Query psy7307
Match_columns 117
No_of_seqs 153 out of 1430
Neff 9.3
Searched_HMMs 46136
Date Fri Aug 16 23:27:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7307hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 99.4 4.4E-12 9.4E-17 87.5 7.9 80 3-83 167-255 (256)
2 cd00190 Tryp_SPc Trypsin-like 99.1 2.3E-10 5.1E-15 76.9 6.0 77 4-81 148-232 (232)
3 COG5640 Secreted trypsin-like 99.1 4.8E-10 1E-14 80.2 6.7 65 21-87 216-283 (413)
4 smart00020 Tryp_SPc Trypsin-li 98.8 1.4E-08 3.1E-13 68.4 5.9 58 19-78 169-229 (229)
5 PF00089 Trypsin: Trypsin; In 98.6 4.8E-08 1E-12 65.2 4.1 58 17-78 161-220 (220)
6 KOG3627|consensus 98.5 1.7E-07 3.7E-12 64.6 4.0 66 47-114 162-234 (256)
7 COG5640 Secreted trypsin-like 97.9 8.8E-06 1.9E-10 58.7 3.4 36 79-115 223-259 (413)
8 cd00190 Tryp_SPc Trypsin-like 97.6 5.9E-05 1.3E-09 50.5 3.4 35 78-113 178-212 (232)
9 smart00020 Tryp_SPc Trypsin-li 97.4 0.00021 4.6E-09 48.0 3.9 34 77-112 178-211 (229)
10 PF00089 Trypsin: Trypsin; In 96.5 0.0025 5.3E-08 42.3 3.0 32 79-114 173-204 (220)
11 PF03761 DUF316: Domain of unk 93.7 0.21 4.6E-06 35.0 5.4 47 28-75 225-272 (282)
12 PF03761 DUF316: Domain of unk 86.6 0.73 1.6E-05 32.3 2.8 30 79-109 226-255 (282)
13 PF02395 Peptidase_S6: Immunog 85.7 0.85 1.8E-05 36.9 3.0 35 76-110 208-243 (769)
14 PF02395 Peptidase_S6: Immunog 83.2 2.1 4.6E-05 34.7 4.2 62 30-93 212-274 (769)
15 PF02907 Peptidase_S29: Hepati 58.5 12 0.00025 24.0 2.5 23 79-105 103-125 (148)
16 PHA02102 hypothetical protein 58.2 8.8 0.00019 21.1 1.7 29 72-100 40-68 (72)
17 PF13365 Trypsin_2: Trypsin-li 45.9 23 0.00049 20.7 2.4 21 80-104 100-120 (120)
18 PF05580 Peptidase_S55: SpoIVB 41.5 27 0.00059 24.1 2.4 26 79-109 175-200 (218)
19 PRK10898 serine endoprotease; 39.8 31 0.00067 25.4 2.6 23 82-108 196-218 (353)
20 PF05579 Peptidase_S32: Equine 39.7 24 0.00053 25.2 2.0 20 83-106 207-226 (297)
21 PRK10139 serine endoprotease; 33.5 43 0.00092 25.6 2.6 23 82-108 210-232 (455)
22 PF08838 DUF1811: Protein of u 32.4 24 0.00053 21.3 0.9 22 82-109 63-84 (102)
23 COG3591 V8-like Glu-specific e 31.8 1.6E+02 0.0035 20.8 5.0 29 27-59 196-224 (251)
24 PF10459 Peptidase_S46: Peptid 31.7 34 0.00074 27.8 1.9 23 79-105 628-650 (698)
25 TIGR02038 protease_degS peripl 29.8 53 0.0012 24.1 2.5 23 82-108 196-218 (351)
26 PF00944 Peptidase_S3: Alphavi 29.3 37 0.00079 21.8 1.4 22 32-57 104-125 (158)
27 KOG3939|consensus 25.8 71 0.0015 22.8 2.4 30 79-108 248-293 (312)
28 PF00947 Pico_P2A: Picornaviru 24.1 88 0.0019 19.7 2.4 21 83-108 89-109 (127)
29 TIGR02037 degP_htrA_DO peripla 21.2 93 0.002 23.4 2.5 23 81-107 176-198 (428)
No 1
>KOG3627|consensus
Probab=99.35 E-value=4.4e-12 Score=87.52 Aligned_cols=80 Identities=34% Similarity=0.706 Sum_probs=62.1
Q ss_pred eeeeccccccCCcc-----cccceeecC-CCCCCcccCCCCCeeEEEcCCCcEEEEEEeecCCC-CCC--CCceeeeccc
Q psy7307 3 LCLVLVLICAAHQL-----VRADYDVFN-RTSRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGIG-CGK--TPGVYVQVNK 73 (117)
Q Consensus 3 ~~~~~~~~C~~~~~-----~~~~~~~~~-~~~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~~-C~~--~p~~~t~v~~ 73 (117)
+.+.+...|..... ....+|+.. ...+++|+||+|+||++.... +++++||+||+.. |.. .|++|+++..
