Query 013490
Match_columns 442
No_of_seqs 167 out of 395
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:22:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013490hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08192 Peptidase_S64: Peptid 99.8 1.1E-18 2.3E-23 187.2 12.3 227 43-287 415-686 (695)
2 TIGR02038 protease_degS peripl 98.2 2.8E-05 6.2E-10 79.5 13.6 93 176-286 147-243 (351)
3 PRK10898 serine endoprotease; 98.0 7E-05 1.5E-09 76.8 13.2 93 176-286 147-244 (353)
4 PRK10139 serine endoprotease; 97.9 8.8E-05 1.9E-09 78.7 12.1 89 176-284 161-253 (455)
5 TIGR02037 degP_htrA_DO peripla 97.9 7.4E-05 1.6E-09 77.9 11.3 91 176-286 128-222 (428)
6 PRK10942 serine endoprotease; 97.8 0.00021 4.5E-09 76.3 12.0 88 176-283 182-273 (473)
7 PF13365 Trypsin_2: Trypsin-li 97.3 0.00092 2E-08 55.3 7.1 24 219-251 97-120 (120)
8 PF00089 Trypsin: Trypsin; In 96.7 0.0077 1.7E-07 54.4 8.6 184 57-284 24-218 (220)
9 PF00944 Peptidase_S3: Alphavi 95.6 0.017 3.6E-07 53.1 4.7 47 204-259 82-130 (158)
10 COG0265 DegQ Trypsin-like seri 95.5 0.12 2.7E-06 52.4 10.8 89 177-285 143-236 (347)
11 KOG1421 Predicted signaling-as 94.8 0.079 1.7E-06 59.2 7.6 44 227-287 213-256 (955)
12 cd00190 Tryp_SPc Trypsin-like 93.9 1.6 3.4E-05 39.6 13.0 29 227-257 181-209 (232)
13 COG3591 V8-like Glu-specific e 92.8 1.4 3E-05 44.2 11.5 28 227-259 200-227 (251)
14 smart00020 Tryp_SPc Trypsin-li 91.9 3.5 7.6E-05 37.6 12.3 28 228-259 183-210 (229)
15 PF00947 Pico_P2A: Picornaviru 91.3 0.21 4.6E-06 45.3 3.5 51 209-283 73-123 (127)
16 PF00863 Peptidase_C4: Peptida 91.2 3.7 8.1E-05 40.8 12.4 72 175-259 103-176 (235)
17 PF05579 Peptidase_S32: Equine 86.2 0.46 9.9E-06 48.2 2.2 29 225-258 203-231 (297)
18 PF10459 Peptidase_S46: Peptid 83.7 1.3 2.8E-05 50.2 4.5 65 212-287 620-684 (698)
19 PF00949 Peptidase_S7: Peptida 80.7 1.8 4E-05 39.4 3.5 27 227-258 94-120 (132)
20 PF12381 Peptidase_C3G: Tungro 63.9 10 0.00022 37.6 4.5 49 208-261 162-210 (231)
21 PF01732 DUF31: Putative pepti 63.0 5.4 0.00012 41.3 2.6 22 228-254 353-374 (374)
22 PF00548 Peptidase_C3: 3C cyst 58.7 11 0.00023 35.4 3.5 39 213-257 134-172 (172)
23 KOG1320 Serine protease [Postt 58.3 40 0.00087 36.9 8.1 77 192-285 268-346 (473)
24 PF02122 Peptidase_S39: Peptid 35.9 41 0.00089 32.8 3.6 42 227-283 144-185 (203)
25 KOG1320 Serine protease [Postt 26.2 2.4E+02 0.0051 31.2 7.7 84 132-237 132-217 (473)
No 1
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=99.77 E-value=1.1e-18 Score=187.16 Aligned_cols=227 Identities=21% Similarity=0.270 Sum_probs=139.1
Q ss_pred CCCCCccccccc-ccceeeeEEEEEeCCC---------CceEEEeecCceeccCCCCCccccCCCCCccCccccC-----
Q 013490 43 DPCIGSGSQVAS-QETYGTLGAIVRSRTG---------NQQVGFLTNRHVAVDLDYPNQKMFHPLPPSLGPGVYL----- 107 (442)
Q Consensus 43 ~p~iG~GisV~~-~~taGTLGclV~D~~G---------~~~~yiLSNnHVla~~n~~~q~~~~~G~pIlQPG~~D----- 107 (442)
.|+|+-.+++.+ ...+||||.++.-.-. .+..|+|||.||+-+.+.+ . -+.+-.|+..+
T Consensus 415 ~pPismSis~~~s~k~SGTlGGyi~p~i~~~~~~l~~ya~s~faiTC~HV~l~~~~~---d---yp~Vs~PS~vl~~~Yk 488 (695)
T PF08192_consen 415 SPPISMSISSENSSKSSGTLGGYIYPKIDQKDPKLSSYANSKFAITCAHVCLSESQA---D---YPNVSVPSSVLISLYK 488 (695)
T ss_pred CCCceEEEeccCCCccccccceeEeeccCccchhHHhhhcccccceeeeEecCcccc---C---CCCcCCchHHHHHHHH
Confidence 366877777765 6689999999942110 1236899999999986531 0 11233454211
Q ss_pred ------------CCee------eeeeeeecc-------cccccccCCCCcccccccccccccccccCCCC-cccccc-cc
Q 013490 108 ------------GAVE------RATSFITDD-------LWYGIFAGTNPETFVRADGAFIPFAEDFNLNN-VTTSVK-GV 160 (442)
Q Consensus 108 ------------GG~~------~L~~fIp~~-------~~~~i~~~~~~~n~vDaD~AlI~~A~~~d~s~-vs~~I~-gi 160 (442)
.-.+ .+.+..|.. |...+|.-..-.+..=.|||||.+.+-..-.+ .-..|. ..
