Query psy10445
Match_columns 425
No_of_seqs 417 out of 1720
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 18:20:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10445hhsearch_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 2.3E-44 4.9E-49 335.7 25.4 227 189-421 1-232 (232)
2 KOG3627|consensus 100.0 3.1E-43 6.8E-48 335.5 25.2 233 186-423 10-255 (256)
3 smart00020 Tryp_SPc Trypsin-li 100.0 5.3E-41 1.2E-45 313.4 24.1 224 188-418 1-229 (229)
4 PF00089 Trypsin: Trypsin; In 100.0 6.5E-39 1.4E-43 296.7 23.7 217 189-418 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 1.2E-32 2.6E-37 260.3 17.1 233 186-423 30-279 (413)
6 PF03761 DUF316: Domain of unk 99.7 7.2E-17 1.6E-21 156.3 16.6 225 165-419 21-276 (282)
7 PF09342 DUF1986: Domain of un 99.5 1E-12 2.2E-17 119.7 15.6 118 196-321 12-131 (267)
8 COG3591 V8-like Glu-specific e 99.0 3.2E-09 7E-14 99.1 12.8 201 195-423 44-251 (251)
9 PF12032 CLIP: Regulatory CLIP 98.6 8.2E-09 1.8E-13 74.1 -0.1 51 44-97 1-54 (54)
10 TIGR02037 degP_htrA_DO peripla 98.3 1.2E-05 2.5E-10 82.7 15.0 142 211-396 57-199 (428)
11 PF13365 Trypsin_2: Trypsin-li 98.3 2.4E-06 5.1E-11 70.9 7.5 22 214-235 1-23 (120)
12 smart00680 CLIP Clip or disulp 98.3 1.9E-07 4E-12 66.4 0.1 51 44-98 1-52 (52)
13 TIGR02038 protease_degS peripl 98.3 3.3E-05 7.2E-10 77.2 16.0 141 212-397 78-219 (351)
14 PRK10898 serine endoprotease; 98.2 8.2E-05 1.8E-09 74.4 16.7 141 212-397 78-219 (353)
15 PRK10139 serine endoprotease; 98.0 0.00018 3.9E-09 74.4 15.2 141 212-396 90-232 (455)
16 PRK10942 serine endoprotease; 97.8 0.00056 1.2E-08 71.0 15.6 141 212-396 111-253 (473)
17 PF02395 Peptidase_S6: Immunog 96.5 0.016 3.5E-07 63.2 10.8 66 215-305 68-133 (769)
18 COG0265 DegQ Trypsin-like seri 86.9 30 0.00066 34.3 15.8 146 211-399 71-217 (347)
19 PF00863 Peptidase_C4: Peptida 78.8 28 0.0006 32.7 10.8 147 218-413 37-186 (235)
20 PF00548 Peptidase_C3: 3C cyst 71.4 20 0.00044 31.9 7.7 71 210-301 23-93 (172)
21 PF00947 Pico_P2A: Picornaviru 63.8 8.1 0.00018 32.5 3.2 34 373-414 89-122 (127)
22 PF05579 Peptidase_S32: Equine 56.9 7.9 0.00017 36.8 2.2 22 373-396 207-228 (297)
23 PF05580 Peptidase_S55: SpoIVB 53.6 15 0.00033 33.8 3.5 26 369-397 175-200 (218)
24 PF02907 Peptidase_S29: Hepati 46.9 15 0.00033 31.2 2.2 22 372-395 106-127 (148)
25 KOG1924|consensus 41.2 70 0.0015 35.1 6.5 12 281-292 719-730 (1102)
26 TIGR02860 spore_IV_B stage IV 32.8 56 0.0012 33.3 4.1 45 369-423 355-400 (402)
27 PF10459 Peptidase_S46: Peptid 30.2 29 0.00063 38.0 1.7 21 213-233 48-69 (698)
28 PF07981 Plasmod_MYXSPDY: Plas 26.8 36 0.00078 17.9 0.8 14 3-16 3-17 (17)
29 PF10459 Peptidase_S46: Peptid 23.2 53 0.0012 36.0 2.2 25 367-393 626-650 (698)
30 PF00944 Peptidase_S3: Alphavi 22.8 48 0.001 28.2 1.4 22 373-396 105-126 (158)
31 KOG1421|consensus 22.2 4.3E+02 0.0092 29.0 8.3 72 213-305 85-158 (955)
32 PF05372 Delta_lysin: Delta ly 21.0 44 0.00096 19.3 0.6 14 411-424 9-22 (25)
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=2.3e-44 Score=335.70 Aligned_cols=227 Identities=47% Similarity=0.902 Sum_probs=194.8
Q ss_pred eeCCeecCCCCCceEEEEeeC-CceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEE
Q psy10445 189 IVGGQNAEQNEWPWVVAIFNS-GKQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRL 267 (425)
Q Consensus 189 I~gG~~a~~~e~Pw~v~i~~~-~~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~i 267 (425)
|+||+++..++|||+|.|+.. ..++|+||||+++||||||||+.... ...+.|++|.+...... .....+.|+++
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~---~~~~~v~~g~~~~~~~~-~~~~~~~v~~~ 76 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSA---PSNYTVRLGSHDLSSNE-GGGQVIKVKKV 76 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCC---CccEEEEeCcccccCCC-CceEEEEEEEE
Confidence 689999999999999999876 77889999999999999999997543 24678999988765432 23456789999
Q ss_pred EecCCCCCCCCCCceEEEEeCCCcccCCCeeeeecCCCC-CCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHh
Q psy10445 268 VRHKAFDMRTLYNDVAILTLDKPVKYSDTIRAICLPRGR-ASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCK 346 (425)
Q Consensus 268 i~Hp~y~~~~~~nDIALLkL~~~v~~~~~v~PIcLp~~~-~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~ 346 (425)
++||+|+.....+|||||||++++.++++++|||||... ....+..+.++|||........+..++...+.+++.+.|.
T Consensus 77 ~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~ 156 (232)
T cd00190 77 IVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECK 156 (232)
T ss_pred EECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhh
Confidence 999999988888999999999999999999999999875 3446789999999987655456778999999999999999
Q ss_pred hhcCCCCCCCCcCCeEEeeCC--CCCCccCccccceeEe-CCcEEEEEEEEeCCCCCCCCCCcEEEeCCchHHHHHHH
Q psy10445 347 ARYGPVAPGGIVDHFLCAGRA--TKDSCTGDSGGPLMVN-DGKWTQVGIVSWGIGCGKGEYPGVYTRVTYFMPWITKN 421 (425)
Q Consensus 347 ~~~~~~~~~~~~~~~iCag~~--~~~~C~GDSGgPL~~~-~g~~~LvGI~S~g~~C~~~~~P~vyt~V~~y~~WI~~~ 421 (425)
..+.. ...+.+.++|++.. ..+.|.|||||||++. +++|+|+||+|+|..|...+.|++|++|+.|++||+++
T Consensus 157 ~~~~~--~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI~~~ 232 (232)
T cd00190 157 RAYSY--GGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232 (232)
T ss_pred hhccC--cccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHhhcC
Confidence 88753 23477899999854 6789999999999986 67899999999999898767899999999999999864
No 2
>KOG3627|consensus
Probab=100.00 E-value=3.1e-43 Score=335.48 Aligned_cols=233 Identities=45% Similarity=0.924 Sum_probs=195.1
Q ss_pred CCceeCCeecCCCCCceEEEEeeCC--ceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccc--eEE
Q psy10445 186 QERIVGGQNAEQNEWPWVVAIFNSG--KQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVK--HVE 261 (425)
Q Consensus 186 ~~rI~gG~~a~~~e~Pw~v~i~~~~--~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~--~~~ 261 (425)
..||+||.++..++|||+|+|.... .++|+|+||+++||||||||+.... .. .+.|++|++......... ...
