Query psy10841
Match_columns 286
No_of_seqs 173 out of 1404
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 19:50:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 100.0 2E-45 4.4E-50 308.0 23.6 225 46-273 1-232 (232)
2 smart00020 Tryp_SPc Trypsin-li 100.0 3.2E-42 7E-47 288.6 22.9 221 45-270 1-229 (229)
3 KOG3627|consensus 100.0 4.9E-41 1.1E-45 286.6 24.4 229 43-275 10-255 (256)
4 PF00089 Trypsin: Trypsin; In 100.0 5.4E-40 1.2E-44 273.1 21.4 215 46-270 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 7.5E-31 1.6E-35 220.9 14.8 227 43-277 30-281 (413)
6 PF03761 DUF316: Domain of unk 99.8 1.1E-17 2.5E-22 144.6 19.1 218 33-274 28-279 (282)
7 PF09342 DUF1986: Domain of un 99.6 4.7E-14 1E-18 114.1 16.5 116 53-175 12-131 (267)
8 COG3591 V8-like Glu-specific e 99.2 1.3E-10 2.7E-15 96.5 11.2 197 52-275 44-251 (251)
9 TIGR02037 degP_htrA_DO peripla 98.6 2.2E-06 4.8E-11 78.5 16.7 166 68-275 57-227 (428)
10 PF13365 Trypsin_2: Trypsin-li 98.6 4.7E-07 1E-11 67.4 8.9 21 71-91 1-22 (120)
11 PRK10898 serine endoprotease; 98.5 1.3E-05 2.9E-10 71.3 18.0 150 57-249 55-219 (353)
12 TIGR02038 protease_degS peripl 98.5 7.6E-06 1.6E-10 72.9 16.3 152 56-249 54-219 (351)
13 PRK10139 serine endoprotease; 98.4 3.9E-05 8.5E-10 70.6 17.9 166 68-275 89-260 (455)
14 PRK10942 serine endoprotease; 98.3 3.3E-05 7.1E-10 71.5 16.1 139 68-248 110-253 (473)
15 PF02395 Peptidase_S6: Immunog 97.5 0.00044 9.6E-09 67.0 8.8 159 72-252 68-245 (769)
16 PF00863 Peptidase_C4: Peptida 95.9 0.16 3.5E-06 42.3 11.2 151 71-265 33-186 (235)
17 PF00548 Peptidase_C3: 3C cyst 93.4 0.49 1.1E-05 37.7 7.7 72 66-154 22-93 (172)
18 COG0265 DegQ Trypsin-like seri 91.4 6 0.00013 35.2 12.9 141 69-251 72-217 (347)
19 PF00947 Pico_P2A: Picornaviru 88.5 0.64 1.4E-05 34.6 3.5 37 219-267 87-123 (127)
20 KOG1421|consensus 84.9 10 0.00023 36.5 10.0 83 71-173 86-171 (955)
21 PF05416 Peptidase_C37: Southa 76.8 8.3 0.00018 34.9 6.2 140 71-249 381-527 (535)
22 PF10459 Peptidase_S46: Peptid 62.5 4.8 0.0001 39.4 1.9 18 71-88 49-67 (698)
23 PF08192 Peptidase_S64: Peptid 61.1 85 0.0018 30.5 9.6 57 217-275 634-690 (695)
24 PF05580 Peptidase_S55: SpoIVB 55.1 13 0.00029 30.5 3.0 27 216-249 174-200 (218)
25 PF02907 Peptidase_S29: Hepati 45.1 22 0.00047 26.9 2.5 23 220-248 106-128 (148)
26 PF05579 Peptidase_S32: Equine 42.7 27 0.00059 29.7 3.0 23 221-249 207-229 (297)
27 KOG1320|consensus 41.8 75 0.0016 29.6 6.0 44 44-89 64-107 (473)
28 PF00944 Peptidase_S3: Alphavi 37.2 29 0.00064 26.2 2.2 24 220-249 104-127 (158)
29 PF14781 BBS2_N: Ciliary BBSom 32.1 1.2E+02 0.0027 23.0 4.8 48 117-172 19-70 (136)
30 TIGR02860 spore_IV_B stage IV 29.5 38 0.00082 30.9 2.1 45 216-273 354-398 (402)
31 PF10459 Peptidase_S46: Peptid 28.0 52 0.0011 32.4 2.8 61 207-277 621-689 (698)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=100.00 E-value=2e-45 Score=308.03 Aligned_cols=225 Identities=43% Similarity=0.832 Sum_probs=192.8
Q ss_pred eecCeeCCCCccceEEEEeeC-CeEEeEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECC
Q psy10841 46 VVGGKKAELGAWPWLIALYRD-GFFHCGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHS 124 (286)
Q Consensus 46 i~~g~~a~~~~~Pw~v~i~~~-~~~~C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 124 (286)
|+||+++..++|||+|.|+.. ..++|+||||+++||||||||+.+.....+.|++|...........+.+.|.++++||
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 80 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHP 80 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECC
Confidence 679999999999999999876 6789999999999999999999876567788999987765543456788999999999
Q ss_pred CCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecc--ccccccc
Q psy10841 125 MFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILP--ACKHYED 202 (286)
Q Consensus 125 ~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~--~c~~~~~ 202 (286)
+|+.....+|||||||++++.++.+++||||+........+..+.++|||...........++...+.+++ .|...+.
T Consensus 81 ~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~ 160 (232)
T cd00190 81 NYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYS 160 (232)
T ss_pred CCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhcc
Confidence 99998889999999999999999999999999865456677899999999876554566778888888877 5876543
Q ss_pred ----CCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcHHHHHhh
Q psy10841 203 ----RIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFVPWLMSN 273 (286)
Q Consensus 203 ----~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~~WI~~~ 273 (286)
..+.++|+.........|.|||||||++.. +++++|+||+|++..|.....|.+|++|++|.+||+++
T Consensus 161 ~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~---~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 161 YGGTITDNMLCAGGLEGGKDACQGDSGGPLVCND---NGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred CcccCCCceEeeCCCCCCCccccCCCCCcEEEEe---CCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 567899998654467899999999999876 58899999999999888656799999999999999864
No 2
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=100.00 E-value=3.2e-42 Score=288.61 Aligned_cols=221 Identities=43% Similarity=0.881 Sum_probs=186.8
Q ss_pred ceecCeeCCCCccceEEEEeeCC-eEEeEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEEC
Q psy10841 45 RVVGGKKAELGAWPWLIALYRDG-FFHCGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMH 123 (286)
Q Consensus 45 ~i~~g~~a~~~~~Pw~v~i~~~~-~~~C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h 123 (286)
||+||+++...+|||+|.++... .+.|+||||++++|||||||+.......+.|++|........ ....+.|..+++|
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~-~~~~~~v~~~~~~ 79 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGE-EGQVIKVSKVIIH 79 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCC-CceEEeeEEEEEC
Confidence 58999999999999999998776 789999999999999999999876656788999977654422 2378899999999
Q ss_pred CCCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCC-CCCCCccceeEeeeecc--ccccc
Q psy10841 124 SMFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFE-HGPDPDHMREVQVPILP--ACKHY 200 (286)
Q Consensus 124 p~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~-~~~~~~~l~~~~~~~~~--~c~~~ 200 (286)
|+|+.....+|||||||++++.+++.++|+||+........+..+.++|||.... .......++...+.+.+ .|...
T Consensus 80 p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~ 159 (229)
T smart00020 80 PNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRA 159 (229)
T ss_pred CCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhh
Confidence 9999888899999999999999999999999998644566678999999998753 23345677778888777 58765
Q ss_pred cc----CCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcHHHH
Q psy10841 201 ED----RIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFVPWL 270 (286)
Q Consensus 201 ~~----~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~~WI 270 (286)
+. ....++|+.........|.||+|+||++.. + +|+|+||++++..|...+.|.+|++|++|.+||
T Consensus 160 ~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~---~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 160 YSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCND---G-RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred hccccccCCCcEeecCCCCCCcccCCCCCCeeEEEC---C-CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 43 567799998654467899999999999865 4 899999999999998667899999999999998
No 3
>KOG3627|consensus
Probab=100.00 E-value=4.9e-41 Score=286.64 Aligned_cols=229 Identities=42% Similarity=0.887 Sum_probs=188.0
Q ss_pred CCceecCeeCCCCccceEEEEeeCC--eEEeEEEEeeCCEEEeccCCcCCC-CCceEEEEEeeeecccC-CCC--ceEEe
Q psy10841 43 SGRVVGGKKAELGAWPWLIALYRDG--FFHCGGVVLDESWVMTAAHCVDGF-EKHYFEVYAGMLRRFSF-SPT--EQVRP 116 (286)
Q Consensus 43 ~~~i~~g~~a~~~~~Pw~v~i~~~~--~~~C~GtLIs~~~VLTaAhC~~~~-~~~~~~v~~g~~~~~~~-~~~--~~~~~ 116 (286)
..+|+||.++..+++||++.+.... .++|+|+||+++||||||||+... .. .+.|++|....... ... .....
