CcEEEEEEEEEeCCCCCCCCCC-CceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEeeecCCC--CCc
Q psy285 490 AP-PVQDIKVIQFLTHENYTDSGTK-NDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWGVTEDG--RSS 565 (842)
Q Consensus 490 ~~-~~~~~~V~~i~~Hp~y~~~~~~-nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG~~~~~--~~~ 565 (842)
.. ......|.++++||+|+..... ||||||+|++++.|+++|+|||||..........+..|.++|||.+..+ ..+
T Consensus 80 ~~~~~~~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~ 159 (256)
T KOG3627|consen 80 EGEEQLVGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLP 159 (256)
T ss_pred cCchhhhceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCC
Confidence 11 1244557788999999998877 9999999999999999999999985544211145689999999998555 678
Q ss_pred cceEEEEEeecChhHHHHHhcC--CCCCCceEEeC-CCCCCCccCCCCCcceeccccCCccccccEEEEEEEeCCC-CCC
Q psy285 566 LELLAVQQKVFNSEECKARYQE--LDPSSQICVGG-KVGKDACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPT-CGT 641 (842)
Q Consensus 566 ~~L~~~~v~~i~~~~C~~~~~~--~~~~~~iCa~~-~~~~~~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~-C~~ 641 (842)
..|+++++++++.++|+..+.. .+++.||||+. ..+.++|+|||||||++ ..+ ++|+++||+|||.. |+.
T Consensus 160 ~~L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~--~~~----~~~~~~GivS~G~~~C~~ 233 (256)
T KOG3627|consen 160 DTLQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVC--EDN----GRWVLVGIVSWGSGGCGQ 233 (256)
T ss_pred ceeEEEEEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEE--eeC----CcEEEEEEEEecCCCCCC
Confidence 8999999999999999988874 57778999997 66788999999999999 544 47899999999998 998
Q ss_pred CCCCCeeEeehhhhHHHHHHhhc
Q psy285 642 KSENPGVYTRMTYFLQWILDHLE 664 (842)
Q Consensus 642 ~~~~p~vyt~V~~~~~WI~~~i~ 664 (842)
... |++||+|+.|.+||++.+.
T Consensus 234 ~~~-P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 234 PNY-PGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred CCC-CeEEeEhHHhHHHHHHHhc
Confidence 866 9999999999999998774
No 2
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=99.97 E-value=7.2e-30 Score=265.39 Aligned_cols=214 Identities=35% Similarity=0.598 Sum_probs=183.8
Q ss_pred eeCCCcccccccceEEEEeec-Cccce----EE---EE----eecCCC-C-eEEEECcccccCCccccccCCccccCCCc
Q psy285 428 VCAPPVQDIKVIQFLTHENYT-GTKND----IA---LL----RLEKSP-D-HIVRLGEQNVITDPDCQNINGHEVCAPPV 493 (842)
Q Consensus 428 i~gG~~a~~~~~~w~V~l~~~-~~~~C----Is---VL----C~~~~~-~-~~V~lG~~~~~~~~dc~~~~~~~~~~~~~ 493 (842)
|+||..++..++||+|+|+.. ..+.| |+ || |+.... . +.|++|...... .....
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~------------~~~~~ 68 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSS------------NEGGG 68 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccC------------CCCce
Confidence 578999988999999999877 78899 77 88 998753 3 899999987765 22356
Q ss_pred EEEEEEEEEeCCCCCCCCCCCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEeeecCC-CCCccceEEEE
Q psy285 494 QDIKVIQFLTHENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWGVTED-GRSSLELLAVQ 572 (842)
Q Consensus 494 ~~~~V~~i~~Hp~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG~~~~-~~~~~~L~~~~ 572 (842)
+.+.|+++++||+|+.....+|||||||++|+.++++++|||||...... ..+..+.++|||.... ...+..++...
T Consensus 69 ~~~~v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~--~~~~~~~~~G~g~~~~~~~~~~~~~~~~ 146 (232)
T cd00190 69 QVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNL--PAGTTCTVSGWGRTSEGGPLPDVLQEVN 146 (232)
T ss_pred EEEEEEEEEECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccccC--CCCCEEEEEeCCcCCCCCCCCceeeEEE
Confidence 78899999999999988889999999999999999999999999875333 5688999999998733 35677899999
Q ss_pred EeecChhHHHHHhc--CCCCCCceEEeCCC-CCCCccCCCCCcceeccccCCccccccEEEEEEEeCCCCCCCCCCCeeE
Q psy285 573 QKVFNSEECKARYQ--ELDPSSQICVGGKV-GKDACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPTCGTKSENPGVY 649 (842)
Q Consensus 573 v~~i~~~~C~~~~~--~~~~~~~iCa~~~~-~~~~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~C~~~~~~p~vy 649 (842)
+.+++.+.|...+. ..+.+.++|++... ..+.|.|||||||++ ..+ ++++|+||+|++..|+.... |.+|
T Consensus 147 ~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~--~~~----~~~~lvGI~s~g~~c~~~~~-~~~~ 219 (232)
T cd00190 147 VPIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVC--NDN----GRGVLVGIVSWGSGCARPNY-PGVY 219 (232)
T ss_pred eeeECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEE--EeC----CEEEEEEEEehhhccCCCCC-CCEE
Confidence 99999999998876 57889999999743 778999999999999 555 78999999999999986454 9999
Q ss_pred eehhhhHHHHHHh
Q psy285 650 TRMTYFLQWILDH 662 (842)
Q Consensus 650 t~V~~~~~WI~~~ 662 (842)
|+|+.|.+||+++
T Consensus 220 t~v~~~~~WI~~~ 232 (232)
T cd00190 220 TRVSSYLDWIQKT 232 (232)
T ss_pred EEcHHhhHHhhcC
Confidence 9999999999863
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.95 E-value=1e-26 Score=241.46 Aligned_cols=210 Identities=34% Similarity=0.610 Sum_probs=178.5
Q ss_pred ceeCCCcccccccceEEEEeecC-ccce----EE---EE----eecCCC-C-eEEEECcccccCCccccccCCccccCCC
Q psy285 427 KVCAPPVQDIKVIQFLTHENYTG-TKND----IA---LL----RLEKSP-D-HIVRLGEQNVITDPDCQNINGHEVCAPP 492 (842)
Q Consensus 427 ri~gG~~a~~~~~~w~V~l~~~~-~~~C----Is---VL----C~~~~~-~-~~V~lG~~~~~~~~dc~~~~~~~~~~~~ 492 (842)
||+||..+.+.++||+|.++... .+.| |+ || |+.... . +.|++|.+..... ..
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~-------------~~ 67 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSG-------------EE 67 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCC-------------CC
Confidence 68999999899999999998876 7889 77 88 998764 3 9999998877651 12
Q ss_pred cEEEEEEEEEeCCCCCCCCCCCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEeeecCC--CCCccceEE
Q psy285 493 VQDIKVIQFLTHENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWGVTED--GRSSLELLA 570 (842)
Q Consensus 493 ~~~~~V~~i~~Hp~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG~~~~--~~~~~~L~~ 570 (842)
.+.+.|.++++||+|+.....+|||||||++|+.+++.++|||||...... ..+..+.++|||.... +.....++.
T Consensus 68 ~~~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~--~~~~~~~~~g~g~~~~~~~~~~~~~~~ 145 (229)
T smart00020 68 GQVIKVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNV--PAGTTCTVSGWGRTSEGAGSLPDTLQE 145 (229)
T ss_pred ceEEeeEEEEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCccccc--CCCCEEEEEeCCCCCCCCCcCCCEeeE
Confidence 278899999999999988889999999999999999999999999874333 4688999999998732 445678999
Q ss_pred EEEeecChhHHHHHhcC--CCCCCceEEeCCC-CCCCccCCCCCcceeccccCCccccccEEEEEEEeCCCCCCCCCCCe
Q psy285 571 VQQKVFNSEECKARYQE--LDPSSQICVGGKV-GKDACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPTCGTKSENPG 647 (842)
Q Consensus 571 ~~v~~i~~~~C~~~~~~--~~~~~~iCa~~~~-~~~~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~C~~~~~~p~ 647 (842)
..+.+++.+.|...+.. .+.+.++|++... ..+.|.|||||||++ .. ++|+|+||+|++..|..... |.
