Query psy8651
Match_columns 302
No_of_seqs 349 out of 2552
Neff 10.0
Searched_HMMs 46136
Date Sat Aug 17 00:16:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8651.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8651hhsearch_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 7.7E-36 1.7E-40 248.8 19.7 191 101-298 1-208 (232)
2 smart00020 Tryp_SPc Trypsin-li 100.0 3.3E-34 7.1E-39 238.8 18.2 190 100-298 1-208 (229)
3 KOG3627|consensus 100.0 3.1E-34 6.7E-39 243.1 18.1 196 98-299 10-229 (256)
4 PF00089 Trypsin: Trypsin; In 100.0 3.7E-31 8E-36 218.8 16.8 182 101-297 1-198 (220)
5 COG5640 Secreted trypsin-like 99.9 3.7E-25 8.1E-30 184.2 13.8 191 97-299 29-253 (413)
6 PF03761 DUF316: Domain of unk 99.5 1.3E-13 2.8E-18 118.5 11.4 186 90-298 29-255 (282)
7 KOG3627|consensus 99.5 1.4E-13 3E-18 116.6 9.8 114 5-119 137-254 (256)
8 PF09342 DUF1986: Domain of un 99.5 1.3E-13 2.9E-18 110.0 7.9 99 109-215 13-113 (267)
9 cd00190 Tryp_SPc Trypsin-like 99.2 1.4E-10 3.1E-15 96.2 9.0 112 4-117 117-231 (232)
10 smart00020 Tryp_SPc Trypsin-li 98.9 9.3E-09 2E-13 85.3 9.0 109 4-115 117-229 (229)
11 PF00089 Trypsin: Trypsin; In 98.8 1E-08 2.2E-13 84.3 7.2 103 6-115 117-220 (220)
12 COG5640 Secreted trypsin-like 98.4 5.1E-07 1.1E-11 76.6 6.9 110 9-121 159-280 (413)
13 COG3591 V8-like Glu-specific e 98.3 1.4E-06 3E-11 71.8 7.0 39 109-147 46-87 (251)
14 PF13365 Trypsin_2: Trypsin-li 97.8 6.3E-05 1.4E-09 55.4 6.2 21 126-146 1-22 (120)
15 TIGR02037 degP_htrA_DO peripla 97.6 0.0033 7.2E-08 57.4 15.1 68 123-215 57-125 (428)
16 PRK10139 serine endoprotease; 97.3 0.0081 1.7E-07 55.1 13.9 58 123-200 89-148 (455)
17 TIGR02038 protease_degS peripl 97.1 0.016 3.4E-07 51.4 13.8 57 124-200 78-135 (351)
18 PRK10898 serine endoprotease; 97.1 0.014 3E-07 51.8 12.8 57 124-200 78-135 (353)
19 PRK10942 serine endoprotease; 96.8 0.051 1.1E-06 50.2 14.7 57 124-200 111-169 (473)
20 PF02395 Peptidase_S6: Immunog 96.6 0.025 5.4E-07 54.8 11.0 65 128-216 69-133 (769)
21 PF00548 Peptidase_C3: 3C cyst 84.0 0.25 5.5E-06 38.9 -0.6 71 122-212 23-93 (172)
22 PF00863 Peptidase_C4: Peptida 79.7 7.2 0.00016 32.4 6.3 25 268-298 149-173 (235)
23 PF00947 Pico_P2A: Picornaviru 68.2 2.6 5.6E-05 31.0 1.0 25 269-301 89-113 (127)
24 PF05579 Peptidase_S32: Equine 48.5 11 0.00024 31.7 1.6 23 269-298 207-229 (297)
25 PF05580 Peptidase_S55: SpoIVB 43.0 23 0.0005 28.9 2.6 24 266-297 176-199 (218)
26 PF10459 Peptidase_S46: Peptid 42.1 17 0.00037 35.4 2.0 20 124-143 47-67 (698)
27 PF02907 Peptidase_S29: Hepati 35.2 28 0.00061 26.0 1.8 13 268-280 106-118 (148)
28 COG0265 DegQ Trypsin-like seri 25.0 3.3E+02 0.0071 24.0 7.2 58 123-200 71-129 (347)
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=7.7e-36 Score=248.82 Aligned_cols=191 Identities=44% Similarity=0.764 Sum_probs=159.6
Q ss_pred ecCCeecccccchhHHhhhcc-CeeeeeEEEeeCCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEe
Q psy8651 101 IVGGNVTKLHEFPWIAALTKK-GKFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIR 179 (302)
Q Consensus 101 i~~g~~~~~~~~pwi~~l~~~-~~~~C~GsLI~~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~ 179 (302)
|.+|..+..++|||++.+... ..+.|+|+||+++||||||||+.......+.|++|........ ...+.+.|.++++
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~--~~~~~~~v~~~~~ 78 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNE--GGGQVIKVKKVIV 78 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCC--CceEEEEEEEEEE
Confidence 457889999999999999876 7889999999999999999999765567889999988765322 1257789999999
Q ss_pred CCCCCCCCCCCCeEEEEEcCCCcCCCCceeeeeeCCCC--CC--------------CCCccCcCceEEEeeeeCHHhHhc
Q psy8651 180 HPDFSLSNFNNDIALLEMESGVDFEAPQIHPACLPGNS--LD--------------ERKPTANSLRKVEVPILSEEECKS 243 (302)
Q Consensus 180 hp~y~~~~~~~DiALl~L~~~~~~~~~~v~picl~~~~--~~--------------~~~~~~~~l~~~~~~~~~~~~C~~ 243 (302)
||+|+.....+|||||||++|+.++. .++|||||... .. .....+..++...+.+++...|..
T Consensus 79 hp~y~~~~~~~DiAll~L~~~~~~~~-~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~ 157 (232)
T cd00190 79 HPNYNPSTYDNDIALLKLKRPVTLSD-NVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKR 157 (232)
T ss_pred CCCCCCCCCcCCEEEEEECCcccCCC-cccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhh
Confidence 99999888899999999999999988 99999999873 21 011345678999999999999998
Q ss_pred cCCCCCCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeEEEEEEeeeee
Q psy8651 244 AGYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEATLSKVVSRVQ 298 (302)
Q Consensus 244 ~~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~ 298 (302)
.+.....+.++++|++......+.|.|||||||++.. ++ +++|+||+|++.