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~--~~-~~~V~~G~~~~~~~~~~~~~~~~ 86 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGAS--AS-LYTVRLGEHDINLSVSEGEEQLV 86 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCC--Cc-ceEEEECccccccccccCchhhh
Confidence 4699999999999999999998765 6799999999999999999997642 11 678999987665542222 244
Q ss_pred EEEEEEEecCCCCCCCCC-CceEEEEeCCCcccCCCeeeeecCCCCC---CCCCCEEEEEEccccCCC-CCCCccceEEE
Q psy10445 262 RKVKRLVRHKAFDMRTLY-NDVAILTLDKPVKYSDTIRAICLPRGRA---SYEGKIATVIGWGSLRES-GPQPAVLQKVN 336 (425)
Q Consensus 262 ~~V~~ii~Hp~y~~~~~~-nDIALLkL~~~v~~~~~v~PIcLp~~~~---~~~~~~~~v~GWG~t~~~-~~~s~~l~~~~ 336 (425)
..|.++++||+|+..... ||||||+|++++.|+++|+|||||.... ...+..+.++|||.+... ...+..|++++
T Consensus 87 ~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~ 166 (256)
T KOG3627|consen 87 GDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVD 166 (256)
T ss_pred ceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEE
Confidence 558889999999998877 9999999999999999999999985543 335588999999987544 25578899999
Q ss_pred EEeeChhhHhhhcCCCCCCCCcCCeEEeeC--CCCCCccCccccceeEeC-CcEEEEEEEEeCCC-CCCCCCCcEEEeCC
Q psy10445 337 IPVWTNADCKARYGPVAPGGIVDHFLCAGR--ATKDSCTGDSGGPLMVND-GKWTQVGIVSWGIG-CGKGEYPGVYTRVT 412 (425)
Q Consensus 337 v~v~~~~~C~~~~~~~~~~~~~~~~iCag~--~~~~~C~GDSGgPL~~~~-g~~~LvGI~S~g~~-C~~~~~P~vyt~V~ 412 (425)
+++++.+.|...+.... .+.+.+|||+. .+.++|+|||||||++.+ ++|+++||+|||.. |+..+.|++||+|+
T Consensus 167 v~i~~~~~C~~~~~~~~--~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~C~~~~~P~vyt~V~ 244 (256)
T KOG3627|consen 167 VPIISNSECRRAYGGLG--TITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGGCGQPNYPGVYTRVS 244 (256)
T ss_pred EeEcChhHhcccccCcc--ccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCCCCCCCCCeEEeEhH
Confidence 99999999998875421 35567899994 567889999999999974 46999999999988 99988999999999
Q ss_pred chHHHHHHHhh
Q psy10445 413 YFMPWITKNLK 423 (425)
Q Consensus 413 ~y~~WI~~~i~ 423 (425)
.|++||++.+.
T Consensus 245 ~y~~WI~~~~~ 255 (256)
T KOG3627|consen 245 SYLDWIKENIG 255 (256)
T ss_pred HhHHHHHHHhc
Confidence 99999999875
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=5.3e-41 Score=313.38 Aligned_cols=224 Identities=47% Similarity=0.909 Sum_probs=190.7
Q ss_pred ceeCCeecCCCCCceEEEEeeCC-ceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEE
Q psy10445 188 RIVGGQNAEQNEWPWVVAIFNSG-KQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKR 266 (425)
Q Consensus 188 rI~gG~~a~~~e~Pw~v~i~~~~-~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ 266 (425)
||+||+++..++|||+|.|+... .+.|+||||++++|||||||+.... ...+.|++|.+......+. ..+.|.+
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~---~~~~~v~~g~~~~~~~~~~--~~~~v~~ 75 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSD---PSNIRVRLGSHDLSSGEEG--QVIKVSK 75 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCC---CcceEEEeCcccCCCCCCc--eEEeeEE
Confidence 68999999999999999998776 7789999999999999999997643 2467899998876544321 4578999
Q ss_pred EEecCCCCCCCCCCceEEEEeCCCcccCCCeeeeecCCCC-CCCCCCEEEEEEccccCC-CCCCCccceEEEEEeeChhh
Q psy10445 267 LVRHKAFDMRTLYNDVAILTLDKPVKYSDTIRAICLPRGR-ASYEGKIATVIGWGSLRE-SGPQPAVLQKVNIPVWTNAD 344 (425)
Q Consensus 267 ii~Hp~y~~~~~~nDIALLkL~~~v~~~~~v~PIcLp~~~-~~~~~~~~~v~GWG~t~~-~~~~s~~l~~~~v~v~~~~~ 344 (425)
++.||+|+.....+|||||||++++.+++.++||||+... ....+..+.++|||.... .+.....++...+.+++.+.
T Consensus 76 ~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (229)
T smart00020 76 VIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNAT 155 (229)
T ss_pred EEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHH
Confidence 9999999988888999999999999999999999999863 344578999999998653 23446678899999999999
Q ss_pred HhhhcCCCCCCCCcCCeEEeeCC--CCCCccCccccceeEeCCcEEEEEEEEeCCCCCCCCCCcEEEeCCchHHHH
Q psy10445 345 CKARYGPVAPGGIVDHFLCAGRA--TKDSCTGDSGGPLMVNDGKWTQVGIVSWGIGCGKGEYPGVYTRVTYFMPWI 418 (425)
Q Consensus 345 C~~~~~~~~~~~~~~~~iCag~~--~~~~C~GDSGgPL~~~~g~~~LvGI~S~g~~C~~~~~P~vyt~V~~y~~WI 418 (425)
|...+... ..+...++|++.. ..+.|.|||||||++..++|+|+||+|+|..|+..+.|.+|++|++|++||
T Consensus 156 C~~~~~~~--~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~WI 229 (229)
T smart00020 156 CRRAYSGG--GAITDNMLCAGGLEGGKDACQGDSGGPLVCNDGRWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229 (229)
T ss_pred hhhhhccc--cccCCCcEeecCCCCCCcccCCCCCCeeEEECCCEEEEEEEEECCCCCCCCCCCEEEEeccccccC
Confidence 99877531 2467889999854 578899999999999855999999999999998777899999999999998
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=6.5e-39 Score=296.71 Aligned_cols=217 Identities=42% Similarity=0.854 Sum_probs=185.1
Q ss_pred eeCCeecCCCCCceEEEEeeCC-ceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEE
Q psy10445 189 IVGGQNAEQNEWPWVVAIFNSG-KQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRL 267 (425)
Q Consensus 189 I~gG~~a~~~e~Pw~v~i~~~~-~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~i 267 (425)
|+||.++..++|||+|.|+... .++|+|+||+++||||||||+.. ...+.+++|...+... +.....+.|+++
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~-----~~~~~v~~g~~~~~~~-~~~~~~~~v~~~ 74 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG-----ASDIKVRLGTYSIRNS-DGSEQTIKVSKI 74 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS-----GGSEEEEESESBTTST-TTTSEEEEEEEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc-----cccccccccccccccc-cccccccccccc
Confidence 7899999999999999999876 88999999999999999999976 1356788888433322 222356889999
Q ss_pred EecCCCCCCCCCCceEEEEeCCCcccCCCeeeeecCCCCC-CCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHh
Q psy10445 268 VRHKAFDMRTLYNDVAILTLDKPVKYSDTIRAICLPRGRA-SYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCK 346 (425)
Q Consensus 268 i~Hp~y~~~~~~nDIALLkL~~~v~~~~~v~PIcLp~~~~-~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~ 346 (425)
+.||.|+.....+|||||||++++.+.+.++|+||+.... ...+..+.++|||.....+ ....++...+.+++.+.|.
