Query psy17339
Match_columns 384
No_of_seqs 407 out of 2216
Neff 9.1
Searched_HMMs 46136
Date Fri Aug 16 19:43:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17339.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17339hhsearch_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 5.9E-45 1.3E-49 327.9 23.1 231 76-377 1-232 (232)
2 KOG3627|consensus 100.0 9.5E-44 2E-48 326.0 24.1 238 73-379 10-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 5.6E-42 1.2E-46 308.5 21.8 228 75-374 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 1.3E-39 2.8E-44 290.9 20.9 219 76-374 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 6.6E-34 1.4E-38 255.6 15.4 246 72-382 29-282 (413)
6 PF03761 DUF316: Domain of unk 99.8 5.8E-20 1.2E-24 170.8 18.3 252 46-376 18-277 (282)
7 PF09342 DUF1986: Domain of un 99.5 2.3E-13 4.9E-18 117.7 14.5 116 84-271 13-131 (267)
8 COG3591 V8-like Glu-specific e 99.2 1.1E-10 2.4E-15 103.7 13.1 199 149-379 48-251 (251)
9 TIGR02037 degP_htrA_DO peripla 98.5 9.7E-06 2.1E-10 79.9 19.7 143 163-352 56-199 (428)
10 cd00190 Tryp_SPc Trypsin-like 98.5 1.1E-07 2.4E-12 85.0 4.1 43 140-184 2-44 (232)
11 smart00020 Tryp_SPc Trypsin-li 98.3 4.2E-07 9.1E-12 81.3 4.4 43 140-184 3-45 (229)
12 TIGR02038 protease_degS peripl 98.2 0.00012 2.5E-09 70.2 19.0 142 164-353 77-219 (351)
13 PF00089 Trypsin: Trypsin; In 98.2 8.5E-07 1.8E-11 78.6 4.0 42 140-183 2-43 (220)
14 PF13365 Trypsin_2: Trypsin-li 98.2 8.4E-06 1.8E-10 65.0 9.3 21 167-187 1-22 (120)
15 PRK10139 serine endoprotease; 98.2 8.3E-05 1.8E-09 73.5 17.5 142 164-352 89-232 (455)
16 PRK10898 serine endoprotease; 98.2 0.00033 7.1E-09 67.1 20.6 142 164-353 77-219 (353)
17 PRK10942 serine endoprotease; 98.1 0.00014 3E-09 72.3 16.7 142 164-352 110-253 (473)
18 KOG3627|consensus 97.6 7.5E-05 1.6E-09 68.1 4.3 45 139-184 13-57 (256)
19 COG5640 Secreted trypsin-like 97.5 3E-05 6.5E-10 71.4 0.5 50 139-188 33-84 (413)
20 PF02395 Peptidase_S6: Immunog 96.9 0.02 4.3E-07 59.9 13.7 65 169-255 69-133 (769)
21 COG3591 V8-like Glu-specific e 96.6 0.0026 5.6E-08 57.1 4.4 45 82-128 44-88 (251)
22 PF03761 DUF316: Domain of unk 96.5 0.0027 5.8E-08 58.9 3.8 47 140-186 43-90 (282)
23 PF00548 Peptidase_C3: 3C cyst 95.0 0.18 3.8E-06 43.1 8.8 151 161-353 21-171 (172)
24 PF09342 DUF1986: Domain of un 94.0 0.076 1.6E-06 47.0 4.3 23 162-184 25-47 (267)
25 PF13365 Trypsin_2: Trypsin-li 93.4 0.025 5.5E-07 44.5 0.3 22 106-127 1-23 (120)
26 PF00863 Peptidase_C4: Peptida 90.4 9.4 0.0002 34.2 13.0 150 169-369 35-186 (235)
27 COG0265 DegQ Trypsin-like seri 86.1 32 0.00069 32.8 16.9 146 164-355 71-217 (347)
28 PF05416 Peptidase_C37: Southa 84.6 3.5 7.5E-05 39.6 7.0 142 168-353 382-527 (535)
29 PF00947 Pico_P2A: Picornaviru 76.1 2 4.4E-05 34.2 2.1 36 326-370 87-122 (127)
30 KOG1320|consensus 62.2 1.7E+02 0.0037 29.2 12.5 47 71-124 61-107 (473)
31 PF05579 Peptidase_S32: Equine 58.8 5.5 0.00012 36.0 1.5 23 328-353 207-229 (297)
32 PF05580 Peptidase_S55: SpoIVB 55.9 14 0.0003 32.5 3.4 25 325-353 176-200 (218)
33 PF02907 Peptidase_S29: Hepati 50.3 11 0.00023 30.5 1.7 21 327-350 106-126 (148)
34 PF10459 Peptidase_S46: Peptid 49.6 10 0.00022 39.7 2.0 22 165-186 47-69 (698)
35 KOG1421|consensus 42.2 2.4E+02 0.0052 29.5 10.0 86 163-268 82-170 (955)
36 TIGR02038 protease_degS peripl 34.2 36 0.00079 32.6 3.0 25 103-127 77-102 (351)
37 PF00944 Peptidase_S3: Alphavi 32.4 11 0.00024 30.4 -0.7 24 327-353 104-127 (158)
38 TIGR02037 degP_htrA_DO peripla 30.4 22 0.00047 35.1 0.8 26 102-127 56-82 (428)
39 TIGR02860 spore_IV_B stage IV 27.3 50 0.0011 32.2 2.6 44 325-378 356-399 (402)
40 PF14903 WG_beta_rep: WG conta 24.7 1E+02 0.0022 17.7 2.8 24 215-238 9-32 (35)
41 PF08048 RepA1_leader: Tap Rep 22.5 12 0.00026 20.2 -1.4 16 1-16 1-16 (25)
42 PF00949 Peptidase_S7: Peptida 21.2 54 0.0012 26.6 1.3 26 325-353 93-118 (132)
43 PRK10898 serine endoprotease; 21.1 80 0.0017 30.3 2.7 24 104-127 78-102 (353)
44 TIGR03475 tap_IncFII_lead RepA 20.8 14 0.0003 20.2 -1.4 15 1-15 1-15 (26)
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=5.9e-45 Score=327.88 Aligned_cols=231 Identities=42% Similarity=0.859 Sum_probs=194.7
Q ss_pred EecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCcccccceeEEEE
Q psy17339 76 IVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEIQ 155 (384)
Q Consensus 76 I~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~v~ 155 (384)
|+||+++.+++|||+|+|+... ..+.|+||||+++||||||||+...
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~----~~~~C~GtlIs~~~VLTaAhC~~~~----------------------------- 47 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTG----GRHFCGGSLISPRWVLTAAHCVYSS----------------------------- 47 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccC----CcEEEEEEEeeCCEEEECHHhcCCC-----------------------------
Confidence 6899999999999999998753 4567888888888888888887653
Q ss_pred EeecCCCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEE
Q psy17339 156 VRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVV 235 (384)
Q Consensus 156 ~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl 235 (384)
....+.|++|.......+...+.+.|.++++||.|+.. ...+|||||
T Consensus 48 --------------------------------~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~-~~~~DiAll 94 (232)
T cd00190 48 --------------------------------APSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHPNYNPS-TYDNDIALL 94 (232)
T ss_pred --------------------------------CCccEEEEeCcccccCCCCceEEEEEEEEEECCCCCCC-CCcCCEEEE
Confidence 24567888888776654445678899999999999887 788999999
Q ss_pred EEcCCcCCCCceeeeccCCCC-CCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCe
Q psy17339 236 KIRGNIEFNQYVQPICIPDRD-NAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSM 314 (384)
Q Consensus 236 ~L~~pv~~~~~v~picLp~~~-~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~ 314 (384)
||++|+.++++++|+|||... ....+..+.++|||..... ...+..+++..+.+++...|... +.. ...+.+++
T Consensus 95 ~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~--~~~~~~~~~~~~~~~~~~~C~~~--~~~-~~~~~~~~ 169 (232)
T cd00190 95 KLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEG--GPLPDVLQEVNVPIVSNAECKRA--YSY-GGTITDNM 169 (232)
T ss_pred EECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCC--CCCCceeeEEEeeeECHHHhhhh--ccC-cccCCCce
Confidence 999999999999999999885 5777899999999987654 23467899999999999999984 321 24677899
Q ss_pred EEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechhhHHHHHHH
Q psy17339 315 LCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSYYTKWINDR 377 (384)
Q Consensus 315 ~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~~~~WI~~~ 377 (384)
+|++......+.|.|||||||++..+++++|+||+|++..|.....|++|++|..|++||+++
T Consensus 170 ~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 170 LCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred EeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 999876556789999999999999999999999999999998767899999999999999863
No 2
>KOG3627|consensus
Probab=100.00 E-value=9.5e-44 Score=326.04 Aligned_cols=238 Identities=42% Similarity=0.854 Sum_probs=190.2
Q ss_pred cceEecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCcccccceeE
Q psy17339 73 NVKIVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKV 152 (384)
Q Consensus 73 ~~rI~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 152 (384)
..||+||.++.+++|||+|+|..+.. ..+.|||+||+++||||||||+....
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~---~~~~Cggsli~~~~vltaaHC~~~~~------------------------- 61 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGN---GRHLCGGSLISPRWVLTAAHCVKGAS------------------------- 61 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCC---cceeeeeEEeeCCEEEEChhhCCCCC-------------------------
Confidence 47999999999999999999998731 25788888888888888888886641
Q ss_pred EEEEeecCCCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCC-Ccc--eEEEEEEEEEEcCCCCCCCCCC
Q psy17339 153 EIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGV-DKF--EKTFKVEKAVLHHRFRKEGTHS 229 (384)
Q Consensus 153 ~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~-~~~--~~~~~v~~i~~hp~y~~~~~~~ 229 (384)
.. .+.|++|.+..... ... .....+.++++||+|+.. ...