T Consensus 167 v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~-~~~~~GivS~G~~~C~~~~~P~vyt~V~~ 245 (256)
T KOG3627|consen 167 VPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG-RWVLVGIVSWGSGGCGQPNYPGVYTRVSS 245 (256)
T ss_pred EeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCC-cEEEEEEEEecCCCCCCCCCCeEEeEhHH
Confidence 45556666765322 223477776 567889999999999998533 7999999999966 987 7999999999
Q ss_pred chHHHHhhcc
Q psy7307 74 YLRWIYNTAK 83 (117)
Q Consensus 74 ~~~wi~~~~~ 83 (117)
|.+||++...
T Consensus 246 y~~WI~~~~~ 255 (256)
T KOG3627|consen 246 YLDWIKENIG 255 (256)
T ss_pred hHHHHHHHhc
Confidence 9999988653
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=99.09 E-value=2.3e-10 Score=76.91 Aligned_cols=77 Identities=35% Similarity=0.674 Sum_probs=58.1
Q ss_pred eeeccccccCCc-----ccccceeecCCC-CCCcccCCCCCeeEEEcCCCcEEEEEEeecCCCCCC--CCceeeecccch
Q psy7307 4 CLVLVLICAAHQ-----LVRADYDVFNRT-SRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYL 75 (117)
Q Consensus 4 ~~~~~~~C~~~~-----~~~~~~~~~~~~-~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~~C~~--~p~~~t~v~~~~ 75 (117)
.+.+...|.... +....+|+.... ..+.|.+|+|+||+... +++++++||++++..|.. .|.+|+++..|.
T Consensus 148 ~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~-~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~ 226 (232)
T cd00190 148 PIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCND-NGRGVLVGIVSWGSGCARPNYPGVYTRVSSYL 226 (232)
T ss_pred eeECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEe-CCEEEEEEEEehhhccCCCCCCCEEEEcHHhh
Confidence 344445555432 223445666554 67899999999999874 478999999999877985 789999999999
Q ss_pred HHHHhh
Q psy7307 76 RWIYNT 81 (117)
Q Consensus 76 ~wi~~~ 81 (117)
+||+++
T Consensus 227 ~WI~~~ 232 (232)
T cd00190 227 DWIQKT 232 (232)
T ss_pred HHhhcC
Confidence 999763
No 3
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.07 E-value=4.8e-10 Score=80.16 Aligned_cols=65 Identities=40% Similarity=0.748 Sum_probs=52.8
Q ss_pred eeecCCCCCCcccCCCCCeeEEEcCCCcEEEEEEeecCCC-CCC--CCceeeecccchHHHHhhccCCCC
Q psy7307 21 YDVFNRTSRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGIG-CGK--TPGVYVQVNKYLRWIYNTAKGDSG 87 (117)
Q Consensus 21 ~~~~~~~~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~~-C~~--~p~~~t~v~~~~~wi~~~~~gdsg 87 (117)
+|+.... ++.|++|+|+|++....+++ .++||+||+.+ |.. .|.+||+++.|.+||...+++-+-
T Consensus 216 ~cag~~~-~daCqGDSGGPi~~~g~~G~-vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~l~~ 283 (413)
T COG5640 216 FCAGRPP-KDACQGDSGGPIFHKGEEGR-VQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTNGLSY 283 (413)
T ss_pred eecCCCC-cccccCCCCCceEEeCCCcc-EEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhcCCCc
Confidence 4444444 99999999999998865554 89999999975 987 888999999999999887765443
No 4
>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=98.79 E-value=1.4e-08 Score=68.41 Aligned_cols=58 Identities=43% Similarity=0.954 Sum_probs=48.4