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~~ 88 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVGD 88 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCc-ceEEEECccccccccccCchhhhce
Confidence 5699999999999999999998765 689999999999999999999774 23 67888887644332 112 24455
Q ss_pred eeEEEECCCCCCCCCC-CceEEEEecCccccCCceeeeecCCCCC--CCCCCCceEEEEecccCCC-CCCCccceeEeee
Q psy10841 117 VSRIVMHSMFKRAEMT-NDLALLQLAAPLRYNRYVRPICLPDVTE--TPEPYSTCTAVGWGAVFEH-GPDPDHMREVQVP 192 (286)
Q Consensus 117 v~~~~~hp~y~~~~~~-~DiAllkL~~~i~~~~~v~picL~~~~~--~~~~~~~~~~~Gwg~~~~~-~~~~~~l~~~~~~ 192 (286)
+.++++||+|+..... +|||||+|.+++.|++.++|||||.... ....+..+.++|||.+... ......+++..++
T Consensus 89 v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v~ 168 (256)
T KOG3627|consen 89 VEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDVP 168 (256)
T ss_pred eeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEEe
Confidence 7788899999998877 9999999999999999999999986443 2455588999999987543 2456788888888
Q ss_pred ecc--ccccccc----CCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCC-CCCCCCCeeEEeCCC
Q psy10841 193 ILP--ACKHYED----RIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEG-CARPNEPGVYTRVSQ 265 (286)
Q Consensus 193 ~~~--~c~~~~~----~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~-c~~~~~p~v~t~v~~ 265 (286)
+++ +|...+. ....++|++......++|.|||||||++... ++++++||+|||.. |.....|++|++|+.
T Consensus 169 i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~---~~~~~~GivS~G~~~C~~~~~P~vyt~V~~ 245 (256)
T KOG3627|consen 169 IISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDN---GRWVLVGIVSWGSGGCGQPNYPGVYTRVSS 245 (256)
T ss_pred EcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeC---CcEEEEEEEEecCCCCCCCCCCeEEeEhHH
Confidence 888 5877664 3356899986556677899999999999873 38999999999997 998778999999999
Q ss_pred cHHHHHhhhc
Q psy10841 266 FVPWLMSNSE 275 (286)
Q Consensus 266 ~~~WI~~~~~ 275 (286)
|.+||++.+.
T Consensus 246 y~~WI~~~~~ 255 (256)
T KOG3627|consen 246 YLDWIKENIG 255 (256)
T ss_pred hHHHHHHHhc
Confidence 9999999875
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=100.00 E-value=5.4e-40 Score=273.07 Aligned_cols=215 Identities=40% Similarity=0.866 Sum_probs=181.8
Q ss_pred eecCeeCCCCccceEEEEeeCC-eEEeEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECC
Q psy10841 46 VVGGKKAELGAWPWLIALYRDG-FFHCGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHS 124 (286)
Q Consensus 46 i~~g~~a~~~~~Pw~v~i~~~~-~~~C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 124 (286)
|.||+++..++|||+|.++... .++|+|+||+++||||||||+.. ...+.+.+|...........+.+.|++++.||
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~--~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~ 78 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG--ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHP 78 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS--GGSEEEEESESBTTSTTTTSEEEEEEEEEEET
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc--cccccccccccccccccccccccccccccccc
Confidence 6899999999999999999877 89999999999999999999977 45678888874444434446889999999999
Q ss_pred CCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecc--cccccc-
Q psy10841 125 MFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILP--ACKHYE- 201 (286)
Q Consensus 125 ~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~--~c~~~~- 201 (286)
+|+.....+|||||||++++.+.+.++|+||+........+..+.++||+.....+ ....++...+.+.+ .|...+
T Consensus 79 ~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~~~~~c~~~~~ 157 (220)
T PF00089_consen 79 KYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVVSRKTCRSSYN 157 (220)
T ss_dssp TSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS-BTSBEEEEEEEEEEHHHHHHHTT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccccccc
Confidence 99998889999999999999999999999999854445677899999999865444 44567777777766 477643
Q ss_pred -cCCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcHHHH
Q psy10841 202 -DRIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFVPWL 270 (286)
Q Consensus 202 -~~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~~WI 270 (286)
.....++|+... .....|.|||||||++... +|+||++++..|...+.|.+|++|+.|++||
T Consensus 158 ~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~------~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 158 DNLTPNMICAGSS-GSGDACQGDSGGPLICNNN------YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TTSTTTEEEEETT-SSSBGGTTTTTSEEEETTE------EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred ccccccccccccc-cccccccccccccccccee------eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 256789999864 5578999999999997541 8999999999999877899999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=7.5e-31 Score=220.89 Aligned_cols=227 Identities=32% Similarity=0.536 Sum_probs=164.1
Q ss_pred CCceecCeeCCCCccceEEEEeeC-----CeEEeEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEee
Q psy10841 43 SGRVVGGKKAELGAWPWLIALYRD-----GFFHCGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPV 117 (286)
Q Consensus 43 ~~~i~~g~~a~~~~~Pw~v~i~~~-----~~~~C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v 117 (286)
+.||+||+.|..++||++|++... +..+|+|+++..|||||||||+....+-...+..+..+..+.. ..+..++
T Consensus 30 s~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~S-q~~rg~v 108 (413)
T COG5640 30 SSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSS-QAERGHV 108 (413)
T ss_pred ceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccc-cccCcce
Confidence 579999999999999999998532 3468999999999999999999776543333444444444422 5677889
Q ss_pred eEEEECCCCCCCCCCCceEEEEecCccccCCceeeeecCCCCC----CCCCCCceEEEEecccCCC---CCC--Ccccee
Q psy10841 118 SRIVMHSMFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTE----TPEPYSTCTAVGWGAVFEH---GPD--PDHMRE 188 (286)
Q Consensus 118 ~~~~~hp~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~----~~~~~~~~~~~Gwg~~~~~---~~~--~~~l~~ 188 (286)
+.+++|..|.+..+.||+|+++|.++..... + .+......+ ........+..+|+.+... ... ...+++
T Consensus 109 r~i~~~efY~~~n~~ND~Av~~l~~~a~~pr-~-ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e 186 (413)
T COG5640 109 RTIYVHEFYSPGNLGNDIAVLELARAASLPR-V-KITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHE 186 (413)
T ss_pred EEEeeecccccccccCcceeeccccccccch-h-heeeccCcccceecccccccccceeeeeeeecCCCCCCCccceeee
Confidence 9999999999999999999999998664321 0 111111111 1222344566677765322 111 246777
Q ss_pred Eeeeecc--ccccccc--------CCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCC-CCCCCCC
Q psy10841 189 VQVPILP--ACKHYED--------RIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEG-CARPNEP 257 (286)
Q Consensus 189 ~~~~~~~--~c~~~~~--------~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~-c~~~~~p 257 (286)
..+...+ .|...+. ..-.-+|++.+ ..+.|+||||||++... +..+.++||+|||.+ |+.+..|
T Consensus 187 ~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~--~~daCqGDSGGPi~~~g---~~G~vQ~GVvSwG~~~Cg~t~~~ 261 (413)
T COG5640 187 VAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP--PKDACQGDSGGPIFHKG---EEGRVQRGVVSWGDGGCGGTLIP 261 (413)
T ss_pred eeeeeechHHhhhhccccccCCCCCCccceecCCC--CcccccCCCCCceEEeC---CCccEEEeEEEecCCCCCCCCcc
Confidence 7777776 4665442 11223999854 47899999999999765 566789999999995 9999999
Q ss_pred eeEEeCCCcHHHHHhhhccc
Q psy10841 258 GVYTRVSQFVPWLMSNSERA 277 (286)
Q Consensus 258 ~v~t~v~~~~~WI~~~~~~~ 277 (286)
.|||+|+.|.+||...++.-
T Consensus 262 gVyT~vsny~~WI~a~~~~l 281 (413)
T COG5640 262 GVYTNVSNYQDWIAAMTNGL 281 (413)
T ss_pred eeEEehhHHHHHHHHHhcCC
Confidence 99999999999999987543
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.79 E-value=1.1e-17 Score=144.56 Aligned_cols=218 Identities=21% Similarity=0.406 Sum_probs=138.2
Q ss_pred cCCCCCC-ccCCCceecCeeCCCCccceEEEEeeCC----eEEeEEEEeeCCEEEeccCCcCCCCCc-------------
Q psy10841 33 TDMAGNP-ILGSGRVVGGKKAELGAWPWLIALYRDG----FFHCGGVVLDESWVMTAAHCVDGFEKH------------- 94 (286)
Q Consensus 33 ~~~~~~~-~~~~~~i~~g~~a~~~~~Pw~v~i~~~~----~~~C~GtLIs~~~VLTaAhC~~~~~~~------------- 94 (286)
-+.||.. ...+.++.+|..+...+.||+|.+...+ .++++|||||+|||||++||+......