T Consensus 62 -----------------------------------~~-~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i~H~~y~~~-~~~ 104 (256)
T KOG3627|consen 62 -----------------------------------AS-LYTVRLGEHDINLSVSEGEEQLVGDVEKIIVHPNYNPR-TLE 104 (256)
T ss_pred -----------------------------------Cc-ceEEEECccccccccccCchhhhceeeEEEECCCCCCC-CCC
Confidence 11 45555565433222 111 234457788899999987 656
Q ss_pred -CceEEEEEcCCcCCCCceeeeccCCCCC---CCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCC
Q psy17339 230 -NDIAVVKIRGNIEFNQYVQPICIPDRDN---AAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGN 305 (384)
Q Consensus 230 -~DIALl~L~~pv~~~~~v~picLp~~~~---~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~ 305 (384)
||||||+|++++.|++.|+|||||.... ...+..+.++|||.+... ....+..|+++++++++.++|... +..
T Consensus 105 ~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~-~~~~~~~L~~~~v~i~~~~~C~~~--~~~ 181 (256)
T KOG3627|consen 105 NNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESG-GGPLPDTLQEVDVPIISNSECRRA--YGG 181 (256)
T ss_pred CCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCC-CCCCCceeEEEEEeEcChhHhccc--ccC
Confidence 9999999999999999999999986542 445589999999988764 234578899999999999999984 331
Q ss_pred CCCCccCCeEEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCC-CCCCCCCeEEEechhhHHHHHHHHH
Q psy17339 306 SNQNILDSMLCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDG-CAKKNKPGVYTRVSYYTKWINDRIQ 379 (384)
Q Consensus 306 ~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~-c~~~~~p~vyt~V~~~~~WI~~~i~ 379 (384)
. ..+.+.|+||+...+..++|+|||||||++..+++|+++||+|||.. |+....|++||+|+.|.+||++.+.
T Consensus 182 ~-~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 182 L-GTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKENIG 255 (256)
T ss_pred c-cccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHHHhc
Confidence 1 14667799999766677899999999999998779999999999997 9987899999999999999999875
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=100.00 E-value=5.6e-42 Score=308.47 Aligned_cols=228 Identities=46% Similarity=0.935 Sum_probs=190.3
Q ss_pred eEecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCcccccceeEEE
Q psy17339 75 KIVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEI 154 (384)
Q Consensus 75 rI~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~v 154 (384)
||+||+++.+++|||+|.++... ..+.|+||||++++|||||||+...
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~----~~~~C~GtlIs~~~VLTaahC~~~~---------------------------- 48 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRG----GRHFCGGSLISPRWVLTAAHCVYGS---------------------------- 48 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcC----CCcEEEEEEecCCEEEECHHHcCCC----------------------------
Confidence 68999999999999999998752 3677888888888888888887653
Q ss_pred EEeecCCCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEE
Q psy17339 155 QVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAV 234 (384)
Q Consensus 155 ~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIAL 234 (384)
....+.|++|..+..... ....+.|.+++.||+|+.. ...+||||
T Consensus 49 ---------------------------------~~~~~~v~~g~~~~~~~~-~~~~~~v~~~~~~p~~~~~-~~~~DiAl 93 (229)
T smart00020 49 ---------------------------------DPSNIRVRLGSHDLSSGE-EGQVIKVSKVIIHPNYNPS-TYDNDIAL 93 (229)
T ss_pred ---------------------------------CCcceEEEeCcccCCCCC-CceEEeeEEEEECCCCCCC-CCcCCEEE
Confidence 235688888887664422 2277899999999999876 78899999
Q ss_pred EEEcCCcCCCCceeeeccCCCC-CCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCC
Q psy17339 235 VKIRGNIEFNQYVQPICIPDRD-NAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDS 313 (384)
Q Consensus 235 l~L~~pv~~~~~v~picLp~~~-~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~ 313 (384)
|+|++|+.+++.++|+|||... ....+..+.++|||..... .......++...+.+++.+.|... +.. ...+.++
T Consensus 94 l~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~-~~~~~~~~~~~~~~~~~~~~C~~~--~~~-~~~~~~~ 169 (229)
T smart00020 94 LKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEG-AGSLPDTLQEVNVPIVSNATCRRA--YSG-GGAITDN 169 (229)
T ss_pred EEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCC-CCcCCCEeeEEEEEEeCHHHhhhh--hcc-ccccCCC
Confidence 9999999999999999999874 4667889999999987652 334567899999999999999983 331 1357889
Q ss_pred eEEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechhhHHHH
Q psy17339 314 MLCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSYYTKWI 374 (384)
Q Consensus 314 ~~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~~~~WI 374 (384)
++|++......+.|.|||||||++..+ +|+|+||+|+|..|...+.|.+|++|.+|++||
T Consensus 170 ~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 170 MLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred cEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 999987654678999999999999887 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=100.00 E-value=1.3e-39 Score=290.86 Aligned_cols=219 Identities=43% Similarity=0.845 Sum_probs=184.6
Q ss_pred EecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCcccccceeEEEE
Q psy17339 76 IVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEIQ 155 (384)
Q Consensus 76 I~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~v~ 155 (384)
|+||.++++++|||+|.++... ..++|+|+||+++||||||||+..
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~----~~~~C~G~li~~~~vLTaahC~~~------------------------------ 46 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSN----GRFFCTGTLISPRWVLTAAHCVDG------------------------------ 46 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETT----TEEEEEEEEEETTEEEEEGGGHTS------------------------------
T ss_pred CCCCEECCCCCCCeEEEEeeCC----CCeeEeEEeccccccccccccccc------------------------------
Confidence 7899999999999999999863 267788888888887777777755
Q ss_pred EeecCCCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEE
Q psy17339 156 VRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVV 235 (384)
Q Consensus 156 ~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl 235 (384)
...+.+++|...........+.+.+.+++.||.|+.. ...+|||||
T Consensus 47 ---------------------------------~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~~~~-~~~~DiAll 92 (220)
T PF00089_consen 47 ---------------------------------ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKYDPS-TYDNDIALL 92 (220)
T ss_dssp ---------------------------------GGSEEEEESESBTTSTTTTSEEEEEEEEEEETTSBTT-TTTTSEEEE
T ss_pred ---------------------------------ccccccccccccccccccccccccccccccccccccc-ccccccccc
Confidence 2357778888544444444688999999999999987 578999999
Q ss_pred EEcCCcCCCCceeeeccCCCC-CCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCe
Q psy17339 236 KIRGNIEFNQYVQPICIPDRD-NAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSM 314 (384)
Q Consensus 236 ~L~~pv~~~~~v~picLp~~~-~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~ 314 (384)
+|++|+.+.+.++|+||+... ....+..+.++|||..... . ....++...+.+++.+.|... +. ..+.+.+
T Consensus 93 ~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~-~--~~~~~~~~~~~~~~~~~c~~~--~~---~~~~~~~ 164 (220)
T PF00089_consen 93 KLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDN-G--YSSNLQSVTVPVVSRKTCRSS--YN---DNLTPNM 164 (220)
T ss_dssp EESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTT-S--BTSBEEEEEEEEEEHHHHHHH--TT---TTSTTTE
T ss_pred ccccccccccccccccccccccccccccccccccccccccc-c--ccccccccccccccccccccc--cc---ccccccc
Confidence 999999999999999999965 4678899999999997655 2 456899999999999999983 43 3478899
Q ss_pred EEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechhhHHHH
Q psy17339 315 LCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSYYTKWI 374 (384)
Q Consensus 315 ~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~~~~WI 374 (384)
+|++.. +..+.|.|||||||++.++ +|+||++++..|...+.|.+|++|+.|++||
T Consensus 165 ~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 165 ICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp EEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred cccccc-cccccccccccccccccee---eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 999875 5578999999999999764 7999999999998887899999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.6e-34 Score=255.59 Aligned_cols=246 Identities=29% Similarity=0.445 Sum_probs=174.3
Q ss_pred CcceEecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCccccccee
Q psy17339 72 ANVKIVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFK 151 (384)
Q Consensus 72 ~~~rI~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 151 (384)
...||+||..|+.++||++|+|..+..+.....+|||+++..|||||||||+.....
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~----------------------- 85 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSP----------------------- 85 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCC-----------------------
Confidence 578999999999999999999987654333456788888888888888888765420
Q ss_pred EEEEEeecCCCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCc
Q psy17339 152 VEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSND 231 (384)
Q Consensus 152 ~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~D 231 (384)
.......|..+..+. ...+...+.+++.|..|... ++.||
T Consensus 86 -----------------------------------is~d~~~vv~~l~d~----Sq~~rg~vr~i~~~efY~~~-n~~ND 125 (413)
T COG5640 86 -----------------------------------ISSDVNRVVVDLNDS----SQAERGHVRTIYVHEFYSPG-NLGND 125 (413)
T ss_pred -----------------------------------ccccceEEEeccccc----ccccCcceEEEeeecccccc-cccCc
Confidence 112233444443332 23567789999999999987 99999
Q ss_pred eEEEEEcCCcCCC-CceeeeccCCC--CCCCCCCeEEEEEeccCCCCCCCcc---cccceEEEEEEecccccccccccCC
Q psy17339 232 IAVVKIRGNIEFN-QYVQPICIPDR--DNAAASDWCVVTGWGAQNAESIDDI---SNTLRAATVKVIDQNTCRSSAVYGN 305 (384)
Q Consensus 232 IALl~L~~pv~~~-~~v~picLp~~--~~~~~~~~~~v~GwG~~~~~~~~~~---~~~l~~~~~~i~~~~~C~~~~~~~~ 305 (384)
||+++|.++.... ..+...--++. .+..........+|+.+........ ...+++..+..++...|.....-..