T Consensus 75 ~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~~~~~c~ 153 (220)
T PF00089_consen 75 IIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVVSRKTCR 153 (220)
T ss_dssp EEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS-BTSBEEEEEEEEEEHHHHH
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccc
Confidence 9999999988889999999999999999999999998432 3467899999999865444 5567899999999999999
Q ss_pred hhcCCCCCCCCcCCeEEeeC-CCCCCccCccccceeEeCCcEEEEEEEEeCCCCCCCCCCcEEEeCCchHHHH
Q psy10445 347 ARYGPVAPGGIVDHFLCAGR-ATKDSCTGDSGGPLMVNDGKWTQVGIVSWGIGCGKGEYPGVYTRVTYFMPWI 418 (425)
Q Consensus 347 ~~~~~~~~~~~~~~~iCag~-~~~~~C~GDSGgPL~~~~g~~~LvGI~S~g~~C~~~~~P~vyt~V~~y~~WI 418 (425)
..+.. .+.+.++|++. ...+.|.|||||||++.++ +|+||++++..|...+.|.+|++|+.|++||
T Consensus 154 ~~~~~----~~~~~~~c~~~~~~~~~~~g~sG~pl~~~~~--~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 154 SSYND----NLTPNMICAGSSGSGDACQGDSGGPLICNNN--YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp HHTTT----TSTTTEEEEETTSSSBGGTTTTTSEEEETTE--EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred ccccc----cccccccccccccccccccccccccccccee--eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 87532 26789999986 5578899999999999875 7999999999999888899999999999999
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-32 Score=260.29 Aligned_cols=233 Identities=31% Similarity=0.528 Sum_probs=169.6
Q ss_pred CCceeCCeecCCCCCceEEEEeeC-----CceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceE
Q psy10445 186 QERIVGGQNAEQNEWPWVVAIFNS-----GKQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHV 260 (425)
Q Consensus 186 ~~rI~gG~~a~~~e~Pw~v~i~~~-----~~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~ 260 (425)
..||+||+.|+.++||+||+|... ...||||++|..|||||||||+............|.. +++..... +
T Consensus 30 s~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~---~l~d~Sq~--~ 104 (413)
T COG5640 30 SSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVV---DLNDSSQA--E 104 (413)
T ss_pred ceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEe---cccccccc--c
Confidence 579999999999999999999632 3468999999999999999999865422222333333 33333332 2
Q ss_pred EEEEEEEEecCCCCCCCCCCceEEEEeCCCcccCC-CeeeeecCCC--CCCCCCCEEEEEEccccCCC---C--CCCccc
Q psy10445 261 ERKVKRLVRHKAFDMRTLYNDVAILTLDKPVKYSD-TIRAICLPRG--RASYEGKIATVIGWGSLRES---G--PQPAVL 332 (425)
Q Consensus 261 ~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~v~~~~-~v~PIcLp~~--~~~~~~~~~~v~GWG~t~~~---~--~~s~~l 332 (425)
...|++++.|..|.+.++.||||+++|+++..... .+.-.--+.. ............+||.+... . +....+
T Consensus 105 rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~p~gt~l 184 (413)
T COG5640 105 RGHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTIL 184 (413)
T ss_pred CcceEEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCCCcccee
Confidence 36799999999999999999999999999765321 1111111110 01112344566777755432 1 122478
Q ss_pred eEEEEEeeChhhHhhhcCC--CCCCCCcCCeEEeeCCCCCCccCccccceeEeC-CcEEEEEEEEeCCC-CCCCCCCcEE
Q psy10445 333 QKVNIPVWTNADCKARYGP--VAPGGIVDHFLCAGRATKDSCTGDSGGPLMVND-GKWTQVGIVSWGIG-CGKGEYPGVY 408 (425)
Q Consensus 333 ~~~~v~v~~~~~C~~~~~~--~~~~~~~~~~iCag~~~~~~C~GDSGgPL~~~~-g~~~LvGI~S~g~~-C~~~~~P~vy 408 (425)
+++.+..++...|...++. .......-.-+|++...+|+|+||||||++.+. ....++||+|||.+ |+....|+||
T Consensus 185 ~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~~~daCqGDSGGPi~~~g~~G~vQ~GVvSwG~~~Cg~t~~~gVy 264 (413)
T COG5640 185 HEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRPPKDACQGDSGGPIFHKGEEGRVQRGVVSWGDGGCGGTLIPGVY 264 (413)
T ss_pred eeeeeeeechHHhhhhccccccCCCCCCccceecCCCCcccccCCCCCceEEeCCCccEEEeEEEecCCCCCCCCcceeE
Confidence 9999999999999988851 112222223499998889999999999999873 34589999999986 9999999999
Q ss_pred EeCCchHHHHHHHhh
Q psy10445 409 TRVTYFMPWITKNLK 423 (425)
Q Consensus 409 t~V~~y~~WI~~~i~ 423 (425)
|+|+.|.+||..+|+
T Consensus 265 T~vsny~~WI~a~~~ 279 (413)
T COG5640 265 TNVSNYQDWIAAMTN 279 (413)
T ss_pred EehhHHHHHHHHHhc
Confidence 999999999999875
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.73 E-value=7.2e-17 Score=156.32 Aligned_cols=225 Identities=25% Similarity=0.498 Sum_probs=141.6
Q ss_pred cccCCcccCCCCCccCCCCCCCCceeCCeecCCCCCceEEEEeeCC----ceeeeeEEeeCCeEEeccccceecc-cc--
Q psy10445 165 TTEAGKVDMSCGQKNGYQDLDQERIVGGQNAEQNEWPWVVAIFNSG----KQFCGGSLIDTQHVLTAAHCVAHMS-SW-- 237 (425)
Q Consensus 165 ~~~~~~~~~~CG~~~~~~~~~~~rI~gG~~a~~~e~Pw~v~i~~~~----~~~CgGtLIs~~~VLTAAHCv~~~~-~~-- 237 (425)
..|+..+...||..... ...++.+|..+..++.||+|.++..+ ..+++|||||+||||||+||+.... .|
T Consensus 21 ~eEN~~rl~~CG~~~~~---~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~ 97 (282)
T PF03761_consen 21 EEENEERLETCGKKKLP---YPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLN 97 (282)
T ss_pred HHHHHHHHHhcCCCCCC---CcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEeccccccc
Confidence 44555566789955321 34568999999999999999997532 3468999999999999999997432 12
Q ss_pred --ceeeEEEEeC-------ccccc---c-----cCccceEEEEEEEEEecCCC----CCCCCCCceEEEEeCCCcccCCC
Q psy10445 238 --DVAKLSVNLG-------DHNIK---Q-----KNEVKHVERKVKRLVRHKAF----DMRTLYNDVAILTLDKPVKYSDT 296 (425)
Q Consensus 238 --~~~~~~V~lG-------~~~~~---~-----~~~~~~~~~~V~~ii~Hp~y----~~~~~~nDIALLkL~~~v~~~~~ 296 (425)
........-+ ...+. . ..........|.++++--.- ......++++||+|+++ +...