T Consensus 28 l~~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~ 107 (282)
T PF03761_consen 28 LETCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCE 107 (282)
T ss_pred HHhcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceee
Confidence 4567744 3345678999999999999999997543 356899999999999999998632210
Q ss_pred ----eEEE---EEeeeec----ccCCCCceEEeeeEEEECC----CCCCCCCCCceEEEEecCccccCCceeeeecCCCC
Q psy10841 95 ----YFEV---YAGMLRR----FSFSPTEQVRPVSRIVMHS----MFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVT 159 (286)
Q Consensus 95 ----~~~v---~~g~~~~----~~~~~~~~~~~v~~~~~hp----~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~ 159 (286)
.+.| .+-.... ..........++.++++-- ........++++||+|+++ +.....|+||+...
T Consensus 108 ~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~ 185 (282)
T PF03761_consen 108 GNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSS 185 (282)
T ss_pred CCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCc
Confidence 0000 0000000 0000111224455554421 1123345689999999998 67889999999876
Q ss_pred CCCCCCCceEEEEecccCCCCCCCccceeEeeeecccccccccCCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcE
Q psy10841 160 ETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHYEDRIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRW 239 (286)
Q Consensus 160 ~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~ 239 (286)
.....+..+.++|+. ....+....+.+.. |.. |..........|.+|+||||+... ++++
T Consensus 186 ~~~~~~~~~~~yg~~-------~~~~~~~~~~~i~~-~~~---------~~~~~~~~~~~~~~d~Gg~lv~~~---~gr~ 245 (282)
T PF03761_consen 186 TNWEKGDEVDVYGFN-------STGKLKHRKLKITN-CTK---------CAYSICTKQYSCKGDRGGPLVKNI---NGRW 245 (282)
T ss_pred cccccCceEEEeecC-------CCCeEEEEEEEEEE-eec---------cceeEecccccCCCCccCeEEEEE---CCCE
Confidence 666667777777771 11223333333332 211 221112345789999999999777 8999
Q ss_pred EEEEEEEecC-CCCCCCCCeeEEeCCCcHHHHHhhh
Q psy10841 240 YVAGVVSHGE-GCARPNEPGVYTRVSQFVPWLMSNS 274 (286)
Q Consensus 240 ~lvGI~s~~~-~c~~~~~p~v~t~v~~~~~WI~~~~ 274 (286)
+|+||.+.+. .|.. ....|.+|..|.+=|-+.+
T Consensus 246 tlIGv~~~~~~~~~~--~~~~f~~v~~~~~~IC~lt 279 (282)
T PF03761_consen 246 TLIGVGASGNYECNK--NNSYFFNVSWYQDEICELT 279 (282)
T ss_pred EEEEEEccCCCcccc--cccEEEEHHHhhhhhccce
Confidence 9999998776 3432 2678999998877665543
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.61 E-value=4.7e-14 Score=114.13 Aligned_cols=116 Identities=33% Similarity=0.670 Sum_probs=92.6
Q ss_pred CCCccceEEEEeeCCeEEeEEEEeeCCEEEeccCCcCCCCC--ceEEEEEeeeec--ccCCCCceEEeeeEEEECCCCCC
Q psy10841 53 ELGAWPWLIALYRDGFFHCGGVVLDESWVMTAAHCVDGFEK--HYFEVYAGMLRR--FSFSPTEQVRPVSRIVMHSMFKR 128 (286)
Q Consensus 53 ~~~~~Pw~v~i~~~~~~~C~GtLIs~~~VLTaAhC~~~~~~--~~~~v~~g~~~~--~~~~~~~~~~~v~~~~~hp~y~~ 128 (286)
....|||++.|+.++.+.|+|+||.++|||++..|+.+... ..+.+++|.... +...+.+|.++|..+..=|
T Consensus 12 e~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~---- 87 (267)
T PF09342_consen 12 EDYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVP---- 87 (267)
T ss_pred ccccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeecc----
Confidence 34579999999999999999999999999999999976443 677888886542 2344567777777653322
Q ss_pred CCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecc
Q psy10841 129 AEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGA 175 (286)
Q Consensus 129 ~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~ 175 (286)
..+++||.|++|+.|+.+|+|..||...........|..+|-..
T Consensus 88 ---~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 88 ---ESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred ---ccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 47899999999999999999999997555566667898888643
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.22 E-value=1.3e-10 Score=96.45 Aligned_cols=197 Identities=17% Similarity=0.224 Sum_probs=108.0
Q ss_pred CCCCccceEEEEee---CCeEEeEEEEeeCCEEEeccCCcCCCCCce--EEEEE-eeeecccCCCCceEEee--eEEEEC
Q psy10841 52 AELGAWPWLIALYR---DGFFHCGGVVLDESWVMTAAHCVDGFEKHY--FEVYA-GMLRRFSFSPTEQVRPV--SRIVMH 123 (286)
Q Consensus 52 a~~~~~Pw~v~i~~---~~~~~C~GtLIs~~~VLTaAhC~~~~~~~~--~~v~~-g~~~~~~~~~~~~~~~v--~~~~~h 123 (286)
....+|||-+-... .+.+-|+++||+++.|||++||+.+...+. +.+.. |.. ........+ ....+.
T Consensus 44 ~dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~G~~~~~~~p~g~~-----~~~~~~~~~~~~~~~~~ 118 (251)
T COG3591 44 TDTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDYGEDDIAAAPPGVN-----SDGGPFYGITKIEIRVY 118 (251)
T ss_pred ccCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCCChhhhhhcCCccc-----CCCCCCCceeeEEEEec
Confidence 34568999876643 234557779999999999999997765432 11221 111 112222222 222223
Q ss_pred C--CCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecccccccc
Q psy10841 124 S--MFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHYE 201 (286)
Q Consensus 124 p--~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~~ 201 (286)
| .|.......|+..++|+....+........++.... ...++...+.||-...... ....+ .|..-.
T Consensus 119 ~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~d~i~v~GYP~dk~~~---~~~~e-------~t~~v~ 187 (251)
T COG3591 119 PGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTASE-AKANDRITVIGYPGDKPNI---GTMWE-------STGKVN 187 (251)
T ss_pred CCceeccCCceeeccHHHhccCCCccccccccccccccc-cccCceeEEEeccCCCCcc---eeEee-------ecceeE
Confidence 3 234445567777777774444444444334433223 3344558889986443210 11111 111111
Q ss_pred cCCCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeC-CCcHHHHHhhhc
Q psy10841 202 DRIADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRV-SQFVPWLMSNSE 275 (286)
Q Consensus 202 ~~~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v-~~~~~WI~~~~~ 275 (286)
......+ ....+++.|+||+|++... + +++||..-+..-.+.....-.+|+ ..+++||++.++
T Consensus 188 ~~~~~~l-----~y~~dT~pG~SGSpv~~~~---~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 188 SIKGNKL-----FYDADTLPGSSGSPVLISK---D---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred EEecceE-----EEEecccCCCCCCceEecC---c---eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 1111111 2245789999999999543 1 799999988753322334556666 446799988764
No 9
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=98.62 E-value=2.2e-06 Score=78.51 Aligned_cols=166 Identities=20% Similarity=0.162 Sum_probs=91.1
Q ss_pred eEEeEEEEeeCC-EEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCcccc
Q psy10841 68 FFHCGGVVLDES-WVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLRY 146 (286)
Q Consensus 68 ~~~C~GtLIs~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~~ 146 (286)
...++|.+|+++ +|||++|++.+.. .+.|.+. ....+..+-+..++ ..|+||||++.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~~--~i~V~~~---------~~~~~~a~vv~~d~-------~~DlAllkv~~~--- 115 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGAD--EITVTLS---------DGREFKAKLVGKDP-------RTDIAVLKIDAK--- 115 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCCC--eEEEEeC---------CCCEEEEEEEEecC-------CCCEEEEEecCC---
Confidence 467999999987 9999999997643 4555443 12334444333333 479999999864
Q ss_pred CCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeeccccccc-cc--CCCCEEEEeeCCCCCCCCCCC
Q psy10841 147 NRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHY-ED--RIADVICAGMPQGGRDTCQGD 223 (286)
Q Consensus 147 ~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~-~~--~~~~~~C~~~~~~~~~~c~gd 223 (286)
..+.++.|... .....++.+.++|+...... . ...-+++..... .. .....+ ..+...-.|.