T Consensus 158 ~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~--~~--~~~lvGI~s~g~ 208 (232)
T cd00190 158 AYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCND--NG--RGVLVGIVSWGS 208 (232)
T ss_pred hccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEe--CC--EEEEEEEEehhh
Confidence 8743357889999998655467899999999999988 43 568999999975
No 2
>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=3.3e-34 Score=238.82 Aligned_cols=190 Identities=43% Similarity=0.772 Sum_probs=157.7
Q ss_pred eecCCeecccccchhHHhhhccC-eeeeeEEEeeCCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEE
Q psy8651 100 RIVGGNVTKLHEFPWIAALTKKG-KFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAI 178 (302)
Q Consensus 100 ~i~~g~~~~~~~~pwi~~l~~~~-~~~C~GsLI~~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~ 178 (302)
++.+|..+...+|||++.+.... .+.|+|+||++++|||||||+.......+.|++|.++...... ...+.|.+++
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~---~~~~~v~~~~ 77 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEE---GQVIKVSKVI 77 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCCC---ceEEeeEEEE
Confidence 46789999999999999998775 7899999999999999999997655568999999887543221 2678999999
Q ss_pred eCCCCCCCCCCCCeEEEEEcCCCcCCCCceeeeeeCCCC--CC---------------CCCccCcCceEEEeeeeCHHhH
Q psy8651 179 RHPDFSLSNFNNDIALLEMESGVDFEAPQIHPACLPGNS--LD---------------ERKPTANSLRKVEVPILSEEEC 241 (302)
Q Consensus 179 ~hp~y~~~~~~~DiALl~L~~~~~~~~~~v~picl~~~~--~~---------------~~~~~~~~l~~~~~~~~~~~~C 241 (302)
.||+|+.....+|||||+|++|+.++. .++|||||... .. ........++...+.+++.+.|
T Consensus 78 ~~p~~~~~~~~~DiAll~L~~~i~~~~-~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C 156 (229)
T smart00020 78 IHPNYNPSTYDNDIALLKLKSPVTLSD-NVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATC 156 (229)
T ss_pred ECCCCCCCCCcCCEEEEEECcccCCCC-ceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHh
Confidence 999999888999999999999999988 99999999762 11 0122345788999999999999
Q ss_pred hccCCCCCCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeEEEEEEeeeee
Q psy8651 242 KSAGYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEATLSKVVSRVQ 298 (302)
Q Consensus 242 ~~~~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~ 298 (302)
...+.....+.+.++|++......+.|.|||||||++.. + +|+|+||+|++.
T Consensus 157 ~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~--~---~~~l~Gi~s~g~ 208 (229)
T smart00020 157 RRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCND--G---RWVLVGIVSWGS 208 (229)
T ss_pred hhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEEC--C---CEEEEEEEEECC
Confidence 987644346788999998655467899999999999987 3 679999999985
No 3
>KOG3627|consensus
Probab=100.00 E-value=3.1e-34 Score=243.13 Aligned_cols=196 Identities=41% Similarity=0.709 Sum_probs=159.0
Q ss_pred CceecCCeecccccchhHHhhhccC--eeeeeEEEeeCCEEEecccccCCC-CCceEEEEEcccccccCCCCCc-eEEEe
Q psy8651 98 NQRIVGGNVTKLHEFPWIAALTKKG--KFYCGATLIAKRHVLTAAHCIEGV-NPKEIKVTLGEHDRLSKNESVP-VIIRK 173 (302)
Q Consensus 98 ~~~i~~g~~~~~~~~pwi~~l~~~~--~~~C~GsLI~~~~VLTaAhC~~~~-~~~~~~v~~g~~~~~~~~~~~~-~~~~~ 173 (302)
..++++|..+..+++||++.+.... .++|+|+||+++||||||||+... .. .+.|++|.+.......... .....
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~~ 88 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVGD 88 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCc-ceEEEECccccccccccCchhhhce
Confidence 4688899999999999999998765 789999999999999999999753 22 7889999876553322221 24455
Q ss_pred EeEEEeCCCCCCCCCC-CCeEEEEEcCCCcCCCCceeeeeeCCCCC---C--------------C--CCccCcCceEEEe
Q psy8651 174 VKRAIRHPDFSLSNFN-NDIALLEMESGVDFEAPQIHPACLPGNSL---D--------------E--RKPTANSLRKVEV 233 (302)
Q Consensus 174 v~~i~~hp~y~~~~~~-~DiALl~L~~~~~~~~~~v~picl~~~~~---~--------------~--~~~~~~~l~~~~~ 233 (302)
|.++++||+|+..... ||||||+|.+++.|++ .|+|||||.... . . ....+..|++.++
T Consensus 89 v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~-~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v 167 (256)
T KOG3627|consen 89 VEKIIVHPNYNPRTLENNDIALLRLSEPVTFSS-HIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDV 167 (256)
T ss_pred eeEEEECCCCCCCCCCCCCEEEEEECCCcccCC-cccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEE
Confidence 7889999999988877 9999999999999998 999999994432 1 1 1146788999999
Q ss_pred eeeCHHhHhccCCCCCCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeEEEEEEeeeeee
Q psy8651 234 PILSEEECKSAGYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEATLSKVVSRVQE 299 (302)
Q Consensus 234 ~~~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~~ 299 (302)
++++.+.|+..+.....+.+.|+||+......++|+|||||||++.. ++ +|+|+||+|||..
T Consensus 168 ~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~--~~--~~~~~GivS~G~~ 229 (256)
T KOG3627|consen 168 PIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCED--NG--RWVLVGIVSWGSG 229 (256)
T ss_pred eEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEee--CC--cEEEEEEEEecCC
Confidence 99999999988754335677799999656777899999999999998 44 6799999999863
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=99.97 E-value=3.7e-31 Score=218.84 Aligned_cols=182 Identities=40% Similarity=0.747 Sum_probs=150.9
Q ss_pred ecCCeecccccchhHHhhhccC-eeeeeEEEeeCCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEe
Q psy8651 101 IVGGNVTKLHEFPWIAALTKKG-KFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIR 179 (302)
Q Consensus 101 i~~g~~~~~~~~pwi~~l~~~~-~~~C~GsLI~~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~ 179 (302)
|.+|..+..+++||++.+.... .++|+|+||+++||||||||+.. ...+.+.+|..... ..... .+.+.|++++.