T Consensus 98 ~~~~~~~~C~~~~~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~ 175 (282)
T PF03761_consen 98 GEEFDNKKCEGNNNHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKN 175 (282)
T ss_pred CcccccceeeCCCceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--cccc
Confidence 0000001111 10000 0 00011122456666653222 23334579999999999 7789
Q ss_pred eeeeecCCCCCCC-CCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCCCCccCc
Q psy10445 297 IRAICLPRGRASY-EGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATKDSCTGD 375 (425)
Q Consensus 297 v~PIcLp~~~~~~-~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~~~C~GD 375 (425)
+.|+||+...... .+....+.|+. ....+....+.+.....|.. .++ .....|.||
T Consensus 176 ~~~~Cl~~~~~~~~~~~~~~~yg~~-------~~~~~~~~~~~i~~~~~~~~-------------~~~---~~~~~~~~d 232 (282)
T PF03761_consen 176 VSPPCLADSSTNWEKGDEVDVYGFN-------STGKLKHRKLKITNCTKCAY-------------SIC---TKQYSCKGD 232 (282)
T ss_pred CCCEEeCCCccccccCceEEEeecC-------CCCeEEEEEEEEEEeeccce-------------eEe---cccccCCCC
Confidence 9999999865432 45566666661 12335555555554332211 122 235678999
Q ss_pred cccceeEe-CCcEEEEEEEEeCC-CCCCCCCCcEEEeCCchHHHHH
Q psy10445 376 SGGPLMVN-DGKWTQVGIVSWGI-GCGKGEYPGVYTRVTYFMPWIT 419 (425)
Q Consensus 376 SGgPL~~~-~g~~~LvGI~S~g~-~C~~~~~P~vyt~V~~y~~WI~ 419 (425)
+||||+.. +|+|+|+||.+.+. .|... ...|.+|..|.+=|-
T Consensus 233 ~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~--~~~f~~v~~~~~~IC 276 (282)
T PF03761_consen 233 RGGPLVKNINGRWTLIGVGASGNYECNKN--NSYFFNVSWYQDEIC 276 (282)
T ss_pred ccCeEEEEECCCEEEEEEEccCCCccccc--ccEEEEHHHhhhhhc
Confidence 99999976 89999999999875 34432 568889988876553
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=99.48 E-value=1e-12 Score=119.72 Aligned_cols=118 Identities=20% Similarity=0.452 Sum_probs=89.3
Q ss_pred CCCCCceEEEEeeCCceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccc-cCccceEEEEEEEEEecCCCC
Q psy10445 196 EQNEWPWVVAIFNSGKQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQ-KNEVKHVERKVKRLVRHKAFD 274 (425)
Q Consensus 196 ~~~e~Pw~v~i~~~~~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~-~~~~~~~~~~V~~ii~Hp~y~ 274 (425)
+.-.|||.|.||..+.+.|+|+||.+.|||++..|+...+- ....+.|.+|...... ......|.++|..+..-|+
T Consensus 12 e~y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L-~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~~-- 88 (267)
T PF09342_consen 12 EDYHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISL-SHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVPE-- 88 (267)
T ss_pred ccccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCccc-ccceEEEEecCcceecccCCChheEEEeeeeeeccc--
Confidence 34569999999999999999999999999999999976532 3356778888765322 2233345566766544433
Q ss_pred CCCCCCceEEEEeCCCcccCCCeeeeecCCCC-CCCCCCEEEEEEccc
Q psy10445 275 MRTLYNDVAILTLDKPVKYSDTIRAICLPRGR-ASYEGKIATVIGWGS 321 (425)
Q Consensus 275 ~~~~~nDIALLkL~~~v~~~~~v~PIcLp~~~-~~~~~~~~~v~GWG~ 321 (425)
.+++||.|++|+.|+.+|+|..||... .......|..+|-..
T Consensus 89 -----S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 89 -----SNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred -----cceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 689999999999999999999999743 233456899888653
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.03 E-value=3.2e-09 Score=99.13 Aligned_cols=201 Identities=16% Similarity=0.246 Sum_probs=109.3
Q ss_pred cCCCCCceEEEEee--C-CceeeeeEEeeCCeEEeccccceeccccceeeEEEEe-CcccccccCccceEEEEEEEEEec
Q psy10445 195 AEQNEWPWVVAIFN--S-GKQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNL-GDHNIKQKNEVKHVERKVKRLVRH 270 (425)
Q Consensus 195 a~~~e~Pw~v~i~~--~-~~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~l-G~~~~~~~~~~~~~~~~V~~ii~H 270 (425)
.....|||-+.... . +..-|+++||+++.||||+||+....... ..+.+.. |... .......+.-.++.+.
T Consensus 44 ~dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~G~-~~~~~~p~g~~~----~~~~~~~~~~~~~~~~ 118 (251)
T COG3591 44 TDTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDYGE-DDIAAAPPGVNS----DGGPFYGITKIEIRVY 118 (251)
T ss_pred ccCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCCCh-hhhhhcCCcccC----CCCCCCceeeEEEEec
Confidence 45678999877643 2 23347779999999999999998654211 2222222 2211 1111111222222223
Q ss_pred CC--CCCCCCCCceEEEEeCCCcccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhh
Q psy10445 271 KA--FDMRTLYNDVAILTLDKPVKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKAR 348 (425)
Q Consensus 271 p~--y~~~~~~nDIALLkL~~~v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~ 348 (425)
|. |.......|+..+.|+....+.+.+...-++.......+....++||=.... ..+++ .+.|...
T Consensus 119 ~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~-----~~~~~-------~e~t~~v 186 (251)
T COG3591 119 PGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKP-----NIGTM-------WESTGKV 186 (251)
T ss_pred CCceeccCCceeeccHHHhccCCCccccccccccccccccccCceeEEEeccCCCC-----cceeE-------eeeccee
Confidence 32 3444555688888887555556666655555554444555588888842211 11111 0111111
Q ss_pred cCCCCCCCCcCCeEEeeCCCCCCccCccccceeEeCCcEEEEEEEEeCCCCCCCCCCcEEEeC-CchHHHHHHHhh
Q psy10445 349 YGPVAPGGIVDHFLCAGRATKDSCTGDSGGPLMVNDGKWTQVGIVSWGIGCGKGEYPGVYTRV-TYFMPWITKNLK 423 (425)
Q Consensus 349 ~~~~~~~~~~~~~iCag~~~~~~C~GDSGgPL~~~~g~~~LvGI~S~g~~C~~~~~P~vyt~V-~~y~~WI~~~i~ 423 (425)
.. +... ......|++.|+||+|++..+. +++||.+-|..-.......-.+|+ ..+++||++.++
T Consensus 187 ~~------~~~~---~l~y~~dT~pG~SGSpv~~~~~--~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 187 NS------IKGN---KLFYDADTLPGSSGSPVLISKD--EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred EE------Eecc---eEEEEecccCCCCCCceEecCc--eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 00 0011 0123458999999999998755 899999988652211122333444 457899998864
No 9
>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=98.59 E-value=8.2e-09 Score=74.11 Aligned_cols=51 Identities=25% Similarity=0.583 Sum_probs=39.6
Q ss_pred cccCCCCceeeEEcccCccccCcCC---CCcccccccccCcceeecCCCCcceeEEe
Q psy10445 44 CVTNRGLLGQCLRFKQCYPYLKLPD---FIWEPVIYDSFDSCSYIAPDGTQGVGVCC 97 (425)
Q Consensus 44 C~tp~~~~G~C~~~~~C~~~~~~~~---~~~~~~~~~~~~~C~~~~~~~~~~~~vCC 97 (425)
|+||+|+.|+|+++++|++++++++ ++.+...++..++|||.+ ...++|||
T Consensus 1 C~tp~g~~G~Cv~i~~C~~l~~~l~~~~~~~~~~~~l~~s~Cg~~~---~~~~~VCC 54 (54)
T PF12032_consen 1 CTTPNGEPGRCVPIRSCPPLLEILRSKPLSPEERNFLRQSQCGFDG---NRDPLVCC 54 (54)
T ss_dssp EE-TTSSEEEEEETTTBHHHHHHHHHS---HHHHHHHHHTESEECS---S-SCEEEE
T ss_pred CcCCCCCcEEEecHHHCHHHHHHHhcCCCCHHHHHHHHHccCCCCC---CCCceeeC
Confidence 8999999999999999999999864 344566778889999944 22458999
No 10
>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=98.32 E-value=1.2e-05 Score=82.71 Aligned_cols=142 Identities=23% Similarity=0.323 Sum_probs=81.9
Q ss_pred ceeeeeEEeeCC-eEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCC
Q psy10445 211 KQFCGGSLIDTQ-HVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDK 289 (425)
Q Consensus 211 ~~~CgGtLIs~~-~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~ 289 (425)
...++|.+|+++ ||||++|.+.... .+.|.+.+- . .+..+-+..++. .||||||++.