Q ss_pred cceeecCCC-CCCcccCCCCCeeEEEcCCCcEEEEEEeecCCCCCC--CCceeeecccchHHH
Q psy7307 19 ADYDVFNRT-SRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWI 78 (117)
Q Consensus 19 ~~~~~~~~~-~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~~C~~--~p~~~t~v~~~~~wi 78 (117)
..+|+.... ..+.|.+|+|+||+.... +|+++||.+++..|.. .+.+|+++..|.+||
T Consensus 169 ~~~C~~~~~~~~~~c~gdsG~pl~~~~~--~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 169 NMLCAGGLEGGKDACQGDSGGPLVCNDG--RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred CcEeecCCCCCCcccCCCCCCeeEEECC--CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 345555544 678999999999998853 8999999999988984 888999999999997
No 5
>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=98.61 E-value=4.8e-08 Score=65.22 Aligned_cols=58 Identities=41% Similarity=0.772 Sum_probs=47.7
Q ss_pred cccceeecCCCCCCcccCCCCCeeEEEcCCCcEEEEEEeecCCCCCC--CCceeeecccchHHH
Q psy7307 17 VRADYDVFNRTSRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWI 78 (117)
Q Consensus 17 ~~~~~~~~~~~~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~~C~~--~p~~~t~v~~~~~wi 78 (117)
....+|+......+.|.+|+|+||++.. . .++||++++..|.. .|.+|+++..|.+||
T Consensus 161 ~~~~~c~~~~~~~~~~~g~sG~pl~~~~---~-~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 161 TPNMICAGSSGSGDACQGDSGGPLICNN---N-YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp TTTEEEEETTSSSBGGTTTTTSEEEETT---E-EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred ccccccccccccccccccccccccccce---e-eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 3445666665567899999999999874 2 79999999878887 579999999999998
No 6
>KOG3627|consensus
Probab=98.48 E-value=1.7e-07 Score=64.64 Aligned_cols=66 Identities=30% Similarity=0.573 Sum_probs=48.5
Q ss_pred CcEEEEEEeecCCCCCC-CCc--ee--eecccch-HHHHhhccCCCCCceeeccCCCcEEEEEeeeeCcc-cccc
Q psy7307 47 KQWTIIGVVSWGIGCGK-TPG--VY--VQVNKYL-RWIYNTAKGDSGGPLLLQRPDKQWTIIGVVSWGIG-CAQV 114 (117)
Q Consensus 47 ~~~~~vgI~s~~~~C~~-~p~--~~--t~v~~~~-~wi~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~~-C~~~ 114 (117)
.+...+.+++.. .|.. +.. .. +.+|... ...+++|+|||||||++.... +|+++||+|||.+ |+..
T Consensus 162 L~~~~v~i~~~~-~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~-~~~~~GivS~G~~~C~~~ 234 (256)
T KOG3627|consen 162 LQEVDVPIISNS-ECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNG-RWVLVGIVSWGSGGCGQP 234 (256)
T ss_pred eEEEEEeEcChh-HhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCC-cEEEEEEEEecCCCCCCC
Confidence 445577788775 7987 332 11 2355543 556778999999999998644 8999999999998 9875
No 7
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=97.94 E-value=8.8e-06 Score=58.74 Aligned_cols=36 Identities=42% Similarity=0.860 Sum_probs=30.8
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEeeeeCcc-ccccc
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVVSWGIG-CAQVL 115 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~~-C~~~~ 115 (117)
+++|++|||+|+.....+++ .+.||+|||.+ |+.+.