T Consensus 489 ~al~~e~~r~~~~~~~~~a~~~e~~~~~~~~~~~~~~~fGqVvwGER~ii~~~LsD~AIIkV~~~~~~~N~LGddi~f~~ 568 (695)
T PF08192_consen 489 KALSEEYTRYPEESVEYQAFLQELDRIFPNKKWQPSNKFGQVVWGERSIINKRLSDWAIIKVNKERKCQNYLGDDIQFNE 568 (695)
T ss_pred HHHHHHHhhccccchHHHHHHHHHHhhccccccCccCccceEEeccchhhcccccceEEEEeCCCceecCCCCccccccC
Confidence 0000 111211111 12244543333333335999988654221111 111111 11
Q ss_pred cccCccee-ccCCC-ccccCCCCcEEEeeeecCceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEe
Q 013490 161 GEIGDVHI-IDLQS-PINSLIGRQVMKVGRSSGLTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILL 238 (442)
Q Consensus 161 G~iG~v~~-idl~g-~~~~~lG~~V~KvGRTTGlT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~ 238 (442)
-.+...+. ++++- ......|+.|+|+|||||+|+|+|+++.+.||.+ |...+.+|+|.+.....|+.+|||||||+.
T Consensus 569 ~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTgyT~G~lNg~klvyw~d-G~i~s~efvV~s~~~~~Fa~~GDSGS~VLt 647 (695)
T PF08192_consen 569 PDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTGYTTGILNGIKLVYWAD-GKIQSSEFVVSSDNNPAFASGGDSGSWVLT 647 (695)
T ss_pred CCccccccccchhhhhhccCCCCeEEEecccCCccceEecceEEEEecC-CCeEEEEEEEecCCCccccCCCCcccEEEe
Confidence 01100000 11111 2244679999999999999999999999999876 556789999999766899999999999996
Q ss_pred eccC-CCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHHhhcC
Q 013490 239 TGQN-GEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 287 (442)
Q Consensus 239 ~~~~-d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L~ 287 (442)
+.++ ...-.+|||+++-.+. ..+|.+|+||..||+.|.
T Consensus 648 k~~d~~~gLgvvGMlhsydge-----------~kqfglftPi~~il~rl~ 686 (695)
T PF08192_consen 648 KLEDNNKGLGVVGMLHSYDGE-----------QKQFGLFTPINEILDRLE 686 (695)
T ss_pred cccccccCceeeEEeeecCCc-----------cceeeccCcHHHHHHHHH
Confidence 5444 3344589999996553 357899999999999875
No 2
>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=98.16 E-value=2.8e-05 Score=79.49 Aligned_cols=93 Identities=15% Similarity=0.192 Sum_probs=64.8
Q ss_pred ccCCCCcEEEeeeecC----ceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 176 NSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 176 ~~~lG~~V~KvGRTTG----lT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
...+|+.|.-+|...| +|.|.|+++.-......+ ..+++.+... -.+|.||..++ |.++++||+
T Consensus 147 ~~~~G~~V~aiG~P~~~~~s~t~GiIs~~~r~~~~~~~---~~~~iqtda~----i~~GnSGGpl~-----n~~G~vIGI 214 (351)
T TIGR02038 147 PPHVGDVVLAIGNPYNLGQTITQGIISATGRNGLSSVG---RQNFIQTDAA----INAGNSGGALI-----NTNGELVGI 214 (351)
T ss_pred ccCCCCEEEEEeCCCCCCCcEEEEEEEeccCcccCCCC---cceEEEECCc----cCCCCCcceEE-----CCCCeEEEE
Confidence 5789999999999876 478999887732221112 2456666655 57899999999 899999999
Q ss_pred EEecCCCCCccccccCCCCccceeeechHHHHhhc
Q 013490 252 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLL 286 (442)
Q Consensus 252 lfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L 286 (442)
..+.-... .+.....+.|+-|++.+...+
T Consensus 215 ~~~~~~~~------~~~~~~g~~faIP~~~~~~vl 243 (351)
T TIGR02038 215 NTASFQKG------GDEGGEGINFAIPIKLAHKIM 243 (351)
T ss_pred Eeeeeccc------CCCCccceEEEecHHHHHHHH
Confidence 87642211 011234568999998877765
No 3
>PRK10898 serine endoprotease; Provisional
Probab=98.02 E-value=7e-05 Score=76.83 Aligned_cols=93 Identities=18% Similarity=0.254 Sum_probs=62.4
Q ss_pred ccCCCCcEEEeeeecC----ceeEEEEEEE-EEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 013490 176 NSLIGRQVMKVGRSSG----LTTGTVMAYA-LEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 250 (442)
Q Consensus 176 ~~~lG~~V~KvGRTTG----lT~G~I~ai~-v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VG 250 (442)
.+..|+.|.-+|.-.| .|.|.|++.. ..+.. .+ ..+++.++.. -.+|.||..++ |.++++||
T Consensus 147 ~~~~G~~V~aiG~P~g~~~~~t~Giis~~~r~~~~~-~~---~~~~iqtda~----i~~GnSGGPl~-----n~~G~vvG 213 (353)
T PRK10898 147 VPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLSP-TG---RQNFLQTDAS----INHGNSGGALV-----NSLGELMG 213 (353)
T ss_pred cCCCCCEEEEEeCCCCcCCCcceeEEEeccccccCC-cc---ccceEEeccc----cCCCCCcceEE-----CCCCeEEE
Confidence 4689999999998766 5889999876 22221 12 1245666655 57899999999 89999999
Q ss_pred EEEecCCCCCccccccCCCCccceeeechHHHHhhc
