Query psy6528
Match_columns 421
No_of_seqs 501 out of 1926
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 20:23:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 100.0 8.2E-44 1.8E-48 327.9 25.0 230 70-301 1-232 (232)
2 KOG3627|consensus 100.0 1.6E-42 3.4E-47 325.5 25.6 235 66-303 9-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 1E-40 2.2E-45 307.4 24.7 226 69-298 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 3.6E-38 7.8E-43 288.0 24.3 218 70-298 1-220 (220)
5 KOG1600|consensus 100.0 4.7E-41 1E-45 305.9 -2.4 114 307-420 71-184 (321)
6 COG5640 Secreted trypsin-like 100.0 2.6E-32 5.7E-37 251.1 15.3 235 66-305 29-281 (413)
7 PLN02220 delta-9 acyl-lipid de 100.0 8.6E-33 1.9E-37 258.4 -7.3 110 310-420 63-172 (299)
8 COG1398 OLE1 Fatty-acid desatu 99.9 2.5E-28 5.4E-33 217.8 -2.9 110 307-420 50-160 (289)
9 cd03505 Delta9-FADS-like The D 99.9 1.3E-26 2.8E-31 200.7 -5.9 79 311-389 11-89 (178)
10 PF03761 DUF316: Domain of unk 99.7 1.9E-16 4.1E-21 150.7 19.5 214 60-302 30-279 (282)
11 PF09342 DUF1986: Domain of un 99.5 1.2E-12 2.5E-17 116.1 14.4 115 78-198 13-131 (267)
12 COG3591 V8-like Glu-specific e 98.9 3.4E-08 7.4E-13 90.0 13.0 199 76-303 44-251 (251)
13 PF13365 Trypsin_2: Trypsin-li 98.1 1.5E-05 3.3E-10 64.9 7.7 20 95-114 1-21 (120)
14 TIGR02037 degP_htrA_DO peripla 97.9 0.00015 3.2E-09 73.3 12.8 85 92-198 57-142 (428)
15 TIGR02038 protease_degS peripl 97.8 0.00064 1.4E-08 66.7 15.3 141 93-277 78-219 (351)
16 PRK10898 serine endoprotease; 97.7 0.0017 3.6E-08 63.8 16.4 141 93-277 78-219 (353)
17 PRK10139 serine endoprotease; 97.6 0.00096 2.1E-08 67.6 12.8 141 93-276 90-232 (455)
18 PRK10942 serine endoprotease; 97.3 0.0034 7.5E-08 64.0 12.9 83 93-197 111-195 (473)
19 PF02395 Peptidase_S6: Immunog 96.2 0.034 7.3E-07 59.5 10.8 33 249-281 213-246 (769)
20 cd01060 Membrane-FADS-like The 95.9 0.0025 5.5E-08 52.1 0.4 64 319-386 15-80 (122)
21 PF00487 FA_desaturase: Fatty 95.3 0.012 2.6E-07 54.1 2.6 57 323-379 23-80 (257)
22 cd03506 Delta6-FADS-like The D 92.6 0.092 2E-06 47.3 2.9 56 327-382 21-77 (204)
23 PF00863 Peptidase_C4: Peptida 89.0 7.6 0.00016 35.6 11.6 161 98-305 36-199 (235)
24 cd03511 Rhizopine-oxygenase-li 88.7 0.19 4E-06 47.8 1.1 50 328-377 66-116 (285)
25 cd03510 Rhizobitoxine-FADS-lik 85.8 0.27 5.9E-06 43.1 0.4 49 329-377 44-93 (175)
26 PF00548 Peptidase_C3: 3C cyst 83.8 8.5 0.00018 33.6 8.9 71 91-177 23-93 (172)
27 cd03514 CrtR_beta-carotene-hyd 83.1 0.45 9.7E-06 43.0 0.6 49 328-376 46-95 (207)
28 cd03513 CrtW_beta-carotene-ket 80.9 0.81 1.8E-05 41.8 1.4 26 351-376 79-104 (225)
29 COG0265 DegQ Trypsin-like seri 78.7 53 0.0011 32.0 13.5 146 93-280 72-218 (347)
30 cd03512 Alkane-hydroxylase Alk 78.5 2.4 5.1E-05 40.9 3.8 25 357-381 118-143 (314)
31 PF00947 Pico_P2A: Picornaviru 75.8 2.1 4.5E-05 34.9 2.2 39 250-299 88-126 (127)
32 cd03507 Delta12-FADS-like The 75.1 1.5 3.2E-05 40.0 1.3 49 328-376 55-104 (222)
33 PLN03199 delta6-acyl-lipid des 73.6 1.6 3.5E-05 44.8 1.3 42 329-370 184-226 (485)
34 PLN03198 delta6-acyl-lipid des 71.5 2.1 4.5E-05 44.3 1.5 44 328-371 258-302 (526)
35 PLN02498 omega-3 fatty acid de 71.4 2 4.4E-05 43.2 1.3 48 328-375 172-220 (450)
36 COG3239 DesA Fatty acid desatu 66.8 3.6 7.7E-05 40.3 2.0 48 328-375 86-133 (343)
37 PLN02598 omega-6 fatty acid de 66.4 3.5 7.5E-05 41.4 1.8 47 328-374 147-194 (421)
38 PLN02505 omega-6 fatty acid de 65.2 3 6.5E-05 41.3 1.1 45 329-374 109-155 (381)
39 PLN02579 sphingolipid delta-4 62.1 3.8 8.3E-05 39.6 1.2 51 328-378 96-148 (323)
40 cd03508 Delta4-sphingolipid-FA 61.8 4 8.6E-05 38.9 1.2 21 356-376 96-117 (289)
41 PF13956 Ibs_toxin: Toxin Ibs, 60.5 5.1 0.00011 20.7 0.9 15 1-15 2-16 (19)
42 TIGR03768 RPA4764 metallophosp 52.9 16 0.00035 36.9 3.8 46 343-388 389-439 (492)
43 PF08194 DIM: DIM protein; In 47.2 29 0.00063 21.7 2.9 30 1-30 1-33 (36)
44 PF05580 Peptidase_S55: SpoIVB 45.2 22 0.00048 32.0 3.1 27 247-278 175-201 (218)
45 KOG4232|consensus 42.5 16 0.00034 36.3 1.9 54 323-376 161-215 (430)
46 cd03509 DesA_FADS-like Fatty a 42.3 12 0.00026 35.6 1.1 49 328-377 49-100 (288)
47 PF02907 Peptidase_S29: Hepati 40.9 21 0.00045 29.6 2.0 21 250-274 106-126 (148)
48 PF05579 Peptidase_S32: Equine 39.5 20 0.00044 33.3 2.0 22 251-276 207-228 (297)
49 PF10459 Peptidase_S46: Peptid 37.9 20 0.00044 38.5 2.0 20 94-113 48-68 (698)
50 PRK13791 lysozyme inhibitor; P 36.5 41 0.00088 27.1 3.1 42 1-42 4-47 (113)
51 TIGR02860 spore_IV_B stage IV 35.1 41 0.00089 33.5 3.5 45 246-301 354-398 (402)
52 COG4982 3-oxoacyl-[acyl-carrie 30.1 38 0.00083 35.5 2.4 87 285-382 460-560 (866)
53 PF00944 Peptidase_S3: Alphavi 25.3 22 0.00049 29.3 -0.1 26 250-279 104-129 (158)
54 PF15240 Pro-rich: Proline-ric 22.4 62 0.0013 28.2 2.0 21 1-21 1-21 (179)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=100.00 E-value=8.2e-44 Score=327.86 Aligned_cols=230 Identities=43% Similarity=0.825 Sum_probs=194.6
Q ss_pred cccCeeCCCCCCceEEEEeec-CeeEEEEEEEeCCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEE-EcC
Q psy6528 70 IVGGQPTEVNQYPWMVRLSYF-NRFYCGGTLINDRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRA-IVG 147 (421)
Q Consensus 70 I~gG~~a~~~~~Pw~v~l~~~-~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~-i~p 147 (421)
|+||+++..++|||+|+|... ..+.|+||||+++||||||||+.+.....+.|++|...............+.++ +||
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 80 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHP 80 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECC
Confidence 689999999999999999887 689999999999999999999977555678899998776543333444445554 469
Q ss_pred CCCCCCCCCceEEEEECCCcccCCCccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccC
Q psy6528 148 DFTFSNFDNDIALLRLNDRVPIVDIIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTN 227 (421)
Q Consensus 148 ~y~~~~~~~DIALlkL~~pv~~s~~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~ 227 (421)
.|+.....+|||||||++|+.++.+++|||||........+..+.++|||.+......+..+++..+.+++.+.|.....
T Consensus 81 ~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~ 160 (232)
T cd00190 81 NYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYS 160 (232)
T ss_pred CCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhcc
Confidence 99988889999999999999999999999999864356668999999999876654567789999999999999985433
Q ss_pred CCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhhhhh
Q psy6528 228 YSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWIKEK 301 (421)
Q Consensus 228 ~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI~~~ 301 (421)
. ...+.++++|++...+..+.|.|||||||++.. +++++|+||+|+|..|...+.|++|++|+.|.+||+++
T Consensus 161 ~-~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~-~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 161 Y-GGTITDNMLCAGGLEGGKDACQGDSGGPLVCND-NGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred C-cccCCCceEeeCCCCCCCccccCCCCCcEEEEe-CCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 2 245789999998765467899999999999987 58999999999999998767899999999999999864
No 2
>KOG3627|consensus
Probab=100.00 E-value=1.6e-42 Score=325.51 Aligned_cols=235 Identities=45% Similarity=0.824 Sum_probs=192.2
Q ss_pred CCCccccCeeCCCCCCceEEEEeecC--eeEEEEEEEeCCEEEEccccccCc-ceeeEEEEEeeeeccCCCC-C--Ccee
Q psy6528 66 DATRIVGGQPTEVNQYPWMVRLSYFN--RFYCGGTLINDRYVLTAAHCVKGR-LWFLIKATFGEYDRCDTSS-K--PESR 139 (421)
Q Consensus 66 ~~~rI~gG~~a~~~~~Pw~v~l~~~~--~~~CgGtLIs~~~VLTAAhC~~~~-~~~~~~v~~G~~~~~~~~~-~--~~~~ 139 (421)
...||+||.++.++++||+|+|.... .+.|+|+||+++||||||||+... .. .+.|++|.+....... . ....
T Consensus 9 ~~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~ 87 (256)
T KOG3627|consen 9 PEGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVG 87 (256)
T ss_pred ccCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCc-ceEEEECccccccccccCchhhhc
Confidence 36799999999999999999998875 789999999999999999999764 22 6788888765443311 1 1233
Q ss_pred EEEEE-EcCCCCCCCCC-CceEEEEECCCcccCCCccccccCCCCC--CCCCCCcEEEEecccCCCC-CCCccceeEEEe
Q psy6528 140 FVIRA-IVGDFTFSNFD-NDIALLRLNDRVPIVDIIKPVCLPTVLN--NTYEDETGVVMGWGTLEES-GRPACIIRDVEV 214 (421)
Q Consensus 140 ~v~~~-i~p~y~~~~~~-~DIALlkL~~pv~~s~~v~picLp~~~~--~~~~~~~~~v~GwG~~~~~-~~~~~~L~~~~~ 214 (421)
.+.++ +||.|+..... ||||||+|++++.|++.|+|||||.... ....+..|.++|||.+... ...+..|+++++
T Consensus 88 ~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v 167 (256)
T KOG3627|consen 88 DVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDV 167 (256)
T ss_pred eeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEE
Confidence 34444 47999998877 9999999999999999999999986433 2444689999999988654 345778999999
Q ss_pred eeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCC-CCCCCCCeEEEEece
Q psy6528 215 PILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAG-CGRAGYPGVYTRITR 293 (421)
Q Consensus 215 ~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~-c~~~~~p~vyt~V~~ 293 (421)
++++.++|+..+.... .+++.|+||+...+..++|+|||||||++... ++++++||+|||.. |+..+.|++||+|+.