T Consensus 126 ~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e~~v~fv~~stc~~~~g~an 205 (413)
T COG5640 126 IAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKGCAN 205 (413)
T ss_pred ceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccceeeeeeeeeechHHhhhhccccc
Confidence 9999999976522 11121111221 1233444566677876655422221 2479999999999999987321010
Q ss_pred C-CCCccCCeEEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCC-CCCCCCCeEEEechhhHHHHHHHHHhhh
Q psy17339 306 S-NQNILDSMLCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDG-CAKKNKPGVYTRVSYYTKWINDRIQMLQ 382 (384)
Q Consensus 306 ~-~~~~~~~~~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~-c~~~~~p~vyt~V~~~~~WI~~~i~~~~ 382 (384)
. .....-.-+|++.. .+++|+||||||++.+.+....++||+|||.+ |+....|+|||+|+.|.+||..+|+.+.
T Consensus 206 ~~dg~~~lT~~cag~~--~~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~l~ 282 (413)
T COG5640 206 ASDGATGLTGFCAGRP--PKDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTNGLS 282 (413)
T ss_pred cCCCCCCccceecCCC--CcccccCCCCCceEEeCCCccEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhcCCC
Confidence 0 01111123999866 47999999999999999888899999999995 9999999999999999999999887654
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.85 E-value=5.8e-20 Score=170.76 Aligned_cols=252 Identities=26% Similarity=0.459 Sum_probs=154.1
Q ss_pred eeeeecCCCccCcCCCccccCCCCcCCcceEecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhccccccc
Q psy17339 46 ELHDLFTHRRAMTCGSRVVNHEPQRAANVKIVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQG 125 (384)
Q Consensus 46 ~~~~~~~~~~~~~Cg~~~~~~~~~~~~~~rI~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~ 125 (384)
+|.+..+..++.+||++.. ....++.+|..++.++.||+|.+....... ....++|||||+||||||+||+..
T Consensus 18 kLt~eEN~~rl~~CG~~~~------~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~-~~~~~~gtlIS~RHiLtss~~~~~ 90 (282)
T PF03761_consen 18 KLTEEENEERLETCGKKKL------PYPSKVFNGTPAESGEAPWAVSVYTKNHNE-GNYFSTGTLISPRHILTSSHCVMN 90 (282)
T ss_pred CCCHHHHHHHHHhcCCCCC------CCcccccCCcccccCCCCCEEEEEeccCcc-cceecceEEeccCeEEEeeeEEEe
Confidence 3334444556778997631 245678999999999999999999875432 446789999999999999999975
Q ss_pred ccccceEEEecccccCCCcccccceeEEEEEeecCCCCceeeEEE---EecCCEEEecccccCCCCCceEEEEEeeeccC
Q psy17339 126 ISKSKLRIIVGKHNLNGVDKFEKTFKVEIQVRSSTGQGEHQCGGA---IISDTVILTAAHCLQGISKSKLRIIVGKHNLN 202 (384)
Q Consensus 126 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~v~~~~~~~~~~~~C~Gt---LIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~ 202 (384)
... .+ +. ........|.+- |+-|.-+ .+.+.+. ....
T Consensus 91 ~~~---~W-~~----------------------~~~~~~~~C~~~~~~l~vP~~~-----------l~~~~v~--~~~~- 130 (282)
T PF03761_consen 91 DKS---KW-LN----------------------GEEFDNKKCEGNNNHLIVPEEV-----------LSKIDVR--CCNC- 130 (282)
T ss_pred ccc---cc-cc----------------------CcccccceeeCCCceEEeCHHH-----------hccEEEE--eecc-
Confidence 321 00 00 111122334432 1111100 1122220 0000
Q ss_pred CCCcceEEEEEEEEEEcCCC---CCCCCCCCceEEEEEcCCcCCCCceeeeccCCCC-CCCCCCeEEEEEeccCCCCCCC
Q psy17339 203 GVDKFEKTFKVEKAVLHHRF---RKEGTHSNDIAVVKIRGNIEFNQYVQPICIPDRD-NAAASDWCVVTGWGAQNAESID 278 (384)
Q Consensus 203 ~~~~~~~~~~v~~i~~hp~y---~~~~~~~~DIALl~L~~pv~~~~~v~picLp~~~-~~~~~~~~~v~GwG~~~~~~~~ 278 (384)
..........+.++++--.- .......++++||+|+++ ++....|+|||+.. ....+..+.+.|+ ..
T Consensus 131 ~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~~~~~~~~~~~yg~----~~--- 201 (282)
T PF03761_consen 131 FSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSSTNWEKGDEVDVYGF----NS--- 201 (282)
T ss_pred cccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCccccccCceEEEeec----CC---
Confidence 01111233456666553222 111145579999999999 67889999999877 4556667777777 11
Q ss_pred cccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecC-CCCC
Q psy17339 279 DISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGD-GCAK 357 (384)
Q Consensus 279 ~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~-~c~~ 357 (384)
...+....+.+.....|.. .+| .....|.||+||||+...+++|+|+||.+.+. .|..
T Consensus 202 --~~~~~~~~~~i~~~~~~~~--------------~~~-----~~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~ 260 (282)
T PF03761_consen 202 --TGKLKHRKLKITNCTKCAY--------------SIC-----TKQYSCKGDRGGPLVKNINGRWTLIGVGASGNYECNK 260 (282)
T ss_pred --CCeEEEEEEEEEEeeccce--------------eEe-----cccccCCCCccCeEEEEECCCEEEEEEEccCCCcccc
Confidence 2234444444443322221 122 24578999999999999999999999998776 3432
Q ss_pred CCCCeEEEechhhHHHHHH
Q psy17339 358 KNKPGVYTRVSYYTKWIND 376 (384)
Q Consensus 358 ~~~p~vyt~V~~~~~WI~~ 376 (384)
....|.+|..|.+=|-+
T Consensus 261 --~~~~f~~v~~~~~~IC~ 277 (282)
T PF03761_consen 261 --NNSYFFNVSWYQDEICE 277 (282)
T ss_pred --cccEEEEHHHhhhhhcc
Confidence 26789999888876543
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.53 E-value=2.3e-13 Score=117.72 Aligned_cols=116 Identities=22% Similarity=0.465 Sum_probs=88.7
Q ss_pred CCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccccceEEEecccccCCCcccccceeEEEEEeecCCCC
Q psy17339 84 YGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEIQVRSSTGQG 163 (384)
Q Consensus 84 ~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~v~~~~~~~~~ 163 (384)
.-.|||.|.|+.. +.+.|+|+||.+.|||++..|+.+..
T Consensus 13 ~y~WPWlA~IYvd-----G~~~CsgvLlD~~WlLvsssCl~~I~------------------------------------ 51 (267)
T PF09342_consen 13 DYHWPWLADIYVD-----GRYWCSGVLLDPHWLLVSSSCLRGIS------------------------------------ 51 (267)
T ss_pred cccCcceeeEEEc-----CeEEEEEEEeccceEEEeccccCCcc------------------------------------
Confidence 3459999999987 88889999999999999999987754
Q ss_pred ceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccC--CCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCc
Q psy17339 164 EHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLN--GVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNI 241 (384)
Q Consensus 164 ~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~--~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv 241 (384)
.....+.|.+|..... -..+.+|.++|..+.. ....+++||.|++|+
T Consensus 52 -----------------------L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~--------V~~S~v~LLHL~~~~ 100 (267)
T PF09342_consen 52 -----------------------LSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKD--------VPESNVLLLHLEQPA 100 (267)
T ss_pred -----------------------cccceEEEEecCcceecccCCChheEEEeeeeee--------ccccceeeeeecCcc
Confidence 2345677888875432 2355677777776554 234689999999999
Q ss_pred CCCCceeeeccCCCC-CCCCCCeEEEEEecc
Q psy17339 242 EFNQYVQPICIPDRD-NAAASDWCVVTGWGA 271 (384)
Q Consensus 242 ~~~~~v~picLp~~~-~~~~~~~~~v~GwG~ 271 (384)
.|+.+|+|..||+.. .......|..+|--.
T Consensus 101 ~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 101 NFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cceeeecccccccccCCCCCCCceEEEEccc
Confidence 999999999999744 455566899888543
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.25 E-value=1.1e-10 Score=103.67 Aligned_cols=199 Identities=18% Similarity=0.190 Sum_probs=112.7
Q ss_pred ceeEEEEEeecCCCCceeeEEEEecCCEEEecccccCCCCCce--EEEEE-eeeccCCCCcceEEEEEEEEEEcCC-CCC
Q psy17339 149 TFKVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISKSK--LRIIV-GKHNLNGVDKFEKTFKVEKAVLHHR-FRK 224 (384)
Q Consensus 149 ~~~~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~--~~v~~-g~~~~~~~~~~~~~~~v~~i~~hp~-y~~ 224 (384)
+||+..-.......+..-|+++||+++.||||+||+....... +.+.. |.. ........+........|. +..
T Consensus 48 ~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~G~~~~~~~p~g~~---~~~~~~~~~~~~~~~~~~g~~~~ 124 (251)
T COG3591 48 QFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDYGEDDIAAAPPGVN---SDGGPFYGITKIEIRVYPGELYK 124 (251)
T ss_pred CCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCCChhhhhhcCCccc---CCCCCCCceeeEEEEecCCceec
Confidence 3444433355566666778889999999999999997644321 22221 111 1111112223333333444 444
Q ss_pred CCCCCCceEEEEEcCCcCCCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccC
Q psy17339 225 EGTHSNDIAVVKIRGNIEFNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYG 304 (384)
Q Consensus 225 ~~~~~~DIALl~L~~pv~~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~ 304 (384)
......|+..+.|+....+........++.......+....++||-..... .++. .+.|...