T Consensus 146 ~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~--~~-----~~~~l~Gi~s~g~~C~~~~~-~~ 217 (229)
T smart00020 146 VNVPIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVC--ND-----GRWVLVGIVSWGSGCARPGK-PG 217 (229)
T ss_pred EEEEEeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEE--EC-----CCEEEEEEEEECCCCCCCCC-CC
Confidence 99999999999987764 5788999999744 678999999999999 32 27899999999999985555 99
Q ss_pred eEeehhhhHHHH
Q psy285 648 VYTRMTYFLQWI 659 (842)
Q Consensus 648 vyt~V~~~~~WI 659 (842)
+|+||+.|.+||
T Consensus 218 ~~~~i~~~~~WI 229 (229)
T smart00020 218 VYTRVSSYLDWI 229 (229)
T ss_pred EEEEeccccccC
Confidence 999999999998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.94 E-value=1.1e-25 Score=231.94 Aligned_cols=208 Identities=33% Similarity=0.624 Sum_probs=177.3
Q ss_pred eeCCCcccccccceEEEEeecC-ccce----EE---EE----eecCCCCeEEEECcccccCCccccccCCccccCCCcEE
Q psy285 428 VCAPPVQDIKVIQFLTHENYTG-TKND----IA---LL----RLEKSPDHIVRLGEQNVITDPDCQNINGHEVCAPPVQD 495 (842)
Q Consensus 428 i~gG~~a~~~~~~w~V~l~~~~-~~~C----Is---VL----C~~~~~~~~V~lG~~~~~~~~dc~~~~~~~~~~~~~~~ 495 (842)
|+||.++.+.+.||+|.++... .++| |+ || |+.....+.|++|...+.. .....+.
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~~~~~~v~~g~~~~~~------------~~~~~~~ 68 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDGASDIKVRLGTYSIRN------------SDGSEQT 68 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTSGGSEEEEESESBTTS------------TTTTSEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEecccccccccccccccccccccccccccccc------------ccccccc
Confidence 6899999899999999999877 8999 66 88 9988323889999854544 2334689
Q ss_pred EEEEEEEeCCCCCCCCCCCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEeeecCCCCCccceEEEEEee
Q psy285 496 IKVIQFLTHENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWGVTEDGRSSLELLAVQQKV 575 (842)
Q Consensus 496 ~~V~~i~~Hp~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~L~~~~v~~ 575 (842)
+.|++++.||+|+.....+|||||+|++++.+.+.++|+||+...... ..+..+.+.|||.......+..++...+.+
T Consensus 69 ~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~ 146 (220)
T PF00089_consen 69 IKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDP--NVGTSCIVVGWGRTSDNGYSSNLQSVTVPV 146 (220)
T ss_dssp EEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTT--TTTSEEEEEESSBSSTTSBTSBEEEEEEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccc--cccccccccccccccccccccccccccccc
Confidence 999999999999998889999999999999999999999999854433 468899999999874333567899999999
Q ss_pred cChhHHHHHhcCCCCCCceEEeCCCCCCCccCCCCCcceeccccCCccccccEEEEEEEeCCCCCCCCCCCeeEeehhhh
Q psy285 576 FNSEECKARYQELDPSSQICVGGKVGKDACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPTCGTKSENPGVYTRMTYF 655 (842)
Q Consensus 576 i~~~~C~~~~~~~~~~~~iCa~~~~~~~~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~C~~~~~~p~vyt~V~~~ 655 (842)
++.+.|...+...+.+.++|++.....+.|.|||||||++ . +. +|+||++++..|..... |.+|+||+.|
T Consensus 147 ~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~g~sG~pl~~--~------~~-~lvGI~s~~~~c~~~~~-~~v~~~v~~~ 216 (220)
T PF00089_consen 147 VSRKTCRSSYNDNLTPNMICAGSSGSGDACQGDSGGPLIC--N------NN-YLVGIVSFGENCGSPNY-PGVYTRVSSY 216 (220)
T ss_dssp EEHHHHHHHTTTTSTTTEEEEETTSSSBGGTTTTTSEEEE--T------TE-EEEEEEEEESSSSBTTS-EEEEEEGGGG
T ss_pred cccccccccccccccccccccccccccccccccccccccc--c------ee-eecceeeecCCCCCCCc-CEEEEEHHHh
Confidence 9999999887666889999999655578999999999999 2 22 79999999999998876 9999999999
Q ss_pred HHHH
Q psy285 656 LQWI 659 (842)
Q Consensus 656 ~~WI 659 (842)
++||
T Consensus 217 ~~WI 220 (220)
T PF00089_consen 217 LDWI 220 (220)
T ss_dssp HHHH
T ss_pred hccC
Confidence 9998
No 5
>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=99.93 E-value=1.1e-25 Score=234.02 Aligned_cols=173 Identities=39% Similarity=0.668 Sum_probs=139.6
Q ss_pred eeCCeeCCCCCCcceeeeecC-----------------CcceecCCCC-ceeEEEEcceeCCCCCCCCCCCCCCCCCceE
Q psy285 211 IIGGYVAKLGSIPWIARIAYS-----------------RTPHCATNPE-QISSVRLGEHDANSDPDCSPDHRQCAPPVQD 272 (842)
Q Consensus 211 I~gG~~a~~~~~Pw~v~i~~~-----------------TAAhC~~~~~-~~~~V~lG~~~~~~~~~~~~~~~~~~~~~~~ 272 (842)
|+||.++.+++|||+|+|+.. |||||+.... ..+.|++|.+...... ...+.
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~----------~~~~~ 70 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNE----------GGGQV 70 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCC----------CceEE
Confidence 689999999999999999763 9999998643 5688999998765432 14678
Q ss_pred EEEEEEEEcCCCCCCCCCccceEEEEeCCCCCCCCCccceeecccc----c------------------------ccc--
Q psy285 273 IRVVKVISHEHFSGEPNMRNDIALLRLERPPRLNGTHLMSCCYYLA----Y------------------------ADN-- 322 (842)
Q Consensus 273 ~~V~~i~~Hp~y~~~~~~~nDIALlkL~~pv~~~~~v~Picl~~l~----~------------------------~~~-- 322 (842)
+.|+++++||+|+. ....+|||||||++|+.++.+++||||+... . ..+
T Consensus 71 ~~v~~~~~hp~y~~-~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~ 149 (232)
T cd00190 71 IKVKKVIVHPNYNP-STYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPI 149 (232)
T ss_pred EEEEEEEECCCCCC-CCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeee
Confidence 99999999999998 6789999999999999999999999994321 0 000
Q ss_pred ---------cee-ecCCCCeeeecCCC-CCCccccCCCCccEEecccCCCccccEEEEEEEEEccCCCCCCCCCeeEEec
Q psy285 323 ---------GIS-IDYNSGQMCVGGNV-GKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPASCGVYEIPGVYSRT 391 (842)
Q Consensus 323 ---------~~~-~~~~~~~lCa~~~~-~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~~C~~~~~p~vyt~V 391 (842)
+.. ....+.++|++... ..+.|.|||||||++ ..++ +++|+||+|++. .|.....|++|++|
T Consensus 150 ~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~--~~~~----~~~lvGI~s~g~-~c~~~~~~~~~t~v 222 (232)
T cd00190 150 VSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVC--NDNG----RGVLVGIVSWGS-GCARPNYPGVYTRV 222 (232)
T ss_pred ECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEE--EeCC----EEEEEEEEehhh-ccCCCCCCCEEEEc
Confidence 000 11234899998764 778999999999999 3345 899999999997 69876789999999
Q ss_pred cccHHHHHHh
Q psy285 392 SYFLRWILDH 401 (842)
Q Consensus 392 ~~~~~WI~~~ 401 (842)
+.|++||+++
T Consensus 223 ~~~~~WI~~~ 232 (232)
T cd00190 223 SSYLDWIQKT 232 (232)
T ss_pred HHhhHHhhcC
Confidence 9999999863
No 6
>KOG3627|consensus
Probab=99.92 E-value=8.6e-25 Score=231.31 Aligned_cols=182 Identities=37% Similarity=0.651 Sum_probs=140.6
Q ss_pred CCCceeCCeeCCCCCCcceeeeecC------------------CcceecCCCCc--eeEEEEcceeCCCCCCCCCCCCCC
Q psy285 207 SEQRIIGGYVAKLGSIPWIARIAYS------------------RTPHCATNPEQ--ISSVRLGEHDANSDPDCSPDHRQC 266 (842)
Q Consensus 207 ~~~rI~gG~~a~~~~~Pw~v~i~~~------------------TAAhC~~~~~~--~~~V~lG~~~~~~~~~~~~~~~~~ 266 (842)
...||+||.++.+++|||+|+|... |||||+... . .+.|++|++......+.
