Query 007476
Match_columns 602
No_of_seqs 190 out of 430
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 00:07:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08192 Peptidase_S64: Peptid 99.7 1.3E-16 2.8E-21 177.2 12.9 100 338-449 586-686 (695)
2 TIGR02038 protease_degS peripl 98.0 0.00013 2.8E-09 77.8 14.1 94 337-448 146-243 (351)
3 PRK10139 serine endoprotease; 97.9 8.4E-05 1.8E-09 82.0 12.8 89 337-446 160-253 (455)
4 PRK10898 serine endoprotease; 97.8 0.00029 6.3E-09 75.3 13.6 93 338-448 147-244 (353)
5 TIGR02037 degP_htrA_DO peripla 97.8 0.00022 4.7E-09 77.6 12.7 93 337-449 127-223 (428)
6 PRK10942 serine endoprotease; 97.8 0.00023 5E-09 78.9 13.0 89 337-445 181-273 (473)
7 PF13365 Trypsin_2: Trypsin-li 97.1 0.0026 5.6E-08 55.0 8.0 21 388-413 100-120 (120)
8 PF00089 Trypsin: Trypsin; In 96.8 0.0029 6.3E-08 59.7 6.6 181 220-446 25-218 (220)
9 PF00863 Peptidase_C4: Peptida 95.4 0.15 3.3E-06 52.4 11.3 85 336-445 102-188 (235)
10 cd00190 Tryp_SPc Trypsin-like 95.2 0.45 9.7E-06 45.2 13.0 30 388-419 180-209 (232)
11 smart00020 Tryp_SPc Trypsin-li 95.1 0.32 7E-06 46.5 11.8 29 389-421 182-210 (229)
12 COG0265 DegQ Trypsin-like seri 94.9 0.21 4.4E-06 53.0 10.9 90 338-447 142-236 (347)
13 KOG1421 Predicted signaling-as 94.7 0.07 1.5E-06 61.7 7.0 45 388-449 212-256 (955)
14 PF00944 Peptidase_S3: Alphavi 94.3 0.056 1.2E-06 51.6 4.5 29 388-421 102-130 (158)
15 COG3591 V8-like Glu-specific e 93.0 1.2 2.6E-05 46.5 11.7 27 389-420 200-226 (251)
16 PF00947 Pico_P2A: Picornaviru 90.3 0.31 6.8E-06 45.9 3.8 50 372-445 74-123 (127)
17 PF05579 Peptidase_S32: Equine 88.3 0.44 9.5E-06 50.1 3.5 27 388-419 204-230 (297)
18 PF00949 Peptidase_S7: Peptida 80.9 1.2 2.5E-05 42.4 2.4 26 389-419 94-119 (132)
19 PF10459 Peptidase_S46: Peptid 79.9 2.3 4.9E-05 50.2 4.9 52 389-449 630-684 (698)
20 PF00548 Peptidase_C3: 3C cyst 78.9 22 0.00047 34.8 10.6 29 389-419 144-172 (172)
21 PF12381 Peptidase_C3G: Tungro 64.3 8.4 0.00018 39.7 4.1 33 388-421 176-208 (231)
22 PF01732 DUF31: Putative pepti 60.7 6.2 0.00013 42.7 2.6 22 390-416 353-374 (374)
23 KOG1320 Serine protease [Postt 40.0 1.1E+02 0.0024 35.1 8.2 47 388-447 300-346 (473)
24 KOG1320 Serine protease [Postt 34.1 1.1E+02 0.0025 34.9 7.1 45 349-399 173-217 (473)
25 PF02122 Peptidase_S39: Peptid 33.4 34 0.00073 34.8 2.7 43 389-446 144-186 (203)
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=99.69 E-value=1.3e-16 Score=177.16 Aligned_cols=100 Identities=30% Similarity=0.448 Sum_probs=84.9
Q ss_pred cccCCCeEEEeeecccceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccC-CCCCceEEEEEe
Q 007476 338 NSLIGRQVMKVGRSSGLTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQN-GEKPRPVGIIWG 416 (602)
Q Consensus 338 ~p~lG~~V~KvGRTTGlT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~-d~~~~aVGLlfG 416 (602)
....|+.|+|+|||||+|+|+|+++++.|+.+ |...+.+++|.+.+...|+.+|||||+|+.+.++ ...-.+|||+++
T Consensus 586 ~~~~G~~VfK~GrTTgyT~G~lNg~klvyw~d-G~i~s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhs 664 (695)
T PF08192_consen 586 NLVPGMEVFKVGRTTGYTTGILNGIKLVYWAD-GKIQSSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHS 664 (695)
