Query psy8662
Match_columns 260
No_of_seqs 265 out of 1679
Neff 8.2
Searched_HMMs 46136
Date Sat Aug 17 00:33:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8662hhsearch_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 2.5E-34 5.4E-39 243.4 18.4 170 87-256 1-232 (232)
2 KOG3627|consensus 100.0 1.2E-32 2.7E-37 238.7 19.6 176 83-258 9-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 5.4E-31 1.2E-35 223.4 16.8 167 86-253 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 2.2E-29 4.8E-34 211.6 18.2 161 87-253 1-220 (220)
5 COG5640 Secreted trypsin-like 99.9 1.2E-26 2.6E-31 202.8 13.4 174 83-258 29-279 (413)
6 PF03761 DUF316: Domain of unk 99.4 2.2E-12 4.8E-17 113.7 14.4 188 65-257 23-279 (282)
7 COG3591 V8-like Glu-specific e 98.7 2.2E-07 4.8E-12 79.8 10.6 54 202-258 197-251 (251)
8 PF09342 DUF1986: Domain of un 98.1 3.8E-06 8.2E-11 71.2 4.5 37 95-131 13-49 (267)
9 PF13365 Trypsin_2: Trypsin-li 97.3 0.0005 1.1E-08 51.7 4.9 20 112-131 1-21 (120)
10 TIGR02038 protease_degS peripl 96.0 0.072 1.6E-06 48.6 10.6 22 110-131 78-100 (351)
11 TIGR02037 degP_htrA_DO peripla 95.9 0.052 1.1E-06 50.8 9.3 23 109-131 57-80 (428)
12 PRK10898 serine endoprotease; 94.7 0.55 1.2E-05 42.9 11.7 22 110-131 78-100 (353)
13 PF02395 Peptidase_S6: Immunog 91.6 0.23 5E-06 49.8 4.4 32 205-236 213-246 (769)
14 PRK10139 serine endoprotease; 91.3 1.4 3.1E-05 41.6 9.3 22 110-131 90-113 (455)
15 PRK10942 serine endoprotease; 87.2 4.7 0.0001 38.4 9.5 23 109-131 110-134 (473)
16 PF00947 Pico_P2A: Picornaviru 73.7 3.1 6.6E-05 32.2 2.5 52 184-249 71-122 (127)
17 PF05580 Peptidase_S55: SpoIVB 56.9 14 0.00031 31.3 3.6 27 202-232 174-200 (218)
18 PF10459 Peptidase_S46: Peptid 53.9 8.3 0.00018 38.5 2.0 21 111-131 48-69 (698)
19 TIGR02860 spore_IV_B stage IV 39.3 39 0.00084 31.5 3.9 46 202-257 354-399 (402)
20 PF05579 Peptidase_S32: Equine 37.0 23 0.00049 31.1 1.8 22 207-231 207-228 (297)
21 PF02907 Peptidase_S29: Hepati 35.6 27 0.00059 27.4 1.9 21 207-230 107-127 (148)
22 PF05416 Peptidase_C37: Southa 34.0 54 0.0012 30.8 3.8 30 203-232 498-527 (535)
23 PF00548 Peptidase_C3: 3C cyst 22.2 43 0.00094 27.2 1.0 28 205-232 144-171 (172)
24 PF02395 Peptidase_S6: Immunog 21.5 60 0.0013 33.0 2.0 16 114-129 69-84 (769)
25 TIGR02841 spore_YyaC putative 20.4 1.3E+02 0.0028 23.7 3.2 51 193-257 5-60 (140)
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=2.5e-34 Score=243.38 Aligned_cols=170 Identities=49% Similarity=0.911 Sum_probs=141.4
Q ss_pred eeCCeeCCCCCCceEEEEEec-CeeeeeeEEEeCCEEEecccccccC---------------------------------
Q psy8662 87 IVGGQVTYVHQYPWMALLMYK-KRFYCGATLINNLYVLTAAHCVHQG--------------------------------- 132 (260)
Q Consensus 87 i~gG~~a~~~~~Pw~v~l~~~-~~~~C~GtLIs~~~VLTAAhCv~~~--------------------------------- 132 (260)
|+||.++..++|||+|.|+.. ..+.|+||||+++||||||||+...