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~--~~~~~v~~g~~~~~-~~~~~-~~~~~v~~~~~ 76 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG--ASDIKVRLGTYSIR-NSDGS-EQTIKVSKIII 76 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS--GGSEEEEESESBTT-STTTT-SEEEEEEEEEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc--cccccccccccccc-ccccc-ccccccccccc
Confidence 5689999999999999998876 89999999999999999999975 56788899983332 22222 57889999999
Q ss_pred CCCCCCCCCCCCeEEEEEcCCCcCCCCceeeeeeCCCCC--C----------CC---CccCcCceEEEeeeeCHHhHhcc
Q psy8651 180 HPDFSLSNFNNDIALLEMESGVDFEAPQIHPACLPGNSL--D----------ER---KPTANSLRKVEVPILSEEECKSA 244 (302)
Q Consensus 180 hp~y~~~~~~~DiALl~L~~~~~~~~~~v~picl~~~~~--~----------~~---~~~~~~l~~~~~~~~~~~~C~~~ 244 (302)
||+|+.....+|||||+|++++.+.+ .++|+||+.... . .. ......++...+.+++.+.|+..
T Consensus 77 h~~~~~~~~~~DiAll~L~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~~~ 155 (220)
T PF00089_consen 77 HPKYDPSTYDNDIALLKLDRPITFGD-NIQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCRSS 155 (220)
T ss_dssp ETTSBTTTTTTSEEEEEESSSSEHBS-SBEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHHHH
T ss_pred cccccccccccccccccccccccccc-ccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 99999988899999999999999888 999999998332 1 11 11345789999999999999987
Q ss_pred CCCCCCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeEEEEEEeeee
Q psy8651 245 GYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEATLSKVVSRV 297 (302)
Q Consensus 245 ~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~ 297 (302)
+ ...+.+.++|++.. ...+.|.|||||||++.. . +|+||+|++
T Consensus 156 ~--~~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~--~-----~lvGI~s~~ 198 (220)
T PF00089_consen 156 Y--NDNLTPNMICAGSS-GSGDACQGDSGGPLICNN--N-----YLVGIVSFG 198 (220)
T ss_dssp T--TTTSTTTEEEEETT-SSSBGGTTTTTSEEEETT--E-----EEEEEEEEE
T ss_pred c--cccccccccccccc-ccccccccccccccccce--e-----eecceeeec
Confidence 4 44478999999854 557899999999999977 1 599999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.7e-25 Score=184.18 Aligned_cols=191 Identities=28% Similarity=0.428 Sum_probs=136.0
Q ss_pred CCceecCCeecccccchhHHhhhcc-----CeeeeeEEEeeCCEEEecccccCCCC---CceEEEEEcccccccCCCCCc
Q psy8651 97 RNQRIVGGNVTKLHEFPWIAALTKK-----GKFYCGATLIAKRHVLTAAHCIEGVN---PKEIKVTLGEHDRLSKNESVP 168 (302)
Q Consensus 97 ~~~~i~~g~~~~~~~~pwi~~l~~~-----~~~~C~GsLI~~~~VLTaAhC~~~~~---~~~~~v~~g~~~~~~~~~~~~ 168 (302)
...+|++|..+..++||.++.+... ...+|||+++..|||||||||+.... .....|.++..+.+ +
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~S---q--- 102 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSS---Q--- 102 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccc---c---
Confidence 4578999999999999999998654 34699999999999999999996543 33444555544432 2
Q ss_pred eEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCCCcCCCCceeeee--------eCCCCCC--------------CCCccCc
Q psy8651 169 VIIRKVKRAIRHPDFSLSNFNNDIALLEMESGVDFEAPQIHPAC--------LPGNSLD--------------ERKPTAN 226 (302)
Q Consensus 169 ~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~~~~~~~~v~pic--------l~~~~~~--------------~~~~~~~ 226 (302)
.+...|.+++.|..|.+.++.||||+++|.++.......+.-.- ++..... ...+...
T Consensus 103 ~~rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt 182 (413)
T COG5640 103 AERGHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGT 182 (413)
T ss_pred ccCcceEEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCccc
Confidence 55678999999999999999999999999997643210111100 0000000 1222335
Q ss_pred CceEEEeeeeCHHhHhccCCCC----CCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeEEEEEEeeeeee
Q psy8651 227 SLRKVEVPILSEEECKSAGYSA----SRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEATLSKVVSRVQE 299 (302)
Q Consensus 227 ~l~~~~~~~~~~~~C~~~~~~~----~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~~ 299 (302)
.|++..+..++...|...+... ....-.-+|++... .++|+||||||++.+. .+|. .++||+|||..
T Consensus 183 ~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~~~g-~~G~---vQ~GVvSwG~~ 253 (413)
T COG5640 183 ILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIFHKG-EEGR---VQRGVVSWGDG 253 (413)
T ss_pred eeeeeeeeeechHHhhhhccccccCCCCCCccceecCCCC--cccccCCCCCceEEeC-CCcc---EEEeEEEecCC
Confidence 8999999999999998876211 11112239998544 7999999999999987 3343 69999999976
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.51 E-value=1.3e-13 Score=118.47 Aligned_cols=186 Identities=27% Similarity=0.412 Sum_probs=111.0
Q ss_pred eeecccc--CCceecCCeecccccchhHHhhhcc----CeeeeeEEEeeCCEEEecccccCCCCCce-------------
Q psy8651 90 IACGQVE--RNQRIVGGNVTKLHEFPWIAALTKK----GKFYCGATLIAKRHVLTAAHCIEGVNPKE------------- 150 (302)
Q Consensus 90 ~~cG~~~--~~~~i~~g~~~~~~~~pwi~~l~~~----~~~~C~GsLI~~~~VLTaAhC~~~~~~~~------------- 150 (302)
..||... ...+..+|..+...+.||.+.+... ...+++|+|||+|||||++||+.......