T Consensus 116 -~~~~~~~l~~~-~~~~~G~~v~aiG~p~g~~~-----~---~t~G~vs~~~~~~~~~~~~~~~i-----~tda~i~~Gn 180 (428)
T TIGR02037 116 -KNLPVIKLGDS-DKLRVGDWVLAIGNPFGLGQ-----T---VTSGIVSALGRSGLGIGDYENFI-----QTDAAINPGN 180 (428)
T ss_pred -CCceEEEccCC-CCCCCCCEEEEEECCCcCCC-----c---EEEEEEEecccCccCCCCccceE-----EECCCCCCCC
Confidence 34567777653 34577899999998532111 1 111111110000 00 001111 1233566799
Q ss_pred CCCeeeeecCCCCCcEEEEEEEEecCC-CCCCCCCeeEEeCCCcHHHHHhhhc
Q psy10841 224 SGGPLLCPVPGSQGRWYVAGVVSHGEG-CARPNEPGVYTRVSQFVPWLMSNSE 275 (286)
Q Consensus 224 sGgPL~~~~~~~~~~~~lvGI~s~~~~-c~~~~~p~v~t~v~~~~~WI~~~~~ 275 (286)
|||||+-. .-.++||.+.... .+.....+.+..+......+++.++
T Consensus 181 SGGpl~n~------~G~viGI~~~~~~~~g~~~g~~faiP~~~~~~~~~~l~~ 227 (428)
T TIGR02037 181 SGGPLVNL------RGEVIGINTAIYSPSGGNVGIGFAIPSNMAKNVVDQLIE 227 (428)
T ss_pred CCCceECC------CCeEEEEEeEEEcCCCCccceEEEEEhHHHHHHHHHHHh
Confidence 99999832 2249999876431 1111112334445444555555444
No 10
>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=98.56 E-value=4.7e-07 Score=67.42 Aligned_cols=21 Identities=29% Similarity=0.658 Sum_probs=19.4
Q ss_pred eEEEEeeCC-EEEeccCCcCCC
Q psy10841 71 CGGVVLDES-WVMTAAHCVDGF 91 (286)
Q Consensus 71 C~GtLIs~~-~VLTaAhC~~~~ 91 (286)
|+|.+|.++ +|||++||+...
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDW 22 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCC
T ss_pred CEEEEEcCCceEEEchhheecc
Confidence 799999999 999999999764
No 11
>PRK10898 serine endoprotease; Provisional
Probab=98.51 E-value=1.3e-05 Score=71.32 Aligned_cols=150 Identities=18% Similarity=0.212 Sum_probs=83.9
Q ss_pred cceEEEEeeCC-----------eEEeEEEEeeCC-EEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECC
Q psy10841 57 WPWLIALYRDG-----------FFHCGGVVLDES-WVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHS 124 (286)
Q Consensus 57 ~Pw~v~i~~~~-----------~~~C~GtLIs~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 124 (286)
-|-+|.|.... ....+|.+|+++ +|||.+|-+.+. ..+.|.+. ....+..+-+..+|
T Consensus 55 ~psvV~v~~~~~~~~~~~~~~~~~~GSGfvi~~~G~IlTn~HVv~~a--~~i~V~~~---------dg~~~~a~vv~~d~ 123 (353)
T PRK10898 55 APAVVNVYNRSLNSTSHNQLEIRTLGSGVIMDQRGYILTNKHVINDA--DQIIVALQ---------DGRVFEALLVGSDS 123 (353)
T ss_pred CCcEEEEEeEeccccCcccccccceeeEEEEeCCeEEEecccEeCCC--CEEEEEeC---------CCCEEEEEEEEEcC
Confidence 47777775321 256999999986 999999999653 34555442 12334444343333
Q ss_pred CCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecc-ccccccc-
Q psy10841 125 MFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILP-ACKHYED- 202 (286)
Q Consensus 125 ~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~-~c~~~~~- 202 (286)
..|+||||++.. . +.++.|... .....++.+..+|+....... ...-+++ .......
T Consensus 124 -------~~DlAvl~v~~~-~----l~~~~l~~~-~~~~~G~~V~aiG~P~g~~~~--------~t~Giis~~~r~~~~~ 182 (353)
T PRK10898 124 -------LTDLAVLKINAT-N----LPVIPINPK-RVPHIGDVVLAIGNPYNLGQT--------ITQGIISATGRIGLSP 182 (353)
T ss_pred -------CCCEEEEEEcCC-C----CCeeeccCc-CcCCCCCEEEEEeCCCCcCCC--------cceeEEEeccccccCC
Confidence 489999999753 1 334455332 345678888888885321110 1111111 0000000
Q ss_pred CC-CCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 203 RI-ADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 203 ~~-~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
.. ...+ ..+.....|.|||||+- ..-.++||.+...
T Consensus 183 ~~~~~~i-----qtda~i~~GnSGGPl~n------~~G~vvGI~~~~~ 219 (353)
T PRK10898 183 TGRQNFL-----QTDASINHGNSGGALVN------SLGELMGINTLSF 219 (353)
T ss_pred ccccceE-----EeccccCCCCCcceEEC------CCCeEEEEEEEEe
Confidence 00 1111 12345678999999993 2234999988654
No 12
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=98.50 E-value=7.6e-06 Score=72.91 Aligned_cols=152 Identities=16% Similarity=0.167 Sum_probs=85.3
Q ss_pred ccceEEEEeeC-----------CeEEeEEEEeeCC-EEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEEC
Q psy10841 56 AWPWLIALYRD-----------GFFHCGGVVLDES-WVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMH 123 (286)
Q Consensus 56 ~~Pw~v~i~~~-----------~~~~C~GtLIs~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h 123 (286)
--|-+|.|... ....++|.+|+++ +|||++|.+.+. +.+.|.+. ....+..+-+..+
T Consensus 54 ~~psVV~I~~~~~~~~~~~~~~~~~~GSG~vi~~~G~IlTn~HVV~~~--~~i~V~~~---------dg~~~~a~vv~~d 122 (351)
T TIGR02038 54 AAPAVVNIYNRSISQNSLNQLSIQGLGSGVIMSKEGYILTNYHVIKKA--DQIVVALQ---------DGRKFEAELVGSD 122 (351)
T ss_pred cCCcEEEEEeEeccccccccccccceEEEEEEeCCeEEEecccEeCCC--CEEEEEEC---------CCCEEEEEEEEec
Confidence 34778877531 1246999999987 999999999653 34445442 1233444433333
Q ss_pred CCCCCCCCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecccc-ccccc
Q psy10841 124 SMFKRAEMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPAC-KHYED 202 (286)
Q Consensus 124 p~y~~~~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c-~~~~~ 202 (286)
| ..|+||||++.+- +.++.|.. ......++.+.++|+...... ....-+++.- .....
T Consensus 123 ~-------~~DlAvlkv~~~~-----~~~~~l~~-s~~~~~G~~V~aiG~P~~~~~--------s~t~GiIs~~~r~~~~ 181 (351)
T TIGR02038 123 P-------LTDLAVLKIEGDN-----LPTIPVNL-DRPPHVGDVVLAIGNPYNLGQ--------TITQGIISATGRNGLS 181 (351)
T ss_pred C-------CCCEEEEEecCCC-----CceEeccC-cCccCCCCEEEEEeCCCCCCC--------cEEEEEEEeccCcccC
Confidence 3 4799999997542 33445533 235678899999998532111 1111111110 00000
Q ss_pred C-CCCEEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 203 R-IADVICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 203 ~-~~~~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
. ....+ . ..+.....|.|||||+- .+-.++||.+...