T Consensus 168 ~i~~~~~C~~~~~~~~-~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~-~~~~~~GivS~G~~~C~~~~~P~vyt~V~~ 245 (256)
T KOG3627|consen 168 PIISNSECRRAYGGLG-TITDTMLCAGGPEGGKDACQGDSGGPLVCEDN-GRWVLVGIVSWGSGGCGQPNYPGVYTRVSS 245 (256)
T ss_pred eEcChhHhcccccCcc-ccCCCEEeeCccCCCCccccCCCCCeEEEeeC-CcEEEEEEEEecCCCCCCCCCCeEEeEhHH
Confidence 9999999985543221 46677999997666788999999999999873 48999999999988 998889999999999
Q ss_pred ehhhhhhhcc
Q psy6528 294 YVEWIKEKSK 303 (421)
Q Consensus 294 y~~WI~~~~~ 303 (421)
|.+||++.+.
T Consensus 246 y~~WI~~~~~ 255 (256)
T KOG3627|consen 246 YLDWIKENIG 255 (256)
T ss_pred hHHHHHHHhc
Confidence 9999999874
No 3
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=100.00 E-value=1e-40 Score=307.35 Aligned_cols=226 Identities=45% Similarity=0.848 Sum_probs=189.3
Q ss_pred ccccCeeCCCCCCceEEEEeecC-eeEEEEEEEeCCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEE-Ec
Q psy6528 69 RIVGGQPTEVNQYPWMVRLSYFN-RFYCGGTLINDRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRA-IV 146 (421)
Q Consensus 69 rI~gG~~a~~~~~Pw~v~l~~~~-~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~-i~ 146 (421)
||+||+++.+++|||+|.++... .+.|+||||++++|||||||+.+.....+.|++|.......... ....+..+ +|
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~-~~~~v~~~~~~ 79 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEG-QVIKVSKVIIH 79 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCCCc-eEEeeEEEEEC
Confidence 68999999999999999998876 78999999999999999999976555578899998765443222 33444444 46
Q ss_pred CCCCCCCCCCceEEEEECCCcccCCCccccccCCCCCCCCCCCcEEEEecccCCC-CCCCccceeEEEeeeechhhhccc
Q psy6528 147 GDFTFSNFDNDIALLRLNDRVPIVDIIKPVCLPTVLNNTYEDETGVVMGWGTLEE-SGRPACIIRDVEVPILSNQYCRTS 225 (421)
Q Consensus 147 p~y~~~~~~~DIALlkL~~pv~~s~~v~picLp~~~~~~~~~~~~~v~GwG~~~~-~~~~~~~L~~~~~~v~~~~~C~~~ 225 (421)
|.|+.....+|||||+|++|+.+++.++|||||........+..+.++|||.... .......++...+.+++.+.|...
T Consensus 80 p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~ 159 (229)
T smart00020 80 PNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRA 159 (229)
T ss_pred CCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhh
Confidence 9999888899999999999999999999999998644566689999999998764 234566799999999999999854
Q ss_pred cCCCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhh
Q psy6528 226 TNYSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWI 298 (421)
Q Consensus 226 ~~~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI 298 (421)
... ...+.+.++|++......+.|.|||||||++.. + +|+|+||+|+|..|...+.|.+|++|.+|.+||
T Consensus 160 ~~~-~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~-~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 160 YSG-GGAITDNMLCAGGLEGGKDACQGDSGGPLVCND-G-RWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred hcc-ccccCCCcEeecCCCCCCcccCCCCCCeeEEEC-C-CEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 332 135788999998765467899999999999987 4 999999999999998777899999999999998
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=100.00 E-value=3.6e-38 Score=288.05 Aligned_cols=218 Identities=42% Similarity=0.872 Sum_probs=184.5
Q ss_pred cccCeeCCCCCCceEEEEeecC-eeEEEEEEEeCCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEE-EcC
Q psy6528 70 IVGGQPTEVNQYPWMVRLSYFN-RFYCGGTLINDRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRA-IVG 147 (421)
Q Consensus 70 I~gG~~a~~~~~Pw~v~l~~~~-~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~-i~p 147 (421)
|+||.++.+++|||+|.+.... .++|+|+||+++||||||||+.. ...+.+.+|...............+.++ +||
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~--~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~ 78 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG--ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHP 78 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS--GGSEEEEESESBTTSTTTTSEEEEEEEEEEET
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc--cccccccccccccccccccccccccccccccc
Confidence 7899999999999999999987 89999999999999999999977 4456788888444444333455666664 569
Q ss_pred CCCCCCCCCceEEEEECCCcccCCCccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccC
Q psy6528 148 DFTFSNFDNDIALLRLNDRVPIVDIIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTN 227 (421)
Q Consensus 148 ~y~~~~~~~DIALlkL~~pv~~s~~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~ 227 (421)
+|+.....+|||||+|++|+.+.+.++|+||+........+..+.++|||.....+ ....++...+.+++.+.|...
T Consensus 79 ~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~~~~~c~~~-- 155 (220)
T PF00089_consen 79 KYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVVSRKTCRSS-- 155 (220)
T ss_dssp TSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS-BTSBEEEEEEEEEEHHHHHHH--
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccccc--
Confidence 99998889999999999999999999999999854445678999999999875554 556799999999999999854
Q ss_pred CCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhh
Q psy6528 228 YSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWI 298 (421)
Q Consensus 228 ~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI 298 (421)
....+.+.++|++.. +..+.|+|||||||++.+. +|+||+|++..|...+.|++|++|+.|.+||
T Consensus 156 -~~~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~----~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 156 -YNDNLTPNMICAGSS-GSGDACQGDSGGPLICNNN----YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp -TTTTSTTTEEEEETT-SSSBGGTTTTTSEEEETTE----EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred -ccccccccccccccc-cccccccccccccccccee----eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 223378899999875 5578999999999999762 7999999999999888899999999999998
No 5
>KOG1600|consensus
Probab=100.00 E-value=4.7e-41 Score=305.93 Aligned_cols=114 Identities=50% Similarity=0.882 Sum_probs=109.6
Q ss_pred eeeEEEEEeeecccccccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCCCCCCcccCceeeeE
Q psy6528 307 FLFFVAYVSVIATTMGAHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDADPHNASRGFFFSHI 386 (421)
Q Consensus 307 ~~~~~~~~~~~~~~~g~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp~~~~~g~~~~~~ 386 (421)
|.++.+.++.++||+|+||+|+||+||+++|+|++|++++++|+||++++|+++||.||+|+|||+||||+.||||||||
T Consensus 71 ~~~~l~~v~glgITag~HRlwsHRSyKa~kpLr~fla~~~~~A~Qg~~~~WvrdHR~HHk~tdTD~DPhn~~rGF~FsHv 150 (321)
T KOG1600|consen 71 FAFFLYAVGGLGITAGYHRLWSHRSYKAPKPLRYFLAYCNTLAFQGDIIDWVRDHRVHHKFTDTDADPHNPRRGFWFSHV 150 (321)
T ss_pred HHHHHHHHhhceeeeehhhhcccccccCCccHHHHHHHHHHHhccCChhHHHhhhhhhccccccCCCCCCcccchhhhhh
Confidence 44556777888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeecCcccccCCCcCCcccccCCCeeEEeee
Q psy6528 387 GWLMVRKHPDVIRGGKLVDMSDLNADPLIMLQKN 420 (421)
Q Consensus 387 ~w~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 420 (421)
|||+.+++|++++.|+.+||+||++||++|||+|
T Consensus 151 gWl~~~k~p~~k~~G~~~dvsDL~~dp~v~Fq~k 184 (321)
T KOG1600|consen 151 GWLLDKKHPQVKECGGRLDVSDLEADPVVRFQRK 184 (321)
T ss_pred hhHhccCChHHHhhcCcCChhHhhhCceeeehhh
Confidence 9999999999999999999999999999999997
No 6
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-32 Score=251.15 Aligned_cols=235 Identities=31% Similarity=0.507 Sum_probs=168.1
Q ss_pred CCCccccCeeCCCCCCceEEEEeec-----CeeEEEEEEEeCCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeE
Q psy6528 66 DATRIVGGQPTEVNQYPWMVRLSYF-----NRFYCGGTLINDRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRF 140 (421)
Q Consensus 66 ~~~rI~gG~~a~~~~~Pw~v~l~~~-----~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~ 140 (421)
...||+||..|..++||++|++... +..+|||+++..|||||||||+....+....+..+..++.+.+..+....
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~Sq~~rg~v 108 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSSQAERGHV 108 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccccccCcce
Confidence 4789999999999999999998543 34699999999999999999997765444445555666655554444333
Q ss_pred EEEEEcCCCCCCCCCCceEEEEECCCcccCCCccccccCCC----CCCCCCCCcEEEEecccCCCCC-----CCccceeE
Q psy6528 141 VIRAIVGDFTFSNFDNDIALLRLNDRVPIVDIIKPVCLPTV----LNNTYEDETGVVMGWGTLEESG-----RPACIIRD 211 (421)
Q Consensus 141 v~~~i~p~y~~~~~~~DIALlkL~~pv~~s~~v~picLp~~----~~~~~~~~~~~v~GwG~~~~~~-----~~~~~L~~ 211 (421)
.....+..|.+.++.||||+++|.++..... + .|-.-.. .............+||.+.... +....|++
T Consensus 109 r~i~~~efY~~~n~~ND~Av~~l~~~a~~pr-~-ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l~e 186 (413)
T COG5640 109 RTIYVHEFYSPGNLGNDIAVLELARAASLPR-V-KITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHE 186 (413)
T ss_pred EEEeeecccccccccCcceeeccccccccch-h-heeeccCcccceecccccccccceeeeeeeecCCCCCCCccceeee
Confidence 3334457788899999999999998764221 0 1111110 0112223455667777654322 12247999
Q ss_pred EEeeeechhhhccccC---CCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCC-CCCCCCCeE
Q psy6528 212 VEVPILSNQYCRTSTN---YSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAG-CGRAGYPGV 287 (421)
Q Consensus 212 ~~~~v~~~~~C~~~~~---~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~-c~~~~~p~v 287 (421)
+.+..++.+.|..... .......-.-+||+... +++|+||||||++...++++ +++||+|||.+ |+.+..|+|
T Consensus 187 ~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~~~g~~G~-vQ~GVvSwG~~~Cg~t~~~gV 263 (413)
T COG5640 187 VAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIFHKGEEGR-VQRGVVSWGDGGCGGTLIPGV 263 (413)
T ss_pred eeeeeechHHhhhhccccccCCCCCCccceecCCCC--cccccCCCCCceEEeCCCcc-EEEeEEEecCCCCCCCCccee
Confidence 9999999999985432 11111222239998554 89999999999999875554 78999999987 999999999
Q ss_pred EEEeceehhhhhhhcccc
Q psy6528 288 YTRITRYVEWIKEKSKEG 305 (421)
Q Consensus 288 yt~V~~y~~WI~~~~~~~ 305 (421)
||+|+.|.+||...+++.