T Consensus 125 ~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~-------~~~~-------~e~t~~v---- 186 (251)
T COG3591 125 EDGASYDVGEAALESGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPN-------IGTM-------WESTGKV---- 186 (251)
T ss_pred cCCceeeccHHHhccCCCccccccccccccccccccCceeEEEeccCCCCc-------ceeE-------eeeccee----
Confidence 335667888888885555555666555555555566666889998544331 1111 1112211
Q ss_pred CCCCCccCCeEEeeecCCCcCCCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEech-hhHHHHHHHHH
Q psy17339 305 NSNQNILDSMLCAGYLNGGIDACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVS-YYTKWINDRIQ 379 (384)
Q Consensus 305 ~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~-~~~~WI~~~i~ 379 (384)
..+....+ .-..+++.|+||+|++...+ +++||.+-|..-.......-.+|+. .+++||++.++
T Consensus 187 ---~~~~~~~l-----~y~~dT~pG~SGSpv~~~~~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 187 ---NSIKGNKL-----FYDADTLPGSSGSPVLISKD---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred ---EEEecceE-----EEEecccCCCCCCceEecCc---eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 01111111 11458899999999998776 8999999887432223344456664 57899998763
No 9
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=98.53 E-value=9.7e-06 Score=79.85 Aligned_cols=143 Identities=24% Similarity=0.355 Sum_probs=84.8
Q ss_pred CceeeEEEEecCC-EEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCc
Q psy17339 163 GEHQCGGAIISDT-VILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNI 241 (384)
Q Consensus 163 ~~~~C~GtLIs~~-~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv 241 (384)
....++|.+|+++ +|||++|++.+ ...+.|.+.. ...+..+-+..+ ...||||||++.+
T Consensus 56 ~~~~GSGfii~~~G~IlTn~Hvv~~--~~~i~V~~~~---------~~~~~a~vv~~d--------~~~DlAllkv~~~- 115 (428)
T TIGR02037 56 VRGLGSGVIISADGYILTNNHVVDG--ADEITVTLSD---------GREFKAKLVGKD--------PRTDIAVLKIDAK- 115 (428)
T ss_pred ccceeeEEEECCCCEEEEcHHHcCC--CCeEEEEeCC---------CCEEEEEEEEec--------CCCCEEEEEecCC-
Confidence 4578999999986 99999999975 4556665432 122333322222 2359999999865
Q ss_pred CCCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecC
Q psy17339 242 EFNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLN 321 (384)
Q Consensus 242 ~~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~ 321 (384)
..+.++.|.+......++.+.++|+.... ........+.-.... . .. ......++=.
T Consensus 116 ---~~~~~~~l~~~~~~~~G~~v~aiG~p~g~-------~~~~t~G~vs~~~~~---~---~~---~~~~~~~i~t---- 172 (428)
T TIGR02037 116 ---KNLPVIKLGDSDKLRVGDWVLAIGNPFGL-------GQTVTSGIVSALGRS---G---LG---IGDYENFIQT---- 172 (428)
T ss_pred ---CCceEEEccCCCCCCCCCEEEEEECCCcC-------CCcEEEEEEEecccC---c---cC---CCCccceEEE----
Confidence 24667888766567899999999985321 111212112111110 0 00 0001111111
Q ss_pred CCcCCCCCCccCeeEEEeCCeEEEEEEEEec
Q psy17339 322 GGIDACGGDSGGPLACKIGGRFVLSGVVSWG 352 (384)
Q Consensus 322 ~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g 352 (384)
+...-+|.|||||+...+ .++||.+..
T Consensus 173 -da~i~~GnSGGpl~n~~G---~viGI~~~~ 199 (428)
T TIGR02037 173 -DAAINPGNSGGPLVNLRG---EVIGINTAI 199 (428)
T ss_pred -CCCCCCCCCCCceECCCC---eEEEEEeEE
Confidence 234567999999996554 899998764
No 10
>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=98.48 E-value=1.1e-07 Score=84.96 Aligned_cols=43 Identities=35% Similarity=0.702 Sum_probs=37.9
Q ss_pred cCCCcccccceeEEEEEeecCCCCceeeEEEEecCCEEEeccccc
Q psy17339 140 LNGVDKFEKTFKVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCL 184 (384)
Q Consensus 140 ~~g~~~~~~~~~~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~ 184 (384)
++|.+.....|||.+.+.... ..+.|+|+||+++||||||||+
T Consensus 2 ~~G~~~~~~~~Pw~v~i~~~~--~~~~C~GtlIs~~~VLTaAhC~ 44 (232)
T cd00190 2 VGGSEAKIGSFPWQVSLQYTG--GRHFCGGSLISPRWVLTAAHCV 44 (232)
T ss_pred cCCeECCCCCCCCEEEEEccC--CcEEEEEEEeeCCEEEECHHhc
Confidence 567888889999999887764 6899999999999999999995
No 11
>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=98.34 E-value=4.2e-07 Score=81.27 Aligned_cols=43 Identities=35% Similarity=0.690 Sum_probs=37.8
Q ss_pred cCCCcccccceeEEEEEeecCCCCceeeEEEEecCCEEEeccccc
Q psy17339 140 LNGVDKFEKTFKVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCL 184 (384)
Q Consensus 140 ~~g~~~~~~~~~~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~ 184 (384)
.+|.+.....|||.+.+.... ..+.|+|+||++++|||||||+
T Consensus 3 ~~G~~~~~~~~Pw~~~i~~~~--~~~~C~GtlIs~~~VLTaahC~ 45 (229)
T smart00020 3 VGGSEANIGSFPWQVSLQYRG--GRHFCGGSLISPRWVLTAAHCV 45 (229)
T ss_pred cCCCcCCCCCCCcEEEEEEcC--CCcEEEEEEecCCEEEECHHHc
Confidence 577888889999999887654 6899999999999999999995
No 12
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=98.25 E-value=0.00012 Score=70.18 Aligned_cols=142 Identities=20% Similarity=0.240 Sum_probs=80.8
Q ss_pred ceeeEEEEecCC-EEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcC
Q psy17339 164 EHQCGGAIISDT-VILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIE 242 (384)
Q Consensus 164 ~~~C~GtLIs~~-~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~ 242 (384)
....+|.+|+++ +|||.+|.+.. ...+.|.+.. ...+..+-+.. ....|+||||++.+-
T Consensus 77 ~~~GSG~vi~~~G~IlTn~HVV~~--~~~i~V~~~d---------g~~~~a~vv~~--------d~~~DlAvlkv~~~~- 136 (351)
T TIGR02038 77 QGLGSGVIMSKEGYILTNYHVIKK--ADQIVVALQD---------GRKFEAELVGS--------DPLTDLAVLKIEGDN- 136 (351)
T ss_pred cceEEEEEEeCCeEEEecccEeCC--CCEEEEEECC---------CCEEEEEEEEe--------cCCCCEEEEEecCCC-
Confidence 357899999977 99999999965 4456665422 12223332222 234699999998642
Q ss_pred CCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecCC
Q psy17339 243 FNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLNG 322 (384)
Q Consensus 243 ~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~ 322 (384)
+.++.+........++.+.+.|+.... ........+.-+... .+. ..-....+- .
T Consensus 137 ----~~~~~l~~s~~~~~G~~V~aiG~P~~~-------~~s~t~GiIs~~~r~------~~~---~~~~~~~iq-----t 191 (351)
T TIGR02038 137 ----LPTIPVNLDRPPHVGDVVLAIGNPYNL-------GQTITQGIISATGRN------GLS---SVGRQNFIQ-----T 191 (351)
T ss_pred ----CceEeccCcCccCCCCEEEEEeCCCCC-------CCcEEEEEEEeccCc------ccC---CCCcceEEE-----E
Confidence 334455443357889999999985321 111222222111110 000 000011111 1
Q ss_pred CcCCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 323 GIDACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 323 ~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
+....+|.|||||+..++ .++||.+...
T Consensus 192 da~i~~GnSGGpl~n~~G---~vIGI~~~~~ 219 (351)
T TIGR02038 192 DAAINAGNSGGALINTNG---ELVGINTASF 219 (351)
T ss_pred CCccCCCCCcceEECCCC---eEEEEEeeee
Confidence 335568999999997654 8999987643
No 13
>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=98.24 E-value=8.5e-07 Score=78.55 Aligned_cols=42 Identities=36% Similarity=0.583 Sum_probs=38.1
Q ss_pred cCCCcccccceeEEEEEeecCCCCceeeEEEEecCCEEEecccc
Q psy17339 140 LNGVDKFEKTFKVEIQVRSSTGQGEHQCGGAIISDTVILTAAHC 183 (384)
Q Consensus 140 ~~g~~~~~~~~~~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC 183 (384)
.+|..+..++|||.+.+....+ .++|+|+||+++||||||||
T Consensus 2 ~~g~~~~~~~~p~~v~i~~~~~--~~~C~G~li~~~~vLTaahC 43 (220)
T PF00089_consen 2 VGGDPASPGEFPWVVSIRYSNG--RFFCTGTLISPRWVLTAAHC 43 (220)
T ss_dssp BSSEECGTTSSTTEEEEEETTT--EEEEEEEEEETTEEEEEGGG
T ss_pred CCCEECCCCCCCeEEEEeeCCC--CeeEeEEecccccccccccc
Confidence 4677888899999999888776 99999999999999999999
No 14
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=98.24 E-value=8.4e-06 Score=64.95 Aligned_cols=21 Identities=38% Similarity=0.472 Sum_probs=19.4
Q ss_pred eEEEEecCC-EEEecccccCCC
Q psy17339 167 CGGAIISDT-VILTAAHCLQGI 187 (384)
Q Consensus 167 C~GtLIs~~-~VLTAAhC~~~~ 187 (384)
|+|.+|.++ +|||+|||+...
