Query psy1243
Match_columns 121
No_of_seqs 130 out of 1395
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 19:04:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1243.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1243hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 99.6 3.5E-15 7.6E-20 106.1 7.0 91 11-103 157-254 (256)
2 cd00190 Tryp_SPc Trypsin-like 99.4 2E-12 4.3E-17 89.6 6.8 89 11-101 137-231 (232)
3 smart00020 Tryp_SPc Trypsin-li 99.3 2.2E-11 4.7E-16 84.6 7.5 87 10-99 137-229 (229)
4 PF00089 Trypsin: Trypsin; In 99.1 4.6E-10 9.9E-15 77.2 6.3 80 12-99 135-220 (220)
5 COG5640 Secreted trypsin-like 99.0 6.5E-10 1.4E-14 82.2 6.1 86 14-103 182-278 (413)
6 PF03761 DUF316: Domain of unk 86.7 0.98 2.1E-05 32.6 3.6 47 50-98 223-274 (282)
7 PF02395 Peptidase_S6: Immunog 76.9 2.7 5.8E-05 35.2 3.0 32 55-86 213-244 (769)
8 COG5640 Secreted trypsin-like 52.6 5.8 0.00013 30.4 0.5 30 69-98 253-283 (413)
9 PF06866 DUF1256: Protein of u 47.1 11 0.00025 25.5 1.2 18 43-65 29-46 (163)
10 TIGR02841 spore_YyaC putative 44.2 12 0.00027 24.7 1.0 18 43-65 5-22 (140)
11 PF13365 Trypsin_2: Trypsin-li 35.4 22 0.00048 21.3 1.2 13 54-66 100-112 (120)
12 PF11245 DUF2544: Protein of u 31.7 43 0.00094 23.9 2.2 35 80-114 163-198 (230)
13 PF02907 Peptidase_S29: Hepati 31.6 29 0.00063 22.9 1.2 14 55-68 105-118 (148)
14 PF05579 Peptidase_S32: Equine 23.0 41 0.00089 24.9 0.9 12 57-68 207-218 (297)
No 1
>KOG3627|consensus
Probab=99.59 E-value=3.5e-15 Score=106.14 Aligned_cols=91 Identities=32% Similarity=0.583 Sum_probs=76.4
Q ss_pred ccccccceEEEeccChhhhcccccCCCCcCCCeEEEeecCCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCC-cc--
Q psy1243 11 SNALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRA-CY-- 87 (121)
Q Consensus 11 ~~~~~L~~~~l~~~~~~~C~~~~~~~~~~~~~~~Cag~~~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~-~~-- 87 (121)
..+..||++.+++++...|+..+.....+.+.+|||+......++|+|||||||++.... .+...||++++.. |.
T Consensus 157 ~~~~~L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~--~~~~~GivS~G~~~C~~~ 234 (256)
T KOG3627|consen 157 PLPDTLQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG--RWVLVGIVSWGSGGCGQP 234 (256)
T ss_pred CCCceeEEEEEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCC--cEEEEEEEEecCCCCCCC
Confidence 568899999999999999999544332567779999965667789999999999999887 6778999999977 64
Q ss_pred ----eeeeccccceecceec
Q psy1243 88 ----VLSKMIRFYASVGIEA 103 (121)
Q Consensus 88 ----wi~~v~~~~~wi~~~~ 103 (121)
.|+++..|.+||...+
T Consensus 235 ~~P~vyt~V~~y~~WI~~~~ 254 (256)
T KOG3627|consen 235 NYPGVYTRVSSYLDWIKENI 254 (256)
T ss_pred CCCeEEeEhHHhHHHHHHHh
Confidence 8999999999998654
No 2
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=99.36 E-value=2e-12 Score=89.61 Aligned_cols=89 Identities=33% Similarity=0.706 Sum_probs=72.9
Q ss_pred ccccccceEEEeccChhhhcccccCCCCcCCCeEEEeecCCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCCcc---
Q psy1243 11 SNALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRACY--- 87 (121)
Q Consensus 11 ~~~~~L~~~~l~~~~~~~C~~~~~~~~~~~~~~~Cag~~~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~~~--- 87 (121)
..+..|++..+.+++...|.+.+.....+.+.++|++......+.|.|||||||++... ..+.+.||++++..|.