T ss_pred ccCCCCeEEEecccCCccceEecceEEEEecC-CCeEEEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeee
Confidence 45679999999999999999999999888876 5567899999997778899999999999965544 334569999999
Q ss_pred ccCCCcccccccCCCCcceEEeechHHHHHhcC
Q 007476 417 GTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 449 (602)
Q Consensus 417 Gs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~L~ 449 (602)
.++.. ..|.+|+||..||+.|+
T Consensus 665 ydge~-----------kqfglftPi~~il~rl~ 686 (695)
T PF08192_consen 665 YDGEQ-----------KQFGLFTPINEILDRLE 686 (695)
T ss_pred cCCcc-----------ceeeccCcHHHHHHHHH
Confidence 88643 48999999999999875
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=97.95 E-value=0.00013 Score=77.82 Aligned_cols=94 Identities=15% Similarity=0.174 Sum_probs=64.1
Q ss_pred ccccCCCeEEEeeeccc----ceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 007476 337 INSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 412 (602)
Q Consensus 337 ~~p~lG~~V~KvGRTTG----lT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVG 412 (602)
....+|+.|.-+|...| +|.|.|.++.-......+ ..+++.+.. --.+|.||+.++ |.++++||
T Consensus 146 ~~~~~G~~V~aiG~P~~~~~s~t~GiIs~~~r~~~~~~~---~~~~iqtda----~i~~GnSGGpl~-----n~~G~vIG 213 (351)
T TIGR02038 146 RPPHVGDVVLAIGNPYNLGQTITQGIISATGRNGLSSVG---RQNFIQTDA----AINAGNSGGALI-----NTNGELVG 213 (351)
T ss_pred CccCCCCEEEEEeCCCCCCCcEEEEEEEeccCcccCCCC---cceEEEECC----ccCCCCCcceEE-----CCCCeEEE
Confidence 35789999999999876 478888887522111112 134555554 256799999999 89999999
Q ss_pred EEEeccCCCcccccccCCCCcceEEeechHHHHHhc
Q 007476 413 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLL 448 (602)
Q Consensus 413 LlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~L 448 (602)
+..+.-... .+....+..|+-|++.+...+
T Consensus 214 I~~~~~~~~------~~~~~~g~~faIP~~~~~~vl 243 (351)
T TIGR02038 214 INTASFQKG------GDEGGEGINFAIPIKLAHKIM 243 (351)
T ss_pred EEeeeeccc------CCCCccceEEEecHHHHHHHH
Confidence 987542211 011234678999998877765
No 3
>PRK10139 serine endoprotease; Provisional
Probab=97.94 E-value=8.4e-05 Score=82.02 Aligned_cols=89 Identities=20% Similarity=0.192 Sum_probs=61.7
Q ss_pred ccccCCCeEEEeeeccc----ceEEEEEEEEEE-EeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceE
Q 007476 337 INSLIGRQVMKVGRSSG----LTTGTVMAYALE-YNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPV 411 (602)
Q Consensus 337 ~~p~lG~~V~KvGRTTG----lT~G~I~ai~V~-y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aV 411 (602)
....+|+.|.-+|.--| .|.|.|.++.-. +.. .+ +.++|.+.. --.+|.||..++ |.++++|
T Consensus 160 ~~~~~G~~V~aiG~P~g~~~tvt~GivS~~~r~~~~~-~~---~~~~iqtda----~in~GnSGGpl~-----n~~G~vI 226 (455)
T PRK10139 160 DKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNL-EG---LENFIQTDA----SINRGNSGGALL-----NLNGELI 226 (455)
T ss_pred cccCCCCEEEEEecCCCCCCceEEEEEccccccccCC-CC---cceEEEECC----ccCCCCCcceEE-----CCCCeEE
Confidence 35688999999988655 478888877522 111 11 356677765 356899999999 8999999
Q ss_pred EEEEeccCCCcccccccCCCCcceEEeechHHHHH
Q 007476 412 GIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLD 446 (602)
Q Consensus 412 GLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~ 446 (602)
|+..+.-... .+..++.|+-|+..+..