T Consensus 9 ~~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~-~~~~~~V~~G~~~~~~~~~~------- 80 (256)
T KOG3627|consen 9 PEGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGA-SASLYTVRLGEHDINLSVSE------- 80 (256)
T ss_pred ccCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCC-CCcceEEEECcccccccccc-------
Confidence 4579999999999999999998752 899999874 2 68899998876554210
Q ss_pred CCCceEEEEEEEEEcCCCCCCCCCc-cceEEEEeCCCCCCCCCccceeeccccc-----c--------------------
Q psy285 267 APPVQDIRVVKVISHEHFSGEPNMR-NDIALLRLERPPRLNGTHLMSCCYYLAY-----A-------------------- 320 (842)
Q Consensus 267 ~~~~~~~~V~~i~~Hp~y~~~~~~~-nDIALlkL~~pv~~~~~v~Picl~~l~~-----~-------------------- 320 (842)
....+...|.++++||+|+. .+.. ||||||+|++++.|+++|+||||+.... .
T Consensus 81 ~~~~~~~~v~~~i~H~~y~~-~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~ 159 (256)
T KOG3627|consen 81 GEEQLVGDVEKIIVHPNYNP-RTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLP 159 (256)
T ss_pred CchhhhceeeEEEECCCCCC-CCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCC
Confidence 00124555888999999998 6666 9999999999999999999999942111 0
Q ss_pred ------cc-----------ceee-cCCCCeeeecC-CCCCCccccCCCCccEEecccCCCccccEEEEEEEEEccCCCCC
Q psy285 321 ------DN-----------GISI-DYNSGQMCVGG-NVGKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPASCGV 381 (842)
Q Consensus 321 ------~~-----------~~~~-~~~~~~lCa~~-~~~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~~C~~ 381 (842)
++ +... ...+.||||+. ....++|+|||||||++. ..+ +|+++||+|||...|+.
T Consensus 160 ~~L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~--~~~----~~~~~GivS~G~~~C~~ 233 (256)
T KOG3627|consen 160 DTLQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCE--DNG----RWVLVGIVSWGSGGCGQ 233 (256)
T ss_pred ceeEEEEEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEe--eCC----cEEEEEEEEecCCCCCC
Confidence 00 0000 11136899998 467788999999999993 233 68999999999733998
Q ss_pred CCCCeeEEeccccHHHHHHhhc
Q psy285 382 YEIPGVYSRTSYFLRWILDHLD 403 (842)
Q Consensus 382 ~~~p~vyt~V~~~~~WI~~~i~ 403 (842)
.+.|++||+|+.|.+||++.+.
T Consensus 234 ~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 234 PNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred CCCCeEEeEhHHhHHHHHHHhc
Confidence 8899999999999999999874
No 7
>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=99.90 E-value=1.9e-23 Score=217.02 Aligned_cols=169 Identities=40% Similarity=0.681 Sum_probs=137.4
Q ss_pred ceeCCeeCCCCCCcceeeeecC-----------------CcceecCCCC-ceeEEEEcceeCCCCCCCCCCCCCCCCCce
Q psy285 210 RIIGGYVAKLGSIPWIARIAYS-----------------RTPHCATNPE-QISSVRLGEHDANSDPDCSPDHRQCAPPVQ 271 (842)
Q Consensus 210 rI~gG~~a~~~~~Pw~v~i~~~-----------------TAAhC~~~~~-~~~~V~lG~~~~~~~~~~~~~~~~~~~~~~ 271 (842)
||+||+++.+++|||+|.|+.. |||||+.... ..+.|++|.++..... ..+
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~-----------~~~ 69 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGE-----------EGQ 69 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCC-----------Cce
Confidence 6899999999999999999765 9999998754 5789999988765432 237
Q ss_pred EEEEEEEEEcCCCCCCCCCccceEEEEeCCCCCCCCCccceeeccc----cc-------------------------ccc
Q psy285 272 DIRVVKVISHEHFSGEPNMRNDIALLRLERPPRLNGTHLMSCCYYL----AY-------------------------ADN 322 (842)
Q Consensus 272 ~~~V~~i~~Hp~y~~~~~~~nDIALlkL~~pv~~~~~v~Picl~~l----~~-------------------------~~~ 322 (842)
.+.|.++++||+|+. ....+|||||+|++|+.++++++||||+.. .. ..+
T Consensus 70 ~~~v~~~~~~p~~~~-~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~ 148 (229)
T smart00020 70 VIKVSKVIIHPNYNP-STYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNV 148 (229)
T ss_pred EEeeEEEEECCCCCC-CCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEE
Confidence 899999999999997 788999999999999999999999999332 00 000
Q ss_pred -----------cee-ecCCCCeeeecCCC-CCCccccCCCCccEEecccCCCccccEEEEEEEEEccCCCCCCCCCeeEE
Q psy285 323 -----------GIS-IDYNSGQMCVGGNV-GKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPASCGVYEIPGVYS 389 (842)
Q Consensus 323 -----------~~~-~~~~~~~lCa~~~~-~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~~C~~~~~p~vyt 389 (842)
+.. ......++|++... ....|.||+||||++. .+ +|+|+||+|++. .|.....|.+|+
T Consensus 149 ~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~---~~----~~~l~Gi~s~g~-~C~~~~~~~~~~ 220 (229)
T smart00020 149 PIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCN---DG----RWVLVGIVSWGS-GCARPGKPGVYT 220 (229)
T ss_pred EEeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEE---CC----CEEEEEEEEECC-CCCCCCCCCEEE
Confidence 000 01234799998764 6789999999999983 11 789999999997 898777899999
Q ss_pred eccccHHHH
Q psy285 390 RTSYFLRWI 398 (842)
Q Consensus 390 ~V~~~~~WI 398 (842)
||+.|++||
T Consensus 221 ~i~~~~~WI 229 (229)
T smart00020 221 RVSSYLDWI 229 (229)
T ss_pred EeccccccC
Confidence 999999998
No 8
>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=99.88 E-value=5.2e-22 Score=204.57 Aligned_cols=166 Identities=37% Similarity=0.705 Sum_probs=133.5
Q ss_pred eeCCeeCCCCCCcceeeeecC-----------------CcceecCCCCceeEEEEcceeCCCCCCCCCCCCCCCCCceEE
Q psy285 211 IIGGYVAKLGSIPWIARIAYS-----------------RTPHCATNPEQISSVRLGEHDANSDPDCSPDHRQCAPPVQDI 273 (842)
Q Consensus 211 I~gG~~a~~~~~Pw~v~i~~~-----------------TAAhC~~~~~~~~~V~lG~~~~~~~~~~~~~~~~~~~~~~~~ 273 (842)
|+||.++.+++|||+|.|+.. |||||+.. ...+.+++|...+.... ...+.+
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~-~~~~~v~~g~~~~~~~~----------~~~~~~ 69 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG-ASDIKVRLGTYSIRNSD----------GSEQTI 69 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS-GGSEEEEESESBTTSTT----------TTSEEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc-ccccccccccccccccc----------cccccc
Confidence 789999999999999999874 99999988 35688899985444332 135899
Q ss_pred EEEEEEEcCCCCCCCCCccceEEEEeCCCCCCCCCccceeeccccc---c------------------------ccce--
Q psy285 274 RVVKVISHEHFSGEPNMRNDIALLRLERPPRLNGTHLMSCCYYLAY---A------------------------DNGI-- 324 (842)
Q Consensus 274 ~V~~i~~Hp~y~~~~~~~nDIALlkL~~pv~~~~~v~Picl~~l~~---~------------------------~~~~-- 324 (842)
.|++++.||+|+. ....+|||||+|++|+.+.+.++|+|++.... . .+..