T Consensus 223 ~daCqGDSGGPi~~~g~~G~-vQ~GVvSwG~~~Cg~t~ 259 (413)
T COG5640 223 KDACQGDSGGPIFHKGEEGR-VQRGVVSWGDGGCGGTL 259 (413)
T ss_pred cccccCCCCCceEEeCCCcc-EEEeEEEecCCCCCCCC
Confidence 89999999999999865554 78899999986 98653
No 8
>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=97.63 E-value=5.9e-05 Score=50.51 Aligned_cols=35 Identities=43% Similarity=0.933 Sum_probs=30.7
Q ss_pred HHhhccCCCCCceeeccCCCcEEEEEeeeeCccccc
Q psy7307 78 IYNTAKGDSGGPLLLQRPDKQWTIIGVVSWGIGCAQ 113 (117)
Q Consensus 78 i~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~~C~~ 113 (117)
....|.+|||+||.+.. +++|+|+||+||+..|..
T Consensus 178 ~~~~c~gdsGgpl~~~~-~~~~~lvGI~s~g~~c~~ 212 (232)
T cd00190 178 GKDACQGDSGGPLVCND-NGRGVLVGIVSWGSGCAR 212 (232)
T ss_pred CCccccCCCCCcEEEEe-CCEEEEEEEEehhhccCC
Confidence 45789999999999984 588999999999988885
No 9
>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=97.41 E-value=0.00021 Score=47.98 Aligned_cols=34 Identities=47% Similarity=1.058 Sum_probs=30.1
Q ss_pred HHHhhccCCCCCceeeccCCCcEEEEEeeeeCcccc
Q psy7307 77 WIYNTAKGDSGGPLLLQRPDKQWTIIGVVSWGIGCA 112 (117)
Q Consensus 77 wi~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~~C~ 112 (117)
+....|.+|+|+||++..+ +|+|+||+|++..|.
T Consensus 178 ~~~~~c~gdsG~pl~~~~~--~~~l~Gi~s~g~~C~ 211 (229)
T smart00020 178 GGKDACQGDSGGPLVCNDG--RWVLVGIVSWGSGCA 211 (229)
T ss_pred CCCcccCCCCCCeeEEECC--CEEEEEEEEECCCCC
Confidence 3567899999999999854 999999999999998
No 10
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=96.54 E-value=0.0025 Score=42.31 Aligned_cols=32 Identities=38% Similarity=0.813 Sum_probs=27.8
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEeeeeCcccccc
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVVSWGIGCAQV 114 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~~C~~~ 114 (117)
.+.|.+|||+||++... +|+||+|++..|...
T Consensus 173 ~~~~~g~sG~pl~~~~~----~lvGI~s~~~~c~~~ 204 (220)
T PF00089_consen 173 GDACQGDSGGPLICNNN----YLVGIVSFGENCGSP 204 (220)
T ss_dssp SBGGTTTTTSEEEETTE----EEEEEEEEESSSSBT
T ss_pred cccccccccccccccee----eecceeeecCCCCCC
Confidence 47899999999999863 799999999888765
No 11
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=93.73 E-value=0.21 Score=35.03 Aligned_cols=47 Identities=34% Similarity=0.661 Sum_probs=33.4
Q ss_pred CCCcccCCCCCeeEEEcCCCcEEEEEEeecCC-CCCCCCceeeecccch
Q psy7307 28 SRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGI-GCGKTPGVYVQVNKYL 75 (117)
Q Consensus 28 ~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~-~C~~~p~~~t~v~~~~ 75 (117)
.+..|.+|+||||+-.. +++++++||.+.+. .|......|.++..|.
T Consensus 225 ~~~~~~~d~Gg~lv~~~-~gr~tlIGv~~~~~~~~~~~~~~f~~v~~~~ 272 (282)
T PF03761_consen 225 KQYSCKGDRGGPLVKNI-NGRWTLIGVGASGNYECNKNNSYFFNVSWYQ 272 (282)
T ss_pred ccccCCCCccCeEEEEE-CCCEEEEEEEccCCCcccccccEEEEHHHhh
Confidence 46789999999999774 68999999998762 3432244555655443
No 12
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=86.57 E-value=0.73 Score=32.33 Aligned_cols=30 Identities=43% Similarity=0.780 Sum_probs=25.6
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEeeeeCc
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVVSWGI 109 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~ 109 (117)
+..|.+|+||||+-. .+++|.|+||.+-+.