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDW 22 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCC
T ss_pred CEEEEEcCCceEEEchhheecc
Confidence 799999999 999999999764
No 15
>PRK10139 serine endoprotease; Provisional
Probab=98.21 E-value=8.3e-05 Score=73.52 Aligned_cols=142 Identities=24% Similarity=0.287 Sum_probs=83.7
Q ss_pred ceeeEEEEecC--CEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCc
Q psy17339 164 EHQCGGAIISD--TVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNI 241 (384)
Q Consensus 164 ~~~C~GtLIs~--~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv 241 (384)
....+|.+|++ -+|||.+|.+.+ ...+.|.+... ..+..+-+-. ....||||||++.+-
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~--a~~i~V~~~dg---------~~~~a~vvg~--------D~~~DlAvlkv~~~~ 149 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQ--AQKISIQLNDG---------REFDAKLIGS--------DDQSDIALLQIQNPS 149 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCC--CCEEEEEECCC---------CEEEEEEEEE--------cCCCCEEEEEecCCC
Confidence 46899999974 699999999975 55677775321 1233332222 234699999998542
Q ss_pred CCCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecC
Q psy17339 242 EFNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLN 321 (384)
Q Consensus 242 ~~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~ 321 (384)
...++.|.+......|+.+..+|+.... .... ..-+++... .. ... ..-....+-+
T Consensus 150 ----~l~~~~lg~s~~~~~G~~V~aiG~P~g~-------~~tv---t~GivS~~~--r~-~~~---~~~~~~~iqt---- 205 (455)
T PRK10139 150 ----KLTQIAIADSDKLRVGDFAVAVGNPFGL-------GQTA---TSGIISALG--RS-GLN---LEGLENFIQT---- 205 (455)
T ss_pred ----CCceeEecCccccCCCCEEEEEecCCCC-------CCce---EEEEEcccc--cc-ccC---CCCcceEEEE----
Confidence 3456777665567889999999874211 1111 122222110 00 000 0000112221
Q ss_pred CCcCCCCCCccCeeEEEeCCeEEEEEEEEec
Q psy17339 322 GGIDACGGDSGGPLACKIGGRFVLSGVVSWG 352 (384)
Q Consensus 322 ~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g 352 (384)
+...-+|.|||||+...+ .++||.+..
T Consensus 206 -da~in~GnSGGpl~n~~G---~vIGi~~~~ 232 (455)
T PRK10139 206 -DASINRGNSGGALLNLNG---ELIGINTAI 232 (455)
T ss_pred -CCccCCCCCcceEECCCC---eEEEEEEEE
Confidence 345568999999997654 899999874
No 16
>PRK10898 serine endoprotease; Provisional
Probab=98.19 E-value=0.00033 Score=67.07 Aligned_cols=142 Identities=18% Similarity=0.237 Sum_probs=79.4
Q ss_pred ceeeEEEEecCC-EEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcC
Q psy17339 164 EHQCGGAIISDT-VILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIE 242 (384)
Q Consensus 164 ~~~C~GtLIs~~-~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~ 242 (384)
...-+|.+|+++ +|||.||=+.+ ...+.|.+.. ...+..+-+.. ...+||||||++.+
T Consensus 77 ~~~GSGfvi~~~G~IlTn~HVv~~--a~~i~V~~~d---------g~~~~a~vv~~--------d~~~DlAvl~v~~~-- 135 (353)
T PRK10898 77 RTLGSGVIMDQRGYILTNKHVIND--ADQIIVALQD---------GRVFEALLVGS--------DSLTDLAVLKINAT-- 135 (353)
T ss_pred cceeeEEEEeCCeEEEecccEeCC--CCEEEEEeCC---------CCEEEEEEEEE--------cCCCCEEEEEEcCC--
Confidence 367999999976 99999999864 4556665532 11223322222 22469999999854
Q ss_pred CCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecCC
Q psy17339 243 FNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLNG 322 (384)
Q Consensus 243 ~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~ 322 (384)
...++.|.+......++.+.+.|+..... .......+.-... . ... ..-....+-.
T Consensus 136 ---~l~~~~l~~~~~~~~G~~V~aiG~P~g~~-------~~~t~Giis~~~r----~--~~~---~~~~~~~iqt----- 191 (353)
T PRK10898 136 ---NLPVIPINPKRVPHIGDVVLAIGNPYNLG-------QTITQGIISATGR----I--GLS---PTGRQNFLQT----- 191 (353)
T ss_pred ---CCCeeeccCcCcCCCCCEEEEEeCCCCcC-------CCcceeEEEeccc----c--ccC---CccccceEEe-----
Confidence 13344454433467889999988753211 1111111111100 0 000 0000111111
Q ss_pred CcCCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 323 GIDACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 323 ~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
+...-+|.|||||+..++ .++||.+...
T Consensus 192 da~i~~GnSGGPl~n~~G---~vvGI~~~~~ 219 (353)
T PRK10898 192 DASINHGNSGGALVNSLG---ELMGINTLSF 219 (353)
T ss_pred ccccCCCCCcceEECCCC---eEEEEEEEEe
Confidence 334567999999997544 8999998654
No 17
>PRK10942 serine endoprotease; Provisional
Probab=98.10 E-value=0.00014 Score=72.31 Aligned_cols=142 Identities=18% Similarity=0.282 Sum_probs=80.6
Q ss_pred ceeeEEEEecC--CEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCc
Q psy17339 164 EHQCGGAIISD--TVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNI 241 (384)
Q Consensus 164 ~~~C~GtLIs~--~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv 241 (384)
....+|.+|++ -+|||.+|.+.+ ...+.|.+... ..+..+-+.. ....||||||++.+-
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~--a~~i~V~~~dg---------~~~~a~vv~~--------D~~~DlAvlki~~~~ 170 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDN--ATKIKVQLSDG---------RKFDAKVVGK--------DPRSDIALIQLQNPK 170 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCC--CCEEEEEECCC---------CEEEEEEEEe--------cCCCCEEEEEecCCC
Confidence 45799999985 499999999975 45677765321 1223322222 224699999997432
Q ss_pred CCCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecC
Q psy17339 242 EFNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLN 321 (384)
Q Consensus 242 ~~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~ 321 (384)
. ..++.|.+......++.+..+|+-... ........+.-+... ... ..-...++-.
T Consensus 171 ~----l~~~~lg~s~~l~~G~~V~aiG~P~g~-------~~tvt~GiVs~~~r~------~~~---~~~~~~~iqt---- 226 (473)
T PRK10942 171 N----LTAIKMADSDALRVGDYTVAIGNPYGL-------GETVTSGIVSALGRS------GLN---VENYENFIQT---- 226 (473)
T ss_pred C----CceeEecCccccCCCCEEEEEcCCCCC-------CcceeEEEEEEeecc------cCC---cccccceEEe----
Confidence 2 346667655567889988888863211 111111111111110 000 0000111211
Q ss_pred CCcCCCCCCccCeeEEEeCCeEEEEEEEEec
Q psy17339 322 GGIDACGGDSGGPLACKIGGRFVLSGVVSWG 352 (384)
Q Consensus 322 ~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g 352 (384)
+...-+|.|||||+...+ .++||.+..
T Consensus 227 -da~i~~GnSGGpL~n~~G---eviGI~t~~ 253 (473)
T PRK10942 227 -DAAINRGNSGGALVNLNG---ELIGINTAI 253 (473)
T ss_pred -ccccCCCCCcCccCCCCC---eEEEEEEEE
Confidence 234557999999997654 899998764
No 18
>KOG3627|consensus
Probab=97.56 E-value=7.5e-05 Score=68.13 Aligned_cols=45 Identities=33% Similarity=0.671 Sum_probs=37.1
Q ss_pred ccCCCcccccceeEEEEEeecCCCCceeeEEEEecCCEEEeccccc
Q psy17339 139 NLNGVDKFEKTFKVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCL 184 (384)
Q Consensus 139 ~~~g~~~~~~~~~~~v~~~~~~~~~~~~C~GtLIs~~~VLTAAhC~ 184 (384)
.++|.++...++||++.+..... ..++|+|+||+++||||||||+
T Consensus 13 i~~g~~~~~~~~Pw~~~l~~~~~-~~~~Cggsli~~~~vltaaHC~ 57 (256)
T KOG3627|consen 13 IVGGTEAEPGSFPWQVSLQYGGN-GRHLCGGSLISPRWVLTAAHCV 57 (256)
T ss_pred EeCCccCCCCCCCCEEEEEECCC-cceeeeeEEeeCCEEEEChhhC
Confidence 44555777778999888877655 5679999999999999999996
No 19
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=3e-05 Score=71.42 Aligned_cols=50 Identities=22% Similarity=0.404 Sum_probs=38.5
Q ss_pred ccCCCcccccceeEEEEEeecCC--CCceeeEEEEecCCEEEecccccCCCC
Q psy17339 139 NLNGVDKFEKTFKVEIQVRSSTG--QGEHQCGGAIISDTVILTAAHCLQGIS 188 (384)
Q Consensus 139 ~~~g~~~~~~~~~~~v~~~~~~~--~~~~~C~GtLIs~~~VLTAAhC~~~~~ 188 (384)
+++|..+..+.||..+.+...-. ....+|+|++|..|||||||||++...
T Consensus 33 IigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s 84 (413)
T COG5640 33 IIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASS 84 (413)
T ss_pred EecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCC
Confidence 34455666777887777654444 578999999999999999999997644
No 20
>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=96.86 E-value=0.02 Score=59.86 Aligned_cols=65 Identities=14% Similarity=0.196 Sum_probs=37.4
Q ss_pred EEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcCCCCcee
Q psy17339 169 GAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIEFNQYVQ 248 (384)
Q Consensus 169 GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~~~~~v~ 248 (384)
+|||+|++|+|++|=.. ..-.|.+|.... ..+.+.+--.|+. .|+.+-||.+=|. -+.
T Consensus 69 aTLigpqYiVSV~HN~~----gy~~v~FG~~g~-------~~Y~iV~RNn~~~--------~Df~~pRLnK~VT---Eva 126 (769)
T PF02395_consen 69 ATLIGPQYIVSVKHNGK----GYNSVSFGNEGQ-------NTYKIVDRNNYPS--------GDFHMPRLNKFVT---EVA 126 (769)
T ss_dssp -EEEETTEEEBETTG-T----SCCEECESCSST-------CEEEEEEEEBETT--------STEBEEEESS------SS-
T ss_pred EEEecCCeEEEEEccCC----CcCceeecccCC-------ceEEEEEccCCCC--------cccceeecCceEE---EEe
Confidence 89999999999999762 223566665332 3445555444443 4999999999665 356
Q ss_pred eeccCCC
Q psy17339 249 PICIPDR 255 (384)
Q Consensus 249 picLp~~ 255 (384)
|+.....