T Consensus 227 Gi~~~~~~~~--------~~~~gigfaIP~~~~~~ 253 (455)
T PRK10139 227 GINTAILAPG--------GGSVGIGFAIPSNMART 253 (455)
T ss_pred EEEEEEEcCC--------CCccceEEEEEhHHHHH
Confidence 9998743211 12246789999865544
No 4
>PRK10898 serine endoprotease; Provisional
Probab=97.80 E-value=0.00029 Score=75.32 Aligned_cols=93 Identities=18% Similarity=0.245 Sum_probs=61.3
Q ss_pred cccCCCeEEEeeeccc----ceEEEEEEEE-EEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 007476 338 NSLIGRQVMKVGRSSG----LTTGTVMAYA-LEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 412 (602)
Q Consensus 338 ~p~lG~~V~KvGRTTG----lT~G~I~ai~-V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVG 412 (602)
.+..|+.|.-+|.-.| .|.|.|.+.. ..+... +. .+++.+.. --.+|.||..++ |.++++||
T Consensus 147 ~~~~G~~V~aiG~P~g~~~~~t~Giis~~~r~~~~~~-~~---~~~iqtda----~i~~GnSGGPl~-----n~~G~vvG 213 (353)
T PRK10898 147 VPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLSPT-GR---QNFLQTDA----SINHGNSGGALV-----NSLGELMG 213 (353)
T ss_pred cCCCCCEEEEEeCCCCcCCCcceeEEEeccccccCCc-cc---cceEEecc----ccCCCCCcceEE-----CCCCeEEE
Confidence 4689999999998766 5789998875 222211 11 23455544 247799999999 89999999
Q ss_pred EEEeccCCCcccccccCCCCcceEEeechHHHHHhc
Q 007476 413 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLL 448 (602)
Q Consensus 413 LlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~L 448 (602)
|..+.-... ..+..+.+..|+-|+..+...+
T Consensus 214 I~~~~~~~~-----~~~~~~~g~~faIP~~~~~~~~ 244 (353)
T PRK10898 214 INTLSFDKS-----NDGETPEGIGFAIPTQLATKIM 244 (353)
T ss_pred EEEEEeccc-----CCCCcccceEEEEchHHHHHHH
Confidence 987532211 0011234678998887755544
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=97.78 E-value=0.00022 Score=77.55 Aligned_cols=93 Identities=17% Similarity=0.178 Sum_probs=62.5
Q ss_pred ccccCCCeEEEeeeccc----ceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 007476 337 INSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 412 (602)
Q Consensus 337 ~~p~lG~~V~KvGRTTG----lT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVG 412 (602)
....+|+.|.-+|.--| +|.|.|+++.-.... ...+.+++.++. --.+|.||+.++ |.++++||
T Consensus 127 ~~~~~G~~v~aiG~p~g~~~~~t~G~vs~~~~~~~~---~~~~~~~i~tda----~i~~GnSGGpl~-----n~~G~viG 194 (428)
T TIGR02037 127 DKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSGLG---IGDYENFIQTDA----AINPGNSGGPLV-----NLRGEVIG 194 (428)
T ss_pred CCCCCCCEEEEEECCCcCCCcEEEEEEEecccCccC---CCCccceEEECC----CCCCCCCCCceE-----CCCCeEEE
Confidence 45689999999998744 578888877522111 112345666655 367899999999 89999999
Q ss_pred EEEeccCCCcccccccCCCCcceEEeechHHHHHhcC
Q 007476 413 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 449 (602)
Q Consensus 413 LlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~L~ 449 (602)
|..+.-... ++..++.|+-|+..+.+.|+
T Consensus 195 I~~~~~~~~--------g~~~g~~faiP~~~~~~~~~ 223 (428)
T TIGR02037 195 INTAIYSPS--------GGNVGIGFAIPSNMAKNVVD 223 (428)
T ss_pred EEeEEEcCC--------CCccceEEEEEhHHHHHHHH
Confidence 987643311 11235688999866655553
No 6
>PRK10942 serine endoprotease; Provisional
Probab=97.78 E-value=0.00023 Score=78.94 Aligned_cols=89 Identities=17% Similarity=0.183 Sum_probs=59.5
Q ss_pred ccccCCCeEEEeeeccc----ceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 007476 337 INSLIGRQVMKVGRSSG----LTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 412 (602)
Q Consensus 337 ~~p~lG~~V~KvGRTTG----lT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVG 412 (602)
....+|++|.-+|..-| .|.|.|+++.-... +...+.++|.+.. --.+|.||..++ |.++++||
T Consensus 181 ~~l~~G~~V~aiG~P~g~~~tvt~GiVs~~~r~~~---~~~~~~~~iqtda----~i~~GnSGGpL~-----n~~GeviG 248 (473)
T PRK10942 181 DALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGL---NVENYENFIQTDA----AINRGNSGGALV-----NLNGELIG 248 (473)
T ss_pred cccCCCCEEEEEcCCCCCCcceeEEEEEEeecccC---CcccccceEEecc----ccCCCCCcCccC-----CCCCeEEE
Confidence 35689999999998765 48888888762210 1112345666655 245899999999 89999999
Q ss_pred EEEeccCCCcccccccCCCCcceEEeechHHHH
Q 007476 413 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 445 (602)
Q Consensus 413 LlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL 445 (602)
|..+.-... + +.....|+-|+..+.