T Consensus 226 ~~~~~~d~Gg~lv~~-~~gr~tlIGv~~~~~ 255 (282)
T PF03761_consen 226 QYSCKGDRGGPLVKN-INGRWTLIGVGASGN 255 (282)
T ss_pred cccCCCCccCeEEEE-ECCCEEEEEEEccCC
Confidence 566899999999987 578999999988665
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=85.73 E-value=0.85 Score=36.93 Aligned_cols=35 Identities=37% Similarity=0.653 Sum_probs=23.3
Q ss_pred HHHHhhccCCCCCceeecc-CCCcEEEEEeeeeCcc
Q psy7307 76 RWIYNTAKGDSGGPLLLQR-PDKQWTIIGVVSWGIG 110 (117)
Q Consensus 76 ~wi~~~~~gdsg~pl~~~~-~~~~~~l~Gi~s~~~~ 110 (117)
++-.....||||+||-..+ ..+.|.|+|+.+.+.+
T Consensus 208 pL~n~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~ 243 (769)
T PF02395_consen 208 PLPNYGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNG 243 (769)
T ss_dssp SSBEB--TT-TT-EEEEEETTTTEEEEEEEEEEECC
T ss_pred ccccccccCcCCCceEEEEccCCeEEEEEEEccccc
Confidence 4445567899999996665 4678999999986543
No 14
>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=83.20 E-value=2.1 Score=34.73 Aligned_cols=62 Identities=27% Similarity=0.508 Sum_probs=35.1
Q ss_pred CcccCCCCCeeEEEc-CCCcEEEEEEeecCCCCCCCCceeeecccchHHHHhhccCCCCCceeec
Q psy7307 30 QAQTGDSGGPLLLQR-PDKQWTIIGVVSWGIGCGKTPGVYVQVNKYLRWIYNTAKGDSGGPLLLQ 93 (117)
Q Consensus 30 ~~C~~dsG~pl~~~~-~~~~~~~vgI~s~~~~C~~~p~~~t~v~~~~~wi~~~~~gdsg~pl~~~ 93 (117)
..=.||||+||..-+ ...+|+++|+++...........+.. ...+++....+.|...|+...
T Consensus 212 ~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~g~~~~~~~--~~~~f~~~~~~~d~~~~v~~~ 274 (769)
T PF02395_consen 212 YGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYNGKGNWWNV--IPPDFINQIKQNDTDGPVKFK 274 (769)
T ss_dssp B--TT-TT-EEEEEETTTTEEEEEEEEEEECCCCHSEEEEEE--ECHHHHHHHHHHCCEEEEECC
T ss_pred ccccCcCCCceEEEEccCCeEEEEEEEccccccCCccceeEE--ecHHHHHHHHhhhcccceeec
Confidence 345799999996543 36899999999876222112222222 224555666666777766653
No 15
>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=58.53 E-value=12 Score=23.99 Aligned_cols=23 Identities=35% Similarity=0.665 Sum_probs=15.9
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEee
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVV 105 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~ 105 (117)
.+..+|.||+|+.|... ..+|+.
