Query psy2626
Match_columns 355
No_of_seqs 457 out of 2165
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 21:01:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2626hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 100.0 5.3E-47 1.1E-51 334.7 25.6 231 108-353 1-232 (232)
2 KOG3627|consensus 100.0 1.1E-45 2.4E-50 332.3 25.0 239 105-355 10-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 6.5E-44 1.4E-48 314.9 23.9 228 107-350 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 4.4E-41 9.5E-46 294.6 22.8 219 108-350 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 1.4E-35 3.1E-40 261.4 17.3 239 104-355 29-279 (413)
6 PF03761 DUF316: Domain of unk 99.8 1.1E-18 2.4E-23 159.0 17.3 218 96-350 30-275 (282)
7 PF09342 DUF1986: Domain of un 99.5 1.2E-12 2.5E-17 111.2 14.0 115 117-251 14-131 (267)
8 PF12032 CLIP: Regulatory CLIP 99.3 1.1E-12 2.3E-17 88.0 2.4 53 10-62 1-54 (54)
9 COG3591 V8-like Glu-specific e 99.3 6.2E-11 1.3E-15 103.2 13.3 204 114-355 44-251 (251)
10 smart00680 CLIP Clip or disulp 99.1 1.7E-10 3.7E-15 76.7 4.0 52 10-63 1-52 (52)
11 TIGR02037 degP_htrA_DO peripla 98.5 3E-06 6.5E-11 81.8 13.7 142 139-328 57-199 (428)
12 PF13365 Trypsin_2: Trypsin-li 98.4 1.4E-06 2.9E-11 68.3 8.3 20 142-161 1-21 (120)
13 TIGR02038 protease_degS peripl 98.3 3E-05 6.5E-10 72.8 15.1 141 139-328 77-218 (351)
14 PRK10898 serine endoprotease; 98.2 8.1E-05 1.8E-09 69.9 16.5 141 140-329 78-219 (353)
15 PRK10139 serine endoprotease; 98.1 5.1E-05 1.1E-09 73.5 13.8 141 140-328 90-232 (455)
16 PRK10942 serine endoprotease; 98.0 0.00013 2.8E-09 71.2 13.7 141 140-328 111-253 (473)
17 PF02395 Peptidase_S6: Immunog 97.2 0.0021 4.5E-08 65.7 9.6 66 143-231 68-133 (769)
18 PF00863 Peptidase_C4: Peptida 89.2 1.6 3.5E-05 38.3 7.0 40 301-345 147-186 (235)
19 PF00947 Pico_P2A: Picornaviru 87.6 0.27 5.8E-06 38.3 1.1 39 303-351 88-126 (127)
20 PF00548 Peptidase_C3: 3C cyst 86.1 4.2 9.1E-05 34.0 7.6 147 138-329 23-171 (172)
21 COG0265 DegQ Trypsin-like seri 82.8 29 0.00062 32.5 12.6 58 140-217 72-130 (347)
22 PF05416 Peptidase_C37: Southa 63.6 20 0.00043 34.1 6.0 143 143-330 382-528 (535)
23 PF05579 Peptidase_S32: Equine 58.1 8.2 0.00018 34.3 2.4 23 304-329 207-229 (297)
24 PF10459 Peptidase_S46: Peptid 55.8 7.2 0.00016 40.1 1.9 21 141-161 48-69 (698)
25 KOG1421|consensus 54.2 56 0.0012 33.3 7.5 71 141-231 85-158 (955)
26 PF02907 Peptidase_S29: Hepati 47.7 13 0.00028 29.4 1.8 22 303-327 106-127 (148)
27 PF05580 Peptidase_S55: SpoIVB 42.9 30 0.00066 29.9 3.4 27 300-330 175-201 (218)
28 PF00944 Peptidase_S3: Alphavi 29.3 30 0.00065 27.4 1.2 24 304-330 105-128 (158)
29 PF10459 Peptidase_S46: Peptid 25.9 68 0.0015 33.2 3.4 24 299-325 627-650 (698)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=100.00 E-value=5.3e-47 Score=334.72 Aligned_cols=231 Identities=43% Similarity=0.846 Sum_probs=199.5
Q ss_pred eecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCC-CCcE
Q psy2626 108 IVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDT-SSGV 186 (355)
Q Consensus 108 i~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~-~~~~ 186 (355)
|+||+++..++|||+|.|++.. ..+.|+||||+++||||||||+.... .....|++|..+.... ...+
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~--------~~~~C~GtlIs~~~VLTaAhC~~~~~---~~~~~v~~g~~~~~~~~~~~~ 69 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTG--------GRHFCGGSLISPRWVLTAAHCVYSSA---PSNYTVRLGSHDLSSNEGGGQ 69 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccC--------CcEEEEEEEeeCCEEEECHHhcCCCC---CccEEEEeCcccccCCCCceE
Confidence 6899999999999999997642 35799999999999999999997632 3568899998877543 3567
Q ss_pred EEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEE
Q psy2626 187 SIEIERPIIHEQYTSARKLNDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQ 266 (355)
Q Consensus 187 ~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~ 266 (355)
.+.|+++++||+|+.....+|||||||++++.++++++|||||.... ....+..+.++|||........+..++...
T Consensus 70 ~~~v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~---~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~ 146 (232)
T cd00190 70 VIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGY---NLPAGTTCTVSGWGRTSEGGPLPDVLQEVN 146 (232)
T ss_pred EEEEEEEEECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccc---cCCCCCEEEEEeCCcCCCCCCCCceeeEEE
Confidence 88999999999999988889999999999999999999999997742 345678899999999876545677899999
Q ss_pred EeeeChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeCccc
Q psy2626 267 ISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNY 346 (355)
Q Consensus 267 ~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V~~y 346 (355)
+.+++...|...+.. ...+.++++|++......+.|.|||||||++..+++++|+||+|+|..|+..+.|++||+|+.|
T Consensus 147 ~~~~~~~~C~~~~~~-~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~ 225 (232)
T cd00190 147 VPIVSNAECKRAYSY-GGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPNYPGVYTRVSSY 225 (232)
T ss_pred eeeECHHHhhhhccC-cccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCCCCCEEEEcHHh
Confidence 999999999988764 2367899999987654678999999999999988999999999999999876789999999999
Q ss_pred HHHHHhH
Q psy2626 347 IQWIADN 353 (355)
Q Consensus 347 ~~WI~~~ 353 (355)
++||+++
T Consensus 226 ~~WI~~~ 232 (232)
T cd00190 226 LDWIQKT 232 (232)
T ss_pred hHHhhcC
Confidence 9999874
No 2
>KOG3627|consensus
Probab=100.00 E-value=1.1e-45 Score=332.29 Aligned_cols=239 Identities=41% Similarity=0.813 Sum_probs=199.0
Q ss_pred CCceecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCC--
Q psy2626 105 SKRIVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDT-- 182 (355)
Q Consensus 105 ~~ri~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~-- 182 (355)
..||+||.++..++|||+|.|.+... ..+.|+|+||+++||||||||+.... .. ...|++|++.....
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~-------~~~~Cggsli~~~~vltaaHC~~~~~--~~-~~~V~~G~~~~~~~~~ 79 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGN-------GRHLCGGSLISPRWVLTAAHCVKGAS--AS-LYTVRLGEHDINLSVS 79 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCC-------cceeeeeEEeeCCEEEEChhhCCCCC--Cc-ceEEEECccccccccc
Confidence 47999999999999999999987531 24699999999999999999998632 12 78899998755443
Q ss_pred CC--cEEEEEeeeEeCCCCCCCCCC-CCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEeccCCCC-CCC
Q psy2626 183 SS--GVSIEIERPIIHEQYTSARKL-NDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFR-GPL 258 (355)
Q Consensus 183 ~~--~~~~~v~~i~~hp~y~~~~~~-~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~-~~~ 258 (355)
.. .....|.++++||+|+..... ||||||+|.+++.|+++|+|||||..... .....+..+.++|||.+... ...