Q 013490 251 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLL 286 (442)
Q Consensus 251 LlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L 286 (442)
|..+.-...+ .+.....+.|+-|++.+...+
T Consensus 214 I~~~~~~~~~-----~~~~~~g~~faIP~~~~~~~~ 244 (353)
T PRK10898 214 INTLSFDKSN-----DGETPEGIGFAIPTQLATKIM 244 (353)
T ss_pred EEEEEecccC-----CCCcccceEEEEchHHHHHHH
Confidence 9875322110 011234678998887755544
No 4
>PRK10139 serine endoprotease; Provisional
Probab=97.92 E-value=8.8e-05 Score=78.69 Aligned_cols=89 Identities=18% Similarity=0.148 Sum_probs=61.8
Q ss_pred ccCCCCcEEEeeeecC----ceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 176 NSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 176 ~~~lG~~V~KvGRTTG----lT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
...+|+.|.-+|.--| .|.|.|++++-...... -+.++|.+... -.+|.||..++ |.++++||+
T Consensus 161 ~~~~G~~V~aiG~P~g~~~tvt~GivS~~~r~~~~~~---~~~~~iqtda~----in~GnSGGpl~-----n~~G~vIGi 228 (455)
T PRK10139 161 KLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLE---GLENFIQTDAS----INRGNSGGALL-----NLNGELIGI 228 (455)
T ss_pred ccCCCCEEEEEecCCCCCCceEEEEEccccccccCCC---CcceEEEECCc----cCCCCCcceEE-----CCCCeEEEE
Confidence 4678999999988555 47888888763211111 14567777765 57899999999 999999999
Q ss_pred EEecCCCCCccccccCCCCccceeeechHHHHh
Q 013490 252 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLD 284 (442)
Q Consensus 252 lfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~ 284 (442)
..+--... +....+.|+-|++.+..
T Consensus 229 ~~~~~~~~--------~~~~gigfaIP~~~~~~ 253 (455)
T PRK10139 229 NTAILAPG--------GGSVGIGFAIPSNMART 253 (455)
T ss_pred EEEEEcCC--------CCccceEEEEEhHHHHH
Confidence 98743221 11235689999865544
No 5
>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=97.91 E-value=7.4e-05 Score=77.92 Aligned_cols=91 Identities=18% Similarity=0.195 Sum_probs=62.1
Q ss_pred ccCCCCcEEEeeeecC----ceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 176 NSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 176 ~~~lG~~V~KvGRTTG----lT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
...+|+.|.-+|.--| +|.|.|+++.-... .. ..+.+++.++.. -.+|.||+.++ +.++++|||
T Consensus 128 ~~~~G~~v~aiG~p~g~~~~~t~G~vs~~~~~~~-~~--~~~~~~i~tda~----i~~GnSGGpl~-----n~~G~viGI 195 (428)
T TIGR02037 128 KLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSGL-GI--GDYENFIQTDAA----INPGNSGGPLV-----NLRGEVIGI 195 (428)
T ss_pred CCCCCCEEEEEECCCcCCCcEEEEEEEecccCcc-CC--CCccceEEECCC----CCCCCCCCceE-----CCCCeEEEE
Confidence 4689999999998744 57888888763211 11 124566776665 67899999999 899999999
Q ss_pred EEecCCCCCccccccCCCCccceeeechHHHHhhc
Q 013490 252 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLL 286 (442)
Q Consensus 252 lfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L 286 (442)
..+.-... | ....+.|+-|++.+.+.|
T Consensus 196 ~~~~~~~~-------g-~~~g~~faiP~~~~~~~~ 222 (428)
T TIGR02037 196 NTAIYSPS-------G-GNVGIGFAIPSNMAKNVV 222 (428)
T ss_pred EeEEEcCC-------C-CccceEEEEEhHHHHHHH
Confidence 87643321 1 112457888876665544
No 6
>PRK10942 serine endoprotease; Provisional
Probab=97.77 E-value=0.00021 Score=76.25 Aligned_cols=88 Identities=17% Similarity=0.210 Sum_probs=59.9
Q ss_pred ccCCCCcEEEeeeecC----ceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 176 NSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 176 ~~~lG~~V~KvGRTTG----lT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
...+|+.|.-+|..-| .|.|.|+++.... .+...+.++|.+... -.+|.||..++ |.++++|||
T Consensus 182 ~l~~G~~V~aiG~P~g~~~tvt~GiVs~~~r~~---~~~~~~~~~iqtda~----i~~GnSGGpL~-----n~~GeviGI 249 (473)
T PRK10942 182 ALRVGDYTVAIGNPYGLGETVTSGIVSALGRSG---LNVENYENFIQTDAA----INRGNSGGALV-----NLNGELIGI 249 (473)
T ss_pred ccCCCCEEEEEcCCCCCCcceeEEEEEEeeccc---CCcccccceEEeccc----cCCCCCcCccC-----CCCCeEEEE
Confidence 4689999999998765 4889998877321 111224566777665 56899999999 899999999
Q ss_pred EEecCCCCCccccccCCCCccceeeechHHHH
Q 013490 252 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 283 (442)
Q Consensus 252 lfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL 283 (442)
..+.-...| ....+.|+-|+..+.