T Consensus 182 ~~~~~~~-i---qtda~i~~GnSGGpl~n------~~G~vIGI~~~~~ 219 (351)
T TIGR02038 182 SVGRQNF-I---QTDAAINAGNSGGALIN------TNGELVGINTASF 219 (351)
T ss_pred CCCcceE-E---EECCccCCCCCcceEEC------CCCeEEEEEeeee
Confidence 0 00111 1 12345678999999992 2234999987643
No 13
>PRK10139 serine endoprotease; Provisional
Probab=98.37 E-value=3.9e-05 Score=70.62 Aligned_cols=166 Identities=18% Similarity=0.157 Sum_probs=91.7
Q ss_pred eEEeEEEEeeC--CEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccc
Q psy10841 68 FFHCGGVVLDE--SWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLR 145 (286)
Q Consensus 68 ~~~C~GtLIs~--~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~ 145 (286)
....+|.+|++ -+|||.+|.+.+. ..+.|.+. ....+..+-+...| ..||||||++.+-
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~a--~~i~V~~~---------dg~~~~a~vvg~D~-------~~DlAvlkv~~~~- 149 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQA--QKISIQLN---------DGREFDAKLIGSDD-------QSDIALLQIQNPS- 149 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCCC--CEEEEEEC---------CCCEEEEEEEEEcC-------CCCEEEEEecCCC-
Confidence 35799999984 5999999999764 35566553 22344444443333 4799999997542
Q ss_pred cCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeeccccccc-ccC--CCCEEEEeeCCCCCCCCCC
Q psy10841 146 YNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHY-EDR--IADVICAGMPQGGRDTCQG 222 (286)
Q Consensus 146 ~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~-~~~--~~~~~C~~~~~~~~~~c~g 222 (286)
.+.++.|... .....++.+..+|+..... .....-+++..... ... ....+ ..+.....|
T Consensus 150 ---~l~~~~lg~s-~~~~~G~~V~aiG~P~g~~--------~tvt~GivS~~~r~~~~~~~~~~~i-----qtda~in~G 212 (455)
T PRK10139 150 ---KLTQIAIADS-DKLRVGDFAVAVGNPFGLG--------QTATSGIISALGRSGLNLEGLENFI-----QTDASINRG 212 (455)
T ss_pred ---CCceeEecCc-cccCCCCEEEEEecCCCCC--------CceEEEEEccccccccCCCCcceEE-----EECCccCCC
Confidence 2456677543 3466788898888742211 11222333321111 110 01112 223566789
Q ss_pred CCCCeeeeecCCCCCcEEEEEEEEecCCCC-CCCCCeeEEeCCCcHHHHHhhhc
Q psy10841 223 DSGGPLLCPVPGSQGRWYVAGVVSHGEGCA-RPNEPGVYTRVSQFVPWLMSNSE 275 (286)
Q Consensus 223 dsGgPL~~~~~~~~~~~~lvGI~s~~~~c~-~~~~p~v~t~v~~~~~WI~~~~~ 275 (286)
.|||||+- .+-.++||.+....-. .....+...-+......+++.++
T Consensus 213 nSGGpl~n------~~G~vIGi~~~~~~~~~~~~gigfaIP~~~~~~v~~~l~~ 260 (455)
T PRK10139 213 NSGGALLN------LNGELIGINTAILAPGGGSVGIGFAIPSNMARTLAQQLID 260 (455)
T ss_pred CCcceEEC------CCCeEEEEEEEEEcCCCCccceEEEEEhHHHHHHHHHHhh
Confidence 99999993 2234999998643211 11112334444444445555444
No 14
>PRK10942 serine endoprotease; Provisional
Probab=98.31 E-value=3.3e-05 Score=71.46 Aligned_cols=139 Identities=22% Similarity=0.237 Sum_probs=78.6
Q ss_pred eEEeEEEEeeC--CEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccc
Q psy10841 68 FFHCGGVVLDE--SWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLR 145 (286)
Q Consensus 68 ~~~C~GtLIs~--~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~ 145 (286)
....+|.+|+. -+|||.+|.+.+. ..+.|.+. ....+..+-+..+| ..||||||++.+-
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~a--~~i~V~~~---------dg~~~~a~vv~~D~-------~~DlAvlki~~~~- 170 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDNA--TKIKVQLS---------DGRKFDAKVVGKDP-------RSDIALIQLQNPK- 170 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCCC--CEEEEEEC---------CCCEEEEEEEEecC-------CCCEEEEEecCCC-
Confidence 35799999986 4999999999654 35556553 12334444344343 4799999997432
Q ss_pred cCCceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeeccccccc-ccC--CCCEEEEeeCCCCCCCCCC
Q psy10841 146 YNRYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHY-EDR--IADVICAGMPQGGRDTCQG 222 (286)
Q Consensus 146 ~~~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~-~~~--~~~~~C~~~~~~~~~~c~g 222 (286)
.+.++.|... .....++.++.+|+...... .+..-+++..... ... ....+ ..+.....|
T Consensus 171 ---~l~~~~lg~s-~~l~~G~~V~aiG~P~g~~~--------tvt~GiVs~~~r~~~~~~~~~~~i-----qtda~i~~G 233 (473)
T PRK10942 171 ---NLTAIKMADS-DALRVGDYTVAIGNPYGLGE--------TVTSGIVSALGRSGLNVENYENFI-----QTDAAINRG 233 (473)
T ss_pred ---CCceeEecCc-cccCCCCEEEEEcCCCCCCc--------ceeEEEEEEeecccCCcccccceE-----EeccccCCC
Confidence 2456667542 34677888888886421110 1111222210000 000 01111 123455689
Q ss_pred CCCCeeeeecCCCCCcEEEEEEEEec
Q psy10841 223 DSGGPLLCPVPGSQGRWYVAGVVSHG 248 (286)
Q Consensus 223 dsGgPL~~~~~~~~~~~~lvGI~s~~ 248 (286)
.|||||+. ..-.++||.+..
T Consensus 234 nSGGpL~n------~~GeviGI~t~~ 253 (473)
T PRK10942 234 NSGGALVN------LNGELIGINTAI 253 (473)
T ss_pred CCcCccCC------CCCeEEEEEEEE
Confidence 99999993 223599998764
No 15
>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=97.51 E-value=0.00044 Score=67.02 Aligned_cols=159 Identities=18% Similarity=0.243 Sum_probs=72.9
Q ss_pred EEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccccCCcee
Q psy10841 72 GGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLRYNRYVR 151 (286)
Q Consensus 72 ~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~~~~~v~ 151 (286)
..|||+|++|+|++|-..... .|.+|... ...+++...-.|+. .|+.+-||++-+. .+.
T Consensus 68 ~aTLigpqYiVSV~HN~~gy~----~v~FG~~g-------~~~Y~iV~RNn~~~-------~Df~~pRLnK~VT---Eva 126 (769)
T PF02395_consen 68 VATLIGPQYIVSVKHNGKGYN----SVSFGNEG-------QNTYKIVDRNNYPS-------GDFHMPRLNKFVT---EVA 126 (769)
T ss_dssp S-EEEETTEEEBETTG-TSCC----EECESCSS-------TCEEEEEEEEBETT-------STEBEEEESS------SS-
T ss_pred eEEEecCCeEEEEEccCCCcC----ceeecccC-------CceEEEEEccCCCC-------cccceeecCceEE---EEe
Confidence 489999999999999873322 46666422 25566666666654 6999999998663 356
Q ss_pred eeecCCCCC------CCCCCCceEEEEecccCCCCCCCccceeEe--eeecc--c-ccccccCCCCEEEEeeC-------
Q psy10841 152 PICLPDVTE------TPEPYSTCTAVGWGAVFEHGPDPDHMREVQ--VPILP--A-CKHYEDRIADVICAGMP------- 213 (286)
Q Consensus 152 picL~~~~~------~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~--~~~~~--~-c~~~~~~~~~~~C~~~~------- 213 (286)
|+-...... ....+....=+|=|................ -.... . -.........++-....
T Consensus 127 P~~~t~~~~~~~~y~d~~rY~~f~R~GsG~Q~i~~~~g~~~~~~~~ay~yltgGt~~~~~~~~n~~~~~~~~~~~~~~~~ 206 (769)
T PF02395_consen 127 PAEMTTAGSDSNTYNDKERYPAFVRVGSGTQYIKDRNGNGTTILGGAYNYLTGGTVYNLPGYGNGSMILSGDLKKFNSYN 206 (769)
T ss_dssp ---BBSSTTSTTGGGHTTTC-EEEEEESSSEEEEECCEEEEEEEEETTSCEEEEEESSEEEEECTCEEEEESTTTCCCCC
T ss_pred ccccccccccccccccchhchheeecCCceEEEEcCCCCeeEEEEeccceecCCccccccccccceEEEecccccccccC
Confidence 666543211 122333333334332211111100000000 00000 0 00000001111111100
Q ss_pred -CCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCC
Q psy10841 214 -QGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCA 252 (286)
Q Consensus 214 -~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~ 252 (286)
.-....-.||||+||+..+. ...+|+|+|+++.+....