T Consensus 80 ~~~~~~~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~-~~~~~~~~~~v~GWG~~~~~~~~~ 158 (256)
T KOG3627|consen 80 EGEEQLVGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADP-YFPPGGTTCLVSGWGRTESGGGPL 158 (256)
T ss_pred cCchhhhceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCccc-CCCCCCCEEEEEeCCCcCCCCCCC
Confidence 12 244557888999999998888 99999999999999999999999855421 12345578899999998765 236
Q ss_pred CccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCC-CCCCCCC
Q psy2626 259 SPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKK-CAEVGFP 337 (355)
Q Consensus 259 ~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~-C~~~~~p 337 (355)
+..|+++++++++...|+..+.... .+.+.||||+......++|+|||||||++..+.+++++||+|||.. |+..+.|
T Consensus 159 ~~~L~~~~v~i~~~~~C~~~~~~~~-~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~~~P 237 (256)
T KOG3627|consen 159 PDTLQEVDVPIISNSECRRAYGGLG-TITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQPNYP 237 (256)
T ss_pred CceeEEEEEeEcChhHhcccccCcc-ccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCCCCC
Confidence 8889999999999999999886422 4667789999865578899999999999988778999999999998 9998899
Q ss_pred cEEEeCcccHHHHHhHhC
Q psy2626 338 GVYTRVTNYIQWIADNIS 355 (355)
Q Consensus 338 ~vyt~V~~y~~WI~~~i~ 355 (355)
++||+|+.|++||++.+.
T Consensus 238 ~vyt~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 238 GVYTRVSSYLDWIKENIG 255 (256)
T ss_pred eEEeEhHHhHHHHHHHhc
Confidence 999999999999999873
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=6.5e-44 Score=314.94 Aligned_cols=228 Identities=43% Similarity=0.844 Sum_probs=195.2
Q ss_pred ceecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCCCCcE
Q psy2626 107 RIVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGV 186 (355)
Q Consensus 107 ri~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~ 186 (355)
||+||+++..++|||+|.|++.. ..+.|+||||++++|||||||+.... ...+.|++|.++........
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~--------~~~~C~GtlIs~~~VLTaahC~~~~~---~~~~~v~~g~~~~~~~~~~~ 69 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRG--------GRHFCGGSLISPRWVLTAAHCVYGSD---PSNIRVRLGSHDLSSGEEGQ 69 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcC--------CCcEEEEEEecCCEEEECHHHcCCCC---CcceEEEeCcccCCCCCCce
Confidence 68999999999999999997542 35789999999999999999998632 34688999988776554447
Q ss_pred EEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEeccCCC-CCCCCccceEE
Q psy2626 187 SIEIERPIIHEQYTSARKLNDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVF-RGPLSPKLRHV 265 (355)
Q Consensus 187 ~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~-~~~~~~~l~~~ 265 (355)
.+.|.++++||+|+.....+|||||+|++|+.+++.++|||||.... ....+..+.++|||.... ....+..++..
T Consensus 70 ~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~---~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~ 146 (229)
T smart00020 70 VIKVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNY---NVPAGTTCTVSGWGRTSEGAGSLPDTLQEV 146 (229)
T ss_pred EEeeEEEEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCccc---ccCCCCEEEEEeCCCCCCCCCcCCCEeeEE
Confidence 88999999999999888889999999999999999999999997632 345678899999998763 23356778899
Q ss_pred EEeeeChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeCcc
Q psy2626 266 QISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTN 345 (355)
Q Consensus 266 ~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V~~ 345 (355)
.+.+++.+.|...+.. ...+...++|++......+.|.|||||||+...+ +|+|+||+|+|..|+..+.|.+|++|+.
T Consensus 147 ~~~~~~~~~C~~~~~~-~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~ 224 (229)
T smart00020 147 NVPIVSNATCRRAYSG-GGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDG-RWVLVGIVSWGSGCARPGKPGVYTRVSS 224 (229)
T ss_pred EEEEeCHHHhhhhhcc-ccccCCCcEeecCCCCCCcccCCCCCCeeEEECC-CEEEEEEEEECCCCCCCCCCCEEEEecc
Confidence 9999999999987754 1357889999987655678999999999999887 9999999999999986778999999999
Q ss_pred cHHHH
Q psy2626 346 YIQWI 350 (355)
Q Consensus 346 y~~WI 350 (355)
|++||
T Consensus 225 ~~~WI 229 (229)
T smart00020 225 YLDWI 229 (229)
T ss_pred ccccC
Confidence 99998
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=4.4e-41 Score=294.62 Aligned_cols=219 Identities=40% Similarity=0.835 Sum_probs=187.8
Q ss_pred eecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCC-CCcE
Q psy2626 108 IVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDT-SSGV 186 (355)
Q Consensus 108 i~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~-~~~~ 186 (355)
|+||.++..++|||+|.|.+... .++|+|+||+++||||||||+.. .....+++|....... ...+
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~--------~~~C~G~li~~~~vLTaahC~~~-----~~~~~v~~g~~~~~~~~~~~~ 67 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNG--------RFFCTGTLISPRWVLTAAHCVDG-----ASDIKVRLGTYSIRNSDGSEQ 67 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTT--------EEEEEEEEEETTEEEEEGGGHTS-----GGSEEEEESESBTTSTTTTSE
T ss_pred CCCCEECCCCCCCeEEEEeeCCC--------CeeEeEEeccccccccccccccc-----ccccccccccccccccccccc
Confidence 78999999999999999977531 68999999999999999999975 2457788998444433 3358
Q ss_pred EEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEE
Q psy2626 187 SIEIERPIIHEQYTSARKLNDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQ 266 (355)
Q Consensus 187 ~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~ 266 (355)
.+.|++++.||+|+.....+|||||+|++++.+.+.++|+||+.... ....+..+.+.|||.....+ ....++...
T Consensus 68 ~~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~---~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~ 143 (220)
T PF00089_consen 68 TIKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGS---DPNVGTSCIVVGWGRTSDNG-YSSNLQSVT 143 (220)
T ss_dssp EEEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTH---TTTTTSEEEEEESSBSSTTS-BTSBEEEEE
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccc---cccccccccccccccccccc-ccccccccc
Confidence 89999999999999988889999999999999999999999997432 23577889999999976544 566889999
Q ss_pred EeeeChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeCccc
Q psy2626 267 ISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNY 346 (355)
Q Consensus 267 ~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V~~y 346 (355)
+.+++.+.|...+.. .+.+.++|++.. ...+.|.|||||||++... +|+||+|++..|...+.|.+|++|+.|
T Consensus 144 ~~~~~~~~c~~~~~~---~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~~---~lvGI~s~~~~c~~~~~~~v~~~v~~~ 216 (220)
T PF00089_consen 144 VPVVSRKTCRSSYND---NLTPNMICAGSS-GSGDACQGDSGGPLICNNN---YLVGIVSFGENCGSPNYPGVYTRVSSY 216 (220)
T ss_dssp EEEEEHHHHHHHTTT---TSTTTEEEEETT-SSSBGGTTTTTSEEEETTE---EEEEEEEEESSSSBTTSEEEEEEGGGG
T ss_pred ccccccccccccccc---cccccccccccc-cccccccccccccccccee---eecceeeecCCCCCCCcCEEEEEHHHh
Confidence 999999999987543 478899999876 4689999999999998664 899999999889988789999999999
Q ss_pred HHHH
Q psy2626 347 IQWI 350 (355)
Q Consensus 347 ~~WI 350 (355)
++||
T Consensus 217 ~~WI 220 (220)
T PF00089_consen 217 LDWI 220 (220)
T ss_dssp HHHH
T ss_pred hccC
Confidence 9999
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-35 Score=261.37 Aligned_cols=239 Identities=31% Similarity=0.475 Sum_probs=179.1
Q ss_pred CCCceecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCCC
Q psy2626 104 SSKRIVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTS 183 (355)
Q Consensus 104 ~~~ri~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~ 183 (355)
.+.||+||..|..++||++|+|..+.. +....-+|||++|..|||||||||+........... .+..+++...