T Consensus 70 ~v~~~~~h~~~~~-~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~ 148 (220)
T PF00089_consen 70 KVSKIIIHPKYDP-STYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVS 148 (220)
T ss_dssp EEEEEEEETTSBT-TTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEE
T ss_pred ccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 9999999999998 66789999999999999999999999943110 0 0000
Q ss_pred -----e-e--cCCCCeeeecCCCCCCccccCCCCccEEecccCCCccccEEEEEEEEEccCCCCCCCCCeeEEeccccHH
Q psy285 325 -----S-I--DYNSGQMCVGGNVGKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPASCGVYEIPGVYSRTSYFLR 396 (842)
Q Consensus 325 -----~-~--~~~~~~lCa~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~~C~~~~~p~vyt~V~~~~~ 396 (842)
. . ...+.++|++.....+.|.|||||||++ .. . +|+||++++. .|.....|.+|++|+.|++
T Consensus 149 ~~~c~~~~~~~~~~~~~c~~~~~~~~~~~g~sG~pl~~----~~----~-~lvGI~s~~~-~c~~~~~~~v~~~v~~~~~ 218 (220)
T PF00089_consen 149 RKTCRSSYNDNLTPNMICAGSSGSGDACQGDSGGPLIC----NN----N-YLVGIVSFGE-NCGSPNYPGVYTRVSSYLD 218 (220)
T ss_dssp HHHHHHHTTTTSTTTEEEEETTSSSBGGTTTTTSEEEE----TT----E-EEEEEEEEES-SSSBTTSEEEEEEGGGGHH
T ss_pred cccccccccccccccccccccccccccccccccccccc----ce----e-eecceeeecC-CCCCCCcCEEEEEHHHhhc
Confidence 0 0 1234899998755578999999999998 22 2 7999999995 8998878999999999999
Q ss_pred HH
Q psy285 397 WI 398 (842)
Q Consensus 397 WI 398 (842)
||
T Consensus 219 WI 220 (220)
T PF00089_consen 219 WI 220 (220)
T ss_dssp HH
T ss_pred cC
Confidence 98
No 9
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=2.4e-21 Score=197.82 Aligned_cols=179 Identities=30% Similarity=0.418 Sum_probs=128.1
Q ss_pred CCCceeCCeeCCCCCCcceeeeecC---------------------CcceecCCCC-ceeEEEEcceeCCCCCCCCCCCC
Q psy285 207 SEQRIIGGYVAKLGSIPWIARIAYS---------------------RTPHCATNPE-QISSVRLGEHDANSDPDCSPDHR 264 (842)
Q Consensus 207 ~~~rI~gG~~a~~~~~Pw~v~i~~~---------------------TAAhC~~~~~-~~~~V~lG~~~~~~~~~~~~~~~ 264 (842)
-+.||+||..|..++||++|++... |||||+.... -...+..+..++....
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~S------- 101 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSS------- 101 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccc-------
Confidence 3679999999999999999998643 9999998765 2222334444444333
Q ss_pred CCCCCceEEEEEEEEEcCCCCCCCCCccceEEEEeCCCCCCCC--------C---------cc-------ceee------
Q psy285 265 QCAPPVQDIRVVKVISHEHFSGEPNMRNDIALLRLERPPRLNG--------T---------HL-------MSCC------ 314 (842)
Q Consensus 265 ~~~~~~~~~~V~~i~~Hp~y~~~~~~~nDIALlkL~~pv~~~~--------~---------v~-------Picl------ 314 (842)
..+...|.+++.|..|.+ .++.||||+++|.++...-. . +. ++-.
T Consensus 102 ----q~~rg~vr~i~~~efY~~-~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~ 176 (413)
T COG5640 102 ----QAERGHVRTIYVHEFYSP-GNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPR 176 (413)
T ss_pred ----cccCcceEEEeeeccccc-ccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCC
Confidence 567889999999999998 89999999999999653210 0 00 0000
Q ss_pred --c---ccccccc----------cee------ecCCCCeeeecCCCCCCccccCCCCccEEecccCCCccccEEEEEEEE
Q psy285 315 --Y---YLAYADN----------GIS------IDYNSGQMCVGGNVGKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVS 373 (842)
Q Consensus 315 --~---~l~~~~~----------~~~------~~~~~~~lCa~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S 373 (842)
+ .|++..+ +.. -...-.-+|++.. .+++|+||||||++.. .+. ...++||+|
T Consensus 177 ~~p~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~-~~daCqGDSGGPi~~~--g~~----G~vQ~GVvS 249 (413)
T COG5640 177 SSPKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP-PKDACQGDSGGPIFHK--GEE----GRVQRGVVS 249 (413)
T ss_pred CCCccceeeeeeeeeechHHhhhhccccccCCCCCCccceecCCC-CcccccCCCCCceEEe--CCC----ccEEEeEEE
Confidence 0 1111111 110 0000123899865 4899999999999983 222 568999999
Q ss_pred EccCCCCCCCCCeeEEeccccHHHHHHhhcc
Q psy285 374 LGPASCGVYEIPGVYSRTSYFLRWILDHLDD 404 (842)
Q Consensus 374 ~g~~~C~~~~~p~vyt~V~~~~~WI~~~i~~ 404 (842)
||..+|+....|+|||+|+.|.+||...++.
T Consensus 250 wG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~ 280 (413)
T COG5640 250 WGDGGCGGTLIPGVYTNVSNYQDWIAAMTNG 280 (413)
T ss_pred ecCCCCCCCCcceeEEehhHHHHHHHHHhcC
Confidence 9987799999999999999999999998763
No 10
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=1.6e-20 Score=191.94 Aligned_cols=217 Identities=22% Similarity=0.264 Sum_probs=155.1
Q ss_pred CCCceeCCCcccccccceEEEEeecC-----ccce----EE---EE----eecCCC--CeEEEECcccccCCccccccCC
Q psy285 424 NGHKVCAPPVQDIKVIQFLTHENYTG-----TKND----IA---LL----RLEKSP--DHIVRLGEQNVITDPDCQNING 485 (842)
Q Consensus 424 ~~~ri~gG~~a~~~~~~w~V~l~~~~-----~~~C----Is---VL----C~~~~~--~~~V~lG~~~~~~~~dc~~~~~ 485 (842)
...||+||..|+..++|++|+|..+. ..+| +. || |+.... +..+.++..++.+
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d--------- 99 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLND--------- 99 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccc---------
Confidence 35799999999777777788886433 4689 44 88 998766 2333333334433
Q ss_pred ccccCCCcEEEEEEEEEeCCCCCCCCCCCceEEEEEcCCCCCCCCcccccCCCCCC--CCCcCCCCeEEEEEeeec--CC
Q psy285 486 HEVCAPPVQDIKVIQFLTHENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNA--MTRNFENENTIVAGWGVT--ED 561 (842)
Q Consensus 486 ~~~~~~~~~~~~V~~i~~Hp~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~--~~~~~~~~~~~v~GWG~~--~~ 561 (842)
....+...|++++.|..|...++.||||+++|.++...- .+ .|-+-.... .............+|+.+ ..
T Consensus 100 ----~Sq~~rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~p-r~-ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~ 173 (413)
T COG5640 100 ----SSQAERGHVRTIYVHEFYSPGNLGNDIAVLELARAASLP-RV-KITSFDASDTFLNSVTTVSPMTNGTFGVTTPSD 173 (413)
T ss_pred ----cccccCcceEEEeeecccccccccCcceeeccccccccc-hh-heeeccCcccceecccccccccceeeeeeeecC
Confidence 223567789999999999999999999999999865432 00 011111111 111123456667788876 11
Q ss_pred C--CCc--cceEEEEEeecChhHHHHHhc--------CCCCCCceEEeCCCCCCCccCCCCCcceeccccCCccccccEE
Q psy285 562 G--RSS--LELLAVQQKVFNSEECKARYQ--------ELDPSSQICVGGKVGKDACKGDSGGPLTWMGSFDSAILARNYL 629 (842)
Q Consensus 562 ~--~~~--~~L~~~~v~~i~~~~C~~~~~--------~~~~~~~iCa~~~~~~~~C~gDsGgPL~~~~~~~~~~~~~~~l 629 (842)
. ..+ ..|+++.+...+...|...+. ..++. +|++. -.+++|+||||||++.+ .+ ....+
T Consensus 174 v~~~~p~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~--~cag~-~~~daCqGDSGGPi~~~--g~----~G~vQ 244 (413)
T COG5640 174 VPRSSPKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTG--FCAGR-PPKDACQGDSGGPIFHK--GE----EGRVQ 244 (413)
T ss_pred CCCCCCccceeeeeeeeeechHHhhhhccccccCCCCCCccc--eecCC-CCcccccCCCCCceEEe--CC----CccEE
Confidence 1 122 479999999999999998774 12333 99995 44899999999999994 34 45689
Q ss_pred EEEEEeCCC-CCCCCCCCeeEeehhhhHHHHHHhhcc
Q psy285 630 IGLVSYGPT-CGTKSENPGVYTRMTYFLQWILDHLED 665 (842)
Q Consensus 630 ~GI~S~g~~-C~~~~~~p~vyt~V~~~~~WI~~~i~~ 665 (842)
+||+|||.+ |+.... |+|||+|+.|.+||..+++.