T Consensus 29 ~~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~~ 108 (282)
T PF03761_consen 29 ETCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCEG 108 (282)
T ss_pred HhcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceeeC
Confidence 4688332 2334567888888889999888654 23567999999999999999995321100
Q ss_pred --EEEEEcccccc--cC-----CCCCceEEEeEeEEEeCCCC----CCCCCCCCeEEEEEcCCCcCCCCceeeeeeCCCC
Q psy8651 151 --IKVTLGEHDRL--SK-----NESVPVIIRKVKRAIRHPDF----SLSNFNNDIALLEMESGVDFEAPQIHPACLPGNS 217 (302)
Q Consensus 151 --~~v~~g~~~~~--~~-----~~~~~~~~~~v~~i~~hp~y----~~~~~~~DiALl~L~~~~~~~~~~v~picl~~~~ 217 (302)
....+-..... .. .........++.++++--.- .......+++||+|+++ ++. ...|+|||...
T Consensus 109 ~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~-~~~~~Cl~~~~ 185 (282)
T PF03761_consen 109 NNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSK-NVSPPCLADSS 185 (282)
T ss_pred CCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccc-cCCCEEeCCCc
Confidence 00111000000 00 00011223456666553222 23445689999999999 656 88999999865
Q ss_pred CCCCC---------ccCcCceEEEeeeeCHHhHhccCCCCCCCCCCeEEeeeCCCCCCCCCCCCCCceEEEecCCCceeE
Q psy8651 218 LDERK---------PTANSLRKVEVPILSEEECKSAGYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPGKMEA 288 (302)
Q Consensus 218 ~~~~~---------~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~gDsGgPL~~~~~~~g~~~~ 288 (302)
..... .....+....+.+..... |+.........|.+|+||||+... +|+ |
T Consensus 186 ~~~~~~~~~~~yg~~~~~~~~~~~~~i~~~~~----------------~~~~~~~~~~~~~~d~Gg~lv~~~--~gr--~ 245 (282)
T PF03761_consen 186 TNWEKGDEVDVYGFNSTGKLKHRKLKITNCTK----------------CAYSICTKQYSCKGDRGGPLVKNI--NGR--W 245 (282)
T ss_pred cccccCceEEEeecCCCCeEEEEEEEEEEeec----------------cceeEecccccCCCCccCeEEEEE--CCC--E
Confidence 43100 022333333444433221 222223345789999999999998 776 5
Q ss_pred EEEEEeeeee
Q psy8651 289 TLSKVVSRVQ 298 (302)
Q Consensus 289 ~l~GI~S~~~ 298 (302)
+|+||.+.+.
T Consensus 246 tlIGv~~~~~ 255 (282)
T PF03761_consen 246 TLIGVGASGN 255 (282)
T ss_pred EEEEEEccCC
Confidence 8999998765
No 7
>KOG3627|consensus
Probab=99.49 E-value=1.4e-13 Score=116.65 Aligned_cols=114 Identities=37% Similarity=0.681 Sum_probs=82.4
Q ss_pred CCCCCEEEEEecCCCCCC-CCCCCCceEEEEeecChhhhccccccCc-CCCCCeEEcccCCCCCCCcccCCCCCceEeec
Q psy8651 5 NYTGKIGIVAGWGRLDER-KPTANSLRKVEVPILSEEECKSAGYSAS-RITNNMLCAGYAEGKRDSCQGDSGGPLQIAVA 82 (302)
Q Consensus 5 ~~~g~~~~v~GWG~~~~~-~~~~~~L~~~~~~~~~~~~C~~~~~~~~-~~~~~~~Cag~~~~~~~~C~gDsGgpl~~~~~ 82 (302)
...+..|.++|||.+... ...+..||++.++++++++|+.. +... .+.++|+||+...+.+++|+|||||||++...
T Consensus 137 ~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v~i~~~~~C~~~-~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~ 215 (256)
T KOG3627|consen 137 PPGGTTCLVSGWGRTESGGGPLPDTLQEVDVPIISNSECRRA-YGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDN 215 (256)
T ss_pred CCCCCEEEEEeCCCcCCCCCCCCceeEEEEEeEcChhHhccc-ccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeC
Confidence 445689999999987654 34689999999999999999973 4332 46678999997566678999999999999754
Q ss_pred cCCC-ceeeeeccccCCceecCCeecccccc-hhHHhhh
Q psy8651 83 RPGK-MEVIACGQVERNQRIVGGNVTKLHEF-PWIAALT 119 (302)
Q Consensus 83 ~~~~-~~~~~cG~~~~~~~i~~g~~~~~~~~-pwi~~l~ 119 (302)
..+. ...+++|...|...-.++.++.+..| +||....
T Consensus 216 ~~~~~~GivS~G~~~C~~~~~P~vyt~V~~y~~WI~~~~ 254 (256)
T KOG3627|consen 216 GRWVLVGIVSWGSGGCGQPNYPGVYTRVSSYLDWIKENI 254 (256)
T ss_pred CcEEEEEEEEecCCCCCCCCCCeEEeEhHHhHHHHHHHh
Confidence 4232 23445555435444345667776666 9987653
No 8
>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=1.3e-13 Score=110.02 Aligned_cols=99 Identities=21% Similarity=0.506 Sum_probs=81.9
Q ss_pred cccchhHHhhhccCeeeeeEEEeeCCEEEecccccCCCC--CceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCC
Q psy8651 109 LHEFPWIAALTKKGKFYCGATLIAKRHVLTAAHCIEGVN--PKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLS 186 (302)
Q Consensus 109 ~~~~pwi~~l~~~~~~~C~GsLI~~~~VLTaAhC~~~~~--~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~ 186 (302)
...|||++.++..+.+.|+|+||.+.|||++-.|+.+.+ ...+.|.+|.......-+....|.++|..+..-|+
T Consensus 13 ~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~~---- 88 (267)
T PF09342_consen 13 DYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVPE---- 88 (267)
T ss_pred cccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeeccc----
Confidence 345899999999999999999999999999999997644 47788999987644333333377888887665544
Q ss_pred CCCCCeEEEEEcCCCcCCCCceeeeeeCC
Q psy8651 187 NFNNDIALLEMESGVDFEAPQIHPACLPG 215 (302)
Q Consensus 187 ~~~~DiALl~L~~~~~~~~~~v~picl~~ 215 (302)
.+++||+|++|+.|+. +|+|.+||.