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~is----d~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~---~vv~~l~d~S 101 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRIS----DYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVN---RVVVDLNDSS 101 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcc----cccceeEeccceecceEEeeehhhccCCCCccccce---EEEecccccc
Confidence 578999999999999999999977654 223456899999999999999999987443222333 3344555555
Q ss_pred CcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCC-CccccccCCCCCccccccCCCceEEEEeccCCCCC-----C
Q psy2626 184 SGVSIEIERPIIHEQYTSARKLNDIALFRLREDAPLSD-LIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRG-----P 257 (355)
Q Consensus 184 ~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~-~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~-----~ 257 (355)
..+...|..++.|..|...++.||||+++|.++..... .+.-.- ..+...............+||.+.... +
T Consensus 102 q~~rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~--~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p 179 (413)
T COG5640 102 QAERGHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFD--ASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSP 179 (413)
T ss_pred cccCcceEEEeeecccccccccCcceeeccccccccchhheeecc--CcccceecccccccccceeeeeeeecCCCCCCC
Confidence 66788999999999999999999999999998765321 111000 011111122333445667787665321 1
Q ss_pred CCccceEEEEeeeChhHHHhhhhcC--C---CCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCC-C
Q psy2626 258 LSPKLRHVQISVVDNPKCRQIFSNY--G---ATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKK-C 331 (355)
Q Consensus 258 ~~~~l~~~~~~~~~~~~C~~~~~~~--~---~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~-C 331 (355)
....+++..+..++...|.+.+... . ..++ -+||+... +++|+||||||++...+..+.++||+|||.+ |
T Consensus 180 ~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT--~~cag~~~--~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~C 255 (413)
T COG5640 180 KGTILHEVAVLFVPLSTCAQYKGCANASDGATGLT--GFCAGRPP--KDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGC 255 (413)
T ss_pred ccceeeeeeeeeechHHhhhhccccccCCCCCCcc--ceecCCCC--cccccCCCCCceEEeCCCccEEEeEEEecCCCC
Confidence 2347899999999999999987411 1 1223 39999754 8999999999999998888999999999998 9
Q ss_pred CCCCCCcEEEeCcccHHHHHhHhC
Q psy2626 332 AEVGFPGVYTRVTNYIQWIADNIS 355 (355)
Q Consensus 332 ~~~~~p~vyt~V~~y~~WI~~~i~ 355 (355)
+.+..|+|||+|+.|.+||...|+
T Consensus 256 g~t~~~gVyT~vsny~~WI~a~~~ 279 (413)
T COG5640 256 GGTLIPGVYTNVSNYQDWIAAMTN 279 (413)
T ss_pred CCCCcceeEEehhHHHHHHHHHhc
Confidence 999999999999999999998764
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.81 E-value=1.1e-18 Score=158.99 Aligned_cols=218 Identities=26% Similarity=0.508 Sum_probs=142.6
Q ss_pred CCCCCCcCCCCceecCeecCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCc------Cc
Q psy2626 96 ECGVNAFNSSKRIVGGTPSERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEY------EP 169 (355)
Q Consensus 96 ~CG~~~~~~~~ri~gG~~a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~------~~ 169 (355)
.||........++.+|..+...+.||++.+..... ....+.++|||||+||||||+||+..... .+ ..
T Consensus 30 ~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~-----~~~~~~~~gtlIS~RHiLtss~~~~~~~~-~W~~~~~~~~ 103 (282)
T PF03761_consen 30 TCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNH-----NEGNYFSTGTLISPRHILTSSHCVMNDKS-KWLNGEEFDN 103 (282)
T ss_pred hcCCCCCCCcccccCCcccccCCCCCEEEEEeccC-----cccceecceEEeccCeEEEeeeEEEeccc-ccccCccccc
Confidence 79976544566789999999999999999977543 22346779999999999999999974211 11 00
Q ss_pred e-------EEEecc-----ccc-----cCCCCcEEEEEeeeEeCCCC----CCCCCCCCeEEEEeCCCCCCCCCcccccc
Q psy2626 170 Y-------IVHVGS-----IDL-----EDTSSGVSIEIERPIIHEQY----TSARKLNDIALFRLREDAPLSDLIQPICL 228 (355)
Q Consensus 170 ~-------~v~~G~-----~~~-----~~~~~~~~~~v~~i~~hp~y----~~~~~~~DIALl~L~~~v~~~~~v~picL 228 (355)
. .+.+-. ... ..........|.++++--.- .......+++||+|+++ ++....|+||
T Consensus 104 ~~C~~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl 181 (282)
T PF03761_consen 104 KKCEGNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCL 181 (282)
T ss_pred ceeeCCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEe
Confidence 0 011100 001 00112233556666664332 23344589999999999 7789999999
Q ss_pred CCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCC
Q psy2626 229 PYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSG 308 (355)
Q Consensus 229 p~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsG 308 (355)
|.+.. ....+..+.+.|+ . ....+....+.+.....|.. .++ .....|.||+|
T Consensus 182 ~~~~~---~~~~~~~~~~yg~--~-----~~~~~~~~~~~i~~~~~~~~------------~~~-----~~~~~~~~d~G 234 (282)
T PF03761_consen 182 ADSST---NWEKGDEVDVYGF--N-----STGKLKHRKLKITNCTKCAY------------SIC-----TKQYSCKGDRG 234 (282)
T ss_pred CCCcc---ccccCceEEEeec--C-----CCCeEEEEEEEEEEeeccce------------eEe-----cccccCCCCcc
Confidence 97654 3345555666666 1 23345555665554322111 122 24678999999
Q ss_pred CcceeeeCCeEEEEEEEEeCCC-CCCCCCCcEEEeCcccHHHH
Q psy2626 309 GPLMYPLDTKYYIIGVVSYGKK-CAEVGFPGVYTRVTNYIQWI 350 (355)
Q Consensus 309 gPL~~~~~~~~~lvGI~S~g~~-C~~~~~p~vyt~V~~y~~WI 350 (355)
|||+...+++|+|+||.+.+.. |... ...|.+|..|.+=|
T Consensus 235 g~lv~~~~gr~tlIGv~~~~~~~~~~~--~~~f~~v~~~~~~I 275 (282)
T PF03761_consen 235 GPLVKNINGRWTLIGVGASGNYECNKN--NSYFFNVSWYQDEI 275 (282)
T ss_pred CeEEEEECCCEEEEEEEccCCCccccc--ccEEEEHHHhhhhh
Confidence 9999999999999999988764 5432 56788988887644
No 7
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=99.47 E-value=1.2e-12 Score=111.22 Aligned_cols=115 Identities=18% Similarity=0.311 Sum_probs=85.5
Q ss_pred CCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEecccccc---CCCCcEEEEEeee
Q psy2626 117 GQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLE---DTSSGVSIEIERP 193 (355)
Q Consensus 117 ~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~---~~~~~~~~~v~~i 193 (355)
-.|||+|.|+..+ .+.|+|+||.+.|||++..|+.+. .....-..|.+|..... ..+..|.+.|..+
T Consensus 14 y~WPWlA~IYvdG---------~~~CsgvLlD~~WlLvsssCl~~I-~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~ 83 (267)
T PF09342_consen 14 YHWPWLADIYVDG---------RYWCSGVLLDPHWLLVSSSCLRGI-SLSHHYVSALLGGGKTYLSVDGPHEQISRVDCF 83 (267)
T ss_pred ccCcceeeEEEcC---------eEEEEEEEeccceEEEeccccCCc-ccccceEEEEecCcceecccCCChheEEEeeee
Confidence 4599999998754 489999999999999999999762 22223456777765422 2255677777776
Q ss_pred EeCCCCCCCCCCCCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEecc
Q psy2626 194 IIHEQYTSARKLNDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGS 251 (355)
Q Consensus 194 ~~hp~y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~ 251 (355)
..-|+ .+++||.|++|+.|+.+|+|..||.... .......|..+|-..