T Consensus 264 yT~vsny~~WI~a~~~~l 281 (413)
T COG5640 264 YTNVSNYQDWIAAMTNGL 281 (413)
T ss_pred EEehhHHHHHHHHHhcCC
Confidence 999999999999988753
No 7
>PLN02220 delta-9 acyl-lipid desaturase
Probab=99.96 E-value=8.6e-33 Score=258.36 Aligned_cols=110 Identities=27% Similarity=0.448 Sum_probs=100.3
Q ss_pred EEEEEeeecccccccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCCCCCCcccCceeeeEEEe
Q psy6528 310 FVAYVSVIATTMGAHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDADPHNASRGFFFSHIGWL 389 (421)
Q Consensus 310 ~~~~~~~~~~~~g~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp~~~~~g~~~~~~~w~ 389 (421)
+.+.++.+++|+|+||+++||+|++++++|.+|+++|++++|+++++|+++||.||+|+|||+|||||.|||||||||||
T Consensus 63 ~~~~it~lGiT~GyHRl~sHrsfka~~~l~~~la~~g~~a~Qgs~~~Wv~~HR~HH~~sDt~~DPHsp~~Gfw~sH~gWl 142 (299)
T PLN02220 63 ILYIVTGLSITFSYHRNLAHRSFKLPKWLEYPFAYSALFALQGDPIDWVSTHRFHHQFTDSDRDPHSPIEGFWFSHVLWI 142 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCcCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCccccccCcHHHHhHhh
Confidence 34566778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCcccccCCCcCCcccccCCCeeEEeee
Q psy6528 390 MVRKHPDVIRGGKLVDMSDLNADPLIMLQKN 420 (421)
Q Consensus 390 ~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 420 (421)
+.+++.. .+.++..|++||.+||+++||+|
T Consensus 143 ~~~~~~~-~~~~~~~~~~Dl~~d~~~~~~~~ 172 (299)
T PLN02220 143 FDTSYIR-EKCGGRDNVMDLKQQWFYRFLRK 172 (299)
T ss_pred cCcchhh-hhcccccchHHHHhCcchHHHHH
Confidence 9866543 33456789999999999999986
No 8
>COG1398 OLE1 Fatty-acid desaturase [Lipid metabolism]
Probab=99.93 E-value=2.5e-28 Score=217.84 Aligned_cols=110 Identities=33% Similarity=0.568 Sum_probs=97.3
Q ss_pred eeeEEEEEeeecccccccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCCCC-CCcccCceeee
Q psy6528 307 FLFFVAYVSVIATTMGAHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDADP-HNASRGFFFSH 385 (421)
Q Consensus 307 ~~~~~~~~~~~~~~~g~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp-~~~~~g~~~~~ 385 (421)
++++.+..+..+||+|+||+++||+|+++++++.+++++|++++||++++|++.||+||+||||++|| |+..|||||||
T Consensus 50 ~~l~~y~~~~igIt~G~HRl~sHRa~~~~k~Le~~la~~g~l~~~G~~~~W~~~HR~HHr~tDTd~DPh~~~~kGfw~sh 129 (289)
T COG1398 50 FTLAYYLIGGIGITLGLHRLWSHRAFKAHKWLEYVLAFWGALTTQGPAIEWVGIHRKHHRKTDTDQDPHYDSFKGFWWSH 129 (289)
T ss_pred HHHHHHHhccceeeeehhhhhhhhhcccchHHHHHHHHHHHhhcCCCceeHHHHHHHhhcccCCCCCCCccccccchhhh
Confidence 44555677778999999999999999999999999999999999999999999999999999999999 66679999999
Q ss_pred EEEeeeecCcccccCCCcCCcccccCCCeeEEeee
Q psy6528 386 IGWLMVRKHPDVIRGGKLVDMSDLNADPLIMLQKN 420 (421)
Q Consensus 386 ~~w~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 420 (421)
||||+.+.. +. ....+..|+-+|+.++||+|
T Consensus 130 igWm~~~~~-~~---~~r~~~~~~~kd~~~~~~~r 160 (289)
T COG1398 130 IGWMLLYSA-EA---KDRETIQKLGKDIPLDWQHR 160 (289)
T ss_pred cceeeecch-hh---cChhHHHHhCCCchhhHHHH
Confidence 999998655 22 23566789999999999875
No 9
>cd03505 Delta9-FADS-like The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide range of bacteria. These enzymes play essential roles in fatty acid metabolism and the regulation of cell membrane fluidity. Acyl-CoA desaturases are the enzymes involved in the CoA-bound desaturation of fatty acids. Mammalian stearoyl-CoA delta-9 desaturase is a key enzyme in the biosynthesis of monounsaturated fatty acids, and in yeast, the delta-9 acyl-CoA desaturase (OLE1) reaction accounts for all de nova unsaturated fatty acid production in Saccharomyces cerevisiae. These non-heme, iron-containing, ER membrane-bound enzymes are part of a three-component enzyme system involving cytochrome b5, cytochrome b5 reductase, and the delta-9 fatty acid desaturase. This complex catalyzes the NADH- and oxygen-dependent i
Probab=99.90 E-value=1.3e-26 Score=200.74 Aligned_cols=79 Identities=49% Similarity=0.928 Sum_probs=75.3
Q ss_pred EEEEeeecccccccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCCCCCCcccCceeeeEEEe
Q psy6528 311 VAYVSVIATTMGAHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDADPHNASRGFFFSHIGWL 389 (421)
Q Consensus 311 ~~~~~~~~~~~g~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp~~~~~g~~~~~~~w~ 389 (421)
.++++.+++++|+||+++||+|++++++|.+|++++++++|+++++|+++||+||+|+|||+|||||.|||||+|+||+
T Consensus 11 ~~~~~~lgit~G~HRl~aHrsfk~~~~l~~~l~~~g~~a~qgs~~~W~~~HR~HH~~sDt~~DPhs~~~gf~~~h~gW~ 89 (178)
T cd03505 11 YYLLTGLGITAGYHRLWAHRSFKAPKPLRIFLAILGSLAGQGSPLWWVADHRLHHRYSDTDGDPHSPKRGFWFSHVGWL 89 (178)
T ss_pred HHHHHHHHHHHHHHHHHhhccCcCcHHHHHHHHHHHHHHcCcCHHHHHHHHHHhhcccCCCCCCCCcccCcHHHHHhhH
Confidence 3445567899999999999999999999999999999999999999999999999999999999999999999999998
No 10
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.73 E-value=1.9e-16 Score=150.74 Aligned_cols=214 Identities=24% Similarity=0.391 Sum_probs=137.0
Q ss_pred CCCCC--CCCCccccCeeCCCCCCceEEEEeecC----eeEEEEEEEeCCEEEEccccccCccee---------------
Q psy6528 60 SCGET--NDATRIVGGQPTEVNQYPWMVRLSYFN----RFYCGGTLINDRYVLTAAHCVKGRLWF--------------- 118 (421)
Q Consensus 60 ~cg~~--~~~~rI~gG~~a~~~~~Pw~v~l~~~~----~~~CgGtLIs~~~VLTAAhC~~~~~~~--------------- 118 (421)
.||.. ....++.+|..+..++.||.|.+...+ ..+++||+||+||||||+||+......
T Consensus 30 ~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~~~ 109 (282)
T PF03761_consen 30 TCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCEGN 109 (282)
T ss_pred hcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceeeCC
Confidence 57743 345568999999999999999997653 356899999999999999999532110
Q ss_pred --eEEE--------EEeeeeccCCCCCCceeEEEEEEcCCCC-----CCCCCCceEEEEECCCcccCCCccccccCCCCC
Q psy6528 119 --LIKA--------TFGEYDRCDTSSKPESRFVIRAIVGDFT-----FSNFDNDIALLRLNDRVPIVDIIKPVCLPTVLN 183 (421)
Q Consensus 119 --~~~v--------~~G~~~~~~~~~~~~~~~v~~~i~p~y~-----~~~~~~DIALlkL~~pv~~s~~v~picLp~~~~ 183 (421)
.+.| .+ ...............+.+++..++- .....++++||+|+++ ++....|+|||....
T Consensus 110 ~~~l~vP~~~l~~~~v-~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~ 186 (282)
T PF03761_consen 110 NNHLIVPEEVLSKIDV-RCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSST 186 (282)
T ss_pred CceEEeCHHHhccEEE-EeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCcc
Confidence 0000 00 0000000111122334444443332 3345689999999999 778899999998655
Q ss_pred CCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEec
Q psy6528 184 NTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFERE 263 (421)
Q Consensus 184 ~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~ 263 (421)
....+....+.|+. ....+....+.+.....|. ..+|. .+..|.||+||||+...
T Consensus 187 ~~~~~~~~~~yg~~-------~~~~~~~~~~~i~~~~~~~------------~~~~~-----~~~~~~~d~Gg~lv~~~- 241 (282)
T PF03761_consen 187 NWEKGDEVDVYGFN-------STGKLKHRKLKITNCTKCA------------YSICT-----KQYSCKGDRGGPLVKNI- 241 (282)
T ss_pred ccccCceEEEeecC-------CCCeEEEEEEEEEEeeccc------------eeEec-----ccccCCCCccCeEEEEE-
Confidence 55567777777771 1223555555554432221 12232 35789999999999987
Q ss_pred CCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhhhhhc
Q psy6528 264 DSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWIKEKS 302 (421)
Q Consensus 264 ~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI~~~~ 302 (421)
+++++++||.+.+...+..+ ...|.+|..|.+=|-+.+
T Consensus 242 ~gr~tlIGv~~~~~~~~~~~-~~~f~~v~~~~~~IC~lt 279 (282)
T PF03761_consen 242 NGRWTLIGVGASGNYECNKN-NSYFFNVSWYQDEICELT 279 (282)
T ss_pred CCCEEEEEEEccCCCccccc-ccEEEEHHHhhhhhccce
Confidence 79999999998775322212 578899988877665543
No 11
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.47 E-value=1.2e-12 Score=116.05 Aligned_cols=115 Identities=19% Similarity=0.388 Sum_probs=87.0
Q ss_pred CCCCceEEEEeecCeeEEEEEEEeCCEEEEccccccCcc--eeeEEEEEeeeeccC--CCCCCceeEEEEEEcCCCCCCC
Q psy6528 78 VNQYPWMVRLSYFNRFYCGGTLINDRYVLTAAHCVKGRL--WFLIKATFGEYDRCD--TSSKPESRFVIRAIVGDFTFSN 153 (421)
Q Consensus 78 ~~~~Pw~v~l~~~~~~~CgGtLIs~~~VLTAAhC~~~~~--~~~~~v~~G~~~~~~--~~~~~~~~~v~~~i~p~y~~~~ 153 (421)
...|||.|.|+..+.+.|+|+||.+.|||++..|+.+.. ..-+.+.+|...... ....+|...|..+.. -
T Consensus 13 ~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~------V 86 (267)
T PF09342_consen 13 DYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKD------V 86 (267)
T ss_pred cccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeee------c
Confidence 456999999999999999999999999999999997633 345677888754222 333344333333221 1
Q ss_pred CCCceEEEEECCCcccCCCccccccCCCCCCCCCCCcEEEEeccc
Q psy6528 154 FDNDIALLRLNDRVPIVDIIKPVCLPTVLNNTYEDETGVVMGWGT 198 (421)
Q Consensus 154 ~~~DIALlkL~~pv~~s~~v~picLp~~~~~~~~~~~~~v~GwG~ 198 (421)
...+++||.|++|+.|+.+|+|..||...........|..+|-..
T Consensus 87 ~~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 87 PESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 257899999999999999999999998545556677999998654
No 12
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.87 E-value=3.4e-08 Score=90.04 Aligned_cols=199 Identities=20% Similarity=0.248 Sum_probs=105.9
Q ss_pred CCCCCCceEEEEeec---CeeEEEEEEEeCCEEEEccccccCccee--eEEEEE-eeeeccCCCCCCceeEEEEEEcC--
Q psy6528 76 TEVNQYPWMVRLSYF---NRFYCGGTLINDRYVLTAAHCVKGRLWF--LIKATF-GEYDRCDTSSKPESRFVIRAIVG-- 147 (421)
Q Consensus 76 a~~~~~Pw~v~l~~~---~~~~CgGtLIs~~~VLTAAhC~~~~~~~--~~~v~~-G~~~~~~~~~~~~~~~v~~~i~p-- 147 (421)
.....|||-+-.... +.+-|+++||+++.||||+||+...... .+.+.. |.. ...........++..+.|
T Consensus 44 ~dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~G~~~~~~~p~g~~--~~~~~~~~~~~~~~~~~~g~ 121 (251)
T COG3591 44 TDTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDYGEDDIAAAPPGVN--SDGGPFYGITKIEIRVYPGE 121 (251)
T ss_pred ccCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCCChhhhhhcCCccc--CCCCCCCceeeEEEEecCCc
Confidence 345689997665442 3456777999999999999999653321 111111 111 011111111112222223
Q ss_pred CCCCCCCCCceEEEEECCCcccCCCccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccC
Q psy6528 148 DFTFSNFDNDIALLRLNDRVPIVDIIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTN 227 (421)
Q Consensus 148 ~y~~~~~~~DIALlkL~~pv~~s~~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~ 227 (421)
.|.......|+..+.|+...++.+......++.. .....+....++||-..... .+++ .+.|....