T Consensus 89 ---S~v~LLHL~~~~~fTr-~VlP~flp~ 113 (267)
T PF09342_consen 89 ---SNVLLLHLEQPANFTR-YVLPTFLPE 113 (267)
T ss_pred ---cceeeeeecCccccee-eeccccccc
Confidence 6899999999999999 999999997
No 9
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=99.16 E-value=1.4e-10 Score=96.23 Aligned_cols=112 Identities=41% Similarity=0.706 Sum_probs=77.2
Q ss_pred CCCCCCEEEEEecCCCCCCCCCCCCceEEEEeecChhhhccccccC-cCCCCCeEEcccCCCCCCCcccCCCCCceEeec
Q psy8651 4 ANYTGKIGIVAGWGRLDERKPTANSLRKVEVPILSEEECKSAGYSA-SRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVA 82 (302)
Q Consensus 4 ~~~~g~~~~v~GWG~~~~~~~~~~~L~~~~~~~~~~~~C~~~~~~~-~~~~~~~~Cag~~~~~~~~C~gDsGgpl~~~~~ 82 (302)
....+..+.++|||.+......+..|++..+++++.+.|... +.. ..+.++++|++......+.|.|||||||++...
T Consensus 117 ~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~-~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~ 195 (232)
T cd00190 117 NLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRA-YSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDN 195 (232)
T ss_pred cCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhh-ccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEeC
Confidence 355689999999998765445678899999999999999873 332 357889999987654568999999999998754
Q ss_pred cCCCcee-eeeccccCCceecCCeecccccc-hhHHh
Q psy8651 83 RPGKMEV-IACGQVERNQRIVGGNVTKLHEF-PWIAA 117 (302)
Q Consensus 83 ~~~~~~~-~~cG~~~~~~~i~~g~~~~~~~~-pwi~~ 117 (302)
..+.+.+ .+.|. .|......+.++....| +||..
T Consensus 196 ~~~~lvGI~s~g~-~c~~~~~~~~~t~v~~~~~WI~~ 231 (232)
T cd00190 196 GRGVLVGIVSWGS-GCARPNYPGVYTRVSSYLDWIQK 231 (232)
T ss_pred CEEEEEEEEehhh-ccCCCCCCCEEEEcHHhhHHhhc
Confidence 2222222 22222 13321234555666666 89864
No 10
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=98.88 E-value=9.3e-09 Score=85.27 Aligned_cols=109 Identities=39% Similarity=0.699 Sum_probs=73.8
Q ss_pred CCCCCCEEEEEecCCCCC-CCCCCCCceEEEEeecChhhhccccccC-cCCCCCeEEcccCCCCCCCcccCCCCCceEee
Q psy8651 4 ANYTGKIGIVAGWGRLDE-RKPTANSLRKVEVPILSEEECKSAGYSA-SRITNNMLCAGYAEGKRDSCQGDSGGPLQIAV 81 (302)
Q Consensus 4 ~~~~g~~~~v~GWG~~~~-~~~~~~~L~~~~~~~~~~~~C~~~~~~~-~~~~~~~~Cag~~~~~~~~C~gDsGgpl~~~~ 81 (302)
....+..+.++|||.... ....+..|+.+.+.+++.+.|... +.. ..+..+++|++......+.|.||||+||++..
T Consensus 117 ~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~-~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~ 195 (229)
T smart00020 117 NVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRA-YSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCND 195 (229)
T ss_pred ccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhh-hccccccCCCcEeecCCCCCCcccCCCCCCeeEEEC
Confidence 455688999999997653 234567899999999999999873 332 24778899998665456899999999999875
Q ss_pred ccCCCc-eeeeeccccCCceecCCeecccccc-hhH
Q psy8651 82 ARPGKM-EVIACGQVERNQRIVGGNVTKLHEF-PWI 115 (302)
Q Consensus 82 ~~~~~~-~~~~cG~~~~~~~i~~g~~~~~~~~-pwi 115 (302)
. ...+ ...+.|. .|......+.++.+..| +||
T Consensus 196 ~-~~~l~Gi~s~g~-~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 196 G-RWVLVGIVSWGS-GCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred C-CEEEEEEEEECC-CCCCCCCCCEEEEeccccccC
Confidence 3 2222 2233333 33322223455555555 776
No 11
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=98.82 E-value=1e-08 Score=84.33 Aligned_cols=103 Identities=36% Similarity=0.675 Sum_probs=72.5
Q ss_pred CCCCEEEEEecCCCCCCCCCCCCceEEEEeecChhhhccccccCcCCCCCeEEcccCCCCCCCcccCCCCCceEeeccCC
Q psy8651 6 YTGKIGIVAGWGRLDERKPTANSLRKVEVPILSEEECKSAGYSASRITNNMLCAGYAEGKRDSCQGDSGGPLQIAVARPG 85 (302)
Q Consensus 6 ~~g~~~~v~GWG~~~~~~~~~~~L~~~~~~~~~~~~C~~~~~~~~~~~~~~~Cag~~~~~~~~C~gDsGgpl~~~~~~~~ 85 (302)
..++.+.+.|||...... .+..+++..+.+++.+.|+.. +.. .+...++|++.. +..+.|.||||+||++...