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~~-----~i~V~~~~~--------~--~~~a~vv~~d~~-------~DlAllkv~~ 114 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGAD-----EITVTLSDG--------R--EFKAKLVGKDPR-------TDIAVLKIDA 114 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCCC-----eEEEEeCCC--------C--EEEEEEEEecCC-------CCEEEEEecC
Confidence 347999999976 9999999997542 355555421 1 123332333433 6999999986
Q ss_pred CcccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCC
Q psy10445 290 PVKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATK 369 (425)
Q Consensus 290 ~v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~ 369 (425)
+ ..+.++.|........++.+++.|+-... ........+.-..... ... . ....++ ..+.
T Consensus 115 ~----~~~~~~~l~~~~~~~~G~~v~aiG~p~g~-----~~~~t~G~vs~~~~~~----~~~---~-~~~~~i---~tda 174 (428)
T TIGR02037 115 K----KNLPVIKLGDSDKLRVGDWVLAIGNPFGL-----GQTVTSGIVSALGRSG----LGI---G-DYENFI---QTDA 174 (428)
T ss_pred C----CCceEEEccCCCCCCCCCEEEEEECCCcC-----CCcEEEEEEEecccCc----cCC---C-CccceE---EECC
Confidence 4 34567777655555678999999985321 1112122222111110 000 0 001111 1123
Q ss_pred CCccCccccceeEeCCcEEEEEEEEeC
Q psy10445 370 DSCTGDSGGPLMVNDGKWTQVGIVSWG 396 (425)
Q Consensus 370 ~~C~GDSGgPL~~~~g~~~LvGI~S~g 396 (425)
..-.|.|||||+..+| .++||.+..
T Consensus 175 ~i~~GnSGGpl~n~~G--~viGI~~~~ 199 (428)
T TIGR02037 175 AINPGNSGGPLVNLRG--EVIGINTAI 199 (428)
T ss_pred CCCCCCCCCceECCCC--eEEEEEeEE
Confidence 4457999999997666 799998764
No 11
>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=98.29 E-value=2.4e-06 Score=70.94 Aligned_cols=22 Identities=41% Similarity=0.481 Sum_probs=19.7
Q ss_pred eeeEEeeCC-eEEeccccceecc
Q psy10445 214 CGGSLIDTQ-HVLTAAHCVAHMS 235 (425)
Q Consensus 214 CgGtLIs~~-~VLTAAHCv~~~~ 235 (425)
|+|.+|+++ +|||||||+....
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~~ 23 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDWN 23 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCCT
T ss_pred CEEEEEcCCceEEEchhheeccc
Confidence 789999999 9999999997643
No 12
>smart00680 CLIP Clip or disulphide knot domain. Present in horseshoe crab proclotting enzyme N-terminal domain, Drosophila Easter and silkworm prophenoloxidase-activating enzyme.
Probab=98.26 E-value=1.9e-07 Score=66.37 Aligned_cols=51 Identities=25% Similarity=0.460 Sum_probs=39.1
Q ss_pred cccCCCCceeeEEcccCccccCcCCCC-cccccccccCcceeecCCCCcceeEEec
Q psy10445 44 CVTNRGLLGQCLRFKQCYPYLKLPDFI-WEPVIYDSFDSCSYIAPDGTQGVGVCCT 98 (425)
Q Consensus 44 C~tp~~~~G~C~~~~~C~~~~~~~~~~-~~~~~~~~~~~C~~~~~~~~~~~~vCC~ 98 (425)
|.||+++.|+|+++++|+++++++... .+...++..+.||+.. ..++||||
T Consensus 1 C~tp~~~~G~Cv~~~~C~~~~~~l~~~~~~~~~~l~~~~Cg~~~----~~~~vCCp 52 (52)
T smart00680 1 CRTPDGERGTCVPISDCPSLLSLLKSDPPEDLNFLRKSQCGFGN----REPLVCCP 52 (52)
T ss_pred CcCCCCCcEEeEEHHhChHHHHHHccCCHHHHHHHHHccCCCCC----CCEeeeCc
Confidence 899999999999999999988876431 2345667778999632 23579997
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=98.25 E-value=3.3e-05 Score=77.21 Aligned_cols=141 Identities=20% Similarity=0.306 Sum_probs=78.3
Q ss_pred eeeeeEEeeCC-eEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCCC
Q psy10445 212 QFCGGSLIDTQ-HVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDKP 290 (425)
Q Consensus 212 ~~CgGtLIs~~-~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~ 290 (425)
...+|.+|+++ ||||++|.+... ..+.|.+.+- . .+..+-+..++. .||||||++..
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~~-----~~i~V~~~dg--------~--~~~a~vv~~d~~-------~DlAvlkv~~~ 135 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKKA-----DQIVVALQDG--------R--KFEAELVGSDPL-------TDLAVLKIEGD 135 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCCC-----CEEEEEECCC--------C--EEEEEEEEecCC-------CCEEEEEecCC
Confidence 36999999976 999999999643 2355555321 1 122332333433 69999999864
Q ss_pred cccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCCC
Q psy10445 291 VKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATKD 370 (425)
Q Consensus 291 v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~~ 370 (425)
- +.++.|-.......++.+++.|+.... + .......+...... .+.. .. ....+ ..+..
T Consensus 136 ~-----~~~~~l~~s~~~~~G~~V~aiG~P~~~--~---~s~t~GiIs~~~r~----~~~~---~~-~~~~i---qtda~ 194 (351)
T TIGR02038 136 N-----LPTIPVNLDRPPHVGDVVLAIGNPYNL--G---QTITQGIISATGRN----GLSS---VG-RQNFI---QTDAA 194 (351)
T ss_pred C-----CceEeccCcCccCCCCEEEEEeCCCCC--C---CcEEEEEEEeccCc----ccCC---CC-cceEE---EECCc
Confidence 2 334445333344578889999985321 1 11222222221110 0000 00 01111 12234
Q ss_pred CccCccccceeEeCCcEEEEEEEEeCC
Q psy10445 371 SCTGDSGGPLMVNDGKWTQVGIVSWGI 397 (425)
Q Consensus 371 ~C~GDSGgPL~~~~g~~~LvGI~S~g~ 397 (425)
.-.|.|||||+..+| .++||.+...
T Consensus 195 i~~GnSGGpl~n~~G--~vIGI~~~~~ 219 (351)
T TIGR02038 195 INAGNSGGALINTNG--ELVGINTASF 219 (351)
T ss_pred cCCCCCcceEECCCC--eEEEEEeeee
Confidence 567999999997766 7999987643
No 14
>PRK10898 serine endoprotease; Provisional
Probab=98.17 E-value=8.2e-05 Score=74.41 Aligned_cols=141 Identities=21% Similarity=0.309 Sum_probs=76.8
Q ss_pred eeeeeEEeeCC-eEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCCC
Q psy10445 212 QFCGGSLIDTQ-HVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDKP 290 (425)
Q Consensus 212 ~~CgGtLIs~~-~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~ 290 (425)
...+|.+|+++ ||||+||=+... ..+.|.+.+- .. +..+-+..+|. +||||||++..
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~a-----~~i~V~~~dg--------~~--~~a~vv~~d~~-------~DlAvl~v~~~ 135 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVINDA-----DQIIVALQDG--------RV--FEALLVGSDSL-------TDLAVLKINAT 135 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCCC-----CEEEEEeCCC--------CE--EEEEEEEEcCC-------CCEEEEEEcCC
Confidence 46999999976 999999988643 3455665321 11 22222333333 79999999854
Q ss_pred cccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCCC
Q psy10445 291 VKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATKD 370 (425)
Q Consensus 291 v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~~ 370 (425)
...++-|........++.+++.|+-.... .......+.-.... .+... . ....+ ..+..
T Consensus 136 -----~l~~~~l~~~~~~~~G~~V~aiG~P~g~~-----~~~t~Giis~~~r~----~~~~~---~-~~~~i---qtda~ 194 (353)
T PRK10898 136 -----NLPVIPINPKRVPHIGDVVLAIGNPYNLG-----QTITQGIISATGRI----GLSPT---G-RQNFL---QTDAS 194 (353)
T ss_pred -----CCCeeeccCcCcCCCCCEEEEEeCCCCcC-----CCcceeEEEecccc----ccCCc---c-ccceE---Eeccc
Confidence 12344443333445688888888752211 11111111111110 00000 0 00111 12234
Q ss_pred CccCccccceeEeCCcEEEEEEEEeCC
Q psy10445 371 SCTGDSGGPLMVNDGKWTQVGIVSWGI 397 (425)
Q Consensus 371 ~C~GDSGgPL~~~~g~~~LvGI~S~g~ 397 (425)
.-.|.|||||+..+| .++||.+...