T Consensus 122 ~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~d~i~v~GYP~dk~~-----~~~~-------~e~t~~v~- 187 (251)
T COG3591 122 LYKEDGASYDVGEAALESGINIGDVVNYLKRNTA-SEAKANDRITVIGYPGDKPN-----IGTM-------WESTGKVN- 187 (251)
T ss_pred eeccCCceeeccHHHhccCCCccccccccccccc-cccccCceeEEEeccCCCCc-----ceeE-------eeecceeE-
Confidence 2344445567777777755566665554445443 33444555889998643321 1111 11121110
Q ss_pred CCCCCCCCCeEEeccCCCCCCCCcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEe-ceehhhhhhhcc
Q psy6528 228 YSSTRISDNMMCAGYPEGMKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRI-TRYVEWIKEKSK 303 (421)
Q Consensus 228 ~~~~~~~~~~lCa~~~~~~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V-~~y~~WI~~~~~ 303 (421)
.+.... ..-..|++.|+||+|++...+ +++||.+-|..-.....-.-.+|+ ....+||++.++
T Consensus 188 ----~~~~~~-----l~y~~dT~pG~SGSpv~~~~~----~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 188 ----SIKGNK-----LFYDADTLPGSSGSPVLISKD----EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred ----EEecce-----EEEEecccCCCCCCceEecCc----eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 011110 112268999999999998763 899999887653221222333454 447788887653
No 13
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=98.07 E-value=1.5e-05 Score=64.93 Aligned_cols=20 Identities=50% Similarity=0.694 Sum_probs=18.7
Q ss_pred EEEEEEeCC-EEEEccccccC
Q psy6528 95 CGGTLINDR-YVLTAAHCVKG 114 (421)
Q Consensus 95 CgGtLIs~~-~VLTAAhC~~~ 114 (421)
|+|.+|+++ +|||||||+.+
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~ 21 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVED 21 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTC
T ss_pred CEEEEEcCCceEEEchhheec
Confidence 789999999 99999999975
No 14
>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=97.90 E-value=0.00015 Score=73.29 Aligned_cols=85 Identities=20% Similarity=0.262 Sum_probs=54.9
Q ss_pred eeEEEEEEEeCC-EEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccC
Q psy6528 92 RFYCGGTLINDR-YVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIV 170 (421)
Q Consensus 92 ~~~CgGtLIs~~-~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s 170 (421)
...++|.+|++. +|||++|++.+.. .+.|.+.. . ... ..+++.. ....||||||++.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~~--~i~V~~~~--------~-~~~-~a~vv~~-----d~~~DlAllkv~~~---- 115 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGAD--EITVTLSD--------G-REF-KAKLVGK-----DPRTDIAVLKIDAK---- 115 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCCC--eEEEEeCC--------C-CEE-EEEEEEe-----cCCCCEEEEEecCC----
Confidence 357999999976 9999999997643 34454421 1 111 1122211 13579999999865
Q ss_pred CCccccccCCCCCCCCCCCcEEEEeccc
Q psy6528 171 DIIKPVCLPTVLNNTYEDETGVVMGWGT 198 (421)
Q Consensus 171 ~~v~picLp~~~~~~~~~~~~~v~GwG~ 198 (421)
..+.++.|... .....|..+.++|+..
T Consensus 116 ~~~~~~~l~~~-~~~~~G~~v~aiG~p~ 142 (428)
T TIGR02037 116 KNLPVIKLGDS-DKLRVGDWVLAIGNPF 142 (428)
T ss_pred CCceEEEccCC-CCCCCCCEEEEEECCC
Confidence 23556777543 3456799999999864
No 15
>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=97.81 E-value=0.00064 Score=66.65 Aligned_cols=141 Identities=16% Similarity=0.149 Sum_probs=75.7
Q ss_pred eEEEEEEEeCC-EEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccCC
Q psy6528 93 FYCGGTLINDR-YVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIVD 171 (421)
Q Consensus 93 ~~CgGtLIs~~-~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s~ 171 (421)
...+|.+|+++ +|||++|.+.+.. .+.|.+.+ . ... ..+++. + ....||||||++.+-
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~~~--~i~V~~~d--------g-~~~-~a~vv~--~---d~~~DlAvlkv~~~~---- 136 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKKAD--QIVVALQD--------G-RKF-EAELVG--S---DPLTDLAVLKIEGDN---- 136 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCCCC--EEEEEECC--------C-CEE-EEEEEE--e---cCCCCEEEEEecCCC----
Confidence 46999999976 9999999996543 34454321 1 111 112221 1 235899999998642
Q ss_pred CccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCc
Q psy6528 172 IIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQ 251 (421)
Q Consensus 172 ~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~ 251 (421)
+.++.+... .....|+.+.++|+...... .. ..-+++...-. .. . ..-....+= -.....+
T Consensus 137 -~~~~~l~~s-~~~~~G~~V~aiG~P~~~~~-----s~---t~GiIs~~~r~-~~--~-~~~~~~~iq-----tda~i~~ 197 (351)
T TIGR02038 137 -LPTIPVNLD-RPPHVGDVVLAIGNPYNLGQ-----TI---TQGIISATGRN-GL--S-SVGRQNFIQ-----TDAAINA 197 (351)
T ss_pred -CceEeccCc-CccCCCCEEEEEeCCCCCCC-----cE---EEEEEEeccCc-cc--C-CCCcceEEE-----ECCccCC
Confidence 234444322 34566999999998642111 11 12222211100 00 0 000011111 1134567
Q ss_pred CCCCCeeEEEecCCceEEEEEEEeCC
Q psy6528 252 GDSGGPMVFEREDSRYEQIGIVSWGA 277 (421)
Q Consensus 252 GDsGgPL~~~~~~~~~~lvGI~S~g~ 277 (421)
|.|||||+-.++ .++||.+...
T Consensus 198 GnSGGpl~n~~G----~vIGI~~~~~ 219 (351)
T TIGR02038 198 GNSGGALINTNG----ELVGINTASF 219 (351)
T ss_pred CCCcceEECCCC----eEEEEEeeee
Confidence 899999986542 7999987643
No 16
>PRK10898 serine endoprotease; Provisional
Probab=97.71 E-value=0.0017 Score=63.76 Aligned_cols=141 Identities=18% Similarity=0.202 Sum_probs=74.8
Q ss_pred eEEEEEEEeCC-EEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccCC
Q psy6528 93 FYCGGTLINDR-YVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIVD 171 (421)
Q Consensus 93 ~~CgGtLIs~~-~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s~ 171 (421)
...+|.+|+++ +|||++|=+.+. ..+.|.+.+ . ... ..+++. + ....||||||++.+ .
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~a--~~i~V~~~d--------g-~~~-~a~vv~--~---d~~~DlAvl~v~~~-~--- 136 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVINDA--DQIIVALQD--------G-RVF-EALLVG--S---DSLTDLAVLKINAT-N--- 136 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCCC--CEEEEEeCC--------C-CEE-EEEEEE--E---cCCCCEEEEEEcCC-C---
Confidence 46899999976 999999998653 334554421 1 111 111221 1 13589999999754 1
Q ss_pred CccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCc
Q psy6528 172 IIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQ 251 (421)
Q Consensus 172 ~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~ 251 (421)
..++.|... .....|..+.++|+...... + .. .-+++.. .+...... . ....+= -....-+
T Consensus 137 -l~~~~l~~~-~~~~~G~~V~aiG~P~g~~~---~--~t---~Giis~~-~r~~~~~~-~--~~~~iq-----tda~i~~ 197 (353)
T PRK10898 137 -LPVIPINPK-RVPHIGDVVLAIGNPYNLGQ---T--IT---QGIISAT-GRIGLSPT-G--RQNFLQ-----TDASINH 197 (353)
T ss_pred -CCeeeccCc-CcCCCCCEEEEEeCCCCcCC---C--cc---eeEEEec-cccccCCc-c--ccceEE-----eccccCC
Confidence 233444332 33556899999998632111 1 11 1122211 00000000 0 011111 1134567
Q ss_pred CCCCCeeEEEecCCceEEEEEEEeCC
Q psy6528 252 GDSGGPMVFEREDSRYEQIGIVSWGA 277 (421)
Q Consensus 252 GDsGgPL~~~~~~~~~~lvGI~S~g~ 277 (421)
|.|||||+..++ .++||.+...
T Consensus 198 GnSGGPl~n~~G----~vvGI~~~~~ 219 (353)
T PRK10898 198 GNSGGALVNSLG----ELMGINTLSF 219 (353)
T ss_pred CCCcceEECCCC----eEEEEEEEEe
Confidence 899999986542 7999988654
No 17
>PRK10139 serine endoprotease; Provisional
Probab=97.57 E-value=0.00096 Score=67.63 Aligned_cols=141 Identities=21% Similarity=0.241 Sum_probs=78.5
Q ss_pred eEEEEEEEeC--CEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccC
Q psy6528 93 FYCGGTLIND--RYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIV 170 (421)
Q Consensus 93 ~~CgGtLIs~--~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s 170 (421)
...+|.+|++ .+|||++|.+.+. ..+.|.+.+ . .. ...+++. .....||||||++.+-
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~a--~~i~V~~~d--------g-~~-~~a~vvg-----~D~~~DlAvlkv~~~~--- 149 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQA--QKISIQLND--------G-RE-FDAKLIG-----SDDQSDIALLQIQNPS--- 149 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCCC--CEEEEEECC--------C-CE-EEEEEEE-----EcCCCCEEEEEecCCC---
Confidence 4799999974 6999999999764 345565421 1 11 1122221 1235799999998542
Q ss_pred CCccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCC
Q psy6528 171 DIIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSC 250 (421)
Q Consensus 171 ~~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C 250 (421)
...++.|... .....|+.+.++|+...... . +..-+++...=. .... .. ....+=+ ....-
T Consensus 150 -~l~~~~lg~s-~~~~~G~~V~aiG~P~g~~~-----t---vt~GivS~~~r~-~~~~--~~-~~~~iqt-----da~in 210 (455)
T PRK10139 150 -KLTQIAIADS-DKLRVGDFAVAVGNPFGLGQ-----T---ATSGIISALGRS-GLNL--EG-LENFIQT-----DASIN 210 (455)
T ss_pred -CCceeEecCc-cccCCCCEEEEEecCCCCCC-----c---eEEEEEcccccc-ccCC--CC-cceEEEE-----CCccC
Confidence 2346666543 34566999999988531111 1 222233321000 0000 00 0111111 23456
Q ss_pred cCCCCCeeEEEecCCceEEEEEEEeC
Q psy6528 251 QGDSGGPMVFEREDSRYEQIGIVSWG 276 (421)
Q Consensus 251 ~GDsGgPL~~~~~~~~~~lvGI~S~g 276 (421)
+|.|||||+-.++ .++||.+..
T Consensus 211 ~GnSGGpl~n~~G----~vIGi~~~~ 232 (455)
T PRK10139 211 RGNSGGALLNLNG----ELIGINTAI 232 (455)
T ss_pred CCCCcceEECCCC----eEEEEEEEE
Confidence 7999999997652 799999874
No 18
>PRK10942 serine endoprotease; Provisional
Probab=97.29 E-value=0.0034 Score=63.97 Aligned_cols=83 Identities=20% Similarity=0.328 Sum_probs=51.9
Q ss_pred eEEEEEEEeC--CEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccC
Q psy6528 93 FYCGGTLIND--RYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIV 170 (421)
Q Consensus 93 ~~CgGtLIs~--~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s 170 (421)
...+|.+|++ .+|||++|.+.+. ..+.|.+.+ .. ....+++. .....||||||++.+-.