T Consensus 103 is~lkGSSGgPiLC~~G----H~vG~f 125 (148)
T PF02907_consen 103 ISDLKGSSGGPILCPSG----HAVGMF 125 (148)
T ss_dssp HHHHTT-TT-EEEETTS----EEEEEE
T ss_pred eEEEecCCCCcccCCCC----CEEEEE
Confidence 46679999999999764 466764
No 16
>PHA02102 hypothetical protein
Probab=58.24 E-value=8.8 Score=21.07 Aligned_cols=29 Identities=14% Similarity=0.572 Sum_probs=22.5
Q ss_pred ccchHHHHhhccCCCCCceeeccCCCcEE
Q psy7307 72 NKYLRWIYNTAKGDSGGPLLLQRPDKQWT 100 (117)
Q Consensus 72 ~~~~~wi~~~~~gdsg~pl~~~~~~~~~~ 100 (117)
..+.+|..+.|-|..+..++.......|+
T Consensus 40 v~f~DWLsSSCYGEg~eaF~~~SDGsvWm 68 (72)
T PHA02102 40 VRFEDWLSSSCYGEGGEAFVARSDGSVWM 68 (72)
T ss_pred EeHHHhhcccccccccceeeeccCCcEec
Confidence 34779999999998888888776555564
No 17
>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=45.86 E-value=23 Score=20.68 Aligned_cols=21 Identities=33% Similarity=0.760 Sum_probs=14.1
Q ss_pred hhccCCCCCceeeccCCCcEEEEEe
Q psy7307 80 NTAKGDSGGPLLLQRPDKQWTIIGV 104 (117)
Q Consensus 80 ~~~~gdsg~pl~~~~~~~~~~l~Gi 104 (117)
.+..|.||+|++-.+ + .++||
T Consensus 100 ~~~~G~SGgpv~~~~--G--~vvGi 120 (120)
T PF13365_consen 100 DTRPGSSGGPVFDSD--G--RVVGI 120 (120)
T ss_dssp S-STTTTTSEEEETT--S--EEEEE
T ss_pred ccCCCcEeHhEECCC--C--EEEeC
Confidence 445799999997643 2 46675
No 18
>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=41.53 E-value=27 Score=24.06 Aligned_cols=26 Identities=27% Similarity=0.477 Sum_probs=20.8
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEeeeeCc
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVVSWGI 109 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~s~~~ 109 (117)
-...+|.||+|.+..+ .|+|=++..+
T Consensus 175 GGIvqGMSGSPI~qdG-----KLiGAVthvf 200 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG-----KLIGAVTHVF 200 (218)
T ss_pred CCEEecccCCCEEECC-----EEEEEEEEEE
Confidence 3568999999999876 8999777543
No 19
>PRK10898 serine endoprotease; Provisional
Probab=39.84 E-value=31 Score=25.38 Aligned_cols=23 Identities=26% Similarity=0.550 Sum_probs=17.3
Q ss_pred ccCCCCCceeeccCCCcEEEEEeeeeC
Q psy7307 82 AKGDSGGPLLLQRPDKQWTIIGVVSWG 108 (117)
Q Consensus 82 ~~gdsg~pl~~~~~~~~~~l~Gi~s~~ 108 (117)
-.|+|||||+-.+. .++||.++.
T Consensus 196 ~~GnSGGPl~n~~G----~vvGI~~~~ 218 (353)
T PRK10898 196 NHGNSGGALVNSLG----ELMGINTLS 218 (353)
T ss_pred CCCCCcceEECCCC----eEEEEEEEE
Confidence 46889999986432 689998754
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=39.74 E-value=24 Score=25.25 Aligned_cols=20 Identities=40% Similarity=0.765 Sum_probs=14.3
Q ss_pred cCCCCCceeeccCCCcEEEEEeee
Q psy7307 83 KGDSGGPLLLQRPDKQWTIIGVVS 106 (117)
Q Consensus 83 ~gdsg~pl~~~~~~~~~~l~Gi~s 106 (117)
-||||+|++..+. .|+||-+
T Consensus 207 ~GDSGSPVVt~dg----~liGVHT 226 (297)
T PF05579_consen 207 PGDSGSPVVTEDG----DLIGVHT 226 (297)
T ss_dssp GGCTT-EEEETTC-----EEEEEE
T ss_pred CCCCCCccCcCCC----CEEEEEe
Confidence 4899999998764 4888754
No 21
>PRK10139 serine endoprotease; Provisional
Probab=33.46 E-value=43 Score=25.62 Aligned_cols=23 Identities=35% Similarity=0.531 Sum_probs=17.5
Q ss_pred ccCCCCCceeeccCCCcEEEEEeeeeC
Q psy7307 82 AKGDSGGPLLLQRPDKQWTIIGVVSWG 108 (117)
Q Consensus 82 ~~gdsg~pl~~~~~~~~~~l~Gi~s~~ 108 (117)
-.|+|||||+-... .++||.++.