T Consensus 250 ~t~~~~~~g--------~~~g~gfaIP~~~~~ 273 (473)
T PRK10942 250 NTAILAPDG--------GNIGIGFAIPSNMVK 273 (473)
T ss_pred EEEEEcCCC--------CcccEEEEEEHHHHH
Confidence 986432211 012357888875443
No 7
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=97.28 E-value=0.00092 Score=55.35 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=20.1
Q ss_pred EcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 219 VGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 219 t~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
+..+ ..+|.||+.++ +.++++|||
T Consensus 97 ~~~~----~~~G~SGgpv~-----~~~G~vvGi 120 (120)
T PF13365_consen 97 TDAD----TRPGSSGGPVF-----DSDGRVVGI 120 (120)
T ss_dssp ESSS-----STTTTTSEEE-----ETTSEEEEE
T ss_pred eecc----cCCCcEeHhEE-----CCCCEEEeC
Confidence 5555 78999999999 899999997
No 8
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=96.74 E-value=0.0077 Score=54.39 Aligned_cols=184 Identities=16% Similarity=0.185 Sum_probs=89.9
Q ss_pred ceeeeEEEEEeCCCCceEEEeecCceeccCCCCCccccCCCCCccCccccCCCeeeeeeeeecccccccccCCCCccccc
Q 013490 57 TYGTLGAIVRSRTGNQQVGFLTNRHVAVDLDYPNQKMFHPLPPSLGPGVYLGAVERATSFITDDLWYGIFAGTNPETFVR 136 (442)
Q Consensus 57 taGTLGclV~D~~G~~~~yiLSNnHVla~~n~~~q~~~~~G~pIlQPG~~DGG~~~L~~fIp~~~~~~i~~~~~~~n~vD 136 (442)
..--.|++|.++ ++||.+|++...+ +.....|...++........-...+++....+ ++.. .+
T Consensus 24 ~~~C~G~li~~~------~vLTaahC~~~~~---~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~-------~~~~-~~ 86 (220)
T PF00089_consen 24 RFFCTGTLISPR------WVLTAAHCVDGAS---DIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKY-------DPST-YD 86 (220)
T ss_dssp EEEEEEEEEETT------EEEEEGGGHTSGG---SEEEEESESBTTSTTTTSEEEEEEEEEEETTS-------BTTT-TT
T ss_pred CeeEeEEecccc------ccccccccccccc---cccccccccccccccccccccccccccccccc-------cccc-cc
Confidence 344557788774 8999999999821 11223343223322111111133343322211 1112 35
Q ss_pred ccccccccccccCCCCcccccccccccCcceeccCCC-ccccCCCCcEEEeeeecCceeE---EEEEEEEEEeCC-----
Q 013490 137 ADGAFIPFAEDFNLNNVTTSVKGVGEIGDVHIIDLQS-PINSLIGRQVMKVGRSSGLTTG---TVMAYALEYNDE----- 207 (442)
Q Consensus 137 aD~AlI~~A~~~d~s~vs~~I~giG~iG~v~~idl~g-~~~~~lG~~V~KvGRTTGlT~G---~I~ai~v~y~~~----- 207 (442)
.|+||+++.+.. .....+..+. +.. ......|+.+.-+|.......+ .+....+.+-..
T Consensus 87 ~DiAll~L~~~~---~~~~~~~~~~---------l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~~ 154 (220)
T PF00089_consen 87 NDIALLKLDRPI---TFGDNIQPIC---------LPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCRS 154 (220)
T ss_dssp TSEEEEEESSSS---EHBSSBEESB---------BTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHHH
T ss_pred cccccccccccc---cccccccccc---------cccccccccccccccccccccccccccccccccccccccccccccc
Confidence 688997766431 2222222221 111 1223677777777776654444 444444322110
Q ss_pred --CCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHHh
Q 013490 208 --KGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLD 284 (442)
Q Consensus 208 --~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~ 284 (442)
... ....++-+..++..-.-.|||||.++. .+..++|++..+.... .+....+|++|...++
T Consensus 155 ~~~~~-~~~~~~c~~~~~~~~~~~g~sG~pl~~-----~~~~lvGI~s~~~~c~---------~~~~~~v~~~v~~~~~ 218 (220)
T PF00089_consen 155 SYNDN-LTPNMICAGSSGSGDACQGDSGGPLIC-----NNNYLVGIVSFGENCG---------SPNYPGVYTRVSSYLD 218 (220)
T ss_dssp HTTTT-STTTEEEEETTSSSBGGTTTTTSEEEE-----TTEEEEEEEEEESSSS---------BTTSEEEEEEGGGGHH
T ss_pred ccccc-ccccccccccccccccccccccccccc-----ceeeecceeeecCCCC---------CCCcCEEEEEHHHhhc
Confidence 000 111222222211122457999999993 3337999999983322 1112388888887654
No 9
>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=95.64 E-value=0.017 Score=53.12 Aligned_cols=47 Identities=30% Similarity=0.494 Sum_probs=35.3
Q ss_pred EeCCCCeEEEEE--EEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCC
Q 013490 204 YNDEKGICFFTD--FLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 259 (442)
Q Consensus 204 y~~~~G~~~f~d--qIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~ 259 (442)
||...|...|++ +.|-+.. ..+||||..++ |.++++||+++||....