T Consensus 245 ~GVvSwG~~~Cg~t~~-~gVyT~vsny~~WI~a~~~~ 280 (413)
T COG5640 245 RGVVSWGDGGCGGTLI-PGVYTNVSNYQDWIAAMTNG 280 (413)
T ss_pred EeEEEecCCCCCCCCc-ceeEEehhHHHHHHHHHhcC
Confidence 999999998 999988 99999999999999998765
No 11
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=98.52 E-value=2.4e-06 Score=91.62 Aligned_cols=207 Identities=21% Similarity=0.302 Sum_probs=123.4
Q ss_pred CCCCC---CCCCceeCCCcccccccceEEEEeecC----ccce----EE---EE----eecCCCC-eEEEECcccccCCc
Q psy285 418 PDCQN---INGHKVCAPPVQDIKVIQFLTHENYTG----TKND----IA---LL----RLEKSPD-HIVRLGEQNVITDP 478 (842)
Q Consensus 418 ~~Cg~---~~~~ri~gG~~a~~~~~~w~V~l~~~~----~~~C----Is---VL----C~~~~~~-~~V~lG~~~~~~~~ 478 (842)
..||. ....++..|..+...+.||.|.+.... ...+ || || |+..... + +...... ..
T Consensus 29 ~~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W---~~~~~~~-~~ 104 (282)
T PF03761_consen 29 ETCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKW---LNGEEFD-NK 104 (282)
T ss_pred HhcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEeccccc---ccCcccc-cc
Confidence 46992 334457888888788899988777543 2344 77 66 7653321 2 1111111 12
Q ss_pred cccccC-Cccc----------------cCCCcEEEEEEEEEeC----CCCCCCCCCCceEEEEEcCCCCCCCCcccccCC
Q psy285 479 DCQNIN-GHEV----------------CAPPVQDIKVIQFLTH----ENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLP 537 (842)
Q Consensus 479 dc~~~~-~~~~----------------~~~~~~~~~V~~i~~H----p~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp 537 (842)
.|.... ...+ .........|.++++- .........++++||+|+++ ++....|+|||
T Consensus 105 ~C~~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~ 182 (282)
T PF03761_consen 105 KCEGNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLA 182 (282)
T ss_pred eeeCCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeC
Confidence 343210 0000 0111223456666552 11223345689999999999 78899999999
Q ss_pred CCCCCCCcCCCCeEEEEEeeecCCCCCccceEEEEEeecChhHHHHHhcCCCCCCceEEeCCCCCCCccCCCCCcceecc
Q psy285 538 YGNAMTRNFENENTIVAGWGVTEDGRSSLELLAVQQKVFNSEECKARYQELDPSSQICVGGKVGKDACKGDSGGPLTWMG 617 (842)
Q Consensus 538 ~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~L~~~~v~~i~~~~C~~~~~~~~~~~~iCa~~~~~~~~C~gDsGgPL~~~~ 617 (842)
...... ..+....+.|+. ....+....+.+.....| ...+| .....|.+|+||||+.
T Consensus 183 ~~~~~~--~~~~~~~~yg~~------~~~~~~~~~~~i~~~~~~---------~~~~~----~~~~~~~~d~Gg~lv~-- 239 (282)
T PF03761_consen 183 DSSTNW--EKGDEVDVYGFN------STGKLKHRKLKITNCTKC---------AYSIC----TKQYSCKGDRGGPLVK-- 239 (282)
T ss_pred CCcccc--ccCceEEEeecC------CCCeEEEEEEEEEEeecc---------ceeEe----cccccCCCCccCeEEE--
Confidence 876544 456666666661 123455555555443321 11222 2357899999999998
Q ss_pred ccCCccccccEEEEEEEeCCC-CCCCCCCCeeEeehhhhHHHHH
Q psy285 618 SFDSAILARNYLIGLVSYGPT-CGTKSENPGVYTRMTYFLQWIL 660 (842)
Q Consensus 618 ~~~~~~~~~~~l~GI~S~g~~-C~~~~~~p~vyt~V~~~~~WI~ 660 (842)
..+ ++|.|+||.+.+.. |... ...|.+|..|.+=|=
T Consensus 240 ~~~----gr~tlIGv~~~~~~~~~~~---~~~f~~v~~~~~~IC 276 (282)
T PF03761_consen 240 NIN----GRWTLIGVGASGNYECNKN---NSYFFNVSWYQDEIC 276 (282)
T ss_pred EEC----CCEEEEEEEccCCCccccc---ccEEEEHHHhhhhhc
Confidence 667 89999999998763 4322 467899998876553
No 12
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=98.41 E-value=1.8e-06 Score=92.67 Aligned_cols=182 Identities=23% Similarity=0.361 Sum_probs=106.7
Q ss_pred CCC---CCCCCceeCCeeCCCCCCcceeeeecC--------------------CcceecCCCCceeEEEEcceeCCCCCC
Q psy285 202 KCG---LASEQRIIGGYVAKLGSIPWIARIAYS--------------------RTPHCATNPEQISSVRLGEHDANSDPD 258 (842)
Q Consensus 202 ~Cg---~~~~~rI~gG~~a~~~~~Pw~v~i~~~--------------------TAAhC~~~~~~~~~V~lG~~~~~~~~~ 258 (842)
+|| .....++..|..+..++.||.|.+... ||+||+......+ +...... ...
T Consensus 30 ~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W---~~~~~~~-~~~ 105 (282)
T PF03761_consen 30 TCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKW---LNGEEFD-NKK 105 (282)
T ss_pred hcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEeccccc---ccCcccc-cce
Confidence 699 334556789999999999999988764 7889987432222 1111111 112
Q ss_pred CCCC--C-----------CC----C--CCCceEEEEEEEEEcCC----CCCCCCCccceEEEEeCCCCCCCCCccceeec
Q psy285 259 CSPD--H-----------RQ----C--APPVQDIRVVKVISHEH----FSGEPNMRNDIALLRLERPPRLNGTHLMSCCY 315 (842)
Q Consensus 259 ~~~~--~-----------~~----~--~~~~~~~~V~~i~~Hp~----y~~~~~~~nDIALlkL~~pv~~~~~v~Picl~ 315 (842)
|..+ + .. + ........|+++++--. ... ....++++||+|+++ ++....|+||+
T Consensus 106 C~~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~-~~~~~~~mIlEl~~~--~~~~~~~~Cl~ 182 (282)
T PF03761_consen 106 CEGNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKN-FNRPYSPMILELEED--FSKNVSPPCLA 182 (282)
T ss_pred eeCCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccc-cccccceEEEEEccc--ccccCCCEEeC
Confidence 3221 0 00 0 00112355666655311 122 345689999999999 88899999993
Q ss_pred cccc-------ccccee----------ecCCCCeeeecCC-CCCCccccCCCCccEEecccCCCccccEEEEEEEEEccC
Q psy285 316 YLAY-------ADNGIS----------IDYNSGQMCVGGN-VGKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPA 377 (842)
Q Consensus 316 ~l~~-------~~~~~~----------~~~~~~~lCa~~~-~~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~ 377 (842)
.-.. ...|.. +......-|+... .....|.+|+||||+. ..+| +|+|+||.+.+..
T Consensus 183 ~~~~~~~~~~~~~~yg~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~d~Gg~lv~--~~~g----r~tlIGv~~~~~~ 256 (282)
T PF03761_consen 183 DSSTNWEKGDEVDVYGFNSTGKLKHRKLKITNCTKCAYSICTKQYSCKGDRGGPLVK--NING----RWTLIGVGASGNY 256 (282)
T ss_pred CCccccccCceEEEeecCCCCeEEEEEEEEEEeeccceeEecccccCCCCccCeEEE--EECC----CEEEEEEEccCCC
Confidence 2111 111111 1100000022211 3467899999999998 5677 9999999998753
Q ss_pred CCCCCCCCeeEEeccccHHHH
Q psy285 378 SCGVYEIPGVYSRTSYFLRWI 398 (842)
Q Consensus 378 ~C~~~~~p~vyt~V~~~~~WI 398 (842)
.|.. ....|.+|+.|.+=|
T Consensus 257 ~~~~--~~~~f~~v~~~~~~I 275 (282)
T PF03761_consen 257 ECNK--NNSYFFNVSWYQDEI 275 (282)
T ss_pred cccc--cccEEEEHHHhhhhh
Confidence 4432 267888988877633
No 13
>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=98.01 E-value=2.8e-05 Score=77.23 Aligned_cols=102 Identities=22% Similarity=0.245 Sum_probs=76.4
Q ss_pred cccceEEEEeecCccce----EE---EE----eecCCC---C-eEEEECcccccCCccccccCCccccCCCcEEEEEEEE
Q psy285 437 KVIQFLTHENYTGTKND----IA---LL----RLEKSP---D-HIVRLGEQNVITDPDCQNINGHEVCAPPVQDIKVIQF 501 (842)
Q Consensus 437 ~~~~w~V~l~~~~~~~C----Is---VL----C~~~~~---~-~~V~lG~~~~~~~~dc~~~~~~~~~~~~~~~~~V~~i 501 (842)
.-.||.|.|+..|.+.| |. || |+.... . ..|.+|...... .+..+.+|.++|..+
T Consensus 14 y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~----------~v~Gp~EQI~rVD~~ 83 (267)
T PF09342_consen 14 YHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYL----------SVDGPHEQISRVDCF 83 (267)
T ss_pred ccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceec----------ccCCChheEEEeeee
Confidence 45799999999999999 44 66 997755 3 788999865332 113456788888776
Q ss_pred EeCCCCCCCCCCCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEee
Q psy285 502 LTHENYTDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWG 557 (842)
Q Consensus 502 ~~Hp~y~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG 557 (842)
..=| +.+++||.|++|+.|+.+|+|..||...... .....|..+|-.