T Consensus 127 P~~~t~~ 133 (769)
T PF02395_consen 127 PAEMTTA 133 (769)
T ss_dssp ---BBSS
T ss_pred ccccccc
Confidence 6655443
No 21
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=96.61 E-value=0.0026 Score=57.05 Aligned_cols=45 Identities=24% Similarity=0.467 Sum_probs=35.6
Q ss_pred CCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccccccc
Q psy17339 82 TPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQGISK 128 (384)
Q Consensus 82 a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~~~~~ 128 (384)
.....|||-+........ +.+-|+++||+|+.||||+||+.+...
T Consensus 44 ~dt~~~Py~av~~~~~~t--G~~~~~~~lI~pntvLTa~Hc~~s~~~ 88 (251)
T COG3591 44 TDTTQFPYSAVVQFEAAT--GRLCTAATLIGPNTVLTAGHCIYSPDY 88 (251)
T ss_pred ccCCCCCcceeEEeecCC--CcceeeEEEEcCceEEEeeeEEecCCC
Confidence 566789998887665442 455677799999999999999988754
No 22
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=96.46 E-value=0.0027 Score=58.93 Aligned_cols=47 Identities=26% Similarity=0.381 Sum_probs=37.5
Q ss_pred cCCCcccccceeEEEEEeecCCC-CceeeEEEEecCCEEEecccccCC
Q psy17339 140 LNGVDKFEKTFKVEIQVRSSTGQ-GEHQCGGAIISDTVILTAAHCLQG 186 (384)
Q Consensus 140 ~~g~~~~~~~~~~~v~~~~~~~~-~~~~C~GtLIs~~~VLTAAhC~~~ 186 (384)
.+|........+|.+.+...... ...+++|+|||+|||||++||+..
T Consensus 43 ~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~ 90 (282)
T PF03761_consen 43 FNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMN 90 (282)
T ss_pred cCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEe
Confidence 46666777778888888776654 457789999999999999999864
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=95.02 E-value=0.18 Score=43.09 Aligned_cols=151 Identities=19% Similarity=0.258 Sum_probs=75.8
Q ss_pred CCCceeeEEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCC
Q psy17339 161 GQGEHQCGGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGN 240 (384)
Q Consensus 161 ~~~~~~C~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~p 240 (384)
..+.+.|.+..|..+|.|-..|. .....+.+ + ...+.+...+..- +.. ....|+++++|+++
T Consensus 21 ~~g~~t~l~~gi~~~~~lvp~H~---~~~~~i~i--~----------g~~~~~~d~~~lv--~~~-~~~~Dl~~v~l~~~ 82 (172)
T PF00548_consen 21 GKGEFTMLALGIYDRYFLVPTHE---EPEDTIYI--D----------GVEYKVDDSVVLV--DRD-GVDTDLTLVKLPRN 82 (172)
T ss_dssp TTEEEEEEEEEEEBTEEEEEGGG---GGCSEEEE--T----------TEEEEEEEEEEEE--ETT-SSEEEEEEEEEESS
T ss_pred CCceEEEecceEeeeEEEEECcC---CCcEEEEE--C----------CEEEEeeeeEEEe--cCC-CcceeEEEEEccCC
Confidence 56778899999999999999992 22222322 2 1222333322221 111 23569999999988
Q ss_pred cCCCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeec
Q psy17339 241 IEFNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYL 320 (384)
Q Consensus 241 v~~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~ 320 (384)
-.|.+..+-++ .. ......+.+.-|... .+..... +.-+.....-. .. ...... |..+.
T Consensus 83 ~kfrDIrk~~~---~~-~~~~~~~~l~v~~~~-------~~~~~~~--v~~v~~~~~i~--~~----g~~~~~--~~~Y~ 141 (172)
T PF00548_consen 83 PKFRDIRKFFP---ES-IPEYPECVLLVNSTK-------FPRMIVE--VGFVTNFGFIN--LS----GTTTPR--SLKYK 141 (172)
T ss_dssp S-B--GGGGSB---SS-GGTEEEEEEEEESSS-------STCEEEE--EEEEEEEEEEE--ET----TEEEEE--EEEEE
T ss_pred cccCchhhhhc---cc-cccCCCcEEEEECCC-------CccEEEE--EEEEeecCccc--cC----CCEeeE--EEEEc
Confidence 88866665555 11 223334444444211 1111111 11111111100 00 011111 12221
Q ss_pred CCCcCCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 321 NGGIDACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 321 ~~~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
..+..|+-||||+.+.++...++||...|.
T Consensus 142 ---~~t~~G~CG~~l~~~~~~~~~i~GiHvaG~ 171 (172)
T PF00548_consen 142 ---APTKPGMCGSPLVSRIGGQGKIIGIHVAGN 171 (172)
T ss_dssp ---SEEETTGTTEEEEESCGGTTEEEEEEEEEE
T ss_pred ---cCCCCCccCCeEEEeeccCccEEEEEeccC
Confidence 234579999999997767779999998764
No 24
>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=93.99 E-value=0.076 Score=47.01 Aligned_cols=23 Identities=26% Similarity=0.702 Sum_probs=21.6
Q ss_pred CCceeeEEEEecCCEEEeccccc
Q psy17339 162 QGEHQCGGAIISDTVILTAAHCL 184 (384)
Q Consensus 162 ~~~~~C~GtLIs~~~VLTAAhC~ 184 (384)
+|.+.|+|+||.+.|||++-.|+
T Consensus 25 dG~~~CsgvLlD~~WlLvsssCl 47 (267)
T PF09342_consen 25 DGRYWCSGVLLDPHWLLVSSSCL 47 (267)
T ss_pred cCeEEEEEEEeccceEEEecccc
Confidence 47899999999999999999996
No 25
>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=93.41 E-value=0.025 Score=44.52 Aligned_cols=22 Identities=36% Similarity=0.465 Sum_probs=20.0
Q ss_pred eeeeeecch-hhhhccccccccc
Q psy17339 106 CGGAIISDT-VILTAAHCLQGIS 127 (384)
Q Consensus 106 CgGtLIs~~-~VLTAAhC~~~~~ 127 (384)
|+|.+|+++ +||||+||+....
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~~ 23 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDWN 23 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCCT
T ss_pred CEEEEEcCCceEEEchhheeccc
Confidence 789999999 9999999998753
No 26
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=90.41 E-value=9.4 Score=34.19 Aligned_cols=150 Identities=19% Similarity=0.268 Sum_probs=66.6
Q ss_pred EEEecCCEEEecccccCCCCCceEEEEE--eeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcCCCCc
Q psy17339 169 GAIISDTVILTAAHCLQGISKSKLRIIV--GKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIEFNQY 246 (384)
Q Consensus 169 GtLIs~~~VLTAAhC~~~~~~~~~~v~~--g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~~~~~ 246 (384)
=-+.--.|+||-+|-+...+. .+.+.. |.+... ...++-+||- ...||.||+|.+.++ +.
T Consensus 35 ~gigyG~~iItn~HLf~~nng-~L~i~s~hG~f~v~---------nt~~lkv~~i------~~~DiviirmPkDfp--Pf 96 (235)
T PF00863_consen 35 YGIGYGSYIITNAHLFKRNNG-ELTIKSQHGEFTVP---------NTTQLKVHPI------EGRDIVIIRMPKDFP--PF 96 (235)
T ss_dssp EEEEETTEEEEEGGGGSSTTC-EEEEEETTEEEEEC---------EGGGSEEEE-------TCSSEEEEE--TTS-----
T ss_pred EEEeECCEEEEChhhhccCCC-eEEEEeCceEEEcC---------CccccceEEe------CCccEEEEeCCcccC--Cc
Confidence 345678899999999865432 344432 222221 1112223332 245999999998765 22
Q ss_pred eeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecCCCcCC
Q psy17339 247 VQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLNGGIDA 326 (384)
Q Consensus 247 v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~~~~~ 326 (384)
-+-+++ . .+..++.+.++|--..... ......+.... .+ +.... .|. . ..++
T Consensus 97 ~~kl~F--R-~P~~~e~v~mVg~~fq~k~----~~s~vSesS~i-~p--~~~~~-fWk--------H---------wIsT 148 (235)
T PF00863_consen 97 PQKLKF--R-APKEGERVCMVGSNFQEKS----ISSTVSESSWI-YP--EENSH-FWK--------H---------WIST 148 (235)
T ss_dssp -S---B-------TT-EEEEEEEECSSCC----CEEEEEEEEEE-EE--ETTTT-EEE--------E----------C--
T ss_pred chhhhc--c-CCCCCCEEEEEEEEEEcCC----eeEEECCceEE-ee--cCCCC-eeE--------E---------EecC
Confidence 222222 1 2556777778876444332 11111111110 11 01000 111 0 1233
Q ss_pred CCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechh
Q psy17339 327 CGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSY 369 (384)
Q Consensus 327 C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~ 369 (384)
=.||=|.||+...++ .+|||.|.+..- ..-.+|+.+..