T Consensus 195 i~~GnSGGPl~n~~G--~vvGI~~~~~ 219 (353)
T PRK10898 195 INHGNSGGALVNSLG--ELMGINTLSF 219 (353)
T ss_pred cCCCCCcceEECCCC--eEEEEEEEEe
Confidence 467999999997666 7999998654
No 15
>PRK10139 serine endoprotease; Provisional
Probab=97.97 E-value=0.00018 Score=74.36 Aligned_cols=141 Identities=22% Similarity=0.356 Sum_probs=80.1
Q ss_pred eeeeeEEeeC--CeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCC
Q psy10445 212 QFCGGSLIDT--QHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDK 289 (425)
Q Consensus 212 ~~CgGtLIs~--~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~ 289 (425)
...+|.+|++ -||||++|.+.+. ..+.|.+.+-. .+..+-+...+. .||||||++.
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~a-----~~i~V~~~dg~----------~~~a~vvg~D~~-------~DlAvlkv~~ 147 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQA-----QKISIQLNDGR----------EFDAKLIGSDDQ-------SDIALLQIQN 147 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCCC-----CEEEEEECCCC----------EEEEEEEEEcCC-------CCEEEEEecC
Confidence 4799999974 6999999999753 34567664211 122332333333 6999999985
Q ss_pred CcccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCC
Q psy10445 290 PVKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATK 369 (425)
Q Consensus 290 ~v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~ 369 (425)
+- ...++.|........++.+++.|+-.- .. .. +..-+++...= .... . ... ...+ ..+.
T Consensus 148 ~~----~l~~~~lg~s~~~~~G~~V~aiG~P~g-~~----~t---vt~GivS~~~r-~~~~-~--~~~-~~~i---qtda 207 (455)
T PRK10139 148 PS----KLTQIAIADSDKLRVGDFAVAVGNPFG-LG----QT---ATSGIISALGR-SGLN-L--EGL-ENFI---QTDA 207 (455)
T ss_pred CC----CCceeEecCccccCCCCEEEEEecCCC-CC----Cc---eEEEEEccccc-cccC-C--CCc-ceEE---EECC
Confidence 42 345667765555557888888887421 11 11 12222221100 0000 0 000 1111 1233
Q ss_pred CCccCccccceeEeCCcEEEEEEEEeC
Q psy10445 370 DSCTGDSGGPLMVNDGKWTQVGIVSWG 396 (425)
Q Consensus 370 ~~C~GDSGgPL~~~~g~~~LvGI~S~g 396 (425)
..-.|.|||||+..+| .++||.+..
T Consensus 208 ~in~GnSGGpl~n~~G--~vIGi~~~~ 232 (455)
T PRK10139 208 SINRGNSGGALLNLNG--ELIGINTAI 232 (455)
T ss_pred ccCCCCCcceEECCCC--eEEEEEEEE
Confidence 4567999999997655 799999874
No 16
>PRK10942 serine endoprotease; Provisional
Probab=97.81 E-value=0.00056 Score=71.02 Aligned_cols=141 Identities=22% Similarity=0.315 Sum_probs=77.6
Q ss_pred eeeeeEEeeC--CeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCC
Q psy10445 212 QFCGGSLIDT--QHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDK 289 (425)
Q Consensus 212 ~~CgGtLIs~--~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~ 289 (425)
...+|.+|+. -||||++|.+.+. ..+.|.+.+- . .+..+-+..++. .||||||++.
T Consensus 111 ~~GSG~ii~~~~G~IlTn~HVv~~a-----~~i~V~~~dg--------~--~~~a~vv~~D~~-------~DlAvlki~~ 168 (473)
T PRK10942 111 ALGSGVIIDADKGYVVTNNHVVDNA-----TKIKVQLSDG--------R--KFDAKVVGKDPR-------SDIALIQLQN 168 (473)
T ss_pred ceEEEEEEECCCCEEEeChhhcCCC-----CEEEEEECCC--------C--EEEEEEEEecCC-------CCEEEEEecC
Confidence 4699999985 5999999998753 3456666421 1 122332333433 6999999974
Q ss_pred CcccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCC
Q psy10445 290 PVKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATK 369 (425)
Q Consensus 290 ~v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~ 369 (425)
+- ...++.|-.......++.++++|+-.. . ........+.-+... .... .. ...++ ..+.
T Consensus 169 ~~----~l~~~~lg~s~~l~~G~~V~aiG~P~g-~----~~tvt~GiVs~~~r~----~~~~---~~-~~~~i---qtda 228 (473)
T PRK10942 169 PK----NLTAIKMADSDALRVGDYTVAIGNPYG-L----GETVTSGIVSALGRS----GLNV---EN-YENFI---QTDA 228 (473)
T ss_pred CC----CCceeEecCccccCCCCEEEEEcCCCC-C----CcceeEEEEEEeecc----cCCc---cc-ccceE---Eecc
Confidence 32 234566655445557888888876311 0 011111112211110 0000 00 01111 1223
Q ss_pred CCccCccccceeEeCCcEEEEEEEEeC
Q psy10445 370 DSCTGDSGGPLMVNDGKWTQVGIVSWG 396 (425)
Q Consensus 370 ~~C~GDSGgPL~~~~g~~~LvGI~S~g 396 (425)
..-.|.|||||+..+| .++||.+..
T Consensus 229 ~i~~GnSGGpL~n~~G--eviGI~t~~ 253 (473)
T PRK10942 229 AINRGNSGGALVNLNG--ELIGINTAI 253 (473)
T ss_pred ccCCCCCcCccCCCCC--eEEEEEEEE
Confidence 4457999999997666 799998763
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=96.53 E-value=0.016 Score=63.21 Aligned_cols=66 Identities=18% Similarity=0.182 Sum_probs=38.3
Q ss_pred eeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCCCcccC
Q psy10445 215 GGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDKPVKYS 294 (425)
Q Consensus 215 gGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~v~~~ 294 (425)
..|||+++||+|++|=.... -.|.+|.+.. ..+.+.+--.|+. .|+.+-||++=|.
T Consensus 68 ~aTLigpqYiVSV~HN~~gy-------~~v~FG~~g~--------~~Y~iV~RNn~~~-------~Df~~pRLnK~VT-- 123 (769)
T PF02395_consen 68 VATLIGPQYIVSVKHNGKGY-------NSVSFGNEGQ--------NTYKIVDRNNYPS-------GDFHMPRLNKFVT-- 123 (769)
T ss_dssp S-EEEETTEEEBETTG-TSC-------CEECESCSST--------CEEEEEEEEBETT-------STEBEEEESS-----
T ss_pred eEEEecCCeEEEEEccCCCc-------CceeecccCC--------ceEEEEEccCCCC-------cccceeecCceEE--
Confidence 38999999999999976222 2377777543 1244444445544 5999999998664
Q ss_pred CCeeeeecCCC
Q psy10445 295 DTIRAICLPRG 305 (425)
Q Consensus 295 ~~v~PIcLp~~ 305 (425)
-+.|+-....
T Consensus 124 -EvaP~~~t~~ 133 (769)
T PF02395_consen 124 -EVAPAEMTTA 133 (769)
T ss_dssp -SS----BBSS
T ss_pred -EEeccccccc
Confidence 4667666443
No 18
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=86.93 E-value=30 Score=34.29 Aligned_cols=146 Identities=22% Similarity=0.273 Sum_probs=73.3
Q ss_pred ceeeeeEEee-CCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCC
Q psy10445 211 KQFCGGSLID-TQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDK 289 (425)
Q Consensus 211 ~~~CgGtLIs-~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~ 289 (425)
....+|.+|+ ..+|||..|=+... ..+.|.+. +.. .+..+-+-.. ...|+|+||.+.