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 579999999999999999987 7899999999999999999998641
Q ss_pred --------CCcee------------------eccC-cccCCceEEEEeeeecCCCCCCCccceEEEEEeeChhhHhhhhc
Q psy8662 133 --------LGIWV------------------TIRG-KSFSNKTGIVTGWGVQKQGGSTSDTLLEVEVPILSNAECKKTAY 185 (260)
Q Consensus 133 --------~~i~l------------------~~~~-~~~~~~~~~v~Gwg~~~~~~~~~~~l~~~~v~vi~~~~C~~~~~ 185 (260)
+|+.| +... ....+..+.++|||...........+++..+.+++.++|...+.
T Consensus 81 ~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~ 160 (232)
T cd00190 81 NYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYS 160 (232)
T ss_pred CCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhcc
Confidence 11222 1111 22346789999999876554566789999999999999998643
Q ss_pred C-CCCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEechhhHHHHHHH
Q psy8662 186 E-NRITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARVNRYLTWIKNN 256 (260)
Q Consensus 186 ~-~~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y~~WI~~~ 256 (260)
. ..+.+++||+.......+.|.|||||||++..+++|+|+||+|++..|...+.|++|++|..|++||+++
T Consensus 161 ~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 161 YGGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred CcccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 2 4678899999876546789999999999999889999999999999998767899999999999999864
No 2
>KOG3627|consensus
Probab=100.00 E-value=1.2e-32 Score=238.68 Aligned_cols=176 Identities=48% Similarity=0.879 Sum_probs=145.4
Q ss_pred CCCceeCCeeCCCCCCceEEEEEecC--eeeeeeEEEeCCEEEecccccccCC---------------------------
Q psy8662 83 KKTRIVGGQVTYVHQYPWMALLMYKK--RFYCGATLINNLYVLTAAHCVHQGL--------------------------- 133 (260)
Q Consensus 83 ~~~ri~gG~~a~~~~~Pw~v~l~~~~--~~~C~GtLIs~~~VLTAAhCv~~~~--------------------------- 133 (260)
...||+||.++..++|||+|+|.... .++|+|+||+++||||||||+....
T Consensus 9 ~~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~~~~V~~G~~~~~~~~~~~~~~~~~~ 88 (256)
T KOG3627|consen 9 PEGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASASLYTVRLGEHDINLSVSEGEEQLVGD 88 (256)
T ss_pred ccCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCcceEEEECccccccccccCchhhhce
Confidence 35689999999999999999999876 7899999999999999999986521
Q ss_pred ------------------Cce------------------eeccCc---ccCCceEEEEeeeecCCC-CCCCccceEEEEE
Q psy8662 134 ------------------GIW------------------VTIRGK---SFSNKTGIVTGWGVQKQG-GSTSDTLLEVEVP 173 (260)
Q Consensus 134 ------------------~i~------------------l~~~~~---~~~~~~~~v~Gwg~~~~~-~~~~~~l~~~~v~ 173 (260)
||. ||.... ...+..+.++|||.+... ...+..|++++++
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 111 111111 223478899999987654 3457889999999
Q ss_pred eeChhhHhhhhcCC-CCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCC-CCCCCCCcEEEechhhHH
Q psy8662 174 ILSNAECKKTAYEN-RITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEG-CAQENYPGVYARVNRYLT 251 (260)
Q Consensus 174 vi~~~~C~~~~~~~-~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~-C~~~~~p~vyt~V~~y~~ 251 (260)
+++.++|+..+... .+++.+||++......++|+|||||||++..+++|+++||+|||.. |+..+.|++||+|+.|++
T Consensus 169 i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~ 248 (256)
T KOG3627|consen 169 IISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLD 248 (256)
T ss_pred EcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCCCCCeEEeEhHHhHH
Confidence 99999999875443 5677899999756667899999999999998779999999999988 998889999999999999
Q ss_pred HHHHHhh
Q psy8662 252 WIKNNTI 258 (260)
Q Consensus 252 WI~~~~~ 258 (260)
||++.+.
T Consensus 249 WI~~~~~ 255 (256)
T KOG3627|consen 249 WIKENIG 255 (256)
T ss_pred HHHHHhc
Confidence 9999875
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.97 E-value=5.4e-31 Score=223.38 Aligned_cols=167 Identities=49% Similarity=0.881 Sum_probs=136.7
Q ss_pred ceeCCeeCCCCCCceEEEEEecC-eeeeeeEEEeCCEEEecccccccC--------------------------------
Q psy8662 86 RIVGGQVTYVHQYPWMALLMYKK-RFYCGATLINNLYVLTAAHCVHQG-------------------------------- 132 (260)
Q Consensus 86 ri~gG~~a~~~~~Pw~v~l~~~~-~~~C~GtLIs~~~VLTAAhCv~~~-------------------------------- 132 (260)
||+||+++..++|||+|.|+... .+.|+||||++++|||||||+...