T Consensus 249 I~t~~~~~~-------g-~~~g~gfaIP~~~~~ 273 (473)
T PRK10942 249 INTAILAPD-------G-GNIGIGFAIPSNMVK 273 (473)
T ss_pred EEEEEEcCC-------C-CcccEEEEEEHHHHH
Confidence 998643211 0 112567888875544
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=97.06 E-value=0.0026 Score=55.02 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=18.6
Q ss_pred CCCCCCccceEEeeccCCCCCceEEE
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGI 413 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGL 413 (602)
...+|.||+.|+ |.++++|||
T Consensus 100 ~~~~G~SGgpv~-----~~~G~vvGi 120 (120)
T PF13365_consen 100 DTRPGSSGGPVF-----DSDGRVVGI 120 (120)
T ss_dssp S-STTTTTSEEE-----ETTSEEEEE
T ss_pred ccCCCcEeHhEE-----CCCCEEEeC
Confidence 588999999999 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=96.80 E-value=0.0029 Score=59.70 Aligned_cols=181 Identities=17% Similarity=0.208 Sum_probs=87.0
Q ss_pred eeeeEEEEEeCCCCceeEEeecCcccccCCCCCccCCCCCCCccCCcccCCCc--cccceeeeeccccccccCCCCcccc
Q 007476 220 YGTLGAIVRSRTGNQQVGFLTNRHVAVDLDYPNQKMFHPLPPSLGPGVYLGAV--ERATSFITDDLWYGIFAGTNPETFV 297 (602)
Q Consensus 220 aGTLGcLV~D~~G~~~~yiLSNnHVla~~n~~~q~~~~pg~pIlQPG~~DGG~--~rl~kfIpl~~~~~i~~g~~p~N~V 297 (602)
.--.|+||.++ ++||++||+...+... . ..+...++.. ++.. -...+++....| ++.+ .
T Consensus 25 ~~C~G~li~~~------~vLTaahC~~~~~~~~--v-~~g~~~~~~~--~~~~~~~~v~~~~~h~~~-------~~~~-~ 85 (220)
T PF00089_consen 25 FFCTGTLISPR------WVLTAAHCVDGASDIK--V-RLGTYSIRNS--DGSEQTIKVSKIIIHPKY-------DPST-Y 85 (220)
T ss_dssp EEEEEEEEETT------EEEEEGGGHTSGGSEE--E-EESESBTTST--TTTSEEEEEEEEEEETTS-------BTTT-T
T ss_pred eeEeEEecccc------cccccccccccccccc--c-cccccccccc--cccccccccccccccccc-------cccc-c
Confidence 34458888874 9999999999921100 0 0111111111 1111 112222222221 1222 3
Q ss_pred cccccccccccccCCCCcccccccccccCcceeecccC-cccccCCCeEEEeeecccceEE---EEEEEEEEEeCC----
Q 007476 298 RADGAFIPFAEDFNLNNVTTSVKGVGEIGDVHIIDLQS-PINSLIGRQVMKVGRSSGLTTG---TVMAYALEYNDE---- 369 (602)
Q Consensus 298 DaD~AlI~va~~~d~s~vs~~I~~vG~IG~~~~vdl~g-~~~p~lG~~V~KvGRTTGlT~G---~I~ai~V~y~~~---- 369 (602)
+.|+||+++.++++ ....+.. + .+.. ...+..|+.+.-+|-......+ .+....+.+-..