T Consensus 71 ~~~gSg~i~~~~g~ivTn~hVi~~a-----~~i~v~l~--------dg~--~~~a~~vg~d-------~~~dlavlki~~ 128 (347)
T COG0265 71 EGLGSGFIISSDGYIVTNNHVIAGA-----EEITVTLA--------DGR--EVPAKLVGKD-------PISDLAVLKIDG 128 (347)
T ss_pred cccccEEEEcCCeEEEecceecCCc-----ceEEEEeC--------CCC--EEEEEEEecC-------CccCEEEEEecc
Confidence 3568888888 78999999988652 34445541 111 1222222222 236999999986
Q ss_pred CcccCCCeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCC
Q psy10445 290 PVKYSDTIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATK 369 (425)
Q Consensus 290 ~v~~~~~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~ 369 (425)
.-. +..+-+........++...+.|-..- . .......-+....+. +...... ....| ..+.
T Consensus 129 ~~~----~~~~~~~~s~~l~vg~~v~aiGnp~g-~----~~tvt~Givs~~~r~-~v~~~~~------~~~~I---qtdA 189 (347)
T COG0265 129 AGG----LPVIALGDSDKLRVGDVVVAIGNPFG-L----GQTVTSGIVSALGRT-GVGSAGG------YVNFI---QTDA 189 (347)
T ss_pred CCC----CceeeccCCCCcccCCEEEEecCCCC-c----ccceeccEEeccccc-cccCccc------ccchh---hccc
Confidence 532 22233333333334555555554211 0 011111122222221 1111000 01111 1224
Q ss_pred CCccCccccceeEeCCcEEEEEEEEeCCCC
Q psy10445 370 DSCTGDSGGPLMVNDGKWTQVGIVSWGIGC 399 (425)
Q Consensus 370 ~~C~GDSGgPL~~~~g~~~LvGI~S~g~~C 399 (425)
..+.|.|||||+..++ .++||.+.....
T Consensus 190 ain~gnsGgpl~n~~g--~~iGint~~~~~ 217 (347)
T COG0265 190 AINPGNSGGPLVNIDG--EVVGINTAIIAP 217 (347)
T ss_pred ccCCCCCCCceEcCCC--cEEEEEEEEecC
Confidence 5688999999997655 789988876543
No 19
>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=78.76 E-value=28 Score=32.72 Aligned_cols=147 Identities=20% Similarity=0.301 Sum_probs=62.2
Q ss_pred EeeCCeEEeccccceeccccceeeEEEE--eCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCCCcccCC
Q psy10445 218 LIDTQHVLTAAHCVAHMSSWDVAKLSVN--LGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDKPVKYSD 295 (425)
Q Consensus 218 LIs~~~VLTAAHCv~~~~~~~~~~~~V~--lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~v~~~~ 295 (425)
+.--.||||-+|-+...++ .+.++ -|++.+..... ..| ||- ...||.||||.+.++ .
T Consensus 37 igyG~~iItn~HLf~~nng----~L~i~s~hG~f~v~nt~~-----lkv-----~~i-----~~~DiviirmPkDfp--P 95 (235)
T PF00863_consen 37 IGYGSYIITNAHLFKRNNG----ELTIKSQHGEFTVPNTTQ-----LKV-----HPI-----EGRDIVIIRMPKDFP--P 95 (235)
T ss_dssp EEETTEEEEEGGGGSSTTC----EEEEEETTEEEEECEGGG-----SEE-----EE------TCSSEEEEE--TTS----
T ss_pred EeECCEEEEChhhhccCCC----eEEEEeCceEEEcCCccc-----cce-----EEe-----CCccEEEEeCCcccC--C
Confidence 5577899999999866543 23332 23333332221 112 222 135999999998764 2
Q ss_pred CeeeeecCCCCCCCCCCEEEEEEccccCCCCCCCccceEEEEEeeChhhHhhhcCCCCCCCCcCCeEEeeCCCCCCccCc
Q psy10445 296 TIRAICLPRGRASYEGKIATVIGWGSLRESGPQPAVLQKVNIPVWTNADCKARYGPVAPGGIVDHFLCAGRATKDSCTGD 375 (425)
Q Consensus 296 ~v~PIcLp~~~~~~~~~~~~v~GWG~t~~~~~~s~~l~~~~v~v~~~~~C~~~~~~~~~~~~~~~~iCag~~~~~~C~GD 375 (425)
+-+-+++ ..+..++.+.++|--..... .+....+... +.+... ...+ .. .-++=.||
T Consensus 96 f~~kl~F---R~P~~~e~v~mVg~~fq~k~--~~s~vSesS~-i~p~~~-~~fW---------kH-------wIsTk~G~ 152 (235)
T PF00863_consen 96 FPQKLKF---RAPKEGERVCMVGSNFQEKS--ISSTVSESSW-IYPEEN-SHFW---------KH-------WISTKDGD 152 (235)
T ss_dssp --S---B-------TT-EEEEEEEECSSCC--CEEEEEEEEE-EEEETT-TTEE---------EE--------C---TT-
T ss_pred cchhhhc---cCCCCCCEEEEEEEEEEcCC--eeEEECCceE-EeecCC-CCee---------EE-------EecCCCCc
Confidence 2222222 22334666777776433211 1111111111 111000 0000 00 01233588
Q ss_pred cccceeEe-CCcEEEEEEEEeCCCCCCCCCCcEEEeCCc
Q psy10445 376 SGGPLMVN-DGKWTQVGIVSWGIGCGKGEYPGVYTRVTY 413 (425)
Q Consensus 376 SGgPL~~~-~g~~~LvGI~S~g~~C~~~~~P~vyt~V~~ 413 (425)
=|.||+.. +| .++||.|.+..-.. -..|+.+..
T Consensus 153 CG~PlVs~~Dg--~IVGiHsl~~~~~~---~N~F~~f~~ 186 (235)
T PF00863_consen 153 CGLPLVSTKDG--KIVGIHSLTSNTSS---RNYFTPFPD 186 (235)
T ss_dssp TT-EEEETTT----EEEEEEEEETTTS---SEEEEE--T
T ss_pred cCCcEEEcCCC--cEEEEEcCccCCCC---eEEEEcCCH
Confidence 89999975 55 79999998753222 347777654
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=71.38 E-value=20 Score=31.92 Aligned_cols=71 Identities=18% Similarity=0.145 Sum_probs=38.2
Q ss_pred CceeeeeEEeeCCeEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCC
Q psy10445 210 GKQFCGGSLIDTQHVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDK 289 (425)
Q Consensus 210 ~~~~CgGtLIs~~~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~ 289 (425)
+.+.|.|..|..+|.|--.|.-. ...+.++.. .+.+.+.+.. .+......||+|++|++
T Consensus 23 g~~t~l~~gi~~~~~lvp~H~~~--------~~~i~i~g~-----------~~~~~d~~~l--v~~~~~~~Dl~~v~l~~ 81 (172)
T PF00548_consen 23 GEFTMLALGIYDRYFLVPTHEEP--------EDTIYIDGV-----------EYKVDDSVVL--VDRDGVDTDLTLVKLPR 81 (172)
T ss_dssp EEEEEEEEEEEBTEEEEEGGGGG--------CSEEEETTE-----------EEEEEEEEEE--EETTSSEEEEEEEEEES
T ss_pred ceEEEecceEeeeEEEEECcCCC--------cEEEEECCE-----------EEEeeeeEEE--ecCCCcceeEEEEEccC
Confidence 44567888999999999999211 112333211 1222221111 11122235999999988
Q ss_pred CcccCCCeeeee
Q psy10445 290 PVKYSDTIRAIC 301 (425)
Q Consensus 290 ~v~~~~~v~PIc 301 (425)
.-.|.+-.+-+.