T Consensus 82 YNwhhGaVqy~~grftip~g~----g~~GDSGRpi~-----DNsGrVVaIVLGG~neG 130 (158)
T PF00944_consen 82 YNWHHGAVQYSNGRFTIPTGV----GKPGDSGRPIF-----DNSGRVVAIVLGGANEG 130 (158)
T ss_dssp EEETTEEEEEETTEEEEETTS-----STTSTTEEEE-----STTSBEEEEEEEEEEET
T ss_pred eccccceEEEeCCeEEeccCC----CCCCCCCCccC-----cCCCCEEEEEecCCCCC
Confidence 455556555654 4454555 78999999999 99999999999998764
No 10
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=95.46 E-value=0.12 Score=52.40 Aligned_cols=89 Identities=20% Similarity=0.280 Sum_probs=60.8
Q ss_pred cCCCCcEEEeeeecC----ceeEEEEEEEEE-EeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 013490 177 SLIGRQVMKVGRSSG----LTTGTVMAYALE-YNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 251 (442)
Q Consensus 177 ~~lG~~V~KvGRTTG----lT~G~I~ai~v~-y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGL 251 (442)
..+|+.|.-+|-..| +|.|.|+++.-. +..... +.++|.+... -.+|.||..++ +.+++.||+
T Consensus 143 l~vg~~v~aiGnp~g~~~tvt~Givs~~~r~~v~~~~~---~~~~IqtdAa----in~gnsGgpl~-----n~~g~~iGi 210 (347)
T COG0265 143 LRVGDVVVAIGNPFGLGQTVTSGIVSALGRTGVGSAGG---YVNFIQTDAA----INPGNSGGPLV-----NIDGEVVGI 210 (347)
T ss_pred cccCCEEEEecCCCCcccceeccEEeccccccccCccc---ccchhhcccc----cCCCCCCCceE-----cCCCcEEEE
Confidence 348898888888888 677777777643 322111 6677765544 68999999999 899999998
Q ss_pred EEecCCCCCccccccCCCCccceeeechHHHHhh
Q 013490 252 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDL 285 (442)
Q Consensus 252 lfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~ 285 (442)
..+.-...+. .....|+-|+..+...
T Consensus 211 nt~~~~~~~~--------~~gigfaiP~~~~~~v 236 (347)
T COG0265 211 NTAIIAPSGG--------SSGIGFAIPVNLVAPV 236 (347)
T ss_pred EEEEecCCCC--------cceeEEEecHHHHHHH
Confidence 8876654310 1224677777665543
No 11
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=94.80 E-value=0.079 Score=59.24 Aligned_cols=44 Identities=23% Similarity=0.244 Sum_probs=38.7
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHHhhcC
Q 013490 227 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 287 (442)
Q Consensus 227 S~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L~ 287 (442)
+.+|-|||.++ +-.+++|+|.-||....+ .++|-||.+|+++|-
T Consensus 213 tsggssgspVv-----~i~gyAVAl~agg~~ssa------------s~ffLpLdrV~RaL~ 256 (955)
T KOG1421|consen 213 TSGGSSGSPVV-----DIPGYAVALNAGGSISSA------------SDFFLPLDRVVRALR 256 (955)
T ss_pred CCCCCCCCcee-----cccceEEeeecCCccccc------------ccceeeccchhhhhh
Confidence 78899999999 899999999999988652 389999999998774
No 12
>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=93.88 E-value=1.6 Score=39.58 Aligned_cols=29 Identities=28% Similarity=0.446 Sum_probs=21.5
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEecCC
Q 013490 227 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 257 (442)
Q Consensus 227 S~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~ 257 (442)
.-+||||+.++.. .+...+++|++..|..
T Consensus 181 ~c~gdsGgpl~~~--~~~~~~lvGI~s~g~~ 209 (232)
T cd00190 181 ACQGDSGGPLVCN--DNGRGVLVGIVSWGSG 209 (232)
T ss_pred cccCCCCCcEEEE--eCCEEEEEEEEehhhc
Confidence 4569999999952 1244789999988764
No 13
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=92.82 E-value=1.4 Score=44.25 Aligned_cols=28 Identities=32% Similarity=0.542 Sum_probs=24.5
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEecCCCC
Q 013490 227 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 259 (442)
Q Consensus 227 S~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~ 259 (442)
..||+|||.++ ..+.+++|++++|-.-.