T Consensus 111 ~~GSG~ii~~~~G~IlTn~HVv~~a--~~i~V~~~d--------g~--~~~a~vv~-----~D~~~DlAvlki~~~~~-- 171 (473)
T PRK10942 111 ALGSGVIIDADKGYVVTNNHVVDNA--TKIKVQLSD--------GR--KFDAKVVG-----KDPRSDIALIQLQNPKN-- 171 (473)
T ss_pred ceEEEEEEECCCCEEEeChhhcCCC--CEEEEEECC--------CC--EEEEEEEE-----ecCCCCEEEEEecCCCC--
Confidence 4699999985 5999999999754 345565432 11 11122222 12358999999974322
Q ss_pred CCccccccCCCCCCCCCCCcEEEEecc
Q psy6528 171 DIIKPVCLPTVLNNTYEDETGVVMGWG 197 (421)
Q Consensus 171 ~~v~picLp~~~~~~~~~~~~~v~GwG 197 (421)
..++.|-.. .....|..+.++|+.
T Consensus 172 --l~~~~lg~s-~~l~~G~~V~aiG~P 195 (473)
T PRK10942 172 --LTAIKMADS-DALRVGDYTVAIGNP 195 (473)
T ss_pred --CceeEecCc-cccCCCCEEEEEcCC
Confidence 345556432 345678998888874
No 19
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=96.21 E-value=0.034 Score=59.54 Aligned_cols=33 Identities=30% Similarity=0.587 Sum_probs=23.9
Q ss_pred CCcCCCCCeeEEEe-cCCceEEEEEEEeCCCCCC
Q psy6528 249 SCQGDSGGPMVFER-EDSRYEQIGIVSWGAGCGR 281 (421)
Q Consensus 249 ~C~GDsGgPL~~~~-~~~~~~lvGI~S~g~~c~~ 281 (421)
.-.||||+||+..+ ..++|+|+|+++.+.+...
T Consensus 213 ~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~g 246 (769)
T PF02395_consen 213 GSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYNG 246 (769)
T ss_dssp --TT-TT-EEEEEETTTTEEEEEEEEEEECCCCH
T ss_pred cccCcCCCceEEEEccCCeEEEEEEEccccccCC
Confidence 46799999998776 4789999999998876543
No 20
>cd01060 Membrane-FADS-like The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would
Probab=95.87 E-value=0.0025 Score=52.06 Aligned_cols=64 Identities=31% Similarity=0.492 Sum_probs=48.0
Q ss_pred ccccccccccccccc-hhHHHHHHHHHHHhhhcCccceeeeccccccccccCCC-CCCCCcccCceeeeE
Q psy6528 319 TTMGAHRLFTHKTFK-ANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTD-ADPHNASRGFFFSHI 386 (421)
Q Consensus 319 ~~~g~hr~~~h~s~~-~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~-~dp~~~~~g~~~~~~ 386 (421)
.....|+. .|++|. ..++.+++..+++. .+..+...|...|..||++++++ +||... ..+..|.
T Consensus 15 ~~~~~H~~-~H~~~~~~~~~n~~~~~~~~~-~~~~~~~~~~~~H~~HH~~~~~~~~D~~~~--~~~~~H~ 80 (122)
T cd01060 15 LTVLAHEL-GHRSFFRSRWLNRLLGALLGL-ALGGSYGWWRRSHRRHHRYTNTPGKDPDSA--VNYLEHY 80 (122)
T ss_pred HHHHHHHH-hhhhhhccccHHHHHHHHHHH-HHcCCHHHHHHHHHHHhcCcCCCCCCCccc--cchHhhc
Confidence 44567887 888887 55566666566666 66788889999999999999997 999998 3344443
No 21
>PF00487 FA_desaturase: Fatty acid desaturase This entry is only a subset of the Pfam family.; InterPro: IPR005804 Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related. Family 1 is composed of: Stearoyl-CoA desaturase (SCD) (1.14.19.1 from EC) []. Family 2 is composed of: Bacterial fatty acid desaturases. Plant stearoyl-acyl-carrier-protein desaturase (1.14.19.1 from EC) [], this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils. Cyanobacterial DesA [], an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids. This entry contains fatty acid desaturases belonging to Family 1. ; GO: 0006629 lipid metabolic process
Probab=95.26 E-value=0.012 Score=54.14 Aligned_cols=57 Identities=21% Similarity=0.245 Sum_probs=47.2
Q ss_pred ccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCC-CCCCccc
Q psy6528 323 AHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDA-DPHNASR 379 (421)
Q Consensus 323 ~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~-dp~~~~~ 379 (421)
.+....|+++..++++..++..+..+....+...|...|..||++++++. ||.+...
T Consensus 23 ~~H~~~H~~~~~~~~~n~~l~~~~~~~~~~~~~~wr~~H~~HH~~~~~~~~Dpd~~~~ 80 (257)
T PF00487_consen 23 LAHDAGHGAFFRSRWLNDLLGRLLGLPIGGPYSSWRISHNRHHHYTNNPDRDPDSWTR 80 (257)
T ss_pred HHHHHhccCCcccChHHHHHHHHHHHHhcCCHhHhheeeeccccccCCccccCccchh
Confidence 34456788888888888888877777777778889999999999999988 9999875
No 22
>cd03506 Delta6-FADS-like The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be required for cold tolerance in bacteria, plants and fish, the primary role of HUFAs in mammals is cell signaling. These enzymes are described as front-end desaturases because they introduce a double bond between the pre-exiting double bond and the carboxyl (front) end of the fatty acid. Various substrates are involved, with both acyl-coenzyme A (CoA) and acyl-lipid desaturases present in this CD. Acyl-lipid desaturases are localized in the membranes of cyanobacterial thylakoid, plant endoplasmic reticulum (ER), and plastid; an
Probab=92.65 E-value=0.092 Score=47.30 Aligned_cols=56 Identities=21% Similarity=0.220 Sum_probs=42.6
Q ss_pred ccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCC-CCCCCCcccCce
Q psy6528 327 FTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDT-DADPHNASRGFF 382 (421)
Q Consensus 327 ~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~-~~dp~~~~~g~~ 382 (421)
..|.++..++++..++..+.......+..+|...|..||+|++. +.||--.....+
T Consensus 21 ~~H~~~~~~~~~n~~~g~~~~~~~g~s~~~w~~~H~~HH~~tn~~~~Dpd~~~~~~~ 77 (204)
T cd03506 21 AGHGQVFKNRWLNKLLGLTVGNLLGASAGWWKNKHNVHHAYTNILGHDPDIDTLPLL 77 (204)
T ss_pred ccCccccCCchHHHHHHHHHHhccCCCHHHHHHHHhhhcCcCCCCCCCCCCCcCceE
Confidence 35667776777777777666666678888999999999999985 589987655443
No 23
>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=89.01 E-value=7.6 Score=35.61 Aligned_cols=161 Identities=20% Similarity=0.259 Sum_probs=69.8
Q ss_pred EEEeCCEEEEccccccCcceeeEEEE--EeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccCCCccc
Q psy6528 98 TLINDRYVLTAAHCVKGRLWFLIKAT--FGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIVDIIKP 175 (421)
Q Consensus 98 tLIs~~~VLTAAhC~~~~~~~~~~v~--~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s~~v~p 175 (421)
-|.--.|+||-+|-+...+.. +.+. -|.+...... ...+..+ ...||.||||.+.++ +.-+-
T Consensus 36 gigyG~~iItn~HLf~~nng~-L~i~s~hG~f~v~nt~----~lkv~~i---------~~~DiviirmPkDfp--Pf~~k 99 (235)
T PF00863_consen 36 GIGYGSYIITNAHLFKRNNGE-LTIKSQHGEFTVPNTT----QLKVHPI---------EGRDIVIIRMPKDFP--PFPQK 99 (235)
T ss_dssp EEEETTEEEEEGGGGSSTTCE-EEEEETTEEEEECEGG----GSEEEE----------TCSSEEEEE--TTS------S-
T ss_pred EEeECCEEEEChhhhccCCCe-EEEEeCceEEEcCCcc----ccceEEe---------CCccEEEEeCCcccC--Ccchh
Confidence 455678999999999654332 3333 2434332111 1112211 257999999988764 22222
Q ss_pred cccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCcCCCC
Q psy6528 176 VCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQGDSG 255 (421)
Q Consensus 176 icLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~GDsG 255 (421)
++. ..+..+..+.++|--...... +....+... +.+.+... .+ ...-++=.||=|
T Consensus 100 l~F----R~P~~~e~v~mVg~~fq~k~~--~s~vSesS~-i~p~~~~~----fW--------------kHwIsTk~G~CG 154 (235)
T PF00863_consen 100 LKF----RAPKEGERVCMVGSNFQEKSI--SSTVSESSW-IYPEENSH----FW--------------KHWISTKDGDCG 154 (235)
T ss_dssp --B--------TT-EEEEEEEECSSCCC--EEEEEEEEE-EEEETTTT----EE--------------EE-C---TT-TT
T ss_pred hhc----cCCCCCCEEEEEEEEEEcCCe--eEEECCceE-EeecCCCC----ee--------------EEEecCCCCccC
Confidence 222 334557777777765432221 111111111 11111111 11 011234457889
Q ss_pred CeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEece-ehhhhhhhcccc
Q psy6528 256 GPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITR-YVEWIKEKSKEG 305 (421)
Q Consensus 256 gPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~-y~~WI~~~~~~~ 305 (421)
.||+... ++ .+|||-|.+..-.. -..|+.+.. +.+-+.+...+.
T Consensus 155 ~PlVs~~-Dg--~IVGiHsl~~~~~~---~N~F~~f~~~f~~~~l~~~~~~ 199 (235)
T PF00863_consen 155 LPLVSTK-DG--KIVGIHSLTSNTSS---RNYFTPFPDDFEEFYLENIEEL 199 (235)
T ss_dssp -EEEETT-T----EEEEEEEEETTTS---SEEEEE--TTHHHHHCC-CCC-
T ss_pred CcEEEcC-CC--cEEEEEcCccCCCC---eEEEEcCCHHHHHHHhcccccC
Confidence 9999876 33 79999998754333 357888754 444444444443
No 24
>cd03511 Rhizopine-oxygenase-like This CD includes the putative hydrocarbon oxygenase, MocD, a bacterial rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and other related proteins. It has been proposed that MocD, MocE (Rieske-like ferredoxin), and MocF (ferredoxin reductase) under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA d
Probab=88.72 E-value=0.19 Score=47.84 Aligned_cols=50 Identities=22% Similarity=0.163 Sum_probs=36.0
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccC-CCCCCCCc
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSD-TDADPHNA 377 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~-~~~dp~~~ 377 (421)
.|+++..++++-.++..+.+.....+...|...|..||+++. +++||-..
T Consensus 66 ~H~~~~~~~~~N~~~g~l~~~~~~~~~~~~~~~H~~HH~~~~~~~~Dpd~~ 116 (285)
T cd03511 66 VHGTAFATRWLNDAVGQIAGLMILLPPDFFRWSHARHHRYTQIPGRDPELA 116 (285)
T ss_pred hcccccCCchHHHHHHHHHHHHhcCChHHHHHHHHHHhcCcCCCCCCCCCC
Confidence 566666666666666655555555666788888999999994 66898654
No 25
>cd03510 Rhizobitoxine-FADS-like This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=85.78 E-value=0.27 Score=43.10 Aligned_cols=49 Identities=27% Similarity=0.282 Sum_probs=31.2
Q ss_pred ccccchhHHHHHHHH-HHHhhhcCccceeeeccccccccccCCCCCCCCc
Q psy6528 329 HKTFKANFALRTVLL-VTSTIAGQNCLWVWVRDHRQHHKYSDTDADPHNA 377 (421)
Q Consensus 329 h~s~~~~~~~~~~l~-~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp~~~ 377 (421)
|+++-.++.+-.++. ++.......+...|...|..||++..+++||--.