T Consensus 84 ~~V~~-------S~v~LLHL~~~~~fTr~VlP~flp~~~~---~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 84 KDVPE-------SNVLLLHLEQPANFTRYVLPTFLPETSN---ENESDDECVAVGHDD 131 (267)
T ss_pred eeccc-------cceeeeeecCcccceeeecccccccccC---CCCCCCceEEEEccc
Confidence 65444 6899999999999999999999996332 334555888888654
No 8
>PF12032 CLIP: Regulatory CLIP domain of proteinases; InterPro: IPR022700 CLIP is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively [, ]. This entry represents the CLIP domain and is found in association with PF00089 from PFAM.; PDB: 2IKE_A 2XXL_A 2IKD_A.
Probab=99.30 E-value=1.1e-12 Score=88.03 Aligned_cols=53 Identities=40% Similarity=0.972 Sum_probs=46.3
Q ss_pred CCCCCCCcceEeecccCHHHHHHhhcCCCChhhhhccccccccCCCC-CceeeC
Q psy2626 10 CSTPRNEIGTCISIRQCRYLYDILNNERNNPRAVQYVKNSHCGLEGR-LPKVCC 62 (355)
Q Consensus 10 C~~~~~~~g~C~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~-~~~vCC 62 (355)
|++|+|+.|+||++++||+++++++....++++.+||++++||+.+. .++|||
T Consensus 1 C~tp~g~~G~Cv~i~~C~~l~~~l~~~~~~~~~~~~l~~s~Cg~~~~~~~~VCC 54 (54)
T PF12032_consen 1 CTTPNGEPGRCVPIRSCPPLLEILRSKPLSPEERNFLRQSQCGFDGNRDPLVCC 54 (54)
T ss_dssp EE-TTSSEEEEEETTTBHHHHHHHHHS---HHHHHHHHHTESEECSS-SCEEEE
T ss_pred CcCCCCCcEEEecHHHCHHHHHHHhcCCCCHHHHHHHHHccCCCCCCCCceeeC
Confidence 78999999999999999999999998888999999999999999766 899998
No 9
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.29 E-value=6.2e-11 Score=103.22 Aligned_cols=204 Identities=20% Similarity=0.246 Sum_probs=112.0
Q ss_pred cCCCCccceEEeceeeeccccCCCCceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEe-ccccccCCCCcEEEEEee
Q psy2626 114 SERGQWPWMAAIGFKIRRRRANGKPEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHV-GSIDLEDTSSGVSIEIER 192 (355)
Q Consensus 114 a~~~e~Pw~v~l~~~~~~~~~~~~~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~-G~~~~~~~~~~~~~~v~~ 192 (355)
.....|||-+...+.. ....+-|+++||+++.||||+||+.....+. ....+.. |.. ........+....
T Consensus 44 ~dt~~~Py~av~~~~~------~tG~~~~~~~lI~pntvLTa~Hc~~s~~~G~-~~~~~~p~g~~--~~~~~~~~~~~~~ 114 (251)
T COG3591 44 TDTTQFPYSAVVQFEA------ATGRLCTAATLIGPNTVLTAGHCIYSPDYGE-DDIAAAPPGVN--SDGGPFYGITKIE 114 (251)
T ss_pred ccCCCCCcceeEEeec------CCCcceeeEEEEcCceEEEeeeEEecCCCCh-hhhhhcCCccc--CCCCCCCceeeEE
Confidence 3456899999985543 2334567789999999999999998733221 2222222 211 1111112222333
Q ss_pred eEeCCC--CCCCCCCCCeEEEEeCCCCCCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeee
Q psy2626 193 PIIHEQ--YTSARKLNDIALFRLREDAPLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVV 270 (355)
Q Consensus 193 i~~hp~--y~~~~~~~DIALl~L~~~v~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~ 270 (355)
..+.|+ |.......|+..+.|+....+.+.+...-++... ....+....+.||-..... .+++.+
T Consensus 115 ~~~~~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~----~~~~~d~i~v~GYP~dk~~-----~~~~~e---- 181 (251)
T COG3591 115 IRVYPGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTAS----EAKANDRITVIGYPGDKPN-----IGTMWE---- 181 (251)
T ss_pred EEecCCceeccCCceeeccHHHhccCCCcccccccccccccc----ccccCceeEEEeccCCCCc-----ceeEee----
Confidence 322443 3444555788888887555555555544444333 2344555788898544321 111110
Q ss_pred ChhHHHhhhhcCCCCCCCCeEEecccCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeC-cccHHH
Q psy2626 271 DNPKCRQIFSNYGATINENILCAGVLSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRV-TNYIQW 349 (355)
Q Consensus 271 ~~~~C~~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V-~~y~~W 349 (355)
.|.... .+....+ .-..|++.|+||+|++...+ +++||.+-|..-.....-.-.+|+ ..+++|
T Consensus 182 ---~t~~v~-----~~~~~~l-----~y~~dT~pG~SGSpv~~~~~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~ 245 (251)
T COG3591 182 ---STGKVN-----SIKGNKL-----FYDADTLPGSSGSPVLISKD---EVIGVHYNGPGANGGSLANNAVRLTPEILNF 245 (251)
T ss_pred ---ecceeE-----EEecceE-----EEEecccCCCCCCceEecCc---eEEEEEecCCCcccccccCcceEecHHHHHH
Confidence 111100 0111111 11578999999999998665 899999988762211122233444 456799
Q ss_pred HHhHhC
Q psy2626 350 IADNIS 355 (355)
Q Consensus 350 I~~~i~ 355 (355)
|++.++
T Consensus 246 I~~~~~ 251 (251)
T COG3591 246 IQQNIK 251 (251)
T ss_pred HHHhhC
Confidence 999875
No 10
>smart00680 CLIP Clip or disulphide knot domain. Present in horseshoe crab proclotting enzyme N-terminal domain, Drosophila Easter and silkworm prophenoloxidase-activating enzyme.
Probab=99.06 E-value=1.7e-10 Score=76.73 Aligned_cols=52 Identities=40% Similarity=1.025 Sum_probs=46.5
Q ss_pred CCCCCCCcceEeecccCHHHHHHhhcCCCChhhhhccccccccCCCCCceeeCC
Q psy2626 10 CSTPRNEIGTCISIRQCRYLYDILNNERNNPRAVQYVKNSHCGLEGRLPKVCCP 63 (355)
Q Consensus 10 C~~~~~~~g~C~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~vCC~ 63 (355)
|.+|++..|.|+++++|+.+.++++... +++.+|++.++|++.+..++||||
T Consensus 1 C~tp~~~~G~Cv~~~~C~~~~~~l~~~~--~~~~~~l~~~~Cg~~~~~~~vCCp 52 (52)
T smart00680 1 CRTPDGERGTCVPISDCPSLLSLLKSDP--PEDLNFLRKSQCGFGNREPLVCCP 52 (52)
T ss_pred CcCCCCCcEEeEEHHhChHHHHHHccCC--HHHHHHHHHccCCCCCCCEeeeCc
Confidence 8899999999999999999999987654 778899999999987677899997
No 11
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=98.46 E-value=3e-06 Score=81.83 Aligned_cols=142 Identities=19% Similarity=0.227 Sum_probs=81.1
Q ss_pred ceeeeEEEEeCC-EEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 139 EWMCGGALITKR-YVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 139 ~~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
...++|.+|++. ||||++|.+.+. ....|.+.. ...+..+-+..++. .||||||++.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~-----~~i~V~~~~--------~~~~~a~vv~~d~~-------~DlAllkv~~~- 115 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGA-----DEITVTLSD--------GREFKAKLVGKDPR-------TDIAVLKIDAK- 115 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCC-----CeEEEEeCC--------CCEEEEEEEEecCC-------CCEEEEEecCC-
Confidence 467999999976 999999999752 234555432 22344444444444 69999999864
Q ss_pred CCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccC
Q psy2626 218 PLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLS 297 (355)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~ 297 (355)
..+.++.|.... ....++..++.|+.... ........+.-..... ... .....++=.