T Consensus 117 ~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~~~~~c~~~-~~~-~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~--- 189 (220)
T PF00089_consen 117 NVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVVSRKTCRSS-YND-NLTPNMICAGSS-GSGDACQGDSGGPLICNNN--- 189 (220)
T ss_dssp TTTSEEEEEESSBSSTTS-BTSBEEEEEEEEEEHHHHHHH-TTT-TSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---
T ss_pred cccccccccccccccccc-ccccccccccccccccccccc-ccc-cccccccccccc-cccccccccccccccccee---
Confidence 578999999999865443 567899999999999999873 322 478899999865 5568999999999998654
Q ss_pred CceeeeeccccCCceecCCeecccccc-hhH
Q psy8651 86 KMEVIACGQVERNQRIVGGNVTKLHEF-PWI 115 (302)
Q Consensus 86 ~~~~~~cG~~~~~~~i~~g~~~~~~~~-pwi 115 (302)
.+.++......+...-..+.++....| +||
T Consensus 190 ~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 190 YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 222222222333322223556666666 887
No 12
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=5.1e-07 Score=76.64 Aligned_cols=110 Identities=24% Similarity=0.388 Sum_probs=74.2
Q ss_pred CEEEEEecCCCCC---CCCCC--CCceEEEEeecChhhhcccccc-----CcCCCCCeEEcccCCCCCCCcccCCCCCce
Q psy8651 9 KIGIVAGWGRLDE---RKPTA--NSLRKVEVPILSEEECKSAGYS-----ASRITNNMLCAGYAEGKRDSCQGDSGGPLQ 78 (302)
Q Consensus 9 ~~~~v~GWG~~~~---~~~~~--~~L~~~~~~~~~~~~C~~~~~~-----~~~~~~~~~Cag~~~~~~~~C~gDsGgpl~ 78 (302)
......+||.+.. ....+ ..|+++.+..++..+|.. .++ .....-.-+|||... +|+|+||||||++
T Consensus 159 s~~~n~t~~~~~~~~v~~~~p~gt~l~e~~v~fv~~stc~~-~~g~an~~dg~~~lT~~cag~~~--~daCqGDSGGPi~ 235 (413)
T COG5640 159 SPMTNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQ-YKGCANASDGATGLTGFCAGRPP--KDACQGDSGGPIF 235 (413)
T ss_pred ccccceeeeeeeecCCCCCCCccceeeeeeeeeechHHhhh-hccccccCCCCCCccceecCCCC--cccccCCCCCceE
Confidence 3445566665432 11223 489999999999999987 232 111222339998555 6999999999999
Q ss_pred Eeecc-CCCceeeeeccccCCceecCCeecccccc-hhHHhhhcc
Q psy8651 79 IAVAR-PGKMEVIACGQVERNQRIVGGNVTKLHEF-PWIAALTKK 121 (302)
Q Consensus 79 ~~~~~-~~~~~~~~cG~~~~~~~i~~g~~~~~~~~-pwi~~l~~~ 121 (302)
..... +-....+++|...|+....+|.++....| .||...+..
T Consensus 236 ~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVyT~vsny~~WI~a~~~~ 280 (413)
T COG5640 236 HKGEEGRVQRGVVSWGDGGCGGTLIPGVYTNVSNYQDWIAAMTNG 280 (413)
T ss_pred EeCCCccEEEeEEEecCCCCCCCCcceeEEehhHHHHHHHHHhcC
Confidence 76422 22334567787777777777888888777 999986543
No 13
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.34 E-value=1.4e-06 Score=71.83 Aligned_cols=39 Identities=38% Similarity=0.643 Sum_probs=27.9
Q ss_pred cccchhHHhhhcc---CeeeeeEEEeeCCEEEecccccCCCC
Q psy8651 109 LHEFPWIAALTKK---GKFYCGATLIAKRHVLTAAHCIEGVN 147 (302)
Q Consensus 109 ~~~~pwi~~l~~~---~~~~C~GsLI~~~~VLTaAhC~~~~~ 147 (302)
...|||-+-.... +..-|+++||+++.||||+||+....
T Consensus 46 t~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~ 87 (251)
T COG3591 46 TTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPD 87 (251)
T ss_pred CCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCC
Confidence 3456775444322 55567779999999999999996544
No 14
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=97.80 E-value=6.3e-05 Score=55.43 Aligned_cols=21 Identities=38% Similarity=0.401 Sum_probs=18.9
Q ss_pred eeEEEeeCC-EEEecccccCCC
Q psy8651 126 CGATLIAKR-HVLTAAHCIEGV 146 (302)
Q Consensus 126 C~GsLI~~~-~VLTaAhC~~~~ 146 (302)
|+|.+|.++ +|||+|||+...
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDW 22 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCC
T ss_pred CEEEEEcCCceEEEchhheecc
Confidence 789999999 999999999653
No 15
>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=97.57 E-value=0.0033 Score=57.36 Aligned_cols=68 Identities=26% Similarity=0.366 Sum_probs=44.8
Q ss_pred eeeeeEEEeeCC-EEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCCC
Q psy8651 123 KFYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESGV 201 (302)
Q Consensus 123 ~~~C~GsLI~~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~~ 201 (302)
...++|.+|+++ +|||++|.+.+ ...+.|.+... ..+..+-+..++ ..||||||++.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~--~~~i~V~~~~~-----------~~~~a~vv~~d~-------~~DlAllkv~~~- 115 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDG--ADEITVTLSDG-----------REFKAKLVGKDP-------RTDIAVLKIDAK- 115 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCC--CCeEEEEeCCC-----------CEEEEEEEEecC-------CCCEEEEEecCC-
Confidence 457999999976 99999999964 35566655421 223333333343 369999999865
Q ss_pred cCCCCceeeeeeCC
Q psy8651 202 DFEAPQIHPACLPG 215 (302)
Q Consensus 202 ~~~~~~v~picl~~ 215 (302)
. .+.++.|..