T Consensus 84 ~~V~-------~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~--~~~~~CVAVg~d 130 (267)
T PF09342_consen 84 KDVP-------ESNVLLLHLEQPANFTRYVLPTFLPETSNEN--ESDDECVAVGHD 130 (267)
T ss_pred eecc-------ccceeeeeecCcccceeeecccccccccCCC--CCCCceEEEEcc
Confidence 4433 4799999999999999999999999743333 455689988854
No 14
>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=97.39 E-value=0.00032 Score=69.90 Aligned_cols=82 Identities=23% Similarity=0.242 Sum_probs=61.5
Q ss_pred CCCCcceeeeecC----------------CcceecCCCC---ceeEEEEcceeCCCCCCCCCCCCCCCCCceEEEEEEEE
Q psy285 219 LGSIPWIARIAYS----------------RTPHCATNPE---QISSVRLGEHDANSDPDCSPDHRQCAPPVQDIRVVKVI 279 (842)
Q Consensus 219 ~~~~Pw~v~i~~~----------------TAAhC~~~~~---~~~~V~lG~~~~~~~~~~~~~~~~~~~~~~~~~V~~i~ 279 (842)
.--|||.|.|+.. ++..|+.... ..++|.||.......-+ .+.+|.++|..+.
T Consensus 13 ~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~--------Gp~EQI~rVD~~~ 84 (267)
T PF09342_consen 13 DYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYLSVD--------GPHEQISRVDCFK 84 (267)
T ss_pred cccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceecccC--------CChheEEEeeeee
Confidence 4459999999976 7888986643 56789999766333211 2466788887765
Q ss_pred EcCCCCCCCCCccceEEEEeCCCCCCCCCccceeecc
Q psy285 280 SHEHFSGEPNMRNDIALLRLERPPRLNGTHLMSCCYY 316 (842)
Q Consensus 280 ~Hp~y~~~~~~~nDIALlkL~~pv~~~~~v~Picl~~ 316 (842)
.-| ..+++||.|++|+.|+.+|+|..|+.
T Consensus 85 ~V~--------~S~v~LLHL~~~~~fTr~VlP~flp~ 113 (267)
T PF09342_consen 85 DVP--------ESNVLLLHLEQPANFTRYVLPTFLPE 113 (267)
T ss_pred ecc--------ccceeeeeecCcccceeeeccccccc
Confidence 333 46899999999999999999999864
No 15
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=91.69 E-value=0.69 Score=47.72 Aligned_cols=54 Identities=24% Similarity=0.412 Sum_probs=36.4
Q ss_pred CCCccccCCCCccEEecccCCCccccEEEEEEEEEccCCCCCCCCCeeEEecc-ccHHHHHHhhc
Q psy285 340 GKDSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGPASCGVYEIPGVYSRTS-YFLRWILDHLD 403 (842)
Q Consensus 340 ~~~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~~~C~~~~~p~vyt~V~-~~~~WI~~~i~ 403 (842)
..+++.|+||+|++.. .-+++||..-+...-+. ....-.+|+. .+++||++.++
T Consensus 197 ~~dT~pG~SGSpv~~~---------~~~vigv~~~g~~~~~~-~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 197 DADTLPGSSGSPVLIS---------KDEVIGVHYNGPGANGG-SLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred EecccCCCCCCceEec---------CceEEEEEecCCCcccc-cccCcceEecHHHHHHHHHhhC
Confidence 4688999999999861 22899999988632222 2333345544 57789988763
No 16
>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=89.20 E-value=1.2 Score=40.30 Aligned_cols=21 Identities=38% Similarity=0.673 Sum_probs=14.6
Q ss_pred CccccCCCCccEEecccCCCccccEEEEEE
Q psy285 342 DSCNGDSGGPLTWMGSFDSAISARTYLIGL 371 (842)
Q Consensus 342 ~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI 371 (842)
..-.|.|||||+- .+| .++||
T Consensus 100 ~~~~G~SGgpv~~---~~G------~vvGi 120 (120)
T PF13365_consen 100 DTRPGSSGGPVFD---SDG------RVVGI 120 (120)
T ss_dssp S-STTTTTSEEEE---TTS------EEEEE
T ss_pred ccCCCcEeHhEEC---CCC------EEEeC
Confidence 3345899999974 355 68886
No 17
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=88.39 E-value=5.9 Score=41.03 Aligned_cols=126 Identities=18% Similarity=0.173 Sum_probs=66.9
Q ss_pred CCCCCCCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEeeecCCCCCccceEEEEEeecChhHHHHHhcC
Q psy285 508 TDSGTKNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWGVTEDGRSSLELLAVQQKVFNSEECKARYQE 587 (842)
Q Consensus 508 ~~~~~~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~L~~~~v~~i~~~~C~~~~~~ 587 (842)
.......|+..+.|+....+.+.+...-++..... ..+....++|+=.. ....+++- +.|.+..
T Consensus 124 ~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~~---~~~d~i~v~GYP~d----k~~~~~~~-------e~t~~v~-- 187 (251)
T COG3591 124 KEDGASYDVGEAALESGINIGDVVNYLKRNTASEA---KANDRITVIGYPGD----KPNIGTMW-------ESTGKVN-- 187 (251)
T ss_pred ccCCceeeccHHHhccCCCcccccccccccccccc---ccCceeEEEeccCC----CCcceeEe-------eecceeE--
Confidence 34455667777777756666666665555544432 24555778887321 11111111 1111100
Q ss_pred CCCCCceEEeCCCCCCCccCCCCCcceeccccCCccccccEEEEEEEeCCCCCCCCCCCeeEeeh-hhhHHHHHHhh
Q psy285 588 LDPSSQICVGGKVGKDACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPTCGTKSENPGVYTRM-TYFLQWILDHL 663 (842)
Q Consensus 588 ~~~~~~iCa~~~~~~~~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~C~~~~~~p~vyt~V-~~~~~WI~~~i 663 (842)
.+....+ .-..+++.|+||+|++. .. -+++||.+-+..-..... -.-.+|+ ..+++||++.+
T Consensus 188 ~~~~~~l----~y~~dT~pG~SGSpv~~--~~-------~~vigv~~~g~~~~~~~~-~n~~vr~t~~~~~~I~~~~ 250 (251)
T COG3591 188 SIKGNKL----FYDADTLPGSSGSPVLI--SK-------DEVIGVHYNGPGANGGSL-ANNAVRLTPEILNFIQQNI 250 (251)
T ss_pred EEecceE----EEEecccCCCCCCceEe--cC-------ceEEEEEecCCCcccccc-cCcceEecHHHHHHHHHhh
Confidence 0111101 12358899999999998 22 279999998875221111 2334454 44678998765
No 18
>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=86.39 E-value=0.25 Score=59.39 Aligned_cols=55 Identities=18% Similarity=0.141 Sum_probs=32.3
Q ss_pred ccCCCCcccccccccccCcCCCcEEEEEEEeCCCCCCCCCCCeEEEecccchHHhhcccC
Q psy285 781 CNGDSGGPLMWMGSFDRSISARTYLLGIVSLGPSTCGMLRIPGVYTRTSYFLRWILATPE 840 (842)
Q Consensus 781 C~GDsGgPL~~~~~~~~~~~~~~~l~GivS~g~~~C~~~~~p~vyt~V~~y~~WI~~~~~ 840 (842)
=.||||+||+... ....+|+|+|++|.+. +....+.--..++..++..|+.+.++
T Consensus 214 ~~GDSGSPlF~YD----~~~kKWvl~Gv~~~~~-~~~g~~~~~~~~~~~f~~~~~~~d~~ 268 (769)
T PF02395_consen 214 SPGDSGSPLFAYD----KEKKKWVLVGVLSGGN-GYNGKGNWWNVIPPDFINQIKQNDTD 268 (769)
T ss_dssp -TT-TT-EEEEEE----TTTTEEEEEEEEEEEC-CCCHSEEEEEEECHHHHHHHHHHCCE
T ss_pred ccCcCCCceEEEE----ccCCeEEEEEEEcccc-ccCCccceeEEecHHHHHHHHhhhcc
Confidence 3899999999853 3578999999999983 33222211122333444566665543
No 19
>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=84.59 E-value=10 Score=43.17 Aligned_cols=25 Identities=32% Similarity=0.438 Sum_probs=18.7
Q ss_pred ccccCCCCccEEecccCCCccccEEEEEEEEEcc
Q psy285 343 SCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGP 376 (842)
Q Consensus 343 ~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~ 376 (842)
.-.|.|||||+- .+| .++||.+...