T Consensus 116 ---~~~~~~~l~~~~----~~~~G~~v~aiG~p~g~-----~~~~t~G~vs~~~~~~----~~~---~~~~~~i~t---- 172 (428)
T TIGR02037 116 ---KNLPVIKLGDSD----KLRVGDWVLAIGNPFGL-----GQTVTSGIVSALGRSG----LGI---GDYENFIQT---- 172 (428)
T ss_pred ---CCceEEEccCCC----CCCCCCEEEEEECCCcC-----CCcEEEEEEEecccCc----cCC---CCccceEEE----
Confidence 235566665333 34678888898986421 1112222222111110 000 000111111
Q ss_pred CCCCCCcCCCCCcceeeeCCeEEEEEEEEeC
Q psy2626 298 GGKDSCGGDSGGPLMYPLDTKYYIIGVVSYG 328 (355)
Q Consensus 298 ~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g 328 (355)
+...-.|.|||||+-..+ .++||.+..
T Consensus 173 -da~i~~GnSGGpl~n~~G---~viGI~~~~ 199 (428)
T TIGR02037 173 -DAAINPGNSGGPLVNLRG---EVIGINTAI 199 (428)
T ss_pred -CCCCCCCCCCCceECCCC---eEEEEEeEE
Confidence 234567999999986543 699998764
No 12
>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=98.41 E-value=1.4e-06 Score=68.26 Aligned_cols=20 Identities=50% Similarity=0.639 Sum_probs=18.9
Q ss_pred eeEEEEeCC-EEEeeccccCC
Q psy2626 142 CGGALITKR-YVLTAAHCVSP 161 (355)
Q Consensus 142 C~GtLIs~~-~VLTAAhCv~~ 161 (355)
|+|.+|+++ +|||||||+..
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 99999999986
No 13
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=98.27 E-value=3e-05 Score=72.77 Aligned_cols=141 Identities=18% Similarity=0.279 Sum_probs=78.4
Q ss_pred ceeeeEEEEeCC-EEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 139 EWMCGGALITKR-YVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 139 ~~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
....+|.+|+++ ||||++|-+... ....|.+.. ...+..+-+..+|. .||||||++.+-
T Consensus 77 ~~~GSG~vi~~~G~IlTn~HVV~~~-----~~i~V~~~d--------g~~~~a~vv~~d~~-------~DlAvlkv~~~~ 136 (351)
T TIGR02038 77 QGLGSGVIMSKEGYILTNYHVIKKA-----DQIVVALQD--------GRKFEAELVGSDPL-------TDLAVLKIEGDN 136 (351)
T ss_pred cceEEEEEEeCCeEEEecccEeCCC-----CEEEEEECC--------CCEEEEEEEEecCC-------CCEEEEEecCCC
Confidence 346999999976 999999999651 234555421 22344444444444 699999997542
Q ss_pred CCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccC
Q psy2626 218 PLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLS 297 (355)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~ 297 (355)
+.++-|-... ....++..++.|+.... ........+....+. .+.. .-....+=
T Consensus 137 -----~~~~~l~~s~----~~~~G~~V~aiG~P~~~-----~~s~t~GiIs~~~r~----~~~~---~~~~~~iq----- 190 (351)
T TIGR02038 137 -----LPTIPVNLDR----PPHVGDVVLAIGNPYNL-----GQTITQGIISATGRN----GLSS---VGRQNFIQ----- 190 (351)
T ss_pred -----CceEeccCcC----ccCCCCEEEEEeCCCCC-----CCcEEEEEEEeccCc----ccCC---CCcceEEE-----
Confidence 2233332221 35678888888886421 111222222221110 0000 00001111
Q ss_pred CCCCCCcCCCCCcceeeeCCeEEEEEEEEeC
Q psy2626 298 GGKDSCGGDSGGPLMYPLDTKYYIIGVVSYG 328 (355)
Q Consensus 298 ~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g 328 (355)
.+...-.|.|||||+-..+ .++||.+..
T Consensus 191 tda~i~~GnSGGpl~n~~G---~vIGI~~~~ 218 (351)
T TIGR02038 191 TDAAINAGNSGGALINTNG---ELVGINTAS 218 (351)
T ss_pred ECCccCCCCCcceEECCCC---eEEEEEeee
Confidence 1345567999999996544 699998764
No 14
>PRK10898 serine endoprotease; Provisional
Probab=98.20 E-value=8.1e-05 Score=69.86 Aligned_cols=141 Identities=19% Similarity=0.247 Sum_probs=76.7
Q ss_pred eeeeEEEEeCC-EEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCC
Q psy2626 140 WMCGGALITKR-YVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDAP 218 (355)
Q Consensus 140 ~~C~GtLIs~~-~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~ 218 (355)
..-+|.+|+++ +|||+||=+.+. ..+.|.+.. ...+..+-+..+|. +||||||++.. .
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~a-----~~i~V~~~d--------g~~~~a~vv~~d~~-------~DlAvl~v~~~-~ 136 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVINDA-----DQIIVALQD--------GRVFEALLVGSDSL-------TDLAVLKINAT-N 136 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCCC-----CEEEEEeCC--------CCEEEEEEEEEcCC-------CCEEEEEEcCC-C
Confidence 57999999976 999999998651 235555532 22344444444444 79999999753 1
Q ss_pred CCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccCC
Q psy2626 219 LSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLSG 298 (355)
Q Consensus 219 ~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~~ 298 (355)
+.++-|.... ....++..++.|+..... .......+.-..+. .....+ ....+= .
T Consensus 137 ----l~~~~l~~~~----~~~~G~~V~aiG~P~g~~-----~~~t~Giis~~~r~----~~~~~~---~~~~iq-----t 191 (353)
T PRK10898 137 ----LPVIPINPKR----VPHIGDVVLAIGNPYNLG-----QTITQGIISATGRI----GLSPTG---RQNFLQ-----T 191 (353)
T ss_pred ----CCeeeccCcC----cCCCCCEEEEEeCCCCcC-----CCcceeEEEecccc----ccCCcc---ccceEE-----e
Confidence 2233332221 345678888888753211 11111111111110 000000 001111 1
Q ss_pred CCCCCcCCCCCcceeeeCCeEEEEEEEEeCC
Q psy2626 299 GKDSCGGDSGGPLMYPLDTKYYIIGVVSYGK 329 (355)
Q Consensus 299 ~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~ 329 (355)
+...-.|.|||||+-..+ .++||.+...