T Consensus 149 k~G~CG~PlVs~~Dg--~IVGiHsl~~~~---~~~N~F~~f~~ 186 (235)
T PF00863_consen 149 KDGDCGLPLVSTKDG--KIVGIHSLTSNT---SSRNYFTPFPD 186 (235)
T ss_dssp -TT-TT-EEEETTT----EEEEEEEEETT---TSSEEEEE--T
T ss_pred CCCccCCcEEEcCCC--cEEEEEcCccCC---CCeEEEEcCCH
Confidence 468999999998766 899999987533 22357888754
No 27
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=86.09 E-value=32 Score=32.76 Aligned_cols=146 Identities=24% Similarity=0.298 Sum_probs=77.5
Q ss_pred ceeeEEEEec-CCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcC
Q psy17339 164 EHQCGGAIIS-DTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIE 242 (384)
Q Consensus 164 ~~~C~GtLIs-~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~ 242 (384)
....+|.+++ ..+|+|-.|=+.. ...+.+.+. + ...+..+-+-. ....|+|++|.+..-.
T Consensus 71 ~~~gSg~i~~~~g~ivTn~hVi~~--a~~i~v~l~-------d--g~~~~a~~vg~--------d~~~dlavlki~~~~~ 131 (347)
T COG0265 71 EGLGSGFIISSDGYIVTNNHVIAG--AEEITVTLA-------D--GREVPAKLVGK--------DPISDLAVLKIDGAGG 131 (347)
T ss_pred cccccEEEEcCCeEEEecceecCC--cceEEEEeC-------C--CCEEEEEEEec--------CCccCEEEEEeccCCC
Confidence 4678888888 7799999998865 555666551 1 12222222221 3356999999986432
Q ss_pred CCCceeeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCccCCeEEeeecCC
Q psy17339 243 FNQYVQPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNILDSMLCAGYLNG 322 (384)
Q Consensus 243 ~~~~v~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~~~~~~Ca~~~~~ 322 (384)
+..+.+........++.....|-... .....-..-+...... +... .. . ....+ ..
T Consensus 132 ----~~~~~~~~s~~l~vg~~v~aiGnp~g-------~~~tvt~Givs~~~r~-~v~~--~~---~--~~~~I-----qt 187 (347)
T COG0265 132 ----LPVIALGDSDKLRVGDVVVAIGNPFG-------LGQTVTSGIVSALGRT-GVGS--AG---G--YVNFI-----QT 187 (347)
T ss_pred ----CceeeccCCCCcccCCEEEEecCCCC-------cccceeccEEeccccc-cccC--cc---c--ccchh-----hc
Confidence 23334444444556666666653221 0111111111212211 1110 00 0 11111 11
Q ss_pred CcCCCCCCccCeeEEEeCCeEEEEEEEEecCCC
Q psy17339 323 GIDACGGDSGGPLACKIGGRFVLSGVVSWGDGC 355 (384)
Q Consensus 323 ~~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c 355 (384)
+...++|.||||++...+ .++||.+.....
T Consensus 188 dAain~gnsGgpl~n~~g---~~iGint~~~~~ 217 (347)
T COG0265 188 DAAINPGNSGGPLVNIDG---EVVGINTAIIAP 217 (347)
T ss_pred ccccCCCCCCCceEcCCC---cEEEEEEEEecC
Confidence 345789999999998654 799998876544
No 28
>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=84.61 E-value=3.5 Score=39.65 Aligned_cols=142 Identities=20% Similarity=0.269 Sum_probs=69.3
Q ss_pred EEEEecCCEEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCCcCCCCce
Q psy17339 168 GGAIISDTVILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGNIEFNQYV 247 (384)
Q Consensus 168 ~GtLIs~~~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~pv~~~~~v 247 (384)
=|.++|+...+|+.|-+...-. -.+|. ++.++.+|. ..++.-++..+|+. +.+
T Consensus 382 WGfWVS~~lfITttHViP~g~~----E~FGv-------------~i~~i~vh~--------sGeF~~~rFpk~iR--PDv 434 (535)
T PF05416_consen 382 WGFWVSPTLFITTTHVIPPGAK----EAFGV-------------PISQIQVHK--------SGEFCRFRFPKPIR--PDV 434 (535)
T ss_dssp EEEESSSSEEEEEGGGS-STTS----EETTE-------------ECGGEEEEE--------ETTEEEEEESS-SS--TTS
T ss_pred eeeeecceEEEEeeeecCCcch----hhhCC-------------ChhHeEEee--------ccceEEEecCCCCC--CCc
Confidence 3789999999999998754221 11221 344445543 23677778777775 223
Q ss_pred eeeccCCCCCCCCCCeEEEEEeccCCCCCCCcccccceEEEEEEecccccccccccCCCCCCc--cCCeEEeeecC--CC
Q psy17339 248 QPICIPDRDNAAASDWCVVTGWGAQNAESIDDISNTLRAATVKVIDQNTCRSSAVYGNSNQNI--LDSMLCAGYLN--GG 323 (384)
Q Consensus 248 ~picLp~~~~~~~~~~~~v~GwG~~~~~~~~~~~~~l~~~~~~i~~~~~C~~~~~~~~~~~~~--~~~~~Ca~~~~--~~ 323 (384)
.-.-|-+. -+.|..|.+.==- .+..|...-++.-....-.. .+ ..+ ...|+-+|... -+
T Consensus 435 tgmiLEeG--apEGtV~siLiKR---------~sGEllpLAvRMgt~AsmkI---qg---r~v~GQ~GMLLTGaNAK~mD 497 (535)
T PF05416_consen 435 TGMILEEG--APEGTVCSILIKR---------PSGELLPLAVRMGTHASMKI---QG---RTVHGQMGMLLTGANAKGMD 497 (535)
T ss_dssp ---EE-SS----TT-EEEEEEE----------TTSBEEEEEEEEEEEEEEEE---TT---EEEEEEEEEETTSTT-SSTT
T ss_pred cceeeccC--CCCceEEEEEEEc---------CCccchhhhhhhccceeEEE---cc---eeecceeeeeeecCCccccc
Confidence 33333221 4567777665321 12223333333222111110 00 001 11233333221 12
Q ss_pred cCCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 324 IDACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 324 ~~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
-++-+||-|.|.++..++.|+++||.....
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 356789999999999999999999987653
No 29
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=76.13 E-value=2 Score=34.18 Aligned_cols=36 Identities=31% Similarity=0.474 Sum_probs=27.6
Q ss_pred CCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechhh
Q psy17339 326 ACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSYY 370 (384)
Q Consensus 326 ~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~~ 370 (384)
+-+||-||+|.|+. =++||++.|. ..-.-|++|+.+
T Consensus 87 ~~PGdCGg~L~C~H----GViGi~Tagg-----~g~VaF~dir~~ 122 (127)
T PF00947_consen 87 AEPGDCGGILRCKH----GVIGIVTAGG-----EGHVAFADIRDL 122 (127)
T ss_dssp SSTT-TCSEEEETT----CEEEEEEEEE-----TTEEEEEECCCG
T ss_pred CCCCCCCceeEeCC----CeEEEEEeCC-----CceEEEEechhh
Confidence 34799999999988 4999999874 234679999875
No 30
>KOG1320|consensus
Probab=62.24 E-value=1.7e+02 Score=29.18 Aligned_cols=47 Identities=28% Similarity=0.375 Sum_probs=38.7
Q ss_pred CCcceEecCccCCCCCCceEEEEeeeccCCCCceeeeeeeecchhhhhcccccc
Q psy17339 71 AANVKIVGGTSTPYGAYPWQVEIQVRSSTGQGEHQCGGAIISDTVILTAAHCLQ 124 (384)
Q Consensus 71 ~~~~rI~gG~~a~~~~~Pw~v~l~~~~~~~~~~~~CgGtLIs~~~VLTAAhC~~ 124 (384)
...-++.-+.......-||+-.-+ ....|.|.-|.-+-+||-||++.
T Consensus 61 ~s~~~v~~~~~~~~~~~pw~~~~q-------~~~~~s~f~i~~~~lltn~~~v~ 107 (473)
T KOG1320|consen 61 QSVVKVFSVSTEPSSVLPWQRTRQ-------FSSGGSGFAIYGKKLLTNAHVVA 107 (473)
T ss_pred cceeEEEeecccccccCcceeeeh-------hcccccchhhcccceeecCcccc
Confidence 355678888888888899987753 44679999999999999999998
No 31
>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=58.78 E-value=5.5 Score=36.03 Aligned_cols=23 Identities=39% Similarity=0.570 Sum_probs=17.6
Q ss_pred CCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 328 GGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 328 ~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
.||||+|++.+++ .|+||.+...
T Consensus 207 ~GDSGSPVVt~dg---~liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTEDG---DLIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETTC----EEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCC
Confidence 5999999998876 7999998653
No 32
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=55.93 E-value=14 Score=32.51 Aligned_cols=25 Identities=28% Similarity=0.239 Sum_probs=22.2
Q ss_pred CCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 325 DACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 325 ~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
..-+|-||+|++.++ .|+|-+++..
T Consensus 176 GIvqGMSGSPI~qdG----KLiGAVthvf 200 (218)
T PF05580_consen 176 GIVQGMSGSPIIQDG----KLIGAVTHVF 200 (218)
T ss_pred CEEecccCCCEEECC----EEEEEEEEEE
Confidence 578999999999877 9999999876
No 33
>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=50.32 E-value=11 Score=30.48 Aligned_cols=21 Identities=38% Similarity=0.773 Sum_probs=15.5
Q ss_pred CCCCccCeeEEEeCCeEEEEEEEE
Q psy17339 327 CGGDSGGPLACKIGGRFVLSGVVS 350 (384)
Q Consensus 327 C~GDsGgPl~~~~~~~~~lvGI~S 350 (384)
-.|.||||++|..+ .++||.-
T Consensus 106 lkGSSGgPiLC~~G---H~vG~f~ 126 (148)
T PF02907_consen 106 LKGSSGGPILCPSG---HAVGMFR 126 (148)
T ss_dssp HTT-TT-EEEETTS---EEEEEEE
T ss_pred EecCCCCcccCCCC---CEEEEEE
Confidence 46999999999876 7888864
No 34
>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=49.62 E-value=10 Score=39.71 Aligned_cols=22 Identities=36% Similarity=0.774 Sum_probs=19.2
Q ss_pred eeeEEEEecCC-EEEecccccCC
Q psy17339 165 HQCGGAIISDT-VILTAAHCLQG 186 (384)
Q Consensus 165 ~~C~GtLIs~~-~VLTAAhC~~~ 186 (384)
..|+|++||++ .|||--||..+
T Consensus 47 gGCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 47 GGCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred CceeEEEEcCCceEEecchhhhh
Confidence 35999999998 99999999853
No 35
>KOG1421|consensus
Probab=42.24 E-value=2.4e+02 Score=29.51 Aligned_cols=86 Identities=21% Similarity=0.298 Sum_probs=49.3
Q ss_pred CceeeEEEEecCC--EEEecccccCCCCCceEEEEEeeeccCCCCcceEEEEEEEEEEcCCCCCCCCCCCceEEEEEcCC
Q psy17339 163 GEHQCGGAIISDT--VILTAAHCLQGISKSKLRIIVGKHNLNGVDKFEKTFKVEKAVLHHRFRKEGTHSNDIAVVKIRGN 240 (384)
Q Consensus 163 ~~~~C~GtLIs~~--~VLTAAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~~DIALl~L~~p 240 (384)
+..--+|.++++. ++||+.|-+...+.....++. . -..+-+.|-|... -||+.+++.+..