T Consensus 86 ~~DiAll~L~~~~~---~~~~~~~---~------~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~ 153 (220)
T PF00089_consen 86 DNDIALLKLDRPIT---FGDNIQP---I------CLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCR 153 (220)
T ss_dssp TTSEEEEEESSSSE---HBSSBEE---S------BBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHH
T ss_pred cccccccccccccc---ccccccc---c------cccccccccccccccccccccccccccccccccccccccccccccc
Confidence 55889999887522 1222211 1 1111 1234677777777766654444 444333222100
Q ss_pred ---CCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEEEEEeccCCCcccccccCCCCcceEEeechHHHHH
Q 007476 370 ---KGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLD 446 (602)
Q Consensus 370 ---~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~ 446 (602)
... ...+++-+...+..-...|||||.++. .++.++|++..+.. + ..+....+|++|...++
T Consensus 154 ~~~~~~-~~~~~~c~~~~~~~~~~~g~sG~pl~~-----~~~~lvGI~s~~~~-c--------~~~~~~~v~~~v~~~~~ 218 (220)
T PF00089_consen 154 SSYNDN-LTPNMICAGSSGSGDACQGDSGGPLIC-----NNNYLVGIVSFGEN-C--------GSPNYPGVYTRVSSYLD 218 (220)
T ss_dssp HHTTTT-STTTEEEEETTSSSBGGTTTTTSEEEE-----TTEEEEEEEEEESS-S--------SBTTSEEEEEEGGGGHH
T ss_pred cccccc-ccccccccccccccccccccccccccc-----ceeeecceeeecCC-C--------CCCCcCEEEEEHHHhhc
Confidence 000 011122111111223567999999993 33379999999833 3 11223588888876653
No 9
>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=95.41 E-value=0.15 Score=52.45 Aligned_cols=85 Identities=18% Similarity=0.181 Sum_probs=53.3
Q ss_pred cccccCCCeEEEeee--cccceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEEE
Q 007476 336 PINSLIGRQVMKVGR--SSGLTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGI 413 (602)
Q Consensus 336 ~~~p~lG~~V~KvGR--TTGlT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVGL 413 (602)
...|..++.|+.+|- .+....-+|+.-...|... +..+++.+|-|.+ ||=|+.++. -.++.+||+
T Consensus 102 FR~P~~~e~v~mVg~~fq~k~~~s~vSesS~i~p~~-~~~fWkHwIsTk~--------G~CG~PlVs----~~Dg~IVGi 168 (235)
T PF00863_consen 102 FRAPKEGERVCMVGSNFQEKSISSTVSESSWIYPEE-NSHFWKHWISTKD--------GDCGLPLVS----TKDGKIVGI 168 (235)
T ss_dssp B----TT-EEEEEEEECSSCCCEEEEEEEEEEEEET-TTTEEEE-C---T--------T-TT-EEEE----TTT--EEEE
T ss_pred ccCCCCCCEEEEEEEEEEcCCeeEEECCceEEeecC-CCCeeEEEecCCC--------CccCCcEEE----cCCCcEEEE
Confidence 368999999999996 7778888888887777633 3466888876544 999999995 578999999
Q ss_pred EEeccCCCcccccccCCCCcceEEeechHHHH
Q 007476 414 IWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 445 (602)
Q Consensus 414 lfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL 445 (602)
|..++... ..-||.|+..=+
T Consensus 169 Hsl~~~~~------------~~N~F~~f~~~f 188 (235)
T PF00863_consen 169 HSLTSNTS------------SRNYFTPFPDDF 188 (235)
T ss_dssp EEEEETTT------------SSEEEEE--TTH
T ss_pred EcCccCCC------------CeEEEEcCCHHH
Confidence 99988754 335777765433
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=95.17 E-value=0.45 Score=45.16 Aligned_cols=30 Identities=27% Similarity=0.381 Sum_probs=22.1
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccC
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 419 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~ 419 (602)
-.-+||||+.++.. .+...+++|++..|..