T Consensus 207 ~pL~n~~~~GDSGSPlF~YD~-~~kKWvl~Gv~~~~~~~~ 245 (769)
T PF02395_consen 207 GPLPNYGSPGDSGSPLFAYDK-EKKKWVLVGVLSGGNGYN 245 (769)
T ss_dssp SSSBEB--TT-TT-EEEEEET-TTTEEEEEEEEEEECCCC
T ss_pred CccccccccCcCCCceEEEEc-cCCeEEEEEEEccccccC
Confidence 01123468999999998774 578999999999877543
No 16
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=95.91 E-value=0.16 Score=42.27 Aligned_cols=151 Identities=14% Similarity=0.156 Sum_probs=67.0
Q ss_pred eEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeee---EEEECCCCCCCCCCCceEEEEecCccccC
Q psy10841 71 CGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVS---RIVMHSMFKRAEMTNDLALLQLAAPLRYN 147 (286)
Q Consensus 71 C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~---~~~~hp~y~~~~~~~DiAllkL~~~i~~~ 147 (286)
..=.|.--.||||-+|-+.... +.+.+..- ...+.+. .+-+||- ...||.||||.+.++
T Consensus 33 ~l~gigyG~~iItn~HLf~~nn-g~L~i~s~----------hG~f~v~nt~~lkv~~i-----~~~DiviirmPkDfp-- 94 (235)
T PF00863_consen 33 SLYGIGYGSYIITNAHLFKRNN-GELTIKSQ----------HGEFTVPNTTQLKVHPI-----EGRDIVIIRMPKDFP-- 94 (235)
T ss_dssp EEEEEEETTEEEEEGGGGSSTT-CEEEEEET----------TEEEEECEGGGSEEEE------TCSSEEEEE--TTS---
T ss_pred EEEEEeECCEEEEChhhhccCC-CeEEEEeC----------ceEEEcCCccccceEEe-----CCccEEEEeCCcccC--
Confidence 3334567899999999986544 33343321 1111121 1222221 257999999998774
Q ss_pred CceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecccccccccCCCCEEEEeeCCCCCCCCCCCCCCe
Q psy10841 148 RYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKHYEDRIADVICAGMPQGGRDTCQGDSGGP 227 (286)
Q Consensus 148 ~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~C~~~~~~~~~~c~gdsGgP 227 (286)
..-+-+++ ..+..++.+.++|...+ .........+...... . ......-- .-.+=.|+-|.|
T Consensus 95 Pf~~kl~F----R~P~~~e~v~mVg~~fq--~k~~~s~vSesS~i~p-~------~~~~fWkH-----wIsTk~G~CG~P 156 (235)
T PF00863_consen 95 PFPQKLKF----RAPKEGERVCMVGSNFQ--EKSISSTVSESSWIYP-E------ENSHFWKH-----WISTKDGDCGLP 156 (235)
T ss_dssp ---S---B--------TT-EEEEEEEECS--SCCCEEEEEEEEEEEE-E------TTTTEEEE------C---TT-TT-E
T ss_pred Ccchhhhc----cCCCCCCEEEEEEEEEE--cCCeeEEECCceEEee-c------CCCCeeEE-----EecCCCCccCCc
Confidence 11122233 34566678888876544 2222222222211110 0 11111111 112346788999
Q ss_pred eeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCC
Q psy10841 228 LLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQ 265 (286)
Q Consensus 228 L~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~ 265 (286)
|+... ++ .+|||.|.+..-. .-..|+.+..
T Consensus 157 lVs~~---Dg--~IVGiHsl~~~~~---~~N~F~~f~~ 186 (235)
T PF00863_consen 157 LVSTK---DG--KIVGIHSLTSNTS---SRNYFTPFPD 186 (235)
T ss_dssp EEETT---T----EEEEEEEEETTT---SSEEEEE--T
T ss_pred EEEcC---CC--cEEEEEcCccCCC---CeEEEEcCCH
Confidence 99755 23 3999999876432 2467888754
No 17
>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=93.40 E-value=0.49 Score=37.66 Aligned_cols=72 Identities=15% Similarity=0.233 Sum_probs=39.9
Q ss_pred CCeEEeEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccc
Q psy10841 66 DGFFHCGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLR 145 (286)
Q Consensus 66 ~~~~~C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~ 145 (286)
.+.+.|.+..|..+|.|-..|.- ... .+.+. ...+++...+.. .+......|+++++|++.-.
T Consensus 22 ~g~~t~l~~gi~~~~~lvp~H~~---~~~--~i~i~----------g~~~~~~d~~~l--v~~~~~~~Dl~~v~l~~~~k 84 (172)
T PF00548_consen 22 KGEFTMLALGIYDRYFLVPTHEE---PED--TIYID----------GVEYKVDDSVVL--VDRDGVDTDLTLVKLPRNPK 84 (172)
T ss_dssp TEEEEEEEEEEEBTEEEEEGGGG---GCS--EEEET----------TEEEEEEEEEEE--EETTSSEEEEEEEEEESSS-
T ss_pred CceEEEecceEeeeEEEEECcCC---CcE--EEEEC----------CEEEEeeeeEEE--ecCCCcceeEEEEEccCCcc
Confidence 34677889999999999999931 112 23332 222333322211 11222346999999988777
Q ss_pred cCCceeeee
Q psy10841 146 YNRYVRPIC 154 (286)
Q Consensus 146 ~~~~v~pic 154 (286)
|.+-.+-++
T Consensus 85 frDIrk~~~ 93 (172)
T PF00548_consen 85 FRDIRKFFP 93 (172)
T ss_dssp B--GGGGSB
T ss_pred cCchhhhhc
Confidence 765444333
No 18
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=91.36 E-value=6 Score=35.20 Aligned_cols=141 Identities=20% Similarity=0.209 Sum_probs=73.1
Q ss_pred EEeEEEEee-CCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccccC
Q psy10841 69 FHCGGVVLD-ESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLRYN 147 (286)
Q Consensus 69 ~~C~GtLIs-~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~~~ 147 (286)
..++|.+++ .-+|||-.|-+.. ...+.+.+. .......+.+-. ....|+|++|.+..-.
T Consensus 72 ~~gSg~i~~~~g~ivTn~hVi~~--a~~i~v~l~---------dg~~~~a~~vg~-------d~~~dlavlki~~~~~-- 131 (347)
T COG0265 72 GLGSGFIISSDGYIVTNNHVIAG--AEEITVTLA---------DGREVPAKLVGK-------DPISDLAVLKIDGAGG-- 131 (347)
T ss_pred ccccEEEEcCCeEEEecceecCC--cceEEEEeC---------CCCEEEEEEEec-------CCccCEEEEEeccCCC--
Confidence 678899998 7799999999866 334444441 223333333322 2347999999986432
Q ss_pred CceeeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecccccc-ccc---CCCCEEEEeeCCCCCCCCCCC
Q psy10841 148 RYVRPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILPACKH-YED---RIADVICAGMPQGGRDTCQGD 223 (286)
Q Consensus 148 ~~v~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~~c~~-~~~---~~~~~~C~~~~~~~~~~c~gd 223 (286)
+..+.+.... ....++.....|-..... +.....+++.-.. ... .....+ ..+...+.|.
T Consensus 132 --~~~~~~~~s~-~l~vg~~v~aiGnp~g~~--------~tvt~Givs~~~r~~v~~~~~~~~~I-----qtdAain~gn 195 (347)
T COG0265 132 --LPVIALGDSD-KLRVGDVVVAIGNPFGLG--------QTVTSGIVSALGRTGVGSAGGYVNFI-----QTDAAINPGN 195 (347)
T ss_pred --CceeeccCCC-CcccCCEEEEecCCCCcc--------cceeccEEeccccccccCcccccchh-----hcccccCCCC
Confidence 2223343322 233455555555422100 1111112221000 000 011111 2235678999
Q ss_pred CCCeeeeecCCCCCcEEEEEEEEecCCC
Q psy10841 224 SGGPLLCPVPGSQGRWYVAGVVSHGEGC 251 (286)
Q Consensus 224 sGgPL~~~~~~~~~~~~lvGI~s~~~~c 251 (286)
||||++- ..-.++||.+.....