T Consensus 44 H~~l~~~~~~N~~~g~~~~~~p~~~~~~~~r~~H~~HH~~~~~~~Dpd~~ 93 (175)
T cd03510 44 HGLLFRNRRLNDFLGNWLAAVPIFQSLAAYRRSHLKHHRHLGTEDDPDLA 93 (175)
T ss_pred HhcccccccHHHHHHHHHHHhhhhCCHHHHHHHHHHHhCccCCCCCCcHH
Confidence 444444444444443 3333333334557888899999999999999875
No 26
>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=83.85 E-value=8.5 Score=33.56 Aligned_cols=71 Identities=21% Similarity=0.143 Sum_probs=38.2
Q ss_pred CeeEEEEEEEeCCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccC
Q psy6528 91 NRFYCGGTLINDRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIV 170 (421)
Q Consensus 91 ~~~~CgGtLIs~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s 170 (421)
+.+.|.|.-|..+|.|--.|.- .... +.+... .......+.. .+......||++++|++.-.|.
T Consensus 23 g~~t~l~~gi~~~~~lvp~H~~---~~~~--i~i~g~---------~~~~~d~~~l--v~~~~~~~Dl~~v~l~~~~kfr 86 (172)
T PF00548_consen 23 GEFTMLALGIYDRYFLVPTHEE---PEDT--IYIDGV---------EYKVDDSVVL--VDRDGVDTDLTLVKLPRNPKFR 86 (172)
T ss_dssp EEEEEEEEEEEBTEEEEEGGGG---GCSE--EEETTE---------EEEEEEEEEE--EETTSSEEEEEEEEEESSS-B-
T ss_pred ceEEEecceEeeeEEEEECcCC---CcEE--EEECCE---------EEEeeeeEEE--ecCCCcceeEEEEEccCCcccC
Confidence 4577888999999999999932 2222 222110 0000111111 1222335699999998887786
Q ss_pred CCccccc
Q psy6528 171 DIIKPVC 177 (421)
Q Consensus 171 ~~v~pic 177 (421)
+..+-++
T Consensus 87 DIrk~~~ 93 (172)
T PF00548_consen 87 DIRKFFP 93 (172)
T ss_dssp -GGGGSB
T ss_pred chhhhhc
Confidence 6555554
No 27
>cd03514 CrtR_beta-carotene-hydroxylase Beta-carotene hydroxylase (CrtR), the carotenoid zeaxanthin biosynthetic enzyme catalyzes the addition of hydroxyl groups to the beta-ionone rings of beta-carotene to form zeaxanthin and is found in bacteria and red algae. Carotenoids are important natural pigments; zeaxanthin and lutein are the only dietary carotenoids that accumulate in the macular region of the retina and lens. It is proposed that these carotenoids protect ocular tissues against photooxidative damage. CrtR does not show overall amino acid sequence similarity to the beta-carotene hydroxylases similar to CrtZ, an astaxanthin biosynthetic beta-carotene hydroxylase. However, CrtR does show sequence similarity to the green alga, Haematococcus pluvialis, beta-carotene ketolase (CrtW), which converts beta-carotene to canthaxanthin. Sequences of the CrtR_beta-carotene-hydroxylase domain family, as well as, the CrtW_beta-carotene-ketolase domain family appear to be structurally related
Probab=83.11 E-value=0.45 Score=42.96 Aligned_cols=49 Identities=24% Similarity=0.228 Sum_probs=31.2
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCC-CCCCC
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTD-ADPHN 376 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~-~dp~~ 376 (421)
.|.++..++++-.++..+..+....+...|...|..||+|+.++ +||-.
T Consensus 46 ~H~~~~~~~~~N~~~g~~~~~~~~~~~~~w~~~H~~HH~~~~~~~~DpD~ 95 (207)
T cd03514 46 SHKAASRNRWINELIGHVSAFFLGFPFPVFRRVHMQHHAHTNDPEKDPDH 95 (207)
T ss_pred ccccccCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCcCcCCcCccH
Confidence 34444444444444444433443455668888899999999874 89864
No 28
>cd03513 CrtW_beta-carotene-ketolase Beta-carotene ketolase/oxygenase (CrtW, also known as CrtO), the carotenoid astaxanthin biosynthetic enzyme, initially catalyzes the addition of two keto groups to carbons C4 and C4' of beta-carotene. Carotenoids are important natural pigments produced by many microorganisms and plants. Astaxanthin is reported to be an antioxidant, an anti-cancer agent, and an immune system stimulant. A number of bacteria and green algae can convert beta-carotene into astaxanthin by using several ketocarotenoids as intermediates and CrtW and a beta-carotene hydroxylase (CrtZ). CrtW initially converts beta-carotene to canthaxanthin via echinenone, and CrtZ initially mediates the conversion of beta-carotene to zeaxanthin via beta-cryptoxanthin. After a few more intermediates are formed, CrtW and CrtZ act in combination to produce astaxanthin. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. Th
Probab=80.88 E-value=0.81 Score=41.81 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=20.5
Q ss_pred CccceeeeccccccccccCCCCCCCC
Q psy6528 351 QNCLWVWVRDHRQHHKYSDTDADPHN 376 (421)
Q Consensus 351 ~~~~~~w~~~hr~hh~~~~~~~dp~~ 376 (421)
..+-..|.+.|..||++..++.||=-
T Consensus 79 g~~~~~~~~~H~~HH~~~~~~~DpD~ 104 (225)
T cd03513 79 GFSYDRLLRKHHLHHRHPGTAKDPDF 104 (225)
T ss_pred cCCHHHHHHHHHHHcCCCCCCCCCCC
Confidence 34555777889999999998888854
No 29
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=78.65 E-value=53 Score=32.00 Aligned_cols=146 Identities=19% Similarity=0.180 Sum_probs=72.7
Q ss_pred eEEEEEEEe-CCEEEEccccccCcceeeEEEEEeeeeccCCCCCCceeEEEEEEcCCCCCCCCCCceEEEEECCCcccCC
Q psy6528 93 FYCGGTLIN-DRYVLTAAHCVKGRLWFLIKATFGEYDRCDTSSKPESRFVIRAIVGDFTFSNFDNDIALLRLNDRVPIVD 171 (421)
Q Consensus 93 ~~CgGtLIs-~~~VLTAAhC~~~~~~~~~~v~~G~~~~~~~~~~~~~~~v~~~i~p~y~~~~~~~DIALlkL~~pv~~s~ 171 (421)
...+|.+++ ..+|+|..|=+.+ ...+.+.+. .. .....+.+- .....|+|++|.+..-.
T Consensus 72 ~~gSg~i~~~~g~ivTn~hVi~~--a~~i~v~l~---------dg-~~~~a~~vg-----~d~~~dlavlki~~~~~--- 131 (347)
T COG0265 72 GLGSGFIISSDGYIVTNNHVIAG--AEEITVTLA---------DG-REVPAKLVG-----KDPISDLAVLKIDGAGG--- 131 (347)
T ss_pred ccccEEEEcCCeEEEecceecCC--cceEEEEeC---------CC-CEEEEEEEe-----cCCccCEEEEEeccCCC---
Confidence 568888888 7899999998765 344444430 11 111111221 12357999999986532
Q ss_pred CccccccCCCCCCCCCCCcEEEEecccCCCCCCCccceeEEEeeeechhhhccccCCCCCCCCCCeEEeccCCCCCCCCc
Q psy6528 172 IIKPVCLPTVLNNTYEDETGVVMGWGTLEESGRPACIIRDVEVPILSNQYCRTSTNYSSTRISDNMMCAGYPEGMKDSCQ 251 (421)
Q Consensus 172 ~v~picLp~~~~~~~~~~~~~v~GwG~~~~~~~~~~~L~~~~~~v~~~~~C~~~~~~~~~~~~~~~lCa~~~~~~~~~C~ 251 (421)
+..+-+... .....++...+.|-... .. ...-..-+....+. +-..... ..+.+ ......++
T Consensus 132 -~~~~~~~~s-~~l~vg~~v~aiGnp~g-~~----~tvt~Givs~~~r~-~v~~~~~-----~~~~I-----qtdAain~ 193 (347)
T COG0265 132 -LPVIALGDS-DKLRVGDVVVAIGNPFG-LG----QTVTSGIVSALGRT-GVGSAGG-----YVNFI-----QTDAAINP 193 (347)
T ss_pred -CceeeccCC-CCcccCCEEEEecCCCC-cc----cceeccEEeccccc-cccCccc-----ccchh-----hcccccCC
Confidence 122223221 22334666666664322 01 11111112222222 1100000 01111 11245788
Q ss_pred CCCCCeeEEEecCCceEEEEEEEeCCCCC
Q psy6528 252 GDSGGPMVFEREDSRYEQIGIVSWGAGCG 280 (421)
Q Consensus 252 GDsGgPL~~~~~~~~~~lvGI~S~g~~c~ 280 (421)
|.||||++...+ .++||.+......
T Consensus 194 gnsGgpl~n~~g----~~iGint~~~~~~ 218 (347)
T COG0265 194 GNSGGPLVNIDG----EVVGINTAIIAPS 218 (347)
T ss_pred CCCCCceEcCCC----cEEEEEEEEecCC
Confidence 999999987552 6889988765543
No 30
>cd03512 Alkane-hydroxylase Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a three-component system comprising a soluble NADH-rubredoxin reductase (AlkT), a soluble rubredoxin (AlkG), and the integral membrane oxygenase (AlkB). AlkB utilizes the oxygen rebound mechanism to hydroxylate alkanes. This mechanism involves homolytic cleavage of the C-H bond by an electrophilic metal-oxo intermediate to generate a substrate-based radical. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. The active
Probab=78.46 E-value=2.4 Score=40.93 Aligned_cols=25 Identities=40% Similarity=0.671 Sum_probs=20.1
Q ss_pred eecc-ccccccccCCCCCCCCcccCc
Q psy6528 357 WVRD-HRQHHKYSDTDADPHNASRGF 381 (421)
Q Consensus 357 w~~~-hr~hh~~~~~~~dp~~~~~g~ 381 (421)
|... |+.||+|..|++||-++.+|=
T Consensus 118 ~~~~H~~~HH~~v~tp~DP~tar~ge 143 (314)
T cd03512 118 FAIEHVRGHHRYVATPEDPATARRGE 143 (314)
T ss_pred eeeeecccCCCCCCCCCCccccccCc
Confidence 4445 558999999999999997654
No 31
>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=75.79 E-value=2.1 Score=34.93 Aligned_cols=39 Identities=28% Similarity=0.523 Sum_probs=27.6
Q ss_pred CcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhhh
Q psy6528 250 CQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWIK 299 (421)
Q Consensus 250 C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI~ 299 (421)
=+||-||+|.|+. =++||++-|.. .-..|++|..+. |++
T Consensus 88 ~PGdCGg~L~C~H-----GViGi~Tagg~-----g~VaF~dir~~~-~~e 126 (127)
T PF00947_consen 88 EPGDCGGILRCKH-----GVIGIVTAGGE-----GHVAFADIRDLL-WLE 126 (127)
T ss_dssp STT-TCSEEEETT-----CEEEEEEEEET-----TEEEEEECCCGS-TTS
T ss_pred CCCCCCceeEeCC-----CeEEEEEeCCC-----ceEEEEechhhh-eec
Confidence 3689999999987 38899988632 235788887754 543
No 32
>cd03507 Delta12-FADS-like The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of organisms including higher plants, green algae, diatoms, nematodes, fungi, and bacteria. The expression of these proteins appears to be temperature dependent: decreases in temperature result in increased levels of fatty acid desaturation within membrane lipids subsequently altering cell membrane fluidity. An important enzyme for the production of polyunsaturates in plants is the oleate delta-12 desaturase (Arabidopsis FAD2) of the endoplasmic reticulum. This enzyme accepts l-acyl-2-oleoyl-sn-glycero-3-phosphocholine as substrate and requires NADH:cytochrome b oxidoreductase, cytochrome b, and oxygen for activity. FAD2 converts oleate(18:1) to linoleate (18:2) and is closely related to oleate 12-hydroxylase which cat
Probab=75.14 E-value=1.5 Score=40.04 Aligned_cols=49 Identities=18% Similarity=0.197 Sum_probs=32.1
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCC-CCCCCC
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDT-DADPHN 376 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~-~~dp~~ 376 (421)
.|+++-.++++-.++..+..+....+...|...|..||+++.. ++||-.