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p 80 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHP 80 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECC
Confidence 58999999999999999999887 889999999999999999999631
Q ss_pred --------CCcee------------------ecc-CcccCCceEEEEeeeecCC-CCCCCccceEEEEEeeChhhHhhhh
Q psy8662 133 --------LGIWV------------------TIR-GKSFSNKTGIVTGWGVQKQ-GGSTSDTLLEVEVPILSNAECKKTA 184 (260)
Q Consensus 133 --------~~i~l------------------~~~-~~~~~~~~~~v~Gwg~~~~-~~~~~~~l~~~~v~vi~~~~C~~~~ 184 (260)
+|+.| +.. .....+..+.++|||.... .......++...+.+++.+.|...+
T Consensus 81 ~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~ 160 (229)
T smart00020 81 NYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAY 160 (229)
T ss_pred CCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhh
Confidence 11222 111 1222457889999998763 2344677899999999999998864
Q ss_pred cC-CCCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEechhhHHHH
Q psy8662 185 YE-NRITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARVNRYLTWI 253 (260)
Q Consensus 185 ~~-~~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y~~WI 253 (260)
.. ..+...++|++........|.||+|+||++..+ +|+|+||+|++..|...+.|.+|++|..|++||
T Consensus 161 ~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 161 SGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred ccccccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 33 257889999987654678999999999999877 999999999999998677899999999999998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.97 E-value=2.2e-29 Score=211.57 Aligned_cols=161 Identities=46% Similarity=0.915 Sum_probs=133.7
Q ss_pred eeCCeeCCCCCCceEEEEEecC-eeeeeeEEEeCCEEEeccccccc--C-------------------------------
Q psy8662 87 IVGGQVTYVHQYPWMALLMYKK-RFYCGATLINNLYVLTAAHCVHQ--G------------------------------- 132 (260)
Q Consensus 87 i~gG~~a~~~~~Pw~v~l~~~~-~~~C~GtLIs~~~VLTAAhCv~~--~------------------------------- 132 (260)
|.||..+..++|||+|.|+... .++|+|+||+++||||||||+.. +
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~ 80 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDGASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKY 80 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTSGGSEEEEESESBTTSTTTTSEEEEEEEEEEETTS
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 6899999999999999999987 89999999999999999999966 1
Q ss_pred ------CCceeeccC-------------------cccCCceEEEEeeeecCCCCCCCccceEEEEEeeChhhHhhhhcCC
Q psy8662 133 ------LGIWVTIRG-------------------KSFSNKTGIVTGWGVQKQGGSTSDTLLEVEVPILSNAECKKTAYEN 187 (260)
Q Consensus 133 ------~~i~l~~~~-------------------~~~~~~~~~v~Gwg~~~~~~~~~~~l~~~~v~vi~~~~C~~~~~~~ 187 (260)
+|+.|.... ....+..+.+.||+.....+ ....++...+.+++.+.|+.. +..
T Consensus 81 ~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~~~~~c~~~-~~~ 158 (220)
T PF00089_consen 81 DPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVVSRKTCRSS-YND 158 (220)
T ss_dssp BTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS-BTSBEEEEEEEEEEHHHHHHH-TTT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccccc-ccc
Confidence 112221000 01346789999999865443 456789999999999999986 445
Q ss_pred CCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEechhhHHHH
Q psy8662 188 RITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARVNRYLTWI 253 (260)
Q Consensus 188 ~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y~~WI 253 (260)
.+.+.++|++.. ...+.|.|||||||++.+. +|+||++++..|...+.|.+|++|+.|++||
T Consensus 159 ~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 159 NLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred cccccccccccc-cccccccccccccccccee---eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 578899999876 5578999999999998764 8999999999999887899999999999999
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.2e-26 Score=202.85 Aligned_cols=174 Identities=34% Similarity=0.572 Sum_probs=129.3
Q ss_pred CCCceeCCeeCCCCCCceEEEEEecC-----eeeeeeEEEeCCEEEecccccccCC------------------------
Q psy8662 83 KKTRIVGGQVTYVHQYPWMALLMYKK-----RFYCGATLINNLYVLTAAHCVHQGL------------------------ 133 (260)
Q Consensus 83 ~~~ri~gG~~a~~~~~Pw~v~l~~~~-----~~~C~GtLIs~~~VLTAAhCv~~~~------------------------ 133 (260)
.+.||+||..|..++||++|+|..+. ..+|||++|..|||||||||+....