T Consensus 137 ~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~--~~~~lvGI~s~g~~c~~~~ 214 (232)
T cd00190 137 PLPDVLQEVNVPIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDN--GRGVLVGIVSWGSGCARPN 214 (232)
T ss_pred CCCceeeEEEeeeECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEeC--CEEEEEEEEehhhccCCCC
Confidence 45677999999999999999854332467899999985443678999999999999876 4567899999987554
Q ss_pred ---eeeeccccceecce
Q psy1243 88 ---VLSKMIRFYASVGI 101 (121)
Q Consensus 88 ---wi~~v~~~~~wi~~ 101 (121)
.|+++..|.+||..
T Consensus 215 ~~~~~t~v~~~~~WI~~ 231 (232)
T cd00190 215 YPGVYTRVSSYLDWIQK 231 (232)
T ss_pred CCCEEEEcHHhhHHhhc
Confidence 79999999999964
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=99.26 E-value=2.2e-11 Score=84.61 Aligned_cols=87 Identities=34% Similarity=0.672 Sum_probs=71.5
Q ss_pred CccccccceEEEeccChhhhcccccCCCCcCCCeEEEeecCCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCCcc--
Q psy1243 10 ASNALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRACY-- 87 (121)
Q Consensus 10 g~~~~~L~~~~l~~~~~~~C~~~~~~~~~~~~~~~Cag~~~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~~~-- 87 (121)
+.....++...+.+++.+.|...+.....+...++|++........|.||||+||++... .+...|+++.+..|.
T Consensus 137 ~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~---~~~l~Gi~s~g~~C~~~ 213 (229)
T smart00020 137 GSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG---RWVLVGIVSWGSGCARP 213 (229)
T ss_pred CcCCCEeeEEEEEEeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEECC---CEEEEEEEEECCCCCCC
Confidence 345668899999999999999854333357889999985444678999999999999876 678999999987554
Q ss_pred ----eeeeccccceec
Q psy1243 88 ----VLSKMIRFYASV 99 (121)
Q Consensus 88 ----wi~~v~~~~~wi 99 (121)
+|+++.+|.+||
T Consensus 214 ~~~~~~~~i~~~~~WI 229 (229)
T smart00020 214 GKPGVYTRVSSYLDWI 229 (229)
T ss_pred CCCCEEEEeccccccC
Confidence 899999999998
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=99.06 E-value=4.6e-10 Score=77.21 Aligned_cols=80 Identities=31% Similarity=0.706 Sum_probs=66.2
Q ss_pred cccccceEEEeccChhhhcccccCCCCcCCCeEEEeecCCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCCcc----
Q psy1243 12 NALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRACY---- 87 (121)
Q Consensus 12 ~~~~L~~~~l~~~~~~~C~~~~~~~~~~~~~~~Cag~~~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~~~---- 87 (121)
....++...+.+++.+.|+.. +...+.+.++|++.. ...+.|.|||||||++.+. .+.|+.+.+..|.
T Consensus 135 ~~~~~~~~~~~~~~~~~c~~~--~~~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~-----~lvGI~s~~~~c~~~~~ 206 (220)
T PF00089_consen 135 YSSNLQSVTVPVVSRKTCRSS--YNDNLTPNMICAGSS-GSGDACQGDSGGPLICNNN-----YLVGIVSFGENCGSPNY 206 (220)
T ss_dssp BTSBEEEEEEEEEEHHHHHHH--TTTTSTTTEEEEETT-SSSBGGTTTTTSEEEETTE-----EEEEEEEEESSSSBTTS
T ss_pred ccccccccccccccccccccc--ccccccccccccccc-cccccccccccccccccee-----eecceeeecCCCCCCCc
Confidence 456889999999999999984 444478899999853 5678999999999998776 6788887776663
Q ss_pred --eeeeccccceec
Q psy1243 88 --VLSKMIRFYASV 99 (121)
Q Consensus 88 --wi~~v~~~~~wi 99 (121)
+|+++..|.+||
T Consensus 207 ~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 207 PGVYTRVSSYLDWI 220 (220)
T ss_dssp EEEEEEGGGGHHHH
T ss_pred CEEEEEHHHhhccC
Confidence 789999999997
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=6.5e-10 Score=82.22 Aligned_cols=86 Identities=23% Similarity=0.368 Sum_probs=67.0
Q ss_pred cccceEEEeccChhhhcccccC----CCCcCCCeEEEeecCCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCC-cc-
Q psy1243 14 LTLKAARVGTLSQESCRKEDAY----GTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRA-CY- 87 (121)
Q Consensus 14 ~~L~~~~l~~~~~~~C~~~~~~----~~~~~~~~~Cag~~~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~-~~- 87 (121)
..|+++.+..++...|...+.. .....-.-+||| ...+++|+||||||++...... ..+.||+||+.. |.