T Consensus 82 g~~~atgfvvd~~~gyiLtnrhvv~pgP~va~avf~-n--------------~ee~ei~pvyrDp---VhdfGf~r~dps 143 (955)
T KOG1421|consen 82 GESEATGFVVDKKLGYILTNRHVVAPGPFVASAVFD-N--------------HEEIEIYPVYRDP---VHDFGFFRYDPS 143 (955)
T ss_pred cccceeEEEEecccceEEEeccccCCCCceeEEEec-c--------------cccCCcccccCCc---hhhcceeecChh
Confidence 4455678888765 899999987654333322221 1 1122344555443 478888887653
Q ss_pred -cCCCCceeeeccCCCCCCCCCCeEEEEE
Q psy17339 241 -IEFNQYVQPICIPDRDNAAASDWCVVTG 268 (384)
Q Consensus 241 -v~~~~~v~picLp~~~~~~~~~~~~v~G 268 (384)
+.| ..+..+||.... -..+....++|
T Consensus 144 ~ir~-s~vt~i~lap~~-akvgseirvvg 170 (955)
T KOG1421|consen 144 TIRF-SIVTEICLAPEL-AKVGSEIRVVG 170 (955)
T ss_pred hcce-eeeeccccCccc-cccCCceEEec
Confidence 333 357788886543 34455555554
No 36
>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=34.22 E-value=36 Score=32.56 Aligned_cols=25 Identities=28% Similarity=0.384 Sum_probs=21.0
Q ss_pred ceeeeeeeecch-hhhhccccccccc
Q psy17339 103 EHQCGGAIISDT-VILTAAHCLQGIS 127 (384)
Q Consensus 103 ~~~CgGtLIs~~-~VLTAAhC~~~~~ 127 (384)
....+|.+|++. +|||++|.+....
T Consensus 77 ~~~GSG~vi~~~G~IlTn~HVV~~~~ 102 (351)
T TIGR02038 77 QGLGSGVIMSKEGYILTNYHVIKKAD 102 (351)
T ss_pred cceEEEEEEeCCeEEEecccEeCCCC
Confidence 346999999976 9999999997654
No 37
>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=32.42 E-value=11 Score=30.36 Aligned_cols=24 Identities=33% Similarity=0.434 Sum_probs=17.5
Q ss_pred CCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 327 CGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 327 C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
-+||||-|++-+.+ .+|||+-.|.
T Consensus 104 ~~GDSGRpi~DNsG---rVVaIVLGG~ 127 (158)
T PF00944_consen 104 KPGDSGRPIFDNSG---RVVAIVLGGA 127 (158)
T ss_dssp STTSTTEEEESTTS---BEEEEEEEEE
T ss_pred CCCCCCCccCcCCC---CEEEEEecCC
Confidence 47999999985433 6778876654
No 38
>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=30.41 E-value=22 Score=35.07 Aligned_cols=26 Identities=35% Similarity=0.423 Sum_probs=22.1
Q ss_pred Cceeeeeeeecch-hhhhccccccccc
Q psy17339 102 GEHQCGGAIISDT-VILTAAHCLQGIS 127 (384)
Q Consensus 102 ~~~~CgGtLIs~~-~VLTAAhC~~~~~ 127 (384)
....++|.+|++. +|||++|++.+..
T Consensus 56 ~~~~GSGfii~~~G~IlTn~Hvv~~~~ 82 (428)
T TIGR02037 56 VRGLGSGVIISADGYILTNNHVVDGAD 82 (428)
T ss_pred ccceeeEEEECCCCEEEEcHHHcCCCC
Confidence 3467999999986 9999999998764
No 39
>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=27.26 E-value=50 Score=32.20 Aligned_cols=44 Identities=23% Similarity=0.296 Sum_probs=31.1
Q ss_pred CCCCCCccCeeEEEeCCeEEEEEEEEecCCCCCCCCCeEEEechhhHHHHHHHH
Q psy17339 325 DACGGDSGGPLACKIGGRFVLSGVVSWGDGCAKKNKPGVYTRVSYYTKWINDRI 378 (384)
Q Consensus 325 ~~C~GDsGgPl~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~~~~WI~~~i 378 (384)
...+|-||+|++.++ .|+|-++.-.--.....+++ |.+|..+..
T Consensus 356 GivqGMSGSPi~q~g----kliGAvtHVfvndpt~GYGi------~ie~Ml~~~ 399 (402)
T TIGR02860 356 GIVQGMSGSPIIQNG----KVIGAVTHVFVNDPTSGYGV------YIEWMLKEA 399 (402)
T ss_pred CEEecccCCCEEECC----EEEEEEEEEEecCCCcceee------hHHHHHHHh
Confidence 678899999999988 99999887542222233555 467876543
No 40
>PF14903 WG_beta_rep: WG containing repeat
Probab=24.72 E-value=1e+02 Score=17.72 Aligned_cols=24 Identities=29% Similarity=0.328 Sum_probs=17.2
Q ss_pred EEEEcCCCCCCCCCCCceEEEEEc
Q psy17339 215 KAVLHHRFRKEGTHSNDIAVVKIR 238 (384)
Q Consensus 215 ~i~~hp~y~~~~~~~~DIALl~L~ 238 (384)
++++.|.|+.-..+.+++|+++.+
T Consensus 9 ~~vi~~~yd~i~~~~~g~~~v~~~ 32 (35)
T PF14903_consen 9 KIVIPPKYDEIYPFSNGYAIVKKD 32 (35)
T ss_pred CEEEEccccCccccCCCEEEEEEC
Confidence 346677887655677889988865
No 41
>PF08048 RepA1_leader: Tap RepA1 leader peptide; InterPro: IPR012605 This entry represents of the RepA1 leader peptide known as Tap found in IncFII plasmids. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid [, ]. The tap gene encodes a 24-amino acid peptide whose translation is required for the translation of repA.
Probab=22.47 E-value=12 Score=20.24 Aligned_cols=16 Identities=31% Similarity=0.702 Sum_probs=12.2
Q ss_pred CCCCceeeeeehhhhc
Q psy17339 1 MFFNPTFVFLCSSILL 16 (384)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (384)
|+.+.-.+|||+.+++
T Consensus 1 MlrK~Q~~FLc~lLL~ 16 (25)
T PF08048_consen 1 MLRKVQYLFLCHLLLP 16 (25)
T ss_pred CchhHHHHHHHHHHhh
Confidence 6777777888888773
No 42
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 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 serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=21.16 E-value=54 Score=26.56 Aligned_cols=26 Identities=31% Similarity=0.434 Sum_probs=17.1
Q ss_pred CCCCCCccCeeEEEeCCeEEEEEEEEecC
Q psy17339 325 DACGGDSGGPLACKIGGRFVLSGVVSWGD 353 (384)
Q Consensus 325 ~~C~GDsGgPl~~~~~~~~~lvGI~S~g~ 353 (384)
+.=.|.||+|++..++ .++||.-.+.
T Consensus 93 d~~~GsSGSpi~n~~g---~ivGlYg~g~ 118 (132)
T PF00949_consen 93 DFPKGSSGSPIFNQNG---EIVGLYGNGV 118 (132)
T ss_dssp -S-TTGTT-EEEETTS---CEEEEEEEEE
T ss_pred ccCCCCCCCceEcCCC---cEEEEEccce
Confidence 4557999999996554 6888876553
No 43
>PRK10898 serine endoprotease; Provisional
Probab=21.12 E-value=80 Score=30.26 Aligned_cols=24 Identities=25% Similarity=0.403 Sum_probs=20.3
Q ss_pred eeeeeeeecch-hhhhccccccccc
Q psy17339 104 HQCGGAIISDT-VILTAAHCLQGIS 127 (384)
Q Consensus 104 ~~CgGtLIs~~-~VLTAAhC~~~~~ 127 (384)
..-+|.+|+++ +|||++|=+.+..
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~a~ 102 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVINDAD 102 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCCCC
Confidence 56899999975 9999999997653
No 44
>TIGR03475 tap_IncFII_lead RepA leader peptide Tap. This protein is a translated leader peptide that actis in the regulation of the expression of the plasmid replication protein RepA in incF2 group plasmids.
Probab=20.80 E-value=14 Score=20.21 Aligned_cols=15 Identities=33% Similarity=0.800 Sum_probs=11.2
Q ss_pred CCCCceeeeeehhhh
Q psy17339 1 MFFNPTFVFLCSSIL 15 (384)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (384)
|+.+.-.+|||+.++
T Consensus 1 M~rKvQ~~FLc~~LL 15 (26)
T TIGR03475 1 MLRKVQYLFLCHLLL 15 (26)
T ss_pred CchhHHHHHHHHHHh
Confidence 667777788888666
Done!