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~Sq~~rg~v 108 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSSQAERGHV 108 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccccccCcce
Confidence 46789999999999999999997643 4689999999999999999997611
Q ss_pred ----------------CceeeccCc----------c-----------cCCceEEEEeeeecCCCC-----CCCccceEEE
Q psy8662 134 ----------------GIWVTIRGK----------S-----------FSNKTGIVTGWGVQKQGG-----STSDTLLEVE 171 (260)
Q Consensus 134 ----------------~i~l~~~~~----------~-----------~~~~~~~v~Gwg~~~~~~-----~~~~~l~~~~ 171 (260)
++.+....+ . .........+|+.+.... .....++++.
T Consensus 109 r~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e~~ 188 (413)
T COG5640 109 RTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHEVA 188 (413)
T ss_pred EEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccceeeeee
Confidence 111100000 0 011222334555443211 1124789999
Q ss_pred EEeeChhhHhhhhcCC-----CCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCC-CCCCCCCcEEEe
Q psy8662 172 VPILSNAECKKTAYEN-----RITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEG-CAQENYPGVYAR 245 (260)
Q Consensus 172 v~vi~~~~C~~~~~~~-----~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~-C~~~~~p~vyt~ 245 (260)
+..++...|...+... ...-.-+|++.+. .++|+||||||++.+.+....++||+|||.+ |+.+..|+|||+
T Consensus 189 v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVyT~ 266 (413)
T COG5640 189 VLFVPLSTCAQYKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGCGGTLIPGVYTN 266 (413)
T ss_pred eeeechHHhhhhccccccCCCCCCccceecCCCC--cccccCCCCCceEEeCCCccEEEeEEEecCCCCCCCCcceeEEe
Confidence 9999999998864211 1112239998654 8999999999999998888899999999986 999999999999
Q ss_pred chhhHHHHHHHhh
Q psy8662 246 VNRYLTWIKNNTI 258 (260)
Q Consensus 246 V~~y~~WI~~~~~ 258 (260)
|+.|.+||..+|+
T Consensus 267 vsny~~WI~a~~~ 279 (413)
T COG5640 267 VSNYQDWIAAMTN 279 (413)
T ss_pred hhHHHHHHHHHhc
Confidence 9999999999886
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.44 E-value=2.2e-12 Score=113.72 Aligned_cols=188 Identities=24% Similarity=0.336 Sum_probs=105.2
Q ss_pred CCCCCcCCCCCCccCCCCCCCceeCCeeCCCCCCceEEEEEecC----eeeeeeEEEeCCEEEecccccccCC-------
Q psy8662 65 VKPVDLEKCGPCTCGAVNKKTRIVGGQVTYVHQYPWMALLMYKK----RFYCGATLINNLYVLTAAHCVHQGL------- 133 (260)
Q Consensus 65 ~~~~~~~~c~~~~cg~~~~~~ri~gG~~a~~~~~Pw~v~l~~~~----~~~C~GtLIs~~~VLTAAhCv~~~~------- 133 (260)
++...++.||.. ......++.+|..+..++.||.|.+.... .++++|||||+|||||++||+..+.
T Consensus 23 EN~~rl~~CG~~---~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~ 99 (282)
T PF03761_consen 23 ENEERLETCGKK---KLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGE 99 (282)
T ss_pred HHHHHHHhcCCC---CCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCc
Confidence 344445555521 12344557899999999999999998753 3568999999999999999997311
Q ss_pred ------------CceeeccCc---cc--------------CCceEEEEeee-ecCC--CCCCCccceEEEEE--eeChhh
Q psy8662 134 ------------GIWVTIRGK---SF--------------SNKTGIVTGWG-VQKQ--GGSTSDTLLEVEVP--ILSNAE 179 (260)
Q Consensus 134 ------------~i~l~~~~~---~~--------------~~~~~~v~Gwg-~~~~--~~~~~~~l~~~~v~--vi~~~~ 179 (260)
.+.+|.... .+ .-..+++.+.= .... .......+.+++-. ....-.