T Consensus 192 da~i~~GnSGGPl~n~~G---~vvGI~~~~~ 219 (353)
T PRK10898 192 DASINHGNSGGALVNSLG---ELMGINTLSF 219 (353)
T ss_pred ccccCCCCCcceEECCCC---eEEEEEEEEe
Confidence 345567999999996543 6999988643
No 15
>PRK10139 serine endoprotease; Provisional
Probab=98.13 E-value=5.1e-05 Score=73.53 Aligned_cols=141 Identities=18% Similarity=0.245 Sum_probs=79.8
Q ss_pred eeeeEEEEeC--CEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 140 WMCGGALITK--RYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 140 ~~C~GtLIs~--~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
...+|.+|++ -||||++|.+.+. ..+.|++.. ...+..+-+-..|. .||||||++.+-
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~a-----~~i~V~~~d--------g~~~~a~vvg~D~~-------~DlAvlkv~~~~ 149 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQA-----QKISIQLND--------GREFDAKLIGSDDQ-------SDIALLQIQNPS 149 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCCC-----CEEEEEECC--------CCEEEEEEEEEcCC-------CCEEEEEecCCC
Confidence 5799999974 6999999999752 345666532 22444444444444 799999998542
Q ss_pred CCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccC
Q psy2626 218 PLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLS 297 (355)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~ 297 (355)
.+.++.|.... ....++..++.|+.... ... +..-+++... ....... . ....+=.
T Consensus 150 ----~l~~~~lg~s~----~~~~G~~V~aiG~P~g~-----~~t---vt~GivS~~~--r~~~~~~-~-~~~~iqt---- 205 (455)
T PRK10139 150 ----KLTQIAIADSD----KLRVGDFAVAVGNPFGL-----GQT---ATSGIISALG--RSGLNLE-G-LENFIQT---- 205 (455)
T ss_pred ----CCceeEecCcc----ccCCCCEEEEEecCCCC-----CCc---eEEEEEcccc--ccccCCC-C-cceEEEE----
Confidence 23455554332 34568888888874321 111 2222332110 0000000 0 0111111
Q ss_pred CCCCCCcCCCCCcceeeeCCeEEEEEEEEeC
Q psy2626 298 GGKDSCGGDSGGPLMYPLDTKYYIIGVVSYG 328 (355)
Q Consensus 298 ~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g 328 (355)
+...-.|.|||||+-..+ .++||.+..
T Consensus 206 -da~in~GnSGGpl~n~~G---~vIGi~~~~ 232 (455)
T PRK10139 206 -DASINRGNSGGALLNLNG---ELIGINTAI 232 (455)
T ss_pred -CCccCCCCCcceEECCCC---eEEEEEEEE
Confidence 345568999999996544 699999864
No 16
>PRK10942 serine endoprotease; Provisional
Probab=97.99 E-value=0.00013 Score=71.15 Aligned_cols=141 Identities=19% Similarity=0.223 Sum_probs=76.9
Q ss_pred eeeeEEEEeC--CEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 140 WMCGGALITK--RYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 140 ~~C~GtLIs~--~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
...+|.+|++ .+|||++|.+.+. ..+.|.+.. ...+..+-+..+|. .||||||++.+-
T Consensus 111 ~~GSG~ii~~~~G~IlTn~HVv~~a-----~~i~V~~~d--------g~~~~a~vv~~D~~-------~DlAvlki~~~~ 170 (473)
T PRK10942 111 ALGSGVIIDADKGYVVTNNHVVDNA-----TKIKVQLSD--------GRKFDAKVVGKDPR-------SDIALIQLQNPK 170 (473)
T ss_pred ceEEEEEEECCCCEEEeChhhcCCC-----CEEEEEECC--------CCEEEEEEEEecCC-------CCEEEEEecCCC
Confidence 4799999985 5999999998751 345566532 22344444444544 799999997432
Q ss_pred CCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeEEecccC
Q psy2626 218 PLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENILCAGVLS 297 (355)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~Ca~~~~ 297 (355)
. +.++-|-... ....++.+++.|+.... ........+.-+.+. ... ..-...++=.
T Consensus 171 ~----l~~~~lg~s~----~l~~G~~V~aiG~P~g~-----~~tvt~GiVs~~~r~----~~~---~~~~~~~iqt---- 226 (473)
T PRK10942 171 N----LTAIKMADSD----ALRVGDYTVAIGNPYGL-----GETVTSGIVSALGRS----GLN---VENYENFIQT---- 226 (473)
T ss_pred C----CceeEecCcc----ccCCCCEEEEEcCCCCC-----CcceeEEEEEEeecc----cCC---cccccceEEe----
Confidence 2 3345554322 34567777777763211 111111122211110 000 0000111111
Q ss_pred CCCCCCcCCCCCcceeeeCCeEEEEEEEEeC
Q psy2626 298 GGKDSCGGDSGGPLMYPLDTKYYIIGVVSYG 328 (355)
Q Consensus 298 ~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g 328 (355)
+...-.|.|||||+...+ .++||.+..
T Consensus 227 -da~i~~GnSGGpL~n~~G---eviGI~t~~ 253 (473)
T PRK10942 227 -DAAINRGNSGGALVNLNG---ELIGINTAI 253 (473)
T ss_pred -ccccCCCCCcCccCCCCC---eEEEEEEEE
Confidence 334557999999996544 699998753
No 17
>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=97.17 E-value=0.0021 Score=65.68 Aligned_cols=66 Identities=17% Similarity=0.136 Sum_probs=40.9
Q ss_pred eEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCCC
Q psy2626 143 GGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDAPLSDL 222 (355)
Q Consensus 143 ~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~ 222 (355)
.+|||+|+||+|++|=... ...|.+|.+.. ..+.+..--.|+. .|+.+-||.+=|. -
T Consensus 68 ~aTLigpqYiVSV~HN~~g-------y~~v~FG~~g~------~~Y~iV~RNn~~~-------~Df~~pRLnK~VT---E 124 (769)
T PF02395_consen 68 VATLIGPQYIVSVKHNGKG-------YNSVSFGNEGQ------NTYKIVDRNNYPS-------GDFHMPRLNKFVT---E 124 (769)
T ss_dssp S-EEEETTEEEBETTG-TS-------CCEECESCSST------CEEEEEEEEBETT-------STEBEEEESS------S
T ss_pred eEEEecCCeEEEEEccCCC-------cCceeecccCC------ceEEEEEccCCCC-------cccceeecCceEE---E
Confidence 4999999999999998632 23577776443 3566666666655 5999999998775 3
Q ss_pred ccccccCCC
Q psy2626 223 IQPICLPYD 231 (355)
Q Consensus 223 v~picLp~~ 231 (355)
+.|+-+...
T Consensus 125 vaP~~~t~~ 133 (769)
T PF02395_consen 125 VAPAEMTTA 133 (769)
T ss_dssp S----BBSS
T ss_pred Eeccccccc
Confidence 667666544
No 18
>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=89.17 E-value=1.6 Score=38.27 Aligned_cols=40 Identities=25% Similarity=0.408 Sum_probs=22.4
Q ss_pred CCCcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeCcc
Q psy2626 301 DSCGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTN 345 (355)
Q Consensus 301 ~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V~~ 345 (355)
++=.||=|.||+...++ .+|||.|.+..-.. -..|+.+..