T Consensus 182 t~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag--~~~~daCqGDSGGPi~~~g~~G--~vQ~GVvSwG~~~Cg~ 257 (413)
T COG5640 182 TILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAG--RPPKDACQGDSGGPIFHKGEEG--RVQRGVVSWGDGGCGG 257 (413)
T ss_pred ceeeeeeeeeechHHhhhhccccccCCCCCCccceecC--CCCcccccCCCCCceEEeCCCc--cEEEeEEEecCCCCCC
Confidence 4789999999999999985421 111222239999 5558999999999999877553 468999999976 64
Q ss_pred -----eeeeccccceecceec
Q psy1243 88 -----VLSKMIRFYASVGIEA 103 (121)
Q Consensus 88 -----wi~~v~~~~~wi~~~~ 103 (121)
+|+++..|.+||...+
T Consensus 258 t~~~gVyT~vsny~~WI~a~~ 278 (413)
T COG5640 258 TLIPGVYTNVSNYQDWIAAMT 278 (413)
T ss_pred CCcceeEEehhHHHHHHHHHh
Confidence 9999999999998766
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=86.67 E-value=0.98 Score=32.60 Aligned_cols=47 Identities=26% Similarity=0.447 Sum_probs=31.6
Q ss_pred CCCCCCccCCCcceEEEeeCCcccCceeEEEEeCCC-c----ceeeecccccee
Q psy1243 50 QGGADSCQGDSGGPIVCDIQGCDKGASLGTDRLSRA-C----YVLSKMIRFYAS 98 (121)
Q Consensus 50 ~~~~~~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~-~----~wi~~v~~~~~w 98 (121)
......|.+|+||||+...++-+ ...|+..-+.+ + .+|-++..|.+-
T Consensus 223 ~~~~~~~~~d~Gg~lv~~~~gr~--tlIGv~~~~~~~~~~~~~~f~~v~~~~~~ 274 (282)
T PF03761_consen 223 CTKQYSCKGDRGGPLVKNINGRW--TLIGVGASGNYECNKNNSYFFNVSWYQDE 274 (282)
T ss_pred ecccccCCCCccCeEEEEECCCE--EEEEEEccCCCcccccccEEEEHHHhhhh
Confidence 34467899999999999887654 45777444432 2 366666665543
No 7
>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=76.94 E-value=2.7 Score=35.22 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=23.6
Q ss_pred CccCCCcceEEEeeCCcccCceeEEEEeCCCc
Q psy1243 55 SCQGDSGGPIVCDIQGCDKGASLGTDRLSRAC 86 (121)
Q Consensus 55 ~C~gDsGgPLv~~~~~~~~~~~~g~~~v~~~~ 86 (121)
.=.||||+||+..+..-..|+..|+++-+...
T Consensus 213 ~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~ 244 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGY 244 (769)
T ss_dssp --TT-TT-EEEEEETTTTEEEEEEEEEEECCC
T ss_pred cccCcCCCceEEEEccCCeEEEEEEEcccccc
Confidence 45799999999999888889999997665544
No 8
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=52.58 E-value=5.8 Score=30.39 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=23.3
Q ss_pred CCcccCceeEE-EEeCCCcceeeecccccee
Q psy1243 69 QGCDKGASLGT-DRLSRACYVLSKMIRFYAS 98 (121)
Q Consensus 69 ~~~~~~~~~g~-~~v~~~~~wi~~v~~~~~w 98 (121)
.+|+....+|+ |+++.|.+||.+++.-...