T Consensus 100 ~~~~~~C~~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~~~~~~~~~ 179 (282)
T PF03761_consen 100 EFDNKKCEGNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEEDFSKNVSPP 179 (282)
T ss_pred ccccceeeCCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEcccccccCCCE
Confidence 111111000 00 01122332221 0000 00111122222222 111222
Q ss_pred Hhhhh------------cCC-----------CCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCC-CC
Q psy8662 180 CKKTA------------YEN-----------RITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEG-CA 235 (260)
Q Consensus 180 C~~~~------------~~~-----------~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~-C~ 235 (260)
|-... ++. .+....-|..........|.+|+||||+...+++|+|+||.+.+.. |.
T Consensus 180 Cl~~~~~~~~~~~~~~~yg~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~ 259 (282)
T PF03761_consen 180 CLADSSTNWEKGDEVDVYGFNSTGKLKHRKLKITNCTKCAYSICTKQYSCKGDRGGPLVKNINGRWTLIGVGASGNYECN 259 (282)
T ss_pred EeCCCccccccCceEEEeecCCCCeEEEEEEEEEEeeccceeEecccccCCCCccCeEEEEECCCEEEEEEEccCCCccc
Confidence 21100 000 0000001333333446789999999999999999999999998763 43
Q ss_pred CCCCCcEEEechhhHHHHHHHh
Q psy8662 236 QENYPGVYARVNRYLTWIKNNT 257 (260)
Q Consensus 236 ~~~~p~vyt~V~~y~~WI~~~~ 257 (260)
.. ...|.+|..|.+=|.+.+
T Consensus 260 ~~--~~~f~~v~~~~~~IC~lt 279 (282)
T PF03761_consen 260 KN--NSYFFNVSWYQDEICELT 279 (282)
T ss_pred cc--ccEEEEHHHhhhhhccce
Confidence 22 578999999998776654
No 7
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.66 E-value=2.2e-07 Score=79.81 Aligned_cols=54 Identities=24% Similarity=0.450 Sum_probs=38.7
Q ss_pred CCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEec-hhhHHHHHHHhh
Q psy8662 202 EKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARV-NRYLTWIKNNTI 258 (260)
Q Consensus 202 ~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V-~~y~~WI~~~~~ 258 (260)
..+++.|+||+|++...+ +++||..-+..=.......-.+|+ ..+++||+++++
T Consensus 197 ~~dT~pG~SGSpv~~~~~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 197 DADTLPGSSGSPVLISKD---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred EecccCCCCCCceEecCc---eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 367899999999998765 899999988652221223344555 567899998764
No 8
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=98.09 E-value=3.8e-06 Score=71.24 Aligned_cols=37 Identities=22% Similarity=0.733 Sum_probs=34.6
Q ss_pred CCCCceEEEEEecCeeeeeeEEEeCCEEEeccccccc
Q psy8662 95 VHQYPWMALLMYKKRFYCGATLINNLYVLTAAHCVHQ 131 (260)
Q Consensus 95 ~~~~Pw~v~l~~~~~~~C~GtLIs~~~VLTAAhCv~~ 131 (260)
...|||+|.|+..|.+.|+|+||.++|||++..|+..
T Consensus 13 ~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~ 49 (267)
T PF09342_consen 13 DYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRG 49 (267)
T ss_pred cccCcceeeEEEcCeEEEEEEEeccceEEEeccccCC
Confidence 4569999999999999999999999999999999865
No 9
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=97.25 E-value=0.0005 Score=51.73 Aligned_cols=20 Identities=45% Similarity=0.527 Sum_probs=18.8
Q ss_pred eeeEEEeCC-EEEeccccccc
Q psy8662 112 CGATLINNL-YVLTAAHCVHQ 131 (260)
Q Consensus 112 C~GtLIs~~-~VLTAAhCv~~ 131 (260)
|+|.+|+++ +|||+|||+..
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~ 21 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVED 21 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTC
T ss_pred CEEEEEcCCceEEEchhheec
Confidence 789999999 99999999985
No 10
>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=96.01 E-value=0.072 Score=48.61 Aligned_cols=22 Identities=18% Similarity=0.365 Sum_probs=19.2
Q ss_pred eeeeeEEEeCC-EEEeccccccc
Q psy8662 110 FYCGATLINNL-YVLTAAHCVHQ 131 (260)
Q Consensus 110 ~~C~GtLIs~~-~VLTAAhCv~~ 131 (260)
...+|.+|+++ +|||++|-+..