T Consensus 147 sTk~G~CG~PlVs~~Dg--~IVGiHsl~~~~~~---~N~F~~f~~ 186 (235)
T PF00863_consen 147 STKDGDCGLPLVSTKDG--KIVGIHSLTSNTSS---RNYFTPFPD 186 (235)
T ss_dssp ---TT-TT-EEEETTT----EEEEEEEEETTTS---SEEEEE--T
T ss_pred cCCCCccCCcEEEcCCC--cEEEEEcCccCCCC---eEEEEcCCH
Confidence 34458889999986654 59999998755332 246777654
No 19
>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=87.60 E-value=0.27 Score=38.32 Aligned_cols=39 Identities=28% Similarity=0.609 Sum_probs=29.2
Q ss_pred CcCCCCCcceeeeCCeEEEEEEEEeCCCCCCCCCCcEEEeCcccHHHHH
Q psy2626 303 CGGDSGGPLMYPLDTKYYIIGVVSYGKKCAEVGFPGVYTRVTNYIQWIA 351 (355)
Q Consensus 303 C~GDsGgPL~~~~~~~~~lvGI~S~g~~C~~~~~p~vyt~V~~y~~WI~ 351 (355)
=.||-||+|.|+.+ ++||++.|.. + -..|++|..+ .|++
T Consensus 88 ~PGdCGg~L~C~HG----ViGi~Tagg~----g-~VaF~dir~~-~~~e 126 (127)
T PF00947_consen 88 EPGDCGGILRCKHG----VIGIVTAGGE----G-HVAFADIRDL-LWLE 126 (127)
T ss_dssp STT-TCSEEEETTC----EEEEEEEEET----T-EEEEEECCCG-STTS
T ss_pred CCCCCCceeEeCCC----eEEEEEeCCC----c-eEEEEechhh-heec
Confidence 36999999999998 9999998733 2 3569999886 4543
No 20
>PF00548 Peptidase_C3: 3C cysteine protease (picornain 3C); InterPro: IPR000199 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This signature defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral C3 cysteine protease. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SJO_E 2H6M_A 1QA7_C 1HAV_B 2HAL_A 2H9H_A 3QZQ_B 3QZR_A 3R0F_B 3SJ9_A ....
Probab=86.11 E-value=4.2 Score=34.00 Aligned_cols=147 Identities=16% Similarity=0.181 Sum_probs=72.4
Q ss_pred CceeeeEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 138 PEWMCGGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 138 ~~~~C~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
..+.+.|..|..+|.|--.|.-. ...+.++. ..+.+...+.. .+......||+|++|++.-
T Consensus 23 g~~t~l~~gi~~~~~lvp~H~~~--------~~~i~i~g---------~~~~~~d~~~l--v~~~~~~~Dl~~v~l~~~~ 83 (172)
T PF00548_consen 23 GEFTMLALGIYDRYFLVPTHEEP--------EDTIYIDG---------VEYKVDDSVVL--VDRDGVDTDLTLVKLPRNP 83 (172)
T ss_dssp EEEEEEEEEEEBTEEEEEGGGGG--------CSEEEETT---------EEEEEEEEEEE--EETTSSEEEEEEEEEESSS
T ss_pred ceEEEecceEeeeEEEEECcCCC--------cEEEEECC---------EEEEeeeeEEE--ecCCCcceeEEEEEccCCc
Confidence 35778899999999999999221 12233321 22333332221 1122223699999999888
Q ss_pred CCCCCccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCCCCeE--Eecc
Q psy2626 218 PLSDLIQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATINENIL--CAGV 295 (355)
Q Consensus 218 ~~~~~v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~~~~~--Ca~~ 295 (355)
.|.+-.+-+.- .......+..+-|... ..... ..+..+.....- ..+...+ +..+
T Consensus 84 kfrDIrk~~~~--------~~~~~~~~~l~v~~~~-----~~~~~--~~v~~v~~~~~i--------~~~g~~~~~~~~Y 140 (172)
T PF00548_consen 84 KFRDIRKFFPE--------SIPEYPECVLLVNSTK-----FPRMI--VEVGFVTNFGFI--------NLSGTTTPRSLKY 140 (172)
T ss_dssp -B--GGGGSBS--------SGGTEEEEEEEEESSS-----STCEE--EEEEEEEEEEEE--------EETTEEEEEEEEE
T ss_pred ccCchhhhhcc--------ccccCCCcEEEEECCC-----CccEE--EEEEEEeecCcc--------ccCCCEeeEEEEE
Confidence 88665555541 1112223333334211 11111 111111000000 0001111 1111
Q ss_pred cCCCCCCCcCCCCCcceeeeCCeEEEEEEEEeCC
Q psy2626 296 LSGGKDSCGGDSGGPLMYPLDTKYYIIGVVSYGK 329 (355)
Q Consensus 296 ~~~~~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~ 329 (355)
...+-.|+=||||+...++...++||...|.
T Consensus 141 ---~~~t~~G~CG~~l~~~~~~~~~i~GiHvaG~ 171 (172)
T PF00548_consen 141 ---KAPTKPGMCGSPLVSRIGGQGKIIGIHVAGN 171 (172)
T ss_dssp ---ESEEETTGTTEEEEESCGGTTEEEEEEEEEE
T ss_pred ---ccCCCCCccCCeEEEeeccCccEEEEEeccC
Confidence 2334568999999997777889999998764
No 21
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=82.78 E-value=29 Score=32.46 Aligned_cols=58 Identities=17% Similarity=0.333 Sum_probs=37.3
Q ss_pred eeeeEEEEe-CCEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCC
Q psy2626 140 WMCGGALIT-KRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDA 217 (355)
Q Consensus 140 ~~C~GtLIs-~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v 217 (355)
...+|.+|+ ..+|||..|=+.. .....|.+ .....+..+-+-..+ ..|+|+||.+..-
T Consensus 72 ~~gSg~i~~~~g~ivTn~hVi~~-----a~~i~v~l--------~dg~~~~a~~vg~d~-------~~dlavlki~~~~ 130 (347)
T COG0265 72 GLGSGFIISSDGYIVTNNHVIAG-----AEEITVTL--------ADGREVPAKLVGKDP-------ISDLAVLKIDGAG 130 (347)
T ss_pred ccccEEEEcCCeEEEecceecCC-----cceEEEEe--------CCCCEEEEEEEecCC-------ccCEEEEEeccCC
Confidence 568899998 7899999998764 13444554 122334444443333 2799999998643
No 22
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=63.60 E-value=20 Score=34.12 Aligned_cols=143 Identities=18% Similarity=0.289 Sum_probs=70.3
Q ss_pred eEEEEeCCEEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCCCCCCCC
Q psy2626 143 GGALITKRYVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLREDAPLSDL 222 (355)
Q Consensus 143 ~GtLIs~~~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~v~~~~~ 222 (355)
=|..+|+...+|+.|-+-.... -.+| .++.+|-+|.. .+..-+++.+|+. +.
T Consensus 382 WGfWVS~~lfITttHViP~g~~-------E~FG------------v~i~~i~vh~s-------GeF~~~rFpk~iR--PD 433 (535)
T PF05416_consen 382 WGFWVSPTLFITTTHVIPPGAK-------EAFG------------VPISQIQVHKS-------GEFCRFRFPKPIR--PD 433 (535)
T ss_dssp EEEESSSSEEEEEGGGS-STTS-------EETT------------EECGGEEEEEE-------TTEEEEEESS-SS--TT
T ss_pred eeeeecceEEEEeeeecCCcch-------hhhC------------CChhHeEEeec-------cceEEEecCCCCC--CC
Confidence 3789999999999998754111 1222 35666666654 5777888887775 22
Q ss_pred ccccccCCCCCccccccCCCceEEEEeccCCCCCCCCccceEEEEeeeChhHHHhhhhcCCCCCC--CCeEEecccCCC-
Q psy2626 223 IQPICLPYDTNLRSELFERKTPFVAGWGSTVFRGPLSPKLRHVQISVVDNPKCRQIFSNYGATIN--ENILCAGVLSGG- 299 (355)
Q Consensus 223 v~picLp~~~~~~~~~~~~~~~~v~GwG~~~~~~~~~~~l~~~~~~~~~~~~C~~~~~~~~~~~~--~~~~Ca~~~~~~- 299 (355)
|.-.-|- +--+++..|.+.==- .+..|...-++.-.... +.-.+..+. ..|+-+|....+
T Consensus 434 vtgmiLE------eGapEGtV~siLiKR-------~sGEllpLAvRMgt~As----mkIqgr~v~GQ~GMLLTGaNAK~m 496 (535)
T PF05416_consen 434 VTGMILE------EGAPEGTVCSILIKR-------PSGELLPLAVRMGTHAS----MKIQGRTVHGQMGMLLTGANAKGM 496 (535)
T ss_dssp S---EE-------SS--TT-EEEEEEE--------TTSBEEEEEEEEEEEEE----EEETTEEEEEEEEEETTSTT-SST
T ss_pred ccceeec------cCCCCceEEEEEEEc-------CCccchhhhhhhcccee----EEEcceeecceeeeeeecCCcccc
Confidence 2222221 122355555554211 23333333222211100 000010111 123333332222
Q ss_pred -CCCCcCCCCCcceeeeCCeEEEEEEEEeCCC
Q psy2626 300 -KDSCGGDSGGPLMYPLDTKYYIIGVVSYGKK 330 (355)
Q Consensus 300 -~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~ 330 (355)
-.+-.||-|-|.++..++.|+++||......