T Consensus 176 i~~GnSGGpl~n---~~G------~viGI~~~~~ 200 (428)
T TIGR02037 176 INPGNSGGPLVN---LRG------EVIGINTAIY 200 (428)
T ss_pred CCCCCCCCceEC---CCC------eEEEEEeEEE
Confidence 345899999984 356 7999987653
No 20
>PRK10139 serine endoprotease; Provisional
Probab=84.13 E-value=11 Score=43.13 Aligned_cols=25 Identities=32% Similarity=0.450 Sum_probs=19.3
Q ss_pred CccccCCCCccEEecccCCCccccEEEEEEEEEc
Q psy285 342 DSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLG 375 (842)
Q Consensus 342 ~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g 375 (842)
..-.|.|||||+- .+| .++||.+..
T Consensus 208 ~in~GnSGGpl~n---~~G------~vIGi~~~~ 232 (455)
T PRK10139 208 SINRGNSGGALLN---LNG------ELIGINTAI 232 (455)
T ss_pred ccCCCCCcceEEC---CCC------eEEEEEEEE
Confidence 3456899999994 356 799999874
No 21
>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=80.72 E-value=1.3 Score=53.49 Aligned_cols=57 Identities=21% Similarity=0.190 Sum_probs=34.8
Q ss_pred CccCCCCCcceeccccCCccccccEEEEEEEeCCCCCCCCCCCeeEeehhhhHHHHHHhhcc
Q psy285 604 ACKGDSGGPLTWMGSFDSAILARNYLIGLVSYGPTCGTKSENPGVYTRMTYFLQWILDHLED 665 (842)
Q Consensus 604 ~C~gDsGgPL~~~~~~~~~~~~~~~l~GI~S~g~~C~~~~~~p~vyt~V~~~~~WI~~~i~~ 665 (842)
.-.||||+||+..+..+ .+|+|+|+.+.+........ --..++..++..|+++....
T Consensus 213 ~~~GDSGSPlF~YD~~~----kKWvl~Gv~~~~~~~~g~~~-~~~~~~~~f~~~~~~~d~~~ 269 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEK----KKWVLVGVLSGGNGYNGKGN-WWNVIPPDFINQIKQNDTDG 269 (769)
T ss_dssp --TT-TT-EEEEEETTT----TEEEEEEEEEEECCCCHSEE-EEEEECHHHHHHHHHHCCEE
T ss_pred cccCcCCCceEEEEccC----CeEEEEEEEccccccCCccc-eeEEecHHHHHHHHhhhccc
Confidence 45799999999977767 89999999998865432211 12333444445666655544
No 22
>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=77.58 E-value=18 Score=41.14 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=26.7
Q ss_pred CCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEee
Q psy285 513 KNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWG 557 (842)
Q Consensus 513 ~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG 557 (842)
..||||||++.+ ..+.++.|..... . ..|+.+++.|+-
T Consensus 104 ~~DlAllkv~~~----~~~~~~~l~~~~~-~--~~G~~v~aiG~p 141 (428)
T TIGR02037 104 RTDIAVLKIDAK----KNLPVIKLGDSDK-L--RVGDWVLAIGNP 141 (428)
T ss_pred CCCEEEEEecCC----CCceEEEccCCCC-C--CCCCEEEEEECC
Confidence 369999999865 2355777754433 2 478889998874
No 23
>PRK10942 serine endoprotease; Provisional
Probab=71.44 E-value=41 Score=38.84 Aligned_cols=23 Identities=35% Similarity=0.527 Sum_probs=17.9
Q ss_pred cccCCCCccEEecccCCCccccEEEEEEEEEc
Q psy285 344 CNGDSGGPLTWMGSFDSAISARTYLIGLVSLG 375 (842)
Q Consensus 344 C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g 375 (842)
-.|.|||||+- .+| .++||.+..
T Consensus 231 ~~GnSGGpL~n---~~G------eviGI~t~~ 253 (473)
T PRK10942 231 NRGNSGGALVN---LNG------ELIGINTAI 253 (473)
T ss_pred CCCCCcCccCC---CCC------eEEEEEEEE
Confidence 46889999984 356 799998764
No 24
>PRK10898 serine endoprotease; Provisional
Probab=67.39 E-value=74 Score=35.16 Aligned_cols=25 Identities=32% Similarity=0.391 Sum_probs=19.1
Q ss_pred ccccCCCCccEEecccCCCccccEEEEEEEEEcc
Q psy285 343 SCNGDSGGPLTWMGSFDSAISARTYLIGLVSLGP 376 (842)
Q Consensus 343 ~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g~ 376 (842)
.-.|.|||||+- .+| .++||.+...
T Consensus 195 i~~GnSGGPl~n---~~G------~vvGI~~~~~ 219 (353)
T PRK10898 195 INHGNSGGALVN---SLG------ELMGINTLSF 219 (353)
T ss_pred cCCCCCcceEEC---CCC------eEEEEEEEEe
Confidence 356899999984 366 7999988653
No 25
>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=65.48 E-value=89 Score=34.52 Aligned_cols=25 Identities=28% Similarity=0.439 Sum_probs=19.0
Q ss_pred CccccCCCCccEEecccCCCccccEEEEEEEEEc
Q psy285 342 DSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLG 375 (842)
Q Consensus 342 ~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g 375 (842)
..-.|.|||||+- .+| .++||.+..
T Consensus 194 ~i~~GnSGGpl~n---~~G------~vIGI~~~~ 218 (351)
T TIGR02038 194 AINAGNSGGALIN---TNG------ELVGINTAS 218 (351)
T ss_pred ccCCCCCcceEEC---CCC------eEEEEEeee
Confidence 3456889999994 356 799998764
No 26
>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=64.23 E-value=6.2 Score=35.95 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=27.1
Q ss_pred cCCCCcccccccccccCcCCCcEEEEEEEeCCCCCCCCCCCeEEEecccch
Q psy285 782 NGDSGGPLMWMGSFDRSISARTYLLGIVSLGPSTCGMLRIPGVYTRTSYFL 832 (842)
Q Consensus 782 ~GDsGgPL~~~~~~~~~~~~~~~l~GivS~g~~~C~~~~~p~vyt~V~~y~ 832 (842)
.||-||+|.|+.+ ++||++-|. +.-..||++..|.
T Consensus 89 PGdCGg~L~C~HG----------ViGi~Tagg------~g~VaF~dir~~~ 123 (127)
T PF00947_consen 89 PGDCGGILRCKHG----------VIGIVTAGG------EGHVAFADIRDLL 123 (127)
T ss_dssp TT-TCSEEEETTC----------EEEEEEEEE------TTEEEEEECCCGS
T ss_pred CCCCCceeEeCCC----------eEEEEEeCC------CceEEEEechhhh
Confidence 5999999999765 899999983 2247899998764
No 27
>PRK10139 serine endoprotease; Provisional
Probab=60.50 E-value=1.1e+02 Score=35.00 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=24.8
Q ss_pred CCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEe
Q psy285 513 KNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGW 556 (842)
Q Consensus 513 ~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GW 556 (842)
..||||||++.+- ...++.|..... . ..|+...+.|.