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~ 100 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKK 100 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCC
Confidence 35999999976 99999999865
No 11
>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=95.88 E-value=0.052 Score=50.79 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=20.1
Q ss_pred eeeeeeEEEeCC-EEEeccccccc
Q psy8662 109 RFYCGATLINNL-YVLTAAHCVHQ 131 (260)
Q Consensus 109 ~~~C~GtLIs~~-~VLTAAhCv~~ 131 (260)
...++|.+|+++ +|||++|.+..
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~ 80 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDG 80 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCC
Confidence 457999999976 99999999976
No 12
>PRK10898 serine endoprotease; Provisional
Probab=94.67 E-value=0.55 Score=42.87 Aligned_cols=22 Identities=18% Similarity=0.465 Sum_probs=19.0
Q ss_pred eeeeeEEEeCC-EEEeccccccc
Q psy8662 110 FYCGATLINNL-YVLTAAHCVHQ 131 (260)
Q Consensus 110 ~~C~GtLIs~~-~VLTAAhCv~~ 131 (260)
...+|.+|+++ +|||.+|=+..
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~ 100 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVIND 100 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCC
Confidence 46999999976 99999999865
No 13
>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=91.57 E-value=0.23 Score=49.76 Aligned_cols=32 Identities=38% Similarity=0.578 Sum_probs=23.1
Q ss_pred CCcCCCCCceEEee--CCeeEEEEEEeeCCCCCC
Q psy8662 205 SCQGDSGGPLHYAN--ETVHHIVGVVSWGEGCAQ 236 (260)
Q Consensus 205 ~C~gDsGgPl~~~~--~~~~~L~GI~S~g~~C~~ 236 (260)
.-.||||+||+.-+ +.+|+|+|+++.+.+...
T Consensus 213 ~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~g 246 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYNG 246 (769)
T ss_dssp --TT-TT-EEEEEETTTTEEEEEEEEEEECCCCH
T ss_pred cccCcCCCceEEEEccCCeEEEEEEEccccccCC
Confidence 45699999999765 589999999998876543
No 14
>PRK10139 serine endoprotease; Provisional
Probab=91.29 E-value=1.4 Score=41.60 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=19.0
Q ss_pred eeeeeEEEeC--CEEEeccccccc
Q psy8662 110 FYCGATLINN--LYVLTAAHCVHQ 131 (260)
Q Consensus 110 ~~C~GtLIs~--~~VLTAAhCv~~ 131 (260)
...+|.+|++ -||||.+|.+..
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~ 113 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQ 113 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCC
Confidence 4799999974 699999999975
No 15
>PRK10942 serine endoprotease; Provisional
Probab=87.25 E-value=4.7 Score=38.40 Aligned_cols=23 Identities=26% Similarity=0.358 Sum_probs=19.4
Q ss_pred eeeeeeEEEeC--CEEEeccccccc
Q psy8662 109 RFYCGATLINN--LYVLTAAHCVHQ 131 (260)
Q Consensus 109 ~~~C~GtLIs~--~~VLTAAhCv~~ 131 (260)
....+|.+|+. -+|||.+|.+..
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~ 134 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDN 134 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCC
Confidence 34699999985 599999999876
No 16
>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=73.68 E-value=3.1 Score=32.16 Aligned_cols=52 Identities=25% Similarity=0.428 Sum_probs=33.2
Q ss_pred hcCCCCCCCeEEeecCCCCCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEechhh
Q psy8662 184 AYENRITPNMLCAGYPKGEKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARVNRY 249 (260)
Q Consensus 184 ~~~~~i~~~~~Ca~~~~~~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y 249 (260)
+++..+..+++=...+. =+||-||+|.|+.+ ++||++.|.. + -.-|++|..+
T Consensus 71 YYP~h~Q~~~l~g~Gp~-----~PGdCGg~L~C~HG----ViGi~Tagg~----g-~VaF~dir~~ 122 (127)
T PF00947_consen 71 YYPKHYQYNLLIGEGPA-----EPGDCGGILRCKHG----VIGIVTAGGE----G-HVAFADIRDL 122 (127)
T ss_dssp TB-SEEEECEEEEE-SS-----STT-TCSEEEETTC----EEEEEEEEET----T-EEEEEECCCG
T ss_pred CchhheecCceeecccC-----CCCCCCceeEeCCC----eEEEEEeCCC----c-eEEEEechhh
Confidence 45555555554443222 24899999999986 9999998732 2 3669999875
No 17
>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=56.90 E-value=14 Score=31.25 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=22.5
Q ss_pred CCCCCcCCCCCceEEeeCCeeEEEEEEeeCC
Q psy8662 202 EKDSCQGDSGGPLHYANETVHHIVGVVSWGE 232 (260)
Q Consensus 202 ~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~ 232 (260)
..+.-+|.||+|++.++ .|+|-++++.