T Consensus 196 sGgpl~n------~~g~~iGint~~~~~ 217 (347)
T COG0265 196 SGGPLVN------IDGEVVGINTAIIAP 217 (347)
T ss_pred CCCceEc------CCCcEEEEEEEEecC
Confidence 9999993 223499998876643
No 19
>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=88.51 E-value=0.64 Score=34.60 Aligned_cols=37 Identities=27% Similarity=0.522 Sum_probs=27.7
Q ss_pred CCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcH
Q psy10841 219 TCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFV 267 (286)
Q Consensus 219 ~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~ 267 (286)
.-+||-||+|.|... ++||++.|-. .-.-|++|+.+.
T Consensus 87 ~~PGdCGg~L~C~HG-------ViGi~Tagg~-----g~VaF~dir~~~ 123 (127)
T PF00947_consen 87 AEPGDCGGILRCKHG-------VIGIVTAGGE-----GHVAFADIRDLL 123 (127)
T ss_dssp SSTT-TCSEEEETTC-------EEEEEEEEET-----TEEEEEECCCGS
T ss_pred CCCCCCCceeEeCCC-------eEEEEEeCCC-----ceEEEEechhhh
Confidence 347899999999773 9999987742 246799999853
No 20
>KOG1421|consensus
Probab=84.87 E-value=10 Score=36.49 Aligned_cols=83 Identities=20% Similarity=0.331 Sum_probs=44.8
Q ss_pred eEEEEeeCC--EEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCc-cccC
Q psy10841 71 CGGVVLDES--WVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAP-LRYN 147 (286)
Q Consensus 71 C~GtLIs~~--~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~-i~~~ 147 (286)
-+|.+++++ ++||+.|-+...+.....++. ......+.-++-.| -||+.++|.+.. +.|.
T Consensus 86 atgfvvd~~~gyiLtnrhvv~pgP~va~avf~----------n~ee~ei~pvyrDp-------VhdfGf~r~dps~ir~s 148 (955)
T KOG1421|consen 86 ATGFVVDKKLGYILTNRHVVAPGPFVASAVFD----------NHEEIEIYPVYRDP-------VHDFGFFRYDPSTIRFS 148 (955)
T ss_pred eeEEEEecccceEEEeccccCCCCceeEEEec----------ccccCCcccccCCc-------hhhcceeecChhhccee
Confidence 457778765 899999998654422222221 12222232222222 368888887543 3443
Q ss_pred CceeeeecCCCCCCCCCCCceEEEEe
Q psy10841 148 RYVRPICLPDVTETPEPYSTCTAVGW 173 (286)
Q Consensus 148 ~~v~picL~~~~~~~~~~~~~~~~Gw 173 (286)
.++.+||.. +....+....++|-
T Consensus 149 -~vt~i~lap--~~akvgseirvvgN 171 (955)
T KOG1421|consen 149 -IVTEICLAP--ELAKVGSEIRVVGN 171 (955)
T ss_pred -eeeccccCc--cccccCCceEEecC
Confidence 467888855 33344555555543
No 21
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=76.82 E-value=8.3 Score=34.89 Aligned_cols=140 Identities=19% Similarity=0.278 Sum_probs=66.7
Q ss_pred eEEEEeeCCEEEeccCCcCCCCCceEEEEEeeeecccCCCCceEEeeeEEEECCCCCCCCCCCceEEEEecCccccCCce
Q psy10841 71 CGGVVLDESWVMTAAHCVDGFEKHYFEVYAGMLRRFSFSPTEQVRPVSRIVMHSMFKRAEMTNDLALLQLAAPLRYNRYV 150 (286)
Q Consensus 71 C~GtLIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAllkL~~~i~~~~~v 150 (286)
-=|-.+|+...+|+.|-+...... .+| ..+.++-+|. ..++.-+++.+|+.. .+
T Consensus 381 GWGfWVS~~lfITttHViP~g~~E----~FG-------------v~i~~i~vh~-------sGeF~~~rFpk~iRP--Dv 434 (535)
T PF05416_consen 381 GWGFWVSPTLFITTTHVIPPGAKE----AFG-------------VPISQIQVHK-------SGEFCRFRFPKPIRP--DV 434 (535)
T ss_dssp EEEEESSSSEEEEEGGGS-STTSE----ETT-------------EECGGEEEEE-------ETTEEEEEESS-SST--TS
T ss_pred ceeeeecceEEEEeeeecCCcchh----hhC-------------CChhHeEEee-------ccceEEEecCCCCCC--Cc
Confidence 348899999999999998543321 111 2344555553 357777788777752 23
Q ss_pred eeeecCCCCCCCCCCCceEEEEecccCCCCCCCccceeEeeeecc--ccc---ccccCCCCEEEEee--CCCCCCCCCCC
Q psy10841 151 RPICLPDVTETPEPYSTCTAVGWGAVFEHGPDPDHMREVQVPILP--ACK---HYEDRIADVICAGM--PQGGRDTCQGD 223 (286)
Q Consensus 151 ~picL~~~~~~~~~~~~~~~~Gwg~~~~~~~~~~~l~~~~~~~~~--~c~---~~~~~~~~~~C~~~--~~~~~~~c~gd 223 (286)
.-.-|- +--+.+..|.+.-=- .+..+...-+++-. .-+ ..-.-+..|+-++. ...+-++-+||
T Consensus 435 tgmiLE---eGapEGtV~siLiKR-------~sGEllpLAvRMgt~AsmkIqgr~v~GQ~GMLLTGaNAK~mDLGT~PGD 504 (535)
T PF05416_consen 435 TGMILE---EGAPEGTVCSILIKR-------PSGELLPLAVRMGTHASMKIQGRTVHGQMGMLLTGANAKGMDLGTIPGD 504 (535)
T ss_dssp ---EE----SS--TT-EEEEEEE--------TTSBEEEEEEEEEEEEEEEETTEEEEEEEEEETTSTT-SSTTTS--TTG
T ss_pred cceeec---cCCCCceEEEEEEEc-------CCccchhhhhhhccceeEEEcceeecceeeeeeecCCccccccCCCCCC
Confidence 333342 122334444433111 11122221111111 000 00001122333321 12334678899
Q ss_pred CCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 224 SGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 224 sGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
-|.|-++.. ++.|+++||.+...
T Consensus 505 CGcPYvyKr---gNd~VV~GVH~AAt 527 (535)
T PF05416_consen 505 CGCPYVYKR---GNDWVVIGVHAAAT 527 (535)
T ss_dssp TT-EEEEEE---TTEEEEEEEEEEE-
T ss_pred CCCceeeec---CCcEEEEEEEehhc
Confidence 999999988 89999999987654
No 22
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=62.51 E-value=4.8 Score=39.36 Aligned_cols=18 Identities=33% Similarity=0.759 Sum_probs=17.3
Q ss_pred eEEEEeeCC-EEEeccCCc
Q psy10841 71 CGGVVLDES-WVMTAAHCV 88 (286)
Q Consensus 71 C~GtLIs~~-~VLTaAhC~ 88 (286)
|+|++||++ .|||--||.
T Consensus 49 CSgsfVS~~GLvlTNHHC~ 67 (698)
T PF10459_consen 49 CSGSFVSPDGLVLTNHHCG 67 (698)
T ss_pred eeEEEEcCCceEEecchhh
Confidence 999999998 899999997
No 23
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=61.10 E-value=85 Score=30.48 Aligned_cols=57 Identities=18% Similarity=0.249 Sum_probs=36.7
Q ss_pred CCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcHHHHHhhhc
Q psy10841 217 RDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFVPWLMSNSE 275 (286)
Q Consensus 217 ~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~~WI~~~~~ 275 (286)
.-.-.||||+=|+...+++.-..-++|++. ..++.. ..-++||.+...++=++++++
T Consensus 634 ~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlh-sydge~-kqfglftPi~~il~rl~~vT~ 690 (695)
T PF08192_consen 634 AFASGGDSGSWVLTKLEDNNKGLGVVGMLH-SYDGEQ-KQFGLFTPINEILDRLEEVTG 690 (695)
T ss_pred cccCCCCcccEEEecccccccCceeeEEee-ecCCcc-ceeeccCcHHHHHHHHHHhhc
Confidence 344579999999976543334456888764 333333 335788888777777766654
No 24
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=55.06 E-value=13 Score=30.49 Aligned_cols=27 Identities=30% Similarity=0.378 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 216 GRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 216 ~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
.....+|-||+|++.+.+ |+|-+++..