T Consensus 180 ~~c~gdsGgpl~~~--~~~~~~lvGI~s~g~~ 209 (232)
T cd00190 180 DACQGDSGGPLVCN--DNGRGVLVGIVSWGSG 209 (232)
T ss_pred ccccCCCCCcEEEE--eCCEEEEEEEEehhhc
Confidence 35579999999952 1234789999988764
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=95.07 E-value=0.32 Score=46.52 Aligned_cols=29 Identities=31% Similarity=0.437 Sum_probs=21.4
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccCCC
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 421 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~ 421 (602)
..+||||+.++... + ..+++|+...|. .+
T Consensus 182 ~c~gdsG~pl~~~~--~-~~~l~Gi~s~g~-~C 210 (229)
T smart00020 182 ACQGDSGGPLVCND--G-RWVLVGIVSWGS-GC 210 (229)
T ss_pred ccCCCCCCeeEEEC--C-CEEEEEEEEECC-CC
Confidence 45699999999421 1 458999998887 44
No 12
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=94.88 E-value=0.21 Score=53.00 Aligned_cols=90 Identities=19% Similarity=0.227 Sum_probs=61.1
Q ss_pred cccCCCeEEEeeeccc----ceEEEEEEEEEE-EeCCCCeEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEE
Q 007476 338 NSLIGRQVMKVGRSSG----LTTGTVMAYALE-YNDEKGICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVG 412 (602)
Q Consensus 338 ~p~lG~~V~KvGRTTG----lT~G~I~ai~V~-y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVG 412 (602)
...+|+.|.-+|-..| +|.|.|.++.-. +.... .+.++|.+.. .-.+|.||..++ +.++.+||
T Consensus 142 ~l~vg~~v~aiGnp~g~~~tvt~Givs~~~r~~v~~~~---~~~~~IqtdA----ain~gnsGgpl~-----n~~g~~iG 209 (347)
T COG0265 142 KLRVGDVVVAIGNPFGLGQTVTSGIVSALGRTGVGSAG---GYVNFIQTDA----AINPGNSGGPLV-----NIDGEVVG 209 (347)
T ss_pred CcccCCEEEEecCCCCcccceeccEEeccccccccCcc---cccchhhccc----ccCCCCCCCceE-----cCCCcEEE
Confidence 3458999999998888 566766666532 32211 1666676554 577899999999 89999999
Q ss_pred EEEeccCCCcccccccCCCCcceEEeechHHHHHh
Q 007476 413 IIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDL 447 (602)
Q Consensus 413 LlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~ 447 (602)
+..+.-... + +.....|+-|+..+...
T Consensus 210 int~~~~~~-------~-~~~gigfaiP~~~~~~v 236 (347)
T COG0265 210 INTAIIAPS-------G-GSSGIGFAIPVNLVAPV 236 (347)
T ss_pred EEEEEecCC-------C-CcceeEEEecHHHHHHH
Confidence 888766533 1 12235677777665543
No 13
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=94.68 E-value=0.07 Score=61.67 Aligned_cols=45 Identities=22% Similarity=0.212 Sum_probs=39.2
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccCCCcccccccCCCCcceEEeechHHHHHhcC
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDLLE 449 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~L~ 449 (602)
-+.+|-|||.|+ +-.+++|.|.-||.... ...+|-||.+|+.+|-
T Consensus 212 stsggssgspVv-----~i~gyAVAl~agg~~ss------------as~ffLpLdrV~RaL~ 256 (955)
T KOG1421|consen 212 STSGGSSGSPVV-----DIPGYAVALNAGGSISS------------ASDFFLPLDRVVRALR 256 (955)
T ss_pred cCCCCCCCCcee-----cccceEEeeecCCcccc------------cccceeeccchhhhhh
Confidence 377899999999 89999999999999754 5579999999998764
No 14
>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=94.34 E-value=0.056 Score=51.57 Aligned_cols=29 Identities=34% Similarity=0.544 Sum_probs=26.3
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccCCC
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 421 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~ 421 (602)
.+.+||||..|+ |.++++||+++||.++.
T Consensus 102 ~g~~GDSGRpi~-----DNsGrVVaIVLGG~neG 130 (158)
T PF00944_consen 102 VGKPGDSGRPIF-----DNSGRVVAIVLGGANEG 130 (158)
T ss_dssp S-STTSTTEEEE-----STTSBEEEEEEEEEEET
T ss_pred CCCCCCCCCccC-----cCCCCEEEEEecCCCCC
Confidence 689999999999 99999999999999865
No 15
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=92.99 E-value=1.2 Score=46.48 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=23.8
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccCC
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTAN 420 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~ 420 (602)
..+|+|||.|+ ..+.+++|++++|..-
T Consensus 200 T~pG~SGSpv~-----~~~~~vigv~~~g~~~ 226 (251)
T COG3591 200 TLPGSSGSPVL-----ISKDEVIGVHYNGPGA 226 (251)
T ss_pred ccCCCCCCceE-----ecCceEEEEEecCCCc
Confidence 67899999999 5677999999999873
No 16
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=90.33 E-value=0.31 Score=45.91 Aligned_cols=50 Identities=22% Similarity=0.291 Sum_probs=38.3
Q ss_pred eEEEEEEEEECCCCCCCCCCCCccceEEeeccCCCCCceEEEEEeccCCCcccccccCCCCcceEEeechHHHH
Q 007476 372 ICFFTDFLVVGENQQTFDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLL 445 (602)
Q Consensus 372 ~~~F~dqIIt~~~~~~fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL 445 (602)
..+..++++..- +++|||-|++++ -+-.++||+-||.. +...|.+|..++
T Consensus 74 ~h~Q~~~l~g~G----p~~PGdCGg~L~------C~HGViGi~Tagg~--------------g~VaF~dir~~~ 123 (127)
T PF00947_consen 74 KHYQYNLLIGEG----PAEPGDCGGILR------CKHGVIGIVTAGGE--------------GHVAFADIRDLL 123 (127)
T ss_dssp SEEEECEEEEE-----SSSTT-TCSEEE------ETTCEEEEEEEEET--------------TEEEEEECCCGS
T ss_pred hheecCceeecc----cCCCCCCCceeE------eCCCeEEEEEeCCC--------------ceEEEEechhhh
Confidence 467788887766 799999999998 46669999999987 447888886653
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=88.26 E-value=0.44 Score=50.12 Aligned_cols=27 Identities=33% Similarity=0.495 Sum_probs=22.1
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccC
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 419 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~ 419 (602)
|+.+|||||.|+ ..++.+||+|-|.+.