T Consensus 497 DLGT~PGDCGcPYvyKrgNd~VV~GVH~AAtr 528 (535)
T PF05416_consen 497 DLGTIPGDCGCPYVYKRGNDWVVIGVHAAATR 528 (535)
T ss_dssp TTS--TTGTT-EEEEEETTEEEEEEEEEEE-S
T ss_pred ccCCCCCCCCCceeeecCCcEEEEEEEehhcc
Confidence 3467899999999999999999999876433
No 23
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=58.11 E-value=8.2 Score=34.32 Aligned_cols=23 Identities=35% Similarity=0.498 Sum_probs=17.3
Q ss_pred cCCCCCcceeeeCCeEEEEEEEEeCC
Q psy2626 304 GGDSGGPLMYPLDTKYYIIGVVSYGK 329 (355)
Q Consensus 304 ~GDsGgPL~~~~~~~~~lvGI~S~g~ 329 (355)
.||||+|++..++ .|+||.+-..
T Consensus 207 ~GDSGSPVVt~dg---~liGVHTGSn 229 (297)
T PF05579_consen 207 PGDSGSPVVTEDG---DLIGVHTGSN 229 (297)
T ss_dssp GGCTT-EEEETTC----EEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCC
Confidence 4899999998776 6999997643
No 24
>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=55.76 E-value=7.2 Score=40.09 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=19.1
Q ss_pred eeeEEEEeCC-EEEeeccccCC
Q psy2626 141 MCGGALITKR-YVLTAAHCVSP 161 (355)
Q Consensus 141 ~C~GtLIs~~-~VLTAAhCv~~ 161 (355)
.|+|++||+. .|||--||..+
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 4999999998 99999999865
No 25
>KOG1421|consensus
Probab=54.20 E-value=56 Score=33.28 Aligned_cols=71 Identities=27% Similarity=0.506 Sum_probs=40.0
Q ss_pred eeeEEEEeCC--EEEeeccccCCCCCCCcCceEEEeccccccCCCCcEEEEEeeeEeCCCCCCCCCCCCeEEEEeCCC-C
Q psy2626 141 MCGGALITKR--YVLTAAHCVSPDTTGEYEPYIVHVGSIDLEDTSSGVSIEIERPIIHEQYTSARKLNDIALFRLRED-A 217 (355)
Q Consensus 141 ~C~GtLIs~~--~VLTAAhCv~~~~~~~~~~~~v~~G~~~~~~~~~~~~~~v~~i~~hp~y~~~~~~~DIALl~L~~~-v 217 (355)
--+|.+++++ ++||+.|-+.. +......++.. -+.+-+.|.|... -||++++|.+.. +
T Consensus 85 ~atgfvvd~~~gyiLtnrhvv~p---gP~va~avf~n--------------~ee~ei~pvyrDp--VhdfGf~r~dps~i 145 (955)
T KOG1421|consen 85 EATGFVVDKKLGYILTNRHVVAP---GPFVASAVFDN--------------HEEIEIYPVYRDP--VHDFGFFRYDPSTI 145 (955)
T ss_pred ceeEEEEecccceEEEeccccCC---CCceeEEEecc--------------cccCCcccccCCc--hhhcceeecChhhc
Confidence 3467788775 89999998864 22222222211 1222334444322 278999887643 3
Q ss_pred CCCCCccccccCCC
Q psy2626 218 PLSDLIQPICLPYD 231 (355)
Q Consensus 218 ~~~~~v~picLp~~ 231 (355)
.| ..+.-+||..+
T Consensus 146 r~-s~vt~i~lap~ 158 (955)
T KOG1421|consen 146 RF-SIVTEICLAPE 158 (955)
T ss_pred ce-eeeeccccCcc
Confidence 33 35677888654
No 26
>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=47.67 E-value=13 Score=29.41 Aligned_cols=22 Identities=32% Similarity=0.670 Sum_probs=15.9
Q ss_pred CcCCCCCcceeeeCCeEEEEEEEEe
Q psy2626 303 CGGDSGGPLMYPLDTKYYIIGVVSY 327 (355)
Q Consensus 303 C~GDsGgPL~~~~~~~~~lvGI~S~ 327 (355)
-.|-||||++|..+ .++||.-.
T Consensus 106 lkGSSGgPiLC~~G---H~vG~f~a 127 (148)
T PF02907_consen 106 LKGSSGGPILCPSG---HAVGMFRA 127 (148)
T ss_dssp HTT-TT-EEEETTS---EEEEEEEE
T ss_pred EecCCCCcccCCCC---CEEEEEEE
Confidence 36899999999876 78888753
No 27
>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=42.92 E-value=30 Score=29.86 Aligned_cols=27 Identities=26% Similarity=0.260 Sum_probs=22.0
Q ss_pred CCCCcCCCCCcceeeeCCeEEEEEEEEeCCC
Q psy2626 300 KDSCGGDSGGPLMYPLDTKYYIIGVVSYGKK 330 (355)
Q Consensus 300 ~~~C~GDsGgPL~~~~~~~~~lvGI~S~g~~ 330 (355)
...-+|-||+|++... .|+|-++++..
T Consensus 175 GGIvqGMSGSPI~qdG----KLiGAVthvf~ 201 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG----KLIGAVTHVFV 201 (218)
T ss_pred CCEEecccCCCEEECC----EEEEEEEEEEe
Confidence 4678999999998765 59999998753
No 28
>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=29.28 E-value=30 Score=27.43 Aligned_cols=24 Identities=29% Similarity=0.502 Sum_probs=17.3
Q ss_pred cCCCCCcceeeeCCeEEEEEEEEeCCC
Q psy2626 304 GGDSGGPLMYPLDTKYYIIGVVSYGKK 330 (355)
Q Consensus 304 ~GDsGgPL~~~~~~~~~lvGI~S~g~~ 330 (355)
.||||-|++-+.+ .+|||+--|..
T Consensus 105 ~GDSGRpi~DNsG---rVVaIVLGG~n 128 (158)
T PF00944_consen 105 PGDSGRPIFDNSG---RVVAIVLGGAN 128 (158)
T ss_dssp TTSTTEEEESTTS---BEEEEEEEEEE
T ss_pred CCCCCCccCcCCC---CEEEEEecCCC
Confidence 6999999985443 57788765543
No 29
>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=25.94 E-value=68 Score=33.19 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=17.1
Q ss_pred CCCCCcCCCCCcceeeeCCeEEEEEEE
Q psy2626 299 GKDSCGGDSGGPLMYPLDTKYYIIGVV 325 (355)
Q Consensus 299 ~~~~C~GDsGgPL~~~~~~~~~lvGI~ 325 (355)
..|+..|.||+|++-.. -.|||++
T Consensus 627 tnDitGGNSGSPvlN~~---GeLVGl~ 650 (698)
T PF10459_consen 627 TNDITGGNSGSPVLNAK---GELVGLA 650 (698)
T ss_pred ccCcCCCCCCCccCCCC---ceEEEEe
Confidence 46777888888887433 3688876
Done!