T Consensus 55 ~H~~~~~~~~~N~~~g~~~~~~~~~p~~~w~~~H~~HH~~~~~~~~D~~~ 104 (222)
T cd03507 55 GHGSFSDNRRLNDIVGHILHSPLLVPYHSWRISHNRHHAHTGNLEGDEVW 104 (222)
T ss_pred CCcccccchhHHHHHHHHHHHHHhCChHHHHHHHHHHHhccCCCCCCCcc
Confidence 4556655555555555433333345566888889999999876 677655
No 33
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=73.58 E-value=1.6 Score=44.78 Aligned_cols=42 Identities=12% Similarity=0.112 Sum_probs=27.2
Q ss_pred ccccchhHHH-HHHHHHHHhhhcCccceeeeccccccccccCC
Q psy6528 329 HKTFKANFAL-RTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDT 370 (421)
Q Consensus 329 h~s~~~~~~~-~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~ 370 (421)
|.++-.++++ +.+-.+++.+....|..+|...|-.||+|+..
T Consensus 184 H~~~~~~~~~N~~~g~~~g~l~~G~S~~wW~~~Hn~HH~~tN~ 226 (485)
T PLN03199 184 HHQVFKKRKHGDLGGIFWGDLMQGFSMQWWKNKHNGHHAVPNL 226 (485)
T ss_pred hhhhhCCchHHHHHHHHHHHhccCCChHHHHHHHhhhhcCcCc
Confidence 3333333333 44333555555567788999999999999983
No 34
>PLN03198 delta6-acyl-lipid desaturase; Provisional
Probab=71.53 E-value=2.1 Score=44.34 Aligned_cols=44 Identities=16% Similarity=0.100 Sum_probs=30.8
Q ss_pred cccccchhHHHHHHHH-HHHhhhcCccceeeeccccccccccCCC
Q psy6528 328 THKTFKANFALRTVLL-VTSTIAGQNCLWVWVRDHRQHHKYSDTD 371 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~-~~~~~~~~~~~~~w~~~hr~hh~~~~~~ 371 (421)
.|.++..++++-.++. +++......+..+|...|..||.++...
T Consensus 258 ~H~s~~~~~~~n~~~g~~~~~~~~G~s~~~W~~~Hn~HH~~tN~~ 302 (526)
T PLN03198 258 LHNQVFETRWLNEVVGYLIGNAVLGFSTGWWKEKHNLHHAAPNEC 302 (526)
T ss_pred ccccccCCcHHHHHHHHHHHHhhcCCCHHHHHHHHHHhccCCCCC
Confidence 3455555555555554 4466665677889999999999999875
No 35
>PLN02498 omega-3 fatty acid desaturase
Probab=71.38 E-value=2 Score=43.16 Aligned_cols=48 Identities=23% Similarity=0.248 Sum_probs=32.0
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCC-CCCCC
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDT-DADPH 375 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~-~~dp~ 375 (421)
.|++|-.++++-.++..+......-+...|-..|+.||+++.. ++||-
T Consensus 172 gHgsf~~~k~lNd~vG~ll~~~ll~py~~Wr~sH~~HH~~Tn~~e~D~~ 220 (450)
T PLN02498 172 GHGSFSNNPKLNSVVGHLLHSSILVPYHGWRISHRTHHQNHGHVENDES 220 (450)
T ss_pred cccccccChHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCCCC
Confidence 3556655556655555444444456667899999999999974 67763
No 36
>COG3239 DesA Fatty acid desaturase [Lipid metabolism]
Probab=66.83 E-value=3.6 Score=40.25 Aligned_cols=48 Identities=19% Similarity=0.151 Sum_probs=37.0
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCCCCCCC
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDTDADPH 375 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~~~dp~ 375 (421)
.|++|..++++-.++..+.+.........|-.-|..||+++.++.||.
T Consensus 86 ~Hgs~~~~r~iNd~ig~l~~~~~~~p~~~wR~~H~~HH~~t~~~~~d~ 133 (343)
T COG3239 86 GHGSFFKNRWINDLIGHLAAALLLAPPVFWRISHNQHHAHTNILDDDP 133 (343)
T ss_pred cccchhhhhhHHHHHHHHHHHHHhcChhhhhhhHHHhhcccCCCCCCH
Confidence 567777778887777766666666667778677999999999887873
No 37
>PLN02598 omega-6 fatty acid desaturase
Probab=66.36 E-value=3.5 Score=41.45 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=31.2
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccC-CCCCC
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSD-TDADP 374 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~-~~~dp 374 (421)
.|++|-.++++-.++..+..+.+.-+...|...|..||+++. .+.||
T Consensus 147 ~H~s~~~~~~lN~~vG~~~~~~ll~p~~~wr~~H~~HH~~tn~~~~D~ 194 (421)
T PLN02598 147 GHNSFSKNQLVEDIVGTIAFTPLIYPFEPWRIKHNTHHAHTNKLVMDT 194 (421)
T ss_pred cccCCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccCcCCCCCCC
Confidence 355555556666665544433334556688889999999997 47785
No 38
>PLN02505 omega-6 fatty acid desaturase
Probab=65.19 E-value=3 Score=41.31 Aligned_cols=45 Identities=22% Similarity=0.334 Sum_probs=29.2
Q ss_pred ccccchhHHHHHHHH-HHHhhhcCccceeeeccccccccccCC-CCCC
Q psy6528 329 HKTFKANFALRTVLL-VTSTIAGQNCLWVWVRDHRQHHKYSDT-DADP 374 (421)
Q Consensus 329 h~s~~~~~~~~~~l~-~~~~~~~~~~~~~w~~~hr~hh~~~~~-~~dp 374 (421)
|++|-.++++-.++. +++.. ...+...|-..|..||+++.. +.||
T Consensus 109 H~s~~~~~~lN~~vG~i~~~~-ll~p~~~Wr~~H~~HH~~tn~~~~D~ 155 (381)
T PLN02505 109 HHAFSDYQWLDDTVGLVLHSA-LLVPYFSWKYSHRRHHSNTGSLERDE 155 (381)
T ss_pred chhhhCChHHHHHHHHHHHHH-HcCCHHHHHHHHHHHhhccCCCCCCc
Confidence 445544445544443 34443 346667899999999999975 7776
No 39
>PLN02579 sphingolipid delta-4 desaturase
Probab=62.05 E-value=3.8 Score=39.62 Aligned_cols=51 Identities=16% Similarity=0.178 Sum_probs=30.3
Q ss_pred cccccchhHHHHHHHHHHHhh-hcCccceeeeccccccccccCC-CCCCCCcc
Q psy6528 328 THKTFKANFALRTVLLVTSTI-AGQNCLWVWVRDHRQHHKYSDT-DADPHNAS 378 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~-~~~~~~~~w~~~hr~hh~~~~~-~~dp~~~~ 378 (421)
.|.++-.++++-.++..+..+ .+.....+|.+.|..||+++.. +.||--+.
T Consensus 96 ~Hg~~f~~~~~N~~lg~~~~l~~g~~~~~~~~~~H~~HH~~~n~~~~D~Di~t 148 (323)
T PLN02579 96 SHNLAFKTPVYNRWLGIFANLPIGIPMSVTFQKYHLEHHRFQGVDGIDMDIPS 148 (323)
T ss_pred hHhhhcCCHHHHHHHHHHHHHhhcCCHhHHHHHHHHHHccCCCCCCCCCCCCc
Confidence 344444455555555544443 3333344687889999999964 45766553
No 40
>cd03508 Delta4-sphingolipid-FADS-like The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, higher plants, and fungi. Studies show that MLD is localized to the endoplasmic reticulum. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for
Probab=61.80 E-value=4 Score=38.88 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=15.9
Q ss_pred eeeccccccccccCCC-CCCCC
Q psy6528 356 VWVRDHRQHHKYSDTD-ADPHN 376 (421)
Q Consensus 356 ~w~~~hr~hh~~~~~~-~dp~~ 376 (421)
.|-..|..||+++.++ .||=-
T Consensus 96 ~~r~~H~~HH~~~n~~~~DpDi 117 (289)
T cd03508 96 SFKKYHLEHHRYLGEDGLDTDI 117 (289)
T ss_pred HHHHHHHHhccCCCCCCCCCCc
Confidence 4677899999999864 47653
No 41
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=60.52 E-value=5.1 Score=20.69 Aligned_cols=15 Identities=27% Similarity=0.416 Sum_probs=11.0
Q ss_pred CchhhhHHHHHHhhh
Q psy6528 1 MELLVLSVLLVTTWT 15 (421)
Q Consensus 1 mk~~~l~~~l~~~~~ 15 (421)
||++.+|++|.+.|+
T Consensus 2 Mk~vIIlvvLLliSf 16 (19)
T PF13956_consen 2 MKLVIILVVLLLISF 16 (19)
T ss_pred ceehHHHHHHHhccc
Confidence 888887777776654
No 42
>TIGR03768 RPA4764 metallophosphoesterase, RPA4764 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this alignment. This model and TIGR03767 divide a narrow clade of pfam00149-related enzymes.
Probab=52.95 E-value=16 Score=36.95 Aligned_cols=46 Identities=22% Similarity=0.422 Sum_probs=28.9
Q ss_pred HHHHhhhcCccceeeeccccccccccC-CCCCCCCcccCce----eeeEEE
Q psy6528 343 LVTSTIAGQNCLWVWVRDHRQHHKYSD-TDADPHNASRGFF----FSHIGW 388 (421)
Q Consensus 343 ~~~~~~~~~~~~~~w~~~hr~hh~~~~-~~~dp~~~~~g~~----~~~~~w 388 (421)
.++..+.-...++.|+.-|+..+...= ...||--|.+||| -||+-|
T Consensus 389 eLlaLL~~hPnVla~LsGHvHrn~v~a~~~p~~~~pe~gFWeveTaSl~Df 439 (492)
T TIGR03768 389 GLVTTLQKYPNLLMWIAGHRHLNTVKAFPSPDPARPEYGFWQVETASLRDF 439 (492)
T ss_pred HHHHHHhcCCCeEEEEcCCcccccccccCCCCCCCCcCceEEEeehhhccc
Confidence 344444445568889998854444442 3456767889999 456555
No 43
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=47.17 E-value=29 Score=21.66 Aligned_cols=30 Identities=20% Similarity=0.088 Sum_probs=16.9
Q ss_pred Cchh---hhHHHHHHhhhcccccceeeeCCcee
Q psy6528 1 MELL---VLSVLLVTTWTGQIGAKAEISDSKWQ 30 (421)
Q Consensus 1 mk~~---~l~~~l~~~~~~~~~~~~~i~~~~~~ 30 (421)
||.| |.+++|++.++.....+..|-+.+|.
T Consensus 1 Mk~l~~a~~l~lLal~~a~~~~pG~ViING~C~ 33 (36)
T PF08194_consen 1 MKCLSLAFALLLLALAAAVPATPGNVIINGKCI 33 (36)
T ss_pred CceeHHHHHHHHHHHHhcccCCCCeEEECceee
Confidence 7743 34444445555555567666666655
No 44
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=45.22 E-value=22 Score=32.01 Aligned_cols=27 Identities=30% Similarity=0.367 Sum_probs=22.7
Q ss_pred CCCCcCCCCCeeEEEecCCceEEEEEEEeCCC
Q psy6528 247 KDSCQGDSGGPMVFEREDSRYEQIGIVSWGAG 278 (421)
Q Consensus 247 ~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~ 278 (421)
.+.-||-||+|++.+. .|+|-++++..