T Consensus 204 fT~~GDSGSPVV-----t~dg~liGVHTGSn~ 230 (297)
T PF05579_consen 204 FTGPGDSGSPVV-----TEDGDLIGVHTGSNK 230 (297)
T ss_dssp SS-GGCTT-EEE-----ETTC-EEEEEEEEET
T ss_pred EcCCCCCCCccC-----cCCCCEEEEEecCCC
Confidence 899999999999 689999999999776
No 18
>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=80.86 E-value=1.2 Score=42.38 Aligned_cols=26 Identities=31% Similarity=0.391 Sum_probs=21.6
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccC
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 419 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~ 419 (602)
-.+|-|||+|+ +.++++|||+++|-.
T Consensus 94 ~~~GsSGSpi~-----n~~g~ivGlYg~g~~ 119 (132)
T PF00949_consen 94 FPKGSSGSPIF-----NQNGEIVGLYGNGVE 119 (132)
T ss_dssp S-TTGTT-EEE-----ETTSCEEEEEEEEEE
T ss_pred cCCCCCCCceE-----cCCCcEEEEEcccee
Confidence 34699999999 899999999999875
No 19
>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=79.90 E-value=2.3 Score=50.22 Aligned_cols=52 Identities=33% Similarity=0.474 Sum_probs=39.6
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccCCC--cccccccCCCC-cceEEeechHHHHHhcC
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR--GRLKLKVGQPP-VNWTSGVDLGRLLDLLE 449 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~--gr~~~~~g~~p-~~~Tl~npI~~VL~~L~ 449 (602)
.-+|-|||.++ |.++++|||.|-|+-.. |-..+ .| .+.++..+|.-||-.|+
T Consensus 630 itGGNSGSPvl-----N~~GeLVGl~FDgn~Esl~~D~~f----dp~~~R~I~VDiRyvL~~ld 684 (698)
T PF10459_consen 630 ITGGNSGSPVL-----NAKGELVGLAFDGNWESLSGDIAF----DPELNRTIHVDIRYVLWALD 684 (698)
T ss_pred cCCCCCCCccC-----CCCceEEEEeecCchhhccccccc----ccccceeEEEEHHHHHHHHH
Confidence 67899999999 99999999999998643 11111 12 46789999998887763
No 20
>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=78.89 E-value=22 Score=34.83 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=23.5
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccC
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTA 419 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~ 419 (602)
+.+||-||+++.. .+....++|||.||++
T Consensus 144 t~~G~CG~~l~~~--~~~~~~i~GiHvaG~G 172 (172)
T PF00548_consen 144 TKPGMCGSPLVSR--IGGQGKIIGIHVAGNG 172 (172)
T ss_dssp EETTGTTEEEEES--CGGTTEEEEEEEEEES
T ss_pred CCCCccCCeEEEe--eccCccEEEEEeccCC
Confidence 6789999999952 3347889999999973
No 21
>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=64.33 E-value=8.4 Score=39.72 Aligned_cols=33 Identities=33% Similarity=0.427 Sum_probs=25.5
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccCCC
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANR 421 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~ 421 (602)
.+..||=||+++.- +...-..+||||.+|+.+.