T Consensus 174 TGGIvqGMSGSPI~qdG----KLiGAVthvf 200 (218)
T PF05580_consen 174 TGGIVQGMSGSPIIQDG----KLIGAVTHVF 200 (218)
T ss_pred hCCEEecccCCCEEECC----EEEEEEEEEE
Confidence 34678999999998876 7999999875
No 18
>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=53.88 E-value=8.3 Score=38.52 Aligned_cols=21 Identities=29% Similarity=0.490 Sum_probs=18.7
Q ss_pred eeeeEEEeCC-EEEeccccccc
Q psy8662 111 YCGATLINNL-YVLTAAHCVHQ 131 (260)
Q Consensus 111 ~C~GtLIs~~-~VLTAAhCv~~ 131 (260)
.|+|++||++ .|||--||...
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 3999999987 89999999865
No 19
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=39.34 E-value=39 Score=31.52 Aligned_cols=46 Identities=24% Similarity=0.401 Sum_probs=31.7
Q ss_pred CCCCCcCCCCCceEEeeCCeeEEEEEEeeCCCCCCCCCCcEEEechhhHHHHHHHh
Q psy8662 202 EKDSCQGDSGGPLHYANETVHHIVGVVSWGEGCAQENYPGVYARVNRYLTWIKNNT 257 (260)
Q Consensus 202 ~~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y~~WI~~~~ 257 (260)
..+.-+|.||+|++.++ .|+|-++...--.....+++ |.+|+.+..
T Consensus 354 tgGivqGMSGSPi~q~g----kliGAvtHVfvndpt~GYGi------~ie~Ml~~~ 399 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQNG----KVIGAVTHVFVNDPTSGYGV------YIEWMLKEA 399 (402)
T ss_pred hCCEEecccCCCEEECC----EEEEEEEEEEecCCCcceee------hHHHHHHHh
Confidence 35678999999999877 69998887542222223454 578887754
No 20
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=36.98 E-value=23 Score=31.10 Aligned_cols=22 Identities=32% Similarity=0.598 Sum_probs=16.7
Q ss_pred cCCCCCceEEeeCCeeEEEEEEeeC
Q psy8662 207 QGDSGGPLHYANETVHHIVGVVSWG 231 (260)
Q Consensus 207 ~gDsGgPl~~~~~~~~~L~GI~S~g 231 (260)
.||||+|++..++ .|+||.+-.
T Consensus 207 ~GDSGSPVVt~dg---~liGVHTGS 228 (297)
T PF05579_consen 207 PGDSGSPVVTEDG---DLIGVHTGS 228 (297)
T ss_dssp GGCTT-EEEETTC----EEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecC
Confidence 3899999998765 599999754
No 21
>PF02907 Peptidase_S29: Hepatitis C virus NS3 protease; InterPro: IPR004109 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies the Hepatitis C virus NS3 protein as a serine protease which belongs to MEROPS peptidase family S29 (hepacivirin family, clan PA(S)), which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. The NS2 proteinase (IPR002518 from INTERPRO), a zinc-dependent enzyme, performs a single proteolytic cut to release the N terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4. It has been suggested that the NS3 serine protease of hepatitus C is involved in cell transformation and that the ability to transform requires an active enzyme [].; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0019087 transformation of host cell by virus; PDB: 2QV1_B 3LOX_C 2OBQ_C 2OC1_C 2OC0_A 3LON_A 3KNX_A 2O8M_A 2OBO_A 2OC8_A ....
Probab=35.56 E-value=27 Score=27.38 Aligned_cols=21 Identities=38% Similarity=0.722 Sum_probs=15.2
Q ss_pred cCCCCCceEEeeCCeeEEEEEEee
Q psy8662 207 QGDSGGPLHYANETVHHIVGVVSW 230 (260)
Q Consensus 207 ~gDsGgPl~~~~~~~~~L~GI~S~ 230 (260)
.|.||||++|..+ .++||.-.