T Consensus 200 T~pG~SGSpv~-----~~~~~vigv~~~g~~~~ 227 (251)
T COG3591 200 TLPGSSGSPVL-----ISKDEVIGVHYNGPGAN 227 (251)
T ss_pred ccCCCCCCceE-----ecCceEEEEEecCCCcc
Confidence 68999999999 56779999999998744
No 14
>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=91.86 E-value=3.5 Score=37.64 Aligned_cols=28 Identities=32% Similarity=0.456 Sum_probs=20.8
Q ss_pred CCCCccceEEeeccCCCCCceEEEEEecCCCC
Q 013490 228 LEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 259 (442)
Q Consensus 228 ~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~ 259 (442)
-+||||+.++... + ..+++|++..|. .+
T Consensus 183 c~gdsG~pl~~~~--~-~~~l~Gi~s~g~-~C 210 (229)
T smart00020 183 CQGDSGGPLVCND--G-RWVLVGIVSWGS-GC 210 (229)
T ss_pred cCCCCCCeeEEEC--C-CEEEEEEEEECC-CC
Confidence 4599999999521 1 458999998887 44
No 15
>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=91.30 E-value=0.21 Score=45.26 Aligned_cols=51 Identities=22% Similarity=0.303 Sum_probs=38.1
Q ss_pred CeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHH
Q 013490 209 GICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 283 (442)
Q Consensus 209 G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL 283 (442)
.+.+.++.++...+ ++|||-|++++ -+.-++||+-||.... ..|.+|+.++
T Consensus 73 P~h~Q~~~l~g~Gp----~~PGdCGg~L~------C~HGViGi~Tagg~g~--------------VaF~dir~~~ 123 (127)
T PF00947_consen 73 PKHYQYNLLIGEGP----AEPGDCGGILR------CKHGVIGIVTAGGEGH--------------VAFADIRDLL 123 (127)
T ss_dssp -SEEEECEEEEE-S----SSTT-TCSEEE------ETTCEEEEEEEEETTE--------------EEEEECCCGS
T ss_pred hhheecCceeeccc----CCCCCCCceeE------eCCCeEEEEEeCCCce--------------EEEEechhhh
Confidence 35678888887776 99999999998 3455999999998754 7788877653
No 16
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=91.20 E-value=3.7 Score=40.84 Aligned_cols=72 Identities=21% Similarity=0.274 Sum_probs=46.2
Q ss_pred cccCCCCcEEEeee--ecCceeEEEEEEEEEEeCCCCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEE
Q 013490 175 INSLIGRQVMKVGR--SSGLTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGII 252 (442)
Q Consensus 175 ~~~~lG~~V~KvGR--TTGlT~G~I~ai~v~y~~~~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLl 252 (442)
..|..++.|+.+|- .+....-+|+.-...|.... ..+.+.+|- +..||=|+.++. -..+.+||+|
T Consensus 103 R~P~~~e~v~mVg~~fq~k~~~s~vSesS~i~p~~~-~~fWkHwIs--------Tk~G~CG~PlVs----~~Dg~IVGiH 169 (235)
T PF00863_consen 103 RAPKEGERVCMVGSNFQEKSISSTVSESSWIYPEEN-SHFWKHWIS--------TKDGDCGLPLVS----TKDGKIVGIH 169 (235)
T ss_dssp ----TT-EEEEEEEECSSCCCEEEEEEEEEEEEETT-TTEEEE-C-----------TT-TT-EEEE----TTT--EEEEE
T ss_pred cCCCCCCEEEEEEEEEEcCCeeEEECCceEEeecCC-CCeeEEEec--------CCCCccCCcEEE----cCCCcEEEEE
Confidence 36899999999986 77777888888876666332 236777765 456999999995 5788999999
Q ss_pred EecCCCC
Q 013490 253 WGGTANR 259 (442)
Q Consensus 253 fGGs~~~ 259 (442)
..++...
T Consensus 170 sl~~~~~ 176 (235)
T PF00863_consen 170 SLTSNTS 176 (235)
T ss_dssp EEEETTT
T ss_pred cCccCCC
Confidence 9988765
No 17
>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=86.20 E-value=0.46 Score=48.22 Aligned_cols=29 Identities=31% Similarity=0.459 Sum_probs=22.4
Q ss_pred CCCCCCCccceEEeeccCCCCCceEEEEEecCCC
Q 013490 225 TFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTAN 258 (442)
Q Consensus 225 ~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~ 258 (442)
-|+.+|||||.++ .+.+.+||+|-|.+..
T Consensus 203 ~fT~~GDSGSPVV-----t~dg~liGVHTGSn~~ 231 (297)
T PF05579_consen 203 CFTGPGDSGSPVV-----TEDGDLIGVHTGSNKR 231 (297)
T ss_dssp ESS-GGCTT-EEE-----ETTC-EEEEEEEEETT
T ss_pred EEcCCCCCCCccC-----cCCCCEEEEEecCCCc
Confidence 4889999999999 6889999999996653
No 18
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=83.73 E-value=1.3 Score=50.19 Aligned_cols=65 Identities=28% Similarity=0.359 Sum_probs=46.0
Q ss_pred EEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHHhhcC
Q 013490 212 FFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 287 (442)
Q Consensus 212 ~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL~~L~ 287 (442)
+--||+-+.+ .-+|-|||.++ |.++++|||.|-|+-..=-.-+.. .+..+.++..+|.-||-.|+
T Consensus 620 ~pv~FlstnD-----itGGNSGSPvl-----N~~GeLVGl~FDgn~Esl~~D~~f-dp~~~R~I~VDiRyvL~~ld 684 (698)
T PF10459_consen 620 VPVNFLSTND-----ITGGNSGSPVL-----NAKGELVGLAFDGNWESLSGDIAF-DPELNRTIHVDIRYVLWALD 684 (698)
T ss_pred eeeEEEeccC-----cCCCCCCCccC-----CCCceEEEEeecCchhhccccccc-ccccceeEEEEHHHHHHHHH
Confidence 3446666555 57899999999 999999999999985430001111 13347799999999988763
No 19
>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=80.66 E-value=1.8 Score=39.45 Aligned_cols=27 Identities=30% Similarity=0.349 Sum_probs=21.6
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEecCCC
Q 013490 227 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTAN 258 (442)
Q Consensus 227 S~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~ 258 (442)
-.+|-|||+++ +.++++|||+++|-..