T Consensus 116 ---~-~~~~~~l~~ 125 (428)
T TIGR02037 116 ---K-NLPVIKLGD 125 (428)
T ss_pred ---C-CceEEEccC
Confidence 2 455666654
No 16
>PRK10139 serine endoprotease; Provisional
Probab=97.29 E-value=0.0081 Score=55.10 Aligned_cols=58 Identities=24% Similarity=0.268 Sum_probs=39.4
Q ss_pred eeeeeEEEeeC--CEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCC
Q psy8651 123 KFYCGATLIAK--RHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESG 200 (302)
Q Consensus 123 ~~~C~GsLI~~--~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~ 200 (302)
....+|.+|++ .+|||.+|.+.+ ...+.|.+... ..++.+-+...| ..||||||++.+
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~--a~~i~V~~~dg-----------~~~~a~vvg~D~-------~~DlAvlkv~~~ 148 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQ--AQKISIQLNDG-----------REFDAKLIGSDD-------QSDIALLQIQNP 148 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCC--CCEEEEEECCC-----------CEEEEEEEEEcC-------CCCEEEEEecCC
Confidence 35789999974 699999999964 45677776421 223333333433 479999999854
No 17
>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=97.14 E-value=0.016 Score=51.40 Aligned_cols=57 Identities=23% Similarity=0.276 Sum_probs=38.0
Q ss_pred eeeeEEEeeCC-EEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCC
Q psy8651 124 FYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESG 200 (302)
Q Consensus 124 ~~C~GsLI~~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~ 200 (302)
...+|.+|+++ +|||.+|.+.. ...+.|.+.. ...++.+-+..+| ..||||||++.+
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~--~~~i~V~~~d-----------g~~~~a~vv~~d~-------~~DlAvlkv~~~ 135 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKK--ADQIVVALQD-----------GRKFEAELVGSDP-------LTDLAVLKIEGD 135 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCC--CCEEEEEECC-----------CCEEEEEEEEecC-------CCCEEEEEecCC
Confidence 46899999976 99999999964 3456665532 1223333333343 479999999854
No 18
>PRK10898 serine endoprotease; Provisional
Probab=97.08 E-value=0.014 Score=51.77 Aligned_cols=57 Identities=19% Similarity=0.275 Sum_probs=38.0
Q ss_pred eeeeEEEeeCC-EEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCC
Q psy8651 124 FYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESG 200 (302)
Q Consensus 124 ~~C~GsLI~~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~ 200 (302)
..-+|.+|+++ +|||.+|-+.. ...+.|.+..- ..+..+-+...| ..||||||++.+
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~--a~~i~V~~~dg-----------~~~~a~vv~~d~-------~~DlAvl~v~~~ 135 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVIND--ADQIIVALQDG-----------RVFEALLVGSDS-------LTDLAVLKINAT 135 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCC--CCEEEEEeCCC-----------CEEEEEEEEEcC-------CCCEEEEEEcCC
Confidence 46899999976 99999999863 45666665321 123333333443 379999999753
No 19
>PRK10942 serine endoprotease; Provisional
Probab=96.84 E-value=0.051 Score=50.19 Aligned_cols=57 Identities=25% Similarity=0.362 Sum_probs=38.3
Q ss_pred eeeeEEEeeC--CEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCC
Q psy8651 124 FYCGATLIAK--RHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESG 200 (302)
Q Consensus 124 ~~C~GsLI~~--~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~ 200 (302)
...+|.+|+. .+|||.+|.+.+ ...+.|.+.+. ..+..+-+..+| ..||||||++.+
T Consensus 111 ~~GSG~ii~~~~G~IlTn~HVv~~--a~~i~V~~~dg-----------~~~~a~vv~~D~-------~~DlAvlki~~~ 169 (473)
T PRK10942 111 ALGSGVIIDADKGYVVTNNHVVDN--ATKIKVQLSDG-----------RKFDAKVVGKDP-------RSDIALIQLQNP 169 (473)
T ss_pred ceEEEEEEECCCCEEEeChhhcCC--CCEEEEEECCC-----------CEEEEEEEEecC-------CCCEEEEEecCC
Confidence 4689999985 599999999864 45677766421 123333333343 379999999743
No 20
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=96.57 E-value=0.025 Score=54.83 Aligned_cols=65 Identities=22% Similarity=0.306 Sum_probs=36.2
Q ss_pred EEEeeCCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCCCcCCCCc
Q psy8651 128 ATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESGVDFEAPQ 207 (302)
Q Consensus 128 GsLI~~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~~~~~~~~ 207 (302)
.|||++++|+|++|=... .-.|.+|.... ..+.+..=-.|+. .|+.+.||.+=|. -
T Consensus 69 aTLigpqYiVSV~HN~~g----y~~v~FG~~g~---------~~Y~iV~RNn~~~-------~Df~~pRLnK~VT----E 124 (769)
T PF02395_consen 69 ATLIGPQYIVSVKHNGKG----YNSVSFGNEGQ---------NTYKIVDRNNYPS-------GDFHMPRLNKFVT----E 124 (769)
T ss_dssp -EEEETTEEEBETTG-TS----CCEECESCSST---------CEEEEEEEEBETT-------STEBEEEESS-------S
T ss_pred EEEecCCeEEEEEccCCC----cCceeecccCC---------ceEEEEEccCCCC-------cccceeecCceEE----E
Confidence 899999999999997622 22456665432 2334433334443 6999999998776 3
Q ss_pred eeeeeeCCC
Q psy8651 208 IHPACLPGN 216 (302)
Q Consensus 208 v~picl~~~ 216 (302)
+.|+-....
T Consensus 125 vaP~~~t~~ 133 (769)
T PF02395_consen 125 VAPAEMTTA 133 (769)
T ss_dssp S----BBSS
T ss_pred Eeccccccc
Confidence 556665544
No 21
>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=84.04 E-value=0.25 Score=38.94 Aligned_cols=71 Identities=17% Similarity=0.167 Sum_probs=38.8
Q ss_pred CeeeeeEEEeeCCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCCC
Q psy8651 122 GKFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESGV 201 (302)
Q Consensus 122 ~~~~C~GsLI~~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~~ 201 (302)
+.+.+.+..|..+|.|-..|.- ... .+.++. ..+++...+.. .+......||++++|.+.-
T Consensus 23 g~~t~l~~gi~~~~~lvp~H~~---~~~--~i~i~g------------~~~~~~d~~~l--v~~~~~~~Dl~~v~l~~~~ 83 (172)
T PF00548_consen 23 GEFTMLALGIYDRYFLVPTHEE---PED--TIYIDG------------VEYKVDDSVVL--VDRDGVDTDLTLVKLPRNP 83 (172)
T ss_dssp EEEEEEEEEEEBTEEEEEGGGG---GCS--EEEETT------------EEEEEEEEEEE--EETTSSEEEEEEEEEESSS
T ss_pred ceEEEecceEeeeEEEEECcCC---CcE--EEEECC------------EEEEeeeeEEE--ecCCCcceeEEEEEccCCc
Confidence 4566778899999999999932 222 233321 22222222111 1122334699999999887
Q ss_pred cCCCCceeeee
Q psy8651 202 DFEAPQIHPAC 212 (302)
Q Consensus 202 ~~~~~~v~pic 212 (302)
.|.+ -.+-++
T Consensus 84 kfrD-Irk~~~ 93 (172)
T PF00548_consen 84 KFRD-IRKFFP 93 (172)
T ss_dssp -B---GGGGSB
T ss_pred ccCc-hhhhhc
Confidence 7754 444443
No 22
>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=79.67 E-value=7.2 Score=32.35 Aligned_cols=25 Identities=32% Similarity=0.401 Sum_probs=17.0
Q ss_pred CCCCCCCceEEEecCCCceeEEEEEEeeeee
Q psy8651 268 CQGDSGGPLQIAVARPGKMEATLSKVVSRVQ 298 (302)
Q Consensus 268 C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~ 298 (302)
=.||=|.||+... +|. ++||.|-+.