T Consensus 253 ~~Cg~t~~~gVyT~vsny~~WI~a~~~~l~~ 283 (413)
T COG5640 253 GGCGGTLIPGVYTNVSNYQDWIAAMTNGLSY 283 (413)
T ss_pred CCCCCCCcceeEEehhHHHHHHHHHhcCCCc
Confidence 34988776666 9999999999998865443
No 9
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=47.06 E-value=11 Score=25.49 Aligned_cols=18 Identities=50% Similarity=1.029 Sum_probs=15.7
Q ss_pred eEEEeecCCCCCCccCCCcceEE
Q psy1243 43 MFCAGSFQGGADSCQGDSGGPIV 65 (121)
Q Consensus 43 ~~Cag~~~~~~~~C~gDsGgPLv 65 (121)
.+|.| .+-|.||+=|||+
T Consensus 29 ~lCIG-----TDRstGDsLGPLV 46 (163)
T PF06866_consen 29 FLCIG-----TDRSTGDSLGPLV 46 (163)
T ss_pred EEEEC-----CCCCccccccchh
Confidence 68987 4789999999999
No 10
>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=44.19 E-value=12 Score=24.66 Aligned_cols=18 Identities=44% Similarity=1.030 Sum_probs=15.4
Q ss_pred eEEEeecCCCCCCccCCCcceEE
Q psy1243 43 MFCAGSFQGGADSCQGDSGGPIV 65 (121)
Q Consensus 43 ~~Cag~~~~~~~~C~gDsGgPLv 65 (121)
.+|.| .+-|.||+=|||+
T Consensus 5 ~lCIG-----TDRstGDsLGPLV 22 (140)
T TIGR02841 5 LLCIG-----TDRSTGDALGPLV 22 (140)
T ss_pred EEEEC-----CCCCcccccchhh
Confidence 57887 4789999999998
No 11
>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=35.39 E-value=22 Score=21.33 Aligned_cols=13 Identities=46% Similarity=0.869 Sum_probs=9.6
Q ss_pred CCccCCCcceEEE
Q psy1243 54 DSCQGDSGGPIVC 66 (121)
Q Consensus 54 ~~C~gDsGgPLv~ 66 (121)
..-.|.|||||+-
T Consensus 100 ~~~~G~SGgpv~~ 112 (120)
T PF13365_consen 100 DTRPGSSGGPVFD 112 (120)
T ss_dssp S-STTTTTSEEEE
T ss_pred ccCCCcEeHhEEC
Confidence 4446899999975
No 12
>PF11245 DUF2544: Protein of unknown function (DUF2544); InterPro: IPR021407 This is a bacterial family of proteins with unknown function.
Probab=31.73 E-value=43 Score=23.92 Aligned_cols=35 Identities=31% Similarity=0.476 Sum_probs=25.1
Q ss_pred EEeCCCcceeeeccccceecceecccccCCC-CCCC
Q psy1243 80 DRLSRACYVLSKMIRFYASVGIEATSSCSPG-DPLT 114 (121)
Q Consensus 80 ~~v~~~~~wi~~v~~~~~wi~~~~~~s~~p~-~~~t 114 (121)
-.-+.||-|+.+++.|...-=++...++.|. +|+|
T Consensus 163 D~RGaYCRfVsq~iTfs~~GCD~akVTvtp~~hPiT 198 (230)
T PF11245_consen 163 DERGAYCRFVSQMITFSSSGCDNAKVTVTPNRHPIT 198 (230)
T ss_pred ccCCceeEEEeeeeEEEeecccCceeeecCCcCccc
Confidence 5567788899999988877666666666555 4544
No 13
>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=31.60 E-value=29 Score=22.94 Aligned_cols=14 Identities=50% Similarity=1.080 Sum_probs=9.3
Q ss_pred CccCCCcceEEEee
Q psy1243 55 SCQGDSGGPIVCDI 68 (121)
Q Consensus 55 ~C~gDsGgPLv~~~ 68 (121)
.-.|.||||++|..
T Consensus 105 ~lkGSSGgPiLC~~ 118 (148)
T PF02907_consen 105 DLKGSSGGPILCPS 118 (148)
T ss_dssp HHTT-TT-EEEETT
T ss_pred EEecCCCCcccCCC
Confidence 45789999999843
No 14
>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=23.04 E-value=41 Score=24.88 Aligned_cols=12 Identities=50% Similarity=0.911 Sum_probs=8.9
Q ss_pred cCCCcceEEEee
Q psy1243 57 QGDSGGPIVCDI 68 (121)
Q Consensus 57 ~gDsGgPLv~~~ 68 (121)
-||||+|++..+
T Consensus 207 ~GDSGSPVVt~d 218 (297)
T PF05579_consen 207 PGDSGSPVVTED 218 (297)
T ss_dssp GGCTT-EEEETT
T ss_pred CCCCCCccCcCC
Confidence 389999999754
Done!