T Consensus 94 ~~~GsSGSpi~-----n~~g~ivGlYg~g~~~ 120 (132)
T PF00949_consen 94 FPKGSSGSPIF-----NQNGEIVGLYGNGVEV 120 (132)
T ss_dssp S-TTGTT-EEE-----ETTSCEEEEEEEEEE-
T ss_pred cCCCCCCCceE-----cCCCcEEEEEccceee
Confidence 36799999999 8999999999998653
No 20
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase; InterPro: IPR024387 This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Probab=63.92 E-value=10 Score=37.62 Aligned_cols=49 Identities=29% Similarity=0.298 Sum_probs=31.5
Q ss_pred CCeEEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCCCc
Q 013490 208 KGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGR 261 (442)
Q Consensus 208 ~G~~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr 261 (442)
+|..+.+.-+-...+ +..||=||++++- +...-..++|||.+|..+.++
T Consensus 162 ~~~ytir~gleY~~~----t~~GdCGs~i~~~-~t~~~RKIvGiHVAG~~~~~~ 210 (231)
T PF12381_consen 162 KGQYTIRQGLEYQMP----TMNGDCGSPIVRN-NTQMVRKIVGIHVAGSANHAM 210 (231)
T ss_pred CCcEEeeeeeeEECC----CcCCCccceeeEc-chhhhhhhheeeecccccccc
Confidence 344444443333333 8999999999962 111234589999999986644
No 21
>PF01732 DUF31: Putative peptidase (DUF31); InterPro: IPR022382 This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas.
Probab=63.01 E-value=5.4 Score=41.29 Aligned_cols=22 Identities=36% Similarity=0.673 Sum_probs=20.6
Q ss_pred CCCCccceEEeeccCCCCCceEEEEEe
Q 013490 228 LEGDSGSLILLTGQNGEKPRPVGIIWG 254 (442)
Q Consensus 228 ~~GDSGSlVl~~~~~d~~~~~VGLlfG 254 (442)
.+|=|||+|+ ++++++|||+||
T Consensus 353 ~gGaSGS~V~-----n~~~~lvGIy~g 374 (374)
T PF01732_consen 353 GGGASGSMVI-----NQNNELVGIYFG 374 (374)
T ss_pred CCCCCcCeEE-----CCCCCEEEEeCC
Confidence 5899999999 999999999997
No 22
>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=58.65 E-value=11 Score=35.41 Aligned_cols=39 Identities=21% Similarity=0.206 Sum_probs=28.6
Q ss_pred EEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCC
Q 013490 213 FTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 257 (442)
Q Consensus 213 f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~ 257 (442)
+...+....+ +.+||-||+++.. ......++|||.||++
T Consensus 134 ~~~~~~Y~~~----t~~G~CG~~l~~~--~~~~~~i~GiHvaG~G 172 (172)
T PF00548_consen 134 TPRSLKYKAP----TKPGMCGSPLVSR--IGGQGKIIGIHVAGNG 172 (172)
T ss_dssp EEEEEEEESE----EETTGTTEEEEES--CGGTTEEEEEEEEEES
T ss_pred eeEEEEEccC----CCCCccCCeEEEe--eccCccEEEEEeccCC
Confidence 4445555555 7789999999952 3447889999999963
No 23
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=58.27 E-value=40 Score=36.93 Aligned_cols=77 Identities=14% Similarity=0.085 Sum_probs=45.4
Q ss_pred ceeEEEEEEEEEEeCCCCe--EEEEEEEEEcCCCCCCCCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCC
Q 013490 192 LTTGTVMAYALEYNDEKGI--CFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQP 269 (442)
Q Consensus 192 lT~G~I~ai~v~y~~~~G~--~~f~dqIIt~~~~~~FS~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~ 269 (442)
+|.|.+++..-.....+.. .+..+.+-+..- ...|-||-++| +..+.+||+.|.--...|-..
T Consensus 268 ~t~g~vs~~~R~~~~lg~~~g~~i~~~~qtd~a----i~~~nsg~~ll-----~~DG~~IgVn~~~~~ri~~~~------ 332 (473)
T KOG1320|consen 268 LTQGMVSGQLRKSFKLGLETGVLISKINQTDAA----INPGNSGGPLL-----NLDGEVIGVNTRKVTRIGFSH------ 332 (473)
T ss_pred eeecccccccccccccCcccceeeeeecccchh----hhcccCCCcEE-----EecCcEeeeeeeeeEEeeccc------
Confidence 3555555544222222222 344455555544 78899999999 889999997776544221112
Q ss_pred CccceeeechHHHHhh
Q 013490 270 PVNWTSGVDLGRLLDL 285 (442)
Q Consensus 270 ~~~~tl~~pI~~VL~~ 285 (442)
-.++.-|+..|+..