T Consensus 210 n~GnSGGpl~n~~G----~vIGi~~~~ 232 (455)
T PRK10139 210 NRGNSGGALLNLNG----ELIGINTAI 232 (455)
T ss_pred CCCCCcceEECCCC----eEEEEEEEE
Confidence 36899999996532 699998863
No 22
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=32.40 E-value=24 Score=21.30 Aligned_cols=22 Identities=27% Similarity=0.598 Sum_probs=16.4
Q ss_pred ccCCCCCceeeccCCCcEEEEEeeeeCc
Q psy7307 82 AKGDSGGPLLLQRPDKQWTIIGVVSWGI 109 (117)
Q Consensus 82 ~~gdsg~pl~~~~~~~~~~l~Gi~s~~~ 109 (117)
..++++.++... +|.||..||.
T Consensus 63 i~~~~~~~F~V~------ylnGVfAWG~ 84 (102)
T PF08838_consen 63 IEGDPEEYFKVD------YLNGVFAWGY 84 (102)
T ss_dssp ETTCCCEEEEEE------EEETTEEEEE
T ss_pred ecCCCCceEEEE------EEeeEEEEEe
Confidence 455666666655 7999999985
No 23
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=31.78 E-value=1.6e+02 Score=20.83 Aligned_cols=29 Identities=31% Similarity=0.546 Sum_probs=22.6
Q ss_pred CCCCcccCCCCCeeEEEcCCCcEEEEEEeecCC
Q psy7307 27 TSRQAQTGDSGGPLLLQRPDKQWTIIGVVSWGI 59 (117)
Q Consensus 27 ~~~~~C~~dsG~pl~~~~~~~~~~~vgI~s~~~ 59 (117)
...+++.|+||+|+.... . .++|+...+.
T Consensus 196 y~~dT~pG~SGSpv~~~~--~--~vigv~~~g~ 224 (251)
T COG3591 196 YDADTLPGSSGSPVLISK--D--EVIGVHYNGP 224 (251)
T ss_pred EEecccCCCCCCceEecC--c--eEEEEEecCC
Confidence 467899999999998763 2 5888887663
No 24
>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=31.72 E-value=34 Score=27.78 Aligned_cols=23 Identities=26% Similarity=0.628 Sum_probs=18.6
Q ss_pred HhhccCCCCCceeeccCCCcEEEEEee
Q psy7307 79 YNTAKGDSGGPLLLQRPDKQWTIIGVV 105 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~~~~~~~l~Gi~ 105 (117)
.+++.|+||+|++-... .|+|+.
T Consensus 628 nDitGGNSGSPvlN~~G----eLVGl~ 650 (698)
T PF10459_consen 628 NDITGGNSGSPVLNAKG----ELVGLA 650 (698)
T ss_pred cCcCCCCCCCccCCCCc----eEEEEe
Confidence 68899999999986543 688974
No 25
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=29.76 E-value=53 Score=24.08 Aligned_cols=23 Identities=26% Similarity=0.550 Sum_probs=17.1
Q ss_pred ccCCCCCceeeccCCCcEEEEEeeeeC
Q psy7307 82 AKGDSGGPLLLQRPDKQWTIIGVVSWG 108 (117)
Q Consensus 82 ~~gdsg~pl~~~~~~~~~~l~Gi~s~~ 108 (117)
-.|+|||||+-... .++||.+..
T Consensus 196 ~~GnSGGpl~n~~G----~vIGI~~~~ 218 (351)
T TIGR02038 196 NAGNSGGALINTNG----ELVGINTAS 218 (351)
T ss_pred CCCCCcceEECCCC----eEEEEEeee
Confidence 46889999986432 689997753
No 26
>PF00944 Peptidase_S3: Alphavirus core protein ; InterPro: IPR000930 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. Togavirin, also known as Sindbis virus core endopeptidase, is a serine protease resident at the N terminus of the p130 polyprotein of togaviruses []. The endopeptidase signature identifies the peptidase as belonging to the MEROPS peptidase family S3 (togavirin family, clan PA(S)). The polyprotein also includes structural proteins for the nucleocapsid core and for the glycoprotein spikes []. Togavirin is only active while part of the polyprotein, cleavage at a Trp-Ser bond resulting in total lack of activity []. Mutagenesis studies have identified the location of the His-Asp-Ser catalytic triad, and X-ray studies have revealed the protein fold to be similar to that of chymotrypsin [, ].; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YEW_D 1EP5_A 3J0C_F 1EP6_C 1WYK_D 1DYL_A 1VCQ_B 1VCP_B 1LD4_D 1KXA_A ....