T Consensus 107 kGSSGgPiLC~~G---H~vG~f~a 127 (148)
T PF02907_consen 107 KGSSGGPILCPSG---HAVGMFRA 127 (148)
T ss_dssp TT-TT-EEEETTS---EEEEEEEE
T ss_pred ecCCCCcccCCCC---CEEEEEEE
Confidence 4889999999876 68888754
No 22
>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=33.99 E-value=54 Score=30.77 Aligned_cols=30 Identities=23% Similarity=0.375 Sum_probs=23.3
Q ss_pred CCCCcCCCCCceEEeeCCeeEEEEEEeeCC
Q psy8662 203 KDSCQGDSGGPLHYANETVHHIVGVVSWGE 232 (260)
Q Consensus 203 ~~~C~gDsGgPl~~~~~~~~~L~GI~S~g~ 232 (260)
-++-+||-|.|.+.+.++.|+++||.....
T Consensus 498 LGT~PGDCGcPYvyKrgNd~VV~GVH~AAt 527 (535)
T PF05416_consen 498 LGTIPGDCGCPYVYKRGNDWVVIGVHAAAT 527 (535)
T ss_dssp TS--TTGTT-EEEEEETTEEEEEEEEEEE-
T ss_pred cCCCCCCCCCceeeecCCcEEEEEEEehhc
Confidence 456679999999999999999999997653
No 23
>PF00548 Peptidase_C3: 3C cysteine protease (picornain 3C); InterPro: IPR000199 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This signature defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral C3 cysteine protease. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SJO_E 2H6M_A 1QA7_C 1HAV_B 2HAL_A 2H9H_A 3QZQ_B 3QZR_A 3R0F_B 3SJ9_A ....
Probab=22.18 E-value=43 Score=27.19 Aligned_cols=28 Identities=25% Similarity=0.323 Sum_probs=22.9
Q ss_pred CCcCCCCCceEEeeCCeeEEEEEEeeCC
Q psy8662 205 SCQGDSGGPLHYANETVHHIVGVVSWGE 232 (260)
Q Consensus 205 ~C~gDsGgPl~~~~~~~~~L~GI~S~g~ 232 (260)
+-.|+=||||+...++...++||...|.
T Consensus 144 t~~G~CG~~l~~~~~~~~~i~GiHvaG~ 171 (172)
T PF00548_consen 144 TKPGMCGSPLVSRIGGQGKIIGIHVAGN 171 (172)
T ss_dssp EETTGTTEEEEESCGGTTEEEEEEEEEE
T ss_pred CCCCccCCeEEEeeccCccEEEEEeccC
Confidence 3458889999997777889999998764
No 24
>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=21.46 E-value=60 Score=32.99 Aligned_cols=16 Identities=38% Similarity=0.534 Sum_probs=13.8
Q ss_pred eEEEeCCEEEeccccc
Q psy8662 114 ATLINNLYVLTAAHCV 129 (260)
Q Consensus 114 GtLIs~~~VLTAAhCv 129 (260)
.|||++++|+|++|=.
T Consensus 69 aTLigpqYiVSV~HN~ 84 (769)
T PF02395_consen 69 ATLIGPQYIVSVKHNG 84 (769)
T ss_dssp -EEEETTEEEBETTG-
T ss_pred EEEecCCeEEEEEccC
Confidence 8999999999999987
No 25
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=20.42 E-value=1.3e+02 Score=23.72 Aligned_cols=51 Identities=29% Similarity=0.442 Sum_probs=33.9
Q ss_pred eEEeecCCCCCCCCcCCCCCceEEe---e--CCeeEEEEEEeeCCCCCCCCCCcEEEechhhHHHHHHHh
Q psy8662 193 MLCAGYPKGEKDSCQGDSGGPLHYA---N--ETVHHIVGVVSWGEGCAQENYPGVYARVNRYLTWIKNNT 257 (260)
Q Consensus 193 ~~Ca~~~~~~~~~C~gDsGgPl~~~---~--~~~~~L~GI~S~g~~C~~~~~p~vyt~V~~y~~WI~~~~ 257 (260)
.+|.+ ++.|.||+=|||+=. . ...+.++|-+. .|-=-.++...++.|++.-
T Consensus 5 ~lCIG-----TDRstGDsLGPLVGt~L~~~~~~~~~VyGTL~---------~PVHA~NL~e~l~~I~~~~ 60 (140)
T TIGR02841 5 LLCIG-----TDRSTGDALGPLVGMKLKFLLLNNFHVFGTLE---------EPVHAKNLEEKLKIIKKKH 60 (140)
T ss_pred EEEEC-----CCCCcccccchhhHHHHHhccCCCCeEEECCC---------CCcccccHHHHHHHHHHhC
Confidence 58986 677889999999721 1 12345666442 3444478888888887753
Done!