T Consensus 174 TGGIvqGMSGSPI~qdGK-------LiGAVthvf 200 (218)
T PF05580_consen 174 TGGIVQGMSGSPIIQDGK-------LIGAVTHVF 200 (218)
T ss_pred hCCEEecccCCCEEECCE-------EEEEEEEEE
Confidence 457889999999997553 999999876
No 25
>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=45.15 E-value=22 Score=26.93 Aligned_cols=23 Identities=39% Similarity=0.858 Sum_probs=15.7
Q ss_pred CCCCCCCeeeeecCCCCCcEEEEEEEEec
Q psy10841 220 CQGDSGGPLLCPVPGSQGRWYVAGVVSHG 248 (286)
Q Consensus 220 c~gdsGgPL~~~~~~~~~~~~lvGI~s~~ 248 (286)
-.|.||||++|..- +++||+...
T Consensus 106 lkGSSGgPiLC~~G------H~vG~f~aa 128 (148)
T PF02907_consen 106 LKGSSGGPILCPSG------HAVGMFRAA 128 (148)
T ss_dssp HTT-TT-EEEETTS------EEEEEEEEE
T ss_pred EecCCCCcccCCCC------CEEEEEEEE
Confidence 46899999999662 589987643
No 26
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=42.70 E-value=27 Score=29.73 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=16.2
Q ss_pred CCCCCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 221 QGDSGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 221 ~gdsGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
.||||+|++..+. .|+||.+-..
T Consensus 207 ~GDSGSPVVt~dg------~liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTEDG------DLIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETTC-------EEEEEEEEE
T ss_pred CCCCCCccCcCCC------CEEEEEecCC
Confidence 5899999996542 3999988543
No 27
>KOG1320|consensus
Probab=41.76 E-value=75 Score=29.62 Aligned_cols=44 Identities=18% Similarity=0.166 Sum_probs=35.3
Q ss_pred CceecCeeCCCCccceEEEEeeCCeEEeEEEEeeCCEEEeccCCcC
Q psy10841 44 GRVVGGKKAELGAWPWLIALYRDGFFHCGGVVLDESWVMTAAHCVD 89 (286)
Q Consensus 44 ~~i~~g~~a~~~~~Pw~v~i~~~~~~~C~GtLIs~~~VLTaAhC~~ 89 (286)
-+++-+...+...-||.-.- .....|+|--|..+-+||-||++.
T Consensus 64 ~~v~~~~~~~~~~~pw~~~~--q~~~~~s~f~i~~~~lltn~~~v~ 107 (473)
T KOG1320|consen 64 VKVFSVSTEPSSVLPWQRTR--QFSSGGSGFAIYGKKLLTNAHVVA 107 (473)
T ss_pred eEEEeecccccccCcceeee--hhcccccchhhcccceeecCcccc
Confidence 36777777777778887654 445679999999999999999986
No 28
>PF00944 Peptidase_S3: Alphavirus core protein ; InterPro: IPR000930 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. Togavirin, also known as Sindbis virus core endopeptidase, is a serine protease resident at the N terminus of the p130 polyprotein of togaviruses []. The endopeptidase signature identifies the peptidase as belonging to the MEROPS peptidase family S3 (togavirin family, clan PA(S)). The polyprotein also includes structural proteins for the nucleocapsid core and for the glycoprotein spikes []. Togavirin is only active while part of the polyprotein, cleavage at a Trp-Ser bond resulting in total lack of activity []. Mutagenesis studies have identified the location of the His-Asp-Ser catalytic triad, and X-ray studies have revealed the protein fold to be similar to that of chymotrypsin [, ].; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YEW_D 1EP5_A 3J0C_F 1EP6_C 1WYK_D 1DYL_A 1VCQ_B 1VCP_B 1LD4_D 1KXA_A ....
Probab=37.15 E-value=29 Score=26.24 Aligned_cols=24 Identities=33% Similarity=0.520 Sum_probs=17.4
Q ss_pred CCCCCCCeeeeecCCCCCcEEEEEEEEecC
Q psy10841 220 CQGDSGGPLLCPVPGSQGRWYVAGVVSHGE 249 (286)
Q Consensus 220 c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~ 249 (286)
-.||||-|++ ++.-.+|||+--|.
T Consensus 104 ~~GDSGRpi~------DNsGrVVaIVLGG~ 127 (158)
T PF00944_consen 104 KPGDSGRPIF------DNSGRVVAIVLGGA 127 (158)
T ss_dssp STTSTTEEEE------STTSBEEEEEEEEE
T ss_pred CCCCCCCccC------cCCCCEEEEEecCC
Confidence 4799999998 23334889887664
No 29
>PF14781 BBS2_N: Ciliary BBSome complex subunit 2, N-terminal
Probab=32.09 E-value=1.2e+02 Score=23.02 Aligned_cols=48 Identities=17% Similarity=0.409 Sum_probs=26.6
Q ss_pred eeEEEECCCCCCC----CCCCceEEEEecCccccCCceeeeecCCCCCCCCCCCceEEEE
Q psy10841 117 VSRIVMHSMFKRA----EMTNDLALLQLAAPLRYNRYVRPICLPDVTETPEPYSTCTAVG 172 (286)
Q Consensus 117 v~~~~~hp~y~~~----~~~~DiAllkL~~~i~~~~~v~picL~~~~~~~~~~~~~~~~G 172 (286)
..++++|-..... ..+.+|++|.+++.+. ||....-.+.....+.++|
T Consensus 19 ~gKV~IH~ph~~~~~~~~~~~~i~~LNin~~it--------alaaG~l~~~~~~D~LliG 70 (136)
T PF14781_consen 19 GGKVFIHNPHERGQRTGRQDSDISFLNINQEIT--------ALAAGRLKPDDGRDCLLIG 70 (136)
T ss_pred CCEEEEECCCccccccccccCceeEEECCCceE--------EEEEEecCCCCCcCEEEEe
Confidence 3566776433221 1568999999987764 3432222223445666665
No 30
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=29.50 E-value=38 Score=30.87 Aligned_cols=45 Identities=27% Similarity=0.454 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCCCCCCCCeeEEeCCCcHHHHHhh
Q psy10841 216 GRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGCARPNEPGVYTRVSQFVPWLMSN 273 (286)
Q Consensus 216 ~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c~~~~~p~v~t~v~~~~~WI~~~ 273 (286)
..+..+|-||+|++.+.+ |+|-+++..-......+++ |.+|..+.
T Consensus 354 tgGivqGMSGSPi~q~gk-------liGAvtHVfvndpt~GYGi------~ie~Ml~~ 398 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQNGK-------VIGAVTHVFVNDPTSGYGV------YIEWMLKE 398 (402)
T ss_pred hCCEEecccCCCEEECCE-------EEEEEEEEEecCCCcceee------hHHHHHHH
Confidence 457789999999997663 9999987652211112333 57787664
No 31
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=27.99 E-value=52 Score=32.39 Aligned_cols=61 Identities=18% Similarity=0.269 Sum_probs=35.5
Q ss_pred EEEEeeCCCCCCCCCCCCCCeeeeecCCCCCcEEEEEEEEecCCC--------CCCCCCeeEEeCCCcHHHHHhhhccc
Q psy10841 207 VICAGMPQGGRDTCQGDSGGPLLCPVPGSQGRWYVAGVVSHGEGC--------ARPNEPGVYTRVSQFVPWLMSNSERA 277 (286)
Q Consensus 207 ~~C~~~~~~~~~~c~gdsGgPL~~~~~~~~~~~~lvGI~s~~~~c--------~~~~~p~v~t~v~~~~~WI~~~~~~~ 277 (286)
-+|... +.++..|.||+|++ +.+-.|||+.=-|.-- .....-.|-++++ |+-|+.+.+...
T Consensus 621 pv~Fls---tnDitGGNSGSPvl------N~~GeLVGl~FDgn~Esl~~D~~fdp~~~R~I~VDiR-yvL~~ldkv~gA 689 (698)
T PF10459_consen 621 PVNFLS---TNDITGGNSGSPVL------NAKGELVGLAFDGNWESLSGDIAFDPELNRTIHVDIR-YVLWALDKVYGA 689 (698)
T ss_pred eeEEEe---ccCcCCCCCCCccC------CCCceEEEEeecCchhhcccccccccccceeEEEEHH-HHHHHHHHHhCh
Confidence 455532 45788999999998 4455699987433210 0001124667765 466776555443
Done!