T Consensus 333 --~iSf~~p~d~vl~~ 346 (473)
T KOG1320|consen 333 --GISFKIPIDTVLVI 346 (473)
T ss_pred --cceeccCchHhhhh
Confidence 23777888887763
No 24
>PF02122 Peptidase_S39: Peptidase S39; InterPro: IPR000382 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) [, ]. ORF2 of Potato leafroll virus (PLrV) encodes a polyprotein which is translated following a -1 frameshift. The polyprotein has a putative linear arrangement of membrane achor-VPg-peptidase-polmerase domains. The serine peptidase domain which is found in this group of sequences belongs to MEROPS peptidase family S39 (clan PA(S)). It is likely that the peptidase domain is involved in the cleavage of the polyprotein []. The nucleotide sequence for the RNA of PLrV has been determined [, ]. The sequence contains six large open reading frames (ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which overlap in different reading frames; it is suggested that the third ORF in the 5' block is translated by frameshift readthrough near the end of the 70K protein, yielding a 118K polypeptide []. Segments of the predicted amino acid sequences of these ORFs resemble those of known viral RNA polymerases, ATP-binding proteins and viral genome-linked proteins. The nucleotide sequence of the genomic RNA of Beet western yellows virus (BWYV) has been determined []. The sequence contains six long ORFs. A cluster of three of these ORFs, including the coat protein cistron, display extensive amino acid sequence similarity to corresponding ORFs of a second luteovirus: Barley yellow dwarf virus [].; GO: 0004252 serine-type endopeptidase activity, 0022415 viral reproductive process, 0016021 integral to membrane; PDB: 1ZYO_A.
Probab=35.88 E-value=41 Score=32.80 Aligned_cols=42 Identities=21% Similarity=0.178 Sum_probs=15.1
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEecCCCCCccccccCCCCccceeeechHHHH
Q 013490 227 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 283 (442)
Q Consensus 227 S~~GDSGSlVl~~~~~d~~~~~VGLlfGGs~~~Gr~~~~~g~~~~~~tl~~pI~~VL 283 (442)
+.+|+||+-++ ..+ ..||+|-|... +...+||-+..||..+.
T Consensus 144 T~~G~SGtp~y-----~g~-~vvGvH~G~~~---------~~~~~n~n~~spip~~~ 185 (203)
T PF02122_consen 144 TSPGWSGTPYY-----SGK-NVVGVHTGSPS---------GSNRENNNRMSPIPPIP 185 (203)
T ss_dssp --TT-TT-EEE------SS--EEEEEEEE----------------------------
T ss_pred CCCCCCCCCeE-----ECC-CceEeecCccc---------ccccccccccccccccc
Confidence 78999999999 344 89999999511 12335667777776664
No 25
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.25 E-value=2.4e+02 Score=31.19 Aligned_cols=84 Identities=15% Similarity=0.137 Sum_probs=46.9
Q ss_pred cccccccccccccccccCCCCcccc-cccccccCcceeccCCCccccCCCCcEEEe-eeecCceeEEEEEEEEEEeCCCC
Q 013490 132 ETFVRADGAFIPFAEDFNLNNVTTS-VKGVGEIGDVHIIDLQSPINSLIGRQVMKV-GRSSGLTTGTVMAYALEYNDEKG 209 (442)
Q Consensus 132 ~n~vDaD~AlI~~A~~~d~s~vs~~-I~giG~iG~v~~idl~g~~~~~lG~~V~Kv-GRTTGlT~G~I~ai~v~y~~~~G 209 (442)
.++..||.|++.+. ....|-.- -...|++ |.+...|+=+ |-+.=+|.|.|.++..+-...++
T Consensus 132 ~~~~~cd~Avv~Ie---~~~f~~~~~~~e~~~i-------------p~l~~S~~Vv~gd~i~VTnghV~~~~~~~y~~~~ 195 (473)
T KOG1320|consen 132 AVFEECDLAVVYIE---SEEFWKGMNPFELGDI-------------PSLNGSGFVVGGDGIIVTNGHVVRVEPRIYAHSS 195 (473)
T ss_pred HhhhcccceEEEEe---eccccCCCcccccCCC-------------cccCccEEEEcCCcEEEEeeEEEEEEeccccCCC
Confidence 36678988986543 22333321 1333443 3333333322 45555899999999955444445
Q ss_pred eEEEEEEEEEcCCCCCCCCCCCccceEE
Q 013490 210 ICFFTDFLVVGENQQTFDLEGDSGSLIL 237 (442)
Q Consensus 210 ~~~f~dqIIt~~~~~~FS~~GDSGSlVl 237 (442)
..+..-||-... .+|.||-..+
T Consensus 196 ~~l~~vqi~aa~------~~~~s~ep~i 217 (473)
T KOG1320|consen 196 TVLLRVQIDAAI------GPGNSGEPVI 217 (473)
T ss_pred cceeeEEEEEee------cCCccCCCeE
Confidence 555555665443 4577777776
Done!