T Consensus 137 ~~DlAvlkv~~~~----~l~~~~lg~s~~-~--~~G~~V~aiG~ 173 (455)
T PRK10139 137 QSDIALLQIQNPS----KLTQIAIADSDK-L--RVGDFAVAVGN 173 (455)
T ss_pred CCCEEEEEecCCC----CCceeEecCccc-c--CCCCEEEEEec
Confidence 4799999998543 234666654433 2 46888888876
No 28
>PRK10898 serine endoprotease; Provisional
Probab=59.48 E-value=1.2e+02 Score=33.61 Aligned_cols=37 Identities=11% Similarity=0.193 Sum_probs=22.8
Q ss_pred CCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEee
Q psy285 513 KNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWG 557 (842)
Q Consensus 513 ~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG 557 (842)
.+||||||++.+ . ..++-|..... . ..|+.+.+.|+-
T Consensus 124 ~~DlAvl~v~~~-~----l~~~~l~~~~~-~--~~G~~V~aiG~P 160 (353)
T PRK10898 124 LTDLAVLKINAT-N----LPVIPINPKRV-P--HIGDVVLAIGNP 160 (353)
T ss_pred CCCEEEEEEcCC-C----CCeeeccCcCc-C--CCCCEEEEEeCC
Confidence 479999999754 1 23344432221 2 468888888864
No 29
>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=57.09 E-value=12 Score=34.11 Aligned_cols=102 Identities=15% Similarity=0.109 Sum_probs=50.9
Q ss_pred ccccceEEEEEeccccCCCCCCccccCCCeeEeEEecc---CCCCCCccceEEEEEEeeccchhhhcCCCCCCCc-eEec
Q psy285 27 FRFYFHVMIIKIKTRARSPFIPNIRFKSPIHLLALFST---EDKRPSLELLAVQQKVFNSEKCKARYQKLDPSSQ-ICVG 102 (842)
Q Consensus 27 ~~~~~di~lvkL~~~~~~~~~~~~~~~~~~~~~~g~~~---~~~~~s~~L~~~~~~i~~~~~C~~~~~~~~~~~~-iCa~ 102 (842)
..++.|++++++...- .+.|+... |. .||.. ...-.+-..+.-... .-+-..+|+.....++ +..
T Consensus 16 ~~~~rDL~V~~t~a~G----~D~I~~C~--Ct-~GvYyCks~~k~yPV~~~~~~~~---~i~~s~YYP~h~Q~~~l~g~- 84 (127)
T PF00947_consen 16 EDYTRDLLVDRTTAHG----CDTIPRCD--CT-TGVYYCKSKNKYYPVTVTGPTWY---WIEESEYYPKHYQYNLLIGE- 84 (127)
T ss_dssp EECCCTEEEEEECCEE----E--BB------S-EEEEEETTTTCEEEEEEEEECEE---EE-SBTTB-SEEEECEEEEE-
T ss_pred hhhCCCEEEEecCCCC----CCcccCcc--CC-CCEEEeeECCeEeeEEEeccceE---EECCccCchhheecCceeec-
Confidence 3578899999997665 33344332 32 24421 111111111111111 1133345554333233 333
Q ss_pred CCCCcccc-ccCCCCCeeecCCcccccCCCcEEEEEEeecCCCCCCCCCCeEEEEcccc
Q psy285 103 GKVGKDSC-YGDSGGPLTWMGSFDSAISARNYLIGLVSYGPEDCGKTENPGVYTRMTYF 160 (842)
Q Consensus 103 ~~~~~~~C-~gDsGgPlv~~~~~~~~~~~~~~l~Gi~S~g~~~C~~~~~p~vyt~v~~y 160 (842)
+.| .||-||+|.|... ++||++-| .+.-..|++|..|
T Consensus 85 -----Gp~~PGdCGg~L~C~HG----------ViGi~Tag------g~g~VaF~dir~~ 122 (127)
T PF00947_consen 85 -----GPAEPGDCGGILRCKHG----------VIGIVTAG------GEGHVAFADIRDL 122 (127)
T ss_dssp ------SSSTT-TCSEEEETTC----------EEEEEEEE------ETTEEEEEECCCG
T ss_pred -----ccCCCCCCCceeEeCCC----------eEEEEEeC------CCceEEEEechhh
Confidence 344 6899999999543 89999988 2345679998776
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=56.58 E-value=1e+02 Score=33.95 Aligned_cols=37 Identities=14% Similarity=0.217 Sum_probs=23.8
Q ss_pred CCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEee
Q psy285 513 KNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGWG 557 (842)
Q Consensus 513 ~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GWG 557 (842)
..||||||++.+- +.++.|.... .. ..|+.+.+.|+.
T Consensus 124 ~~DlAvlkv~~~~-----~~~~~l~~s~-~~--~~G~~V~aiG~P 160 (351)
T TIGR02038 124 LTDLAVLKIEGDN-----LPTIPVNLDR-PP--HVGDVVLAIGNP 160 (351)
T ss_pred CCCEEEEEecCCC-----CceEeccCcC-cc--CCCCEEEEEeCC
Confidence 4799999998542 2344443222 22 578888888874
No 31
>PRK10942 serine endoprotease; Provisional
Probab=49.92 E-value=1.5e+02 Score=34.20 Aligned_cols=37 Identities=22% Similarity=0.369 Sum_probs=23.4
Q ss_pred CCceEEEEEcCCCCCCCCcccccCCCCCCCCCcCCCCeEEEEEe
Q psy285 513 KNDIALLRLEKSPEWNGYVHPVCLPYGNAMTRNFENENTIVAGW 556 (842)
Q Consensus 513 ~nDIALlkL~~~v~~s~~v~PicLp~~~~~~~~~~~~~~~v~GW 556 (842)
..||||||++.+-. ..++-|-.... . ..|+.+.+.|.
T Consensus 158 ~~DlAvlki~~~~~----l~~~~lg~s~~-l--~~G~~V~aiG~ 194 (473)
T PRK10942 158 RSDIALIQLQNPKN----LTAIKMADSDA-L--RVGDYTVAIGN 194 (473)
T ss_pred CCCEEEEEecCCCC----CceeEecCccc-c--CCCCEEEEEcC
Confidence 47999999975332 33565643332 2 46787777775
No 32
>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=25.04 E-value=1.3e+02 Score=29.46 Aligned_cols=28 Identities=25% Similarity=0.409 Sum_probs=20.9
Q ss_pred CccccCCCCccEEecccCCCccccEEEEEEEEEc
Q psy285 342 DSCNGDSGGPLTWMGSFDSAISARTYLIGLVSLG 375 (842)
Q Consensus 342 ~~C~gDsGgPL~~~~~~~g~~~~~~~l~GI~S~g 375 (842)
.+-.|+-||||+. ..++ ...++||-.-|
T Consensus 143 ~t~~G~CG~~l~~--~~~~----~~~i~GiHvaG 170 (172)
T PF00548_consen 143 PTKPGMCGSPLVS--RIGG----QGKIIGIHVAG 170 (172)
T ss_dssp EEETTGTTEEEEE--SCGG----TTEEEEEEEEE
T ss_pred CCCCCccCCeEEE--eecc----CccEEEEEecc
Confidence 3557899999998 3344 55899998766
No 33
>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=23.18 E-value=54 Score=29.06 Aligned_cols=18 Identities=33% Similarity=0.650 Sum_probs=13.9
Q ss_pred ccCCCCCeeecCCcccccCCCcEEEEE
Q psy285 111 YGDSGGPLTWMGSFDSAISARNYLIGL 137 (842)
Q Consensus 111 ~gDsGgPlv~~~~~~~~~~~~~~l~Gi 137 (842)
.|.||||++- ....++||
T Consensus 103 ~G~SGgpv~~---------~~G~vvGi 120 (120)
T PF13365_consen 103 PGSSGGPVFD---------SDGRVVGI 120 (120)
T ss_dssp TTTTTSEEEE---------TTSEEEEE
T ss_pred CCcEeHhEEC---------CCCEEEeC
Confidence 5789999983 45568886
No 34
>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=21.85 E-value=74 Score=29.44 Aligned_cols=24 Identities=25% Similarity=0.491 Sum_probs=16.3
Q ss_pred cccccCCCCCeeecCCcccccCCCcEEEEEEee
Q psy285 108 DSCYGDSGGPLTWMGSFDSAISARNYLIGLVSY 140 (842)
Q Consensus 108 ~~C~gDsGgPlv~~~~~~~~~~~~~~l~Gi~S~ 140 (842)
+.-+|-||||++| ....++||.--
T Consensus 104 s~lkGSSGgPiLC---------~~GH~vG~f~a 127 (148)
T PF02907_consen 104 SDLKGSSGGPILC---------PSGHAVGMFRA 127 (148)
T ss_dssp HHHTT-TT-EEEE---------TTSEEEEEEEE
T ss_pred EEEecCCCCcccC---------CCCCEEEEEEE
Confidence 3458999999999 34579998533
Done!