T Consensus 175 GGIvqGMSGSPI~qdG-----KLiGAVthvf~ 201 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG-----KLIGAVTHVFV 201 (218)
T ss_pred CCEEecccCCCEEECC-----EEEEEEEEEEe
Confidence 4689999999998865 89999998753
No 45
>KOG4232|consensus
Probab=42.50 E-value=16 Score=36.29 Aligned_cols=54 Identities=20% Similarity=0.179 Sum_probs=43.8
Q ss_pred ccccccccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccCC-CCCCCC
Q psy6528 323 AHRLFTHKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSDT-DADPHN 376 (421)
Q Consensus 323 ~hr~~~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~~-~~dp~~ 376 (421)
.|-+.-++.|+.++|-..+=.+.+..+-..+.-||...|-.||+++.. +.||=.
T Consensus 161 ~Hd~gH~~i~~~~~wN~~~~~fv~n~L~G~sa~WW~~~H~~HHa~pN~~~~DpDi 215 (430)
T KOG4232|consen 161 QHDYGHLSIFKNSKWNHLAQKFVGNHLKGFSAAWWKSHHNQHHAAPNSLDKDPDI 215 (430)
T ss_pred hcccccccccccccHHHHHHHHHhhhcccccHHHHHHHHhhhhccCccCCCCccc
Confidence 466777788999999888888888888777888999999999999874 556644
No 46
>cd03509 DesA_FADS-like Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=42.27 E-value=12 Score=35.57 Aligned_cols=49 Identities=16% Similarity=0.095 Sum_probs=28.5
Q ss_pred cccccchhHHHHHHHHHHHhhhcCccceeeeccccccccccC---CCCCCCCc
Q psy6528 328 THKTFKANFALRTVLLVTSTIAGQNCLWVWVRDHRQHHKYSD---TDADPHNA 377 (421)
Q Consensus 328 ~h~s~~~~~~~~~~l~~~~~~~~~~~~~~w~~~hr~hh~~~~---~~~dp~~~ 377 (421)
.|.++-.++++-.++..+.... ..+...|-..|-.||++++ .+.||-..
T Consensus 49 ~Hg~~~~~~~~N~~~g~~~~~l-~~p~~~wr~~H~~HH~~~nl~~~~~Dpd~~ 100 (288)
T cd03509 49 LHGHPTRSRWVNEALGYPPLAL-WYPYTRYRDTHLAHHRDEDLTDPGDDPESN 100 (288)
T ss_pred hccCcccChHHHHHHHHHHHHH-hcCHHHHHHHHHHHcCCCCCCCCCCCCccc
Confidence 3455555555555554332111 1344488888999999985 34687643
No 47
>PF02907 Peptidase_S29: Hepatitis C virus NS3 protease; InterPro: IPR004109 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies the Hepatitis C virus NS3 protein as a serine protease which belongs to MEROPS peptidase family S29 (hepacivirin family, clan PA(S)), which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. The NS2 proteinase (IPR002518 from INTERPRO), a zinc-dependent enzyme, performs a single proteolytic cut to release the N terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4. It has been suggested that the NS3 serine protease of hepatitus C is involved in cell transformation and that the ability to transform requires an active enzyme [].; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0019087 transformation of host cell by virus; PDB: 2QV1_B 3LOX_C 2OBQ_C 2OC1_C 2OC0_A 3LON_A 3KNX_A 2O8M_A 2OBO_A 2OC8_A ....
Probab=40.90 E-value=21 Score=29.58 Aligned_cols=21 Identities=29% Similarity=0.705 Sum_probs=14.8
Q ss_pred CcCCCCCeeEEEecCCceEEEEEEE
Q psy6528 250 CQGDSGGPMVFEREDSRYEQIGIVS 274 (421)
Q Consensus 250 C~GDsGgPL~~~~~~~~~~lvGI~S 274 (421)
-.|.||||++|..+ .++||.-
T Consensus 106 lkGSSGgPiLC~~G----H~vG~f~ 126 (148)
T PF02907_consen 106 LKGSSGGPILCPSG----HAVGMFR 126 (148)
T ss_dssp HTT-TT-EEEETTS----EEEEEEE
T ss_pred EecCCCCcccCCCC----CEEEEEE
Confidence 45789999999763 7889874
No 48
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=39.49 E-value=20 Score=33.30 Aligned_cols=22 Identities=41% Similarity=0.665 Sum_probs=16.0
Q ss_pred cCCCCCeeEEEecCCceEEEEEEEeC
Q psy6528 251 QGDSGGPMVFEREDSRYEQIGIVSWG 276 (421)
Q Consensus 251 ~GDsGgPL~~~~~~~~~~lvGI~S~g 276 (421)
.||||+|++..++ .++||-+-.
T Consensus 207 ~GDSGSPVVt~dg----~liGVHTGS 228 (297)
T PF05579_consen 207 PGDSGSPVVTEDG----DLIGVHTGS 228 (297)
T ss_dssp GGCTT-EEEETTC-----EEEEEEEE
T ss_pred CCCCCCccCcCCC----CEEEEEecC
Confidence 5899999998763 689998754
No 49
>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=37.93 E-value=20 Score=38.46 Aligned_cols=20 Identities=35% Similarity=0.698 Sum_probs=18.1
Q ss_pred EEEEEEEeCC-EEEEcccccc
Q psy6528 94 YCGGTLINDR-YVLTAAHCVK 113 (421)
Q Consensus 94 ~CgGtLIs~~-~VLTAAhC~~ 113 (421)
.|+|++||++ .|||--||..
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~ 68 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGY 68 (698)
T ss_pred ceeEEEEcCCceEEecchhhh
Confidence 4999999987 9999999984
No 50
>PRK13791 lysozyme inhibitor; Provisional
Probab=36.50 E-value=41 Score=27.11 Aligned_cols=42 Identities=19% Similarity=0.298 Sum_probs=22.2
Q ss_pred CchhhhHH--HHHHhhhcccccceeeeCCceeeCCCceEEEeec
Q psy6528 1 MELLVLSV--LLVTTWTGQIGAKAEISDSKWQADNGQTKTISLF 42 (421)
Q Consensus 1 mk~~~l~~--~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~ 42 (421)
||.+++.+ ++++.+.........+....++|.+++..++...
T Consensus 4 mk~~~~~~~~~~ls~~~~~~~~~~~~~t~~YqC~~~~~l~V~y~ 47 (113)
T PRK13791 4 RKLIPFTLFLAALSASTTSIAASQEITKSIYTCNDNQVLEVIYV 47 (113)
T ss_pred HHHHHHHHHHHHHhhhhhhccCCCCcccEEEECCCCCeEEEEEe
Confidence 67655333 3333333322245667777778877665555333
No 51
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=35.07 E-value=41 Score=33.51 Aligned_cols=45 Identities=29% Similarity=0.446 Sum_probs=30.6
Q ss_pred CCCCCcCCCCCeeEEEecCCceEEEEEEEeCCCCCCCCCCeEEEEeceehhhhhhh
Q psy6528 246 MKDSCQGDSGGPMVFEREDSRYEQIGIVSWGAGCGRAGYPGVYTRITRYVEWIKEK 301 (421)
Q Consensus 246 ~~~~C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c~~~~~p~vyt~V~~y~~WI~~~ 301 (421)
..+.-||-||+|++.+. .|+|-++--.--......++ |.+|+.+.
T Consensus 354 tgGivqGMSGSPi~q~g-----kliGAvtHVfvndpt~GYGi------~ie~Ml~~ 398 (402)
T TIGR02860 354 TGGIVQGMSGSPIIQNG-----KVIGAVTHVFVNDPTSGYGV------YIEWMLKE 398 (402)
T ss_pred hCCEEecccCCCEEECC-----EEEEEEEEEEecCCCcceee------hHHHHHHH
Confidence 35789999999999876 89998876433222222355 57787664
No 52
>COG4982 3-oxoacyl-[acyl-carrier protein]
Probab=30.06 E-value=38 Score=35.52 Aligned_cols=87 Identities=26% Similarity=0.381 Sum_probs=46.9
Q ss_pred CeEEEEeceehhhhhhhcccc--------------eeeeEEEEEeeecccccccccccccccchhHHHHHHHHHHHhhhc
Q psy6528 285 PGVYTRITRYVEWIKEKSKEG--------------CFLFFVAYVSVIATTMGAHRLFTHKTFKANFALRTVLLVTSTIAG 350 (421)
Q Consensus 285 p~vyt~V~~y~~WI~~~~~~~--------------~~~~~~~~~~~~~~~~g~hr~~~h~s~~~~~~~~~~l~~~~~~~~ 350 (421)
-+-|++|...++||-+.-++. ...+....+...+.-.++. +...|.....+-.++.+++.+.-
T Consensus 460 ~~SysDVdAlIewIg~eq~~t~g~~s~~~k~a~~ptll~PFAAp~v~G~l~~ag---sraE~~~rilLw~V~Rliggl~~ 536 (866)
T COG4982 460 MGSYSDVDALIEWIGDEQTETVGPQSIHIKLAWTPTLLFPFAAPRVSGELADAG---SRAEFAMRILLWNVLRLIGGLKK 536 (866)
T ss_pred ccchhhHHHHHHHhccccccccCCcceecccccCcceeeecccCCccCccccCC---chHHHHHHHHHHHHHHHHHHhhh
Confidence 467899999999997665431 0111111111112111111 12234444555556678888888
Q ss_pred CccceeeeccccccccccCCCCCCCCcccCce
Q psy6528 351 QNCLWVWVRDHRQHHKYSDTDADPHNASRGFF 382 (421)
Q Consensus 351 ~~~~~~w~~~hr~hh~~~~~~~dp~~~~~g~~ 382 (421)
|++.+. -.||.|=. =|-||+||.|
T Consensus 537 ~~s~r~--v~~R~hVV------LPgSPNrG~F 560 (866)
T COG4982 537 QGSSRG--VDTRLHVV------LPGSPNRGMF 560 (866)
T ss_pred hccccC--cccceEEE------ecCCCCCCcc
Confidence 887532 24775544 4777777766
No 53
>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=25.33 E-value=22 Score=29.33 Aligned_cols=26 Identities=35% Similarity=0.425 Sum_probs=18.4
Q ss_pred CcCCCCCeeEEEecCCceEEEEEEEeCCCC
Q psy6528 250 CQGDSGGPMVFEREDSRYEQIGIVSWGAGC 279 (421)
Q Consensus 250 C~GDsGgPL~~~~~~~~~~lvGI~S~g~~c 279 (421)
-.||||-|++-+. + .+|||+--|..-
T Consensus 104 ~~GDSGRpi~DNs--G--rVVaIVLGG~ne 129 (158)
T PF00944_consen 104 KPGDSGRPIFDNS--G--RVVAIVLGGANE 129 (158)
T ss_dssp STTSTTEEEESTT--S--BEEEEEEEEEEE
T ss_pred CCCCCCCccCcCC--C--CEEEEEecCCCC
Confidence 4689999987543 3 578998766543
No 54
>PF15240 Pro-rich: Proline-rich
Probab=22.43 E-value=62 Score=28.25 Aligned_cols=21 Identities=33% Similarity=0.350 Sum_probs=11.0
Q ss_pred CchhhhHHHHHHhhhcccccc
Q psy6528 1 MELLVLSVLLVTTWTGQIGAK 21 (421)
Q Consensus 1 mk~~~l~~~l~~~~~~~~~~~ 21 (421)
|-|+||.++|++-|..+-..+
T Consensus 1 MLlVLLSvALLALSSAQ~~dE 21 (179)
T PF15240_consen 1 MLLVLLSVALLALSSAQSTDE 21 (179)
T ss_pred ChhHHHHHHHHHhhhcccccc
Confidence 666666555555444444433
Done!