T Consensus 176 ~t~~GdCGs~i~~~-~t~~~RKIvGiHVAG~~~~ 208 (231)
T PF12381_consen 176 PTMNGDCGSPIVRN-NTQMVRKIVGIHVAGSANH 208 (231)
T ss_pred CCcCCCccceeeEc-chhhhhhhheeeecccccc
Confidence 69999999999951 1123467999999999865
No 22
>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=60.65 E-value=6.2 Score=42.67 Aligned_cols=22 Identities=36% Similarity=0.673 Sum_probs=20.5
Q ss_pred CCCCccceEEeeccCCCCCceEEEEEe
Q 007476 390 LEGDSGSLILLTGQNGEKPRPVGIIWG 416 (602)
Q Consensus 390 ~~GDSGSlVl~~~~~d~~~~aVGLlfG 416 (602)
.+|=|||+|+ +.++.+|||+||
T Consensus 353 ~gGaSGS~V~-----n~~~~lvGIy~g 374 (374)
T PF01732_consen 353 GGGASGSMVI-----NQNNELVGIYFG 374 (374)
T ss_pred CCCCCcCeEE-----CCCCCEEEEeCC
Confidence 4799999999 999999999997
No 23
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=40.02 E-value=1.1e+02 Score=35.07 Aligned_cols=47 Identities=15% Similarity=0.190 Sum_probs=34.0
Q ss_pred CCCCCCccceEEeeccCCCCCceEEEEEeccCCCcccccccCCCCcceEEeechHHHHHh
Q 007476 388 FDLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLDL 447 (602)
Q Consensus 388 fS~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~~ 447 (602)
-...|-||-+++ +.++.+||+.|.--. |..|.. ..++.-|+..|+..
T Consensus 300 ai~~~nsg~~ll-----~~DG~~IgVn~~~~~---ri~~~~-----~iSf~~p~d~vl~~ 346 (473)
T KOG1320|consen 300 AINPGNSGGPLL-----NLDGEVIGVNTRKVT---RIGFSH-----GISFKIPIDTVLVI 346 (473)
T ss_pred hhhcccCCCcEE-----EecCcEeeeeeeeeE---Eeeccc-----cceeccCchHhhhh
Confidence 577899999999 889999997776554 222222 34788888888764
No 24
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=34.07 E-value=1.1e+02 Score=34.93 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=29.8
Q ss_pred eecccceEEEEEEEEEEEeCCCCeEEEEEEEEECCCCCCCCCCCCccceEE
Q 007476 349 GRSSGLTTGTVMAYALEYNDEKGICFFTDFLVVGENQQTFDLEGDSGSLIL 399 (602)
Q Consensus 349 GRTTGlT~G~I~ai~V~y~~~~G~~~F~dqIIt~~~~~~fS~~GDSGSlVl 399 (602)
|-+.=+|.|.|.++..+-+..++..+..-||.+.. .+|.||-..+
T Consensus 173 gd~i~VTnghV~~~~~~~y~~~~~~l~~vqi~aa~------~~~~s~ep~i 217 (473)
T KOG1320|consen 173 GDGIIVTNGHVVRVEPRIYAHSSTVLLRVQIDAAI------GPGNSGEPVI 217 (473)
T ss_pred CCcEEEEeeEEEEEEeccccCCCcceeeEEEEEee------cCCccCCCeE
Confidence 56666899999999865433334555666666544 3467777776
No 25
>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=33.40 E-value=34 Score=34.80 Aligned_cols=43 Identities=21% Similarity=0.175 Sum_probs=15.1
Q ss_pred CCCCCccceEEeeccCCCCCceEEEEEeccCCCcccccccCCCCcceEEeechHHHHH
Q 007476 389 DLEGDSGSLILLTGQNGEKPRPVGIIWGGTANRGRLKLKVGQPPVNWTSGVDLGRLLD 446 (602)
Q Consensus 389 S~~GDSGSlVl~~~~~d~~~~aVGLlfGGs~~~gr~~~~~g~~p~~~Tl~npI~~VL~ 446 (602)
+.+|+||+-++ ..+ .+||+|-|... +...++|-+..||..+..
T Consensus 144 T~~G~SGtp~y-----~g~-~vvGvH~G~~~---------~~~~~n~n~~spip~~~g 186 (203)
T PF02122_consen 144 TSPGWSGTPYY-----SGK-NVVGVHTGSPS---------GSNRENNNRMSPIPPIPG 186 (203)
T ss_dssp --TT-TT-EEE------SS--EEEEEEEE-----------------------------
T ss_pred CCCCCCCCCeE-----ECC-CceEeecCccc---------cccccccccccccccccc
Confidence 78999999999 344 89999999521 112347778888877654
Done!