T Consensus 149 k~G~CG~PlVs~~--Dg~----IVGiHsl~~ 173 (235)
T PF00863_consen 149 KDGDCGLPLVSTK--DGK----IVGIHSLTS 173 (235)
T ss_dssp -TT-TT-EEEETT--T------EEEEEEEEE
T ss_pred CCCccCCcEEEcC--CCc----EEEEEcCcc
Confidence 3588999999987 774 999998765
No 23
>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=68.20 E-value=2.6 Score=31.04 Aligned_cols=25 Identities=28% Similarity=0.337 Sum_probs=19.7
Q ss_pred CCCCCCceEEEecCCCceeEEEEEEeeeeeeec
Q psy8651 269 QGDSGGPLQIAVARPGKMEATLSKVVSRVQETV 301 (302)
Q Consensus 269 ~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~~~~ 301 (302)
.||-||+|.|+- -++||++-|.+..
T Consensus 89 PGdCGg~L~C~H--------GViGi~Tagg~g~ 113 (127)
T PF00947_consen 89 PGDCGGILRCKH--------GVIGIVTAGGEGH 113 (127)
T ss_dssp TT-TCSEEEETT--------CEEEEEEEEETTE
T ss_pred CCCCCceeEeCC--------CeEEEEEeCCCce
Confidence 489999999976 4899998887654
No 24
>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=48.49 E-value=11 Score=31.69 Aligned_cols=23 Identities=35% Similarity=0.494 Sum_probs=16.1
Q ss_pred CCCCCCceEEEecCCCceeEEEEEEeeeee
Q psy8651 269 QGDSGGPLQIAVARPGKMEATLSKVVSRVQ 298 (302)
Q Consensus 269 ~gDsGgPL~~~~~~~g~~~~~l~GI~S~~~ 298 (302)
.||||+|++.++ | .|+||.+-..
T Consensus 207 ~GDSGSPVVt~d---g----~liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTED---G----DLIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETT---C-----EEEEEEEEE
T ss_pred CCCCCCccCcCC---C----CEEEEEecCC
Confidence 489999999865 2 3999987543
No 25
>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=43.02 E-value=23 Score=28.89 Aligned_cols=24 Identities=33% Similarity=0.376 Sum_probs=20.2
Q ss_pred CCCCCCCCCceEEEecCCCceeEEEEEEeeee
Q psy8651 266 DSCQGDSGGPLQIAVARPGKMEATLSKVVSRV 297 (302)
Q Consensus 266 ~~C~gDsGgPL~~~~~~~g~~~~~l~GI~S~~ 297 (302)
..-+|-||+|++.+. .|+|-++++
T Consensus 176 GIvqGMSGSPI~qdG--------KLiGAVthv 199 (218)
T PF05580_consen 176 GIVQGMSGSPIIQDG--------KLIGAVTHV 199 (218)
T ss_pred CEEecccCCCEEECC--------EEEEEEEEE
Confidence 678899999998755 699998876
No 26
>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=42.13 E-value=17 Score=35.44 Aligned_cols=20 Identities=30% Similarity=0.499 Sum_probs=18.2
Q ss_pred eeeeEEEeeCC-EEEeccccc
Q psy8651 124 FYCGATLIAKR-HVLTAAHCI 143 (302)
Q Consensus 124 ~~C~GsLI~~~-~VLTaAhC~ 143 (302)
..|+|++||++ .|||=-||.
T Consensus 47 gGCSgsfVS~~GLvlTNHHC~ 67 (698)
T PF10459_consen 47 GGCSGSFVSPDGLVLTNHHCG 67 (698)
T ss_pred CceeEEEEcCCceEEecchhh
Confidence 35999999987 899999998
No 27
>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=35.23 E-value=28 Score=26.03 Aligned_cols=13 Identities=38% Similarity=0.756 Sum_probs=9.2
Q ss_pred CCCCCCCceEEEe
Q psy8651 268 CQGDSGGPLQIAV 280 (302)
Q Consensus 268 C~gDsGgPL~~~~ 280 (302)
-+|-||||++|..
T Consensus 106 lkGSSGgPiLC~~ 118 (148)
T PF02907_consen 106 LKGSSGGPILCPS 118 (148)
T ss_dssp HTT-TT-EEEETT
T ss_pred EecCCCCcccCCC
Confidence 5688999999976
No 28
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.02 E-value=3.3e+02 Score=24.00 Aligned_cols=58 Identities=26% Similarity=0.299 Sum_probs=37.1
Q ss_pred eeeeeEEEee-CCEEEecccccCCCCCceEEEEEcccccccCCCCCceEEEeEeEEEeCCCCCCCCCCCCeEEEEEcCC
Q psy8651 123 KFYCGATLIA-KRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNESVPVIIRKVKRAIRHPDFSLSNFNNDIALLEMESG 200 (302)
Q Consensus 123 ~~~C~GsLI~-~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DiALl~L~~~ 200 (302)
....+|.+++ ..+|+|-.|=+.. ...+.+.+. + ...++.+-+-.. ...|+|++|.+..
T Consensus 71 ~~~gSg~i~~~~g~ivTn~hVi~~--a~~i~v~l~--d---------g~~~~a~~vg~d-------~~~dlavlki~~~ 129 (347)
T COG0265 71 EGLGSGFIISSDGYIVTNNHVIAG--AEEITVTLA--D---------GREVPAKLVGKD-------PISDLAVLKIDGA 129 (347)
T ss_pred cccccEEEEcCCeEEEecceecCC--cceEEEEeC--C---------CCEEEEEEEecC-------CccCEEEEEeccC
Confidence 3567888888 7799999998764 556666551 1 222333333322 2479999999864
Done!