Probab=29.33 E-value=37 Score=21.82 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=15.5
Q ss_pred ccCCCCCeeEEEcCCCcEEEEEEeec
Q psy7307 32 QTGDSGGPLLLQRPDKQWTIIGVVSW 57 (117)
Q Consensus 32 C~~dsG~pl~~~~~~~~~~~vgI~s~ 57 (117)
-.||||.|++.+ .++ .++|+--
T Consensus 104 ~~GDSGRpi~DN--sGr--VVaIVLG 125 (158)
T PF00944_consen 104 KPGDSGRPIFDN--SGR--VVAIVLG 125 (158)
T ss_dssp STTSTTEEEEST--TSB--EEEEEEE
T ss_pred CCCCCCCccCcC--CCC--EEEEEec
Confidence 358999999866 366 6666643
No 27
>KOG3939|consensus
Probab=25.77 E-value=71 Score=22.81 Aligned_cols=30 Identities=37% Similarity=0.412 Sum_probs=21.3
Q ss_pred HhhccCCCCCceeecc----------------CCCcEEEEEeeeeC
Q psy7307 79 YNTAKGDSGGPLLLQR----------------PDKQWTIIGVVSWG 108 (117)
Q Consensus 79 ~~~~~gdsg~pl~~~~----------------~~~~~~l~Gi~s~~ 108 (117)
+.++.+.|||+|+|-. .++..+++||+-=|
T Consensus 248 qGts~ETsGGlLIclP~eqaakfcaei~s~k~gegqAWIIGiVekg 293 (312)
T KOG3939|consen 248 QGTSAETSGGLLICLPREQAAKFCAEIKSPKNGEGQAWIIGIVEKG 293 (312)
T ss_pred cCCCccCCCceEEEccHHHHHHHHHHhcCCccCCCceEEEEEEecC
Confidence 5667788999998832 23457889987654
No 28
>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=24.12 E-value=88 Score=19.73 Aligned_cols=21 Identities=43% Similarity=0.744 Sum_probs=15.1
Q ss_pred cCCCCCceeeccCCCcEEEEEeeeeC
Q psy7307 83 KGDSGGPLLLQRPDKQWTIIGVVSWG 108 (117)
Q Consensus 83 ~gdsg~pl~~~~~~~~~~l~Gi~s~~ 108 (117)
-||-||+|.|+-. ++||++-|
T Consensus 89 PGdCGg~L~C~HG-----ViGi~Tag 109 (127)
T PF00947_consen 89 PGDCGGILRCKHG-----VIGIVTAG 109 (127)
T ss_dssp TT-TCSEEEETTC-----EEEEEEEE
T ss_pred CCCCCceeEeCCC-----eEEEEEeC
Confidence 5999999999742 77777643
No 29
>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=21.18 E-value=93 Score=23.38 Aligned_cols=23 Identities=39% Similarity=0.689 Sum_probs=16.6
Q ss_pred hccCCCCCceeeccCCCcEEEEEeeee
Q psy7307 81 TAKGDSGGPLLLQRPDKQWTIIGVVSW 107 (117)
Q Consensus 81 ~~~gdsg~pl~~~~~~~~~~l~Gi~s~ 107 (117)
.-.|+|||||+-.. + .++||.+.
T Consensus 176 i~~GnSGGpl~n~~--G--~viGI~~~ 198 (428)
T TIGR02037 176 INPGNSGGPLVNLR--G--EVIGINTA 198 (428)
T ss_pred CCCCCCCCceECCC--C--eEEEEEeE
Confidence 34689999998543 2 68898764
Done!