T Consensus 82 ~~kfrDIrk~~~ 93 (172)
T PF00548_consen 82 NPKFRDIRKFFP 93 (172)
T ss_dssp SS-B--GGGGSB
T ss_pred CcccCchhhhhc
Confidence 777876555554
No 21
>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=63.76 E-value=8.1 Score=32.47 Aligned_cols=34 Identities=29% Similarity=0.454 Sum_probs=26.0
Q ss_pred cCccccceeEeCCcEEEEEEEEeCCCCCCCCCCcEEEeCCch
Q psy10445 373 TGDSGGPLMVNDGKWTQVGIVSWGIGCGKGEYPGVYTRVTYF 414 (425)
Q Consensus 373 ~GDSGgPL~~~~g~~~LvGI~S~g~~C~~~~~P~vyt~V~~y 414 (425)
.||-||+|.|+.| ++||++.|.. .-.-|++|..|
T Consensus 89 PGdCGg~L~C~HG---ViGi~Tagg~-----g~VaF~dir~~ 122 (127)
T PF00947_consen 89 PGDCGGILRCKHG---VIGIVTAGGE-----GHVAFADIRDL 122 (127)
T ss_dssp TT-TCSEEEETTC---EEEEEEEEET-----TEEEEEECCCG
T ss_pred CCCCCceeEeCCC---eEEEEEeCCC-----ceEEEEechhh
Confidence 6999999999874 8999998722 23678998875
No 22
>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=56.86 E-value=7.9 Score=36.79 Aligned_cols=22 Identities=36% Similarity=0.771 Sum_probs=17.1
Q ss_pred cCccccceeEeCCcEEEEEEEEeC
Q psy10445 373 TGDSGGPLMVNDGKWTQVGIVSWG 396 (425)
Q Consensus 373 ~GDSGgPL~~~~g~~~LvGI~S~g 396 (425)
.||||+|++.++| .|+||.+-.
T Consensus 207 ~GDSGSPVVt~dg--~liGVHTGS 228 (297)
T PF05579_consen 207 PGDSGSPVVTEDG--DLIGVHTGS 228 (297)
T ss_dssp GGCTT-EEEETTC---EEEEEEEE
T ss_pred CCCCCCccCcCCC--CEEEEEecC
Confidence 5999999999877 689999754
No 23
>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=53.61 E-value=15 Score=33.81 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=22.2
Q ss_pred CCCccCccccceeEeCCcEEEEEEEEeCC
Q psy10445 369 KDSCTGDSGGPLMVNDGKWTQVGIVSWGI 397 (425)
Q Consensus 369 ~~~C~GDSGgPL~~~~g~~~LvGI~S~g~ 397 (425)
...-+|-||+|++.++ .|+|-++++.
T Consensus 175 GGIvqGMSGSPI~qdG---KLiGAVthvf 200 (218)
T PF05580_consen 175 GGIVQGMSGSPIIQDG---KLIGAVTHVF 200 (218)
T ss_pred CCEEecccCCCEEECC---EEEEEEEEEE
Confidence 3568899999999876 8999999875
No 24
>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=46.93 E-value=15 Score=31.19 Aligned_cols=22 Identities=36% Similarity=0.739 Sum_probs=15.7
Q ss_pred ccCccccceeEeCCcEEEEEEEEe
Q psy10445 372 CTGDSGGPLMVNDGKWTQVGIVSW 395 (425)
Q Consensus 372 C~GDSGgPL~~~~g~~~LvGI~S~ 395 (425)
-.|-||||++|..| .++||.--
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 35889999999876 78888743
No 25
>KOG1924|consensus
Probab=41.20 E-value=70 Score=35.14 Aligned_cols=12 Identities=25% Similarity=0.338 Sum_probs=7.0
Q ss_pred ceEEEEeCCCcc
Q psy10445 281 DVAILTLDKPVK 292 (425)
Q Consensus 281 DIALLkL~~~v~ 292 (425)
-++||+.++.+.
T Consensus 719 k~~ILevne~vL 730 (1102)
T KOG1924|consen 719 KNVILEVNEDVL 730 (1102)
T ss_pred HHHHhhccHHHH
Confidence 356666666553
No 26
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=32.76 E-value=56 Score=33.31 Aligned_cols=45 Identities=24% Similarity=0.426 Sum_probs=31.5
Q ss_pred CCCccCccccceeEeCCcEEEEEEEEeCCC-CCCCCCCcEEEeCCchHHHHHHHhh
Q psy10445 369 KDSCTGDSGGPLMVNDGKWTQVGIVSWGIG-CGKGEYPGVYTRVTYFMPWITKNLK 423 (425)
Q Consensus 369 ~~~C~GDSGgPL~~~~g~~~LvGI~S~g~~-C~~~~~P~vyt~V~~y~~WI~~~i~ 423 (425)
...-+|-||+|++.++ .|+|-++.-.- -...+ +++ |.+|+.+...
T Consensus 355 gGivqGMSGSPi~q~g---kliGAvtHVfvndpt~G-YGi------~ie~Ml~~~~ 400 (402)
T TIGR02860 355 GGIVQGMSGSPIIQNG---KVIGAVTHVFVNDPTSG-YGV------YIEWMLKEAG 400 (402)
T ss_pred CCEEecccCCCEEECC---EEEEEEEEEEecCCCcc-eee------hHHHHHHHhc
Confidence 4668999999999887 89999987542 12222 233 6789887643
No 27
>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=30.15 E-value=29 Score=38.02 Aligned_cols=21 Identities=38% Similarity=0.629 Sum_probs=18.6
Q ss_pred eeeeEEeeCC-eEEecccccee
Q psy10445 213 FCGGSLIDTQ-HVLTAAHCVAH 233 (425)
Q Consensus 213 ~CgGtLIs~~-~VLTAAHCv~~ 233 (425)
.|+|++||++ .|||--||..+
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 3999999987 99999999853
No 28
>PF07981 Plasmod_MYXSPDY: Plasmodium repeat_MYXSPDY; InterPro: IPR012598 This repeat is found in two hypothetical Plasmodium proteins.
Probab=26.84 E-value=36 Score=17.88 Aligned_cols=14 Identities=57% Similarity=0.854 Sum_probs=10.5
Q ss_pred CCCC-eeeecCCCCC
Q psy10445 3 GTPD-QVRLSGLPDT 16 (425)
Q Consensus 3 ~~~~-~~~~~~~~~~ 16 (425)
-.|| -+||..||+|
T Consensus 3 ~SPdytL~~v~Lpdt 17 (17)
T PF07981_consen 3 FSPDYTLRLVQLPDT 17 (17)
T ss_pred cCCCceEEEEecCCC
Confidence 3455 4799999986
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=23.16 E-value=53 Score=36.02 Aligned_cols=25 Identities=36% Similarity=0.690 Sum_probs=19.6
Q ss_pred CCCCCccCccccceeEeCCcEEEEEEE
Q psy10445 367 ATKDSCTGDSGGPLMVNDGKWTQVGIV 393 (425)
Q Consensus 367 ~~~~~C~GDSGgPL~~~~g~~~LvGI~ 393 (425)
...|+..|.||+|++..+| .|||++
T Consensus 626 stnDitGGNSGSPvlN~~G--eLVGl~ 650 (698)
T PF10459_consen 626 STNDITGGNSGSPVLNAKG--ELVGLA 650 (698)
T ss_pred eccCcCCCCCCCccCCCCc--eEEEEe
Confidence 3467888999999987655 789987
No 30
>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=22.80 E-value=48 Score=28.24 Aligned_cols=22 Identities=50% Similarity=0.747 Sum_probs=16.6
Q ss_pred cCccccceeEeCCcEEEEEEEEeC
Q psy10445 373 TGDSGGPLMVNDGKWTQVGIVSWG 396 (425)
Q Consensus 373 ~GDSGgPL~~~~g~~~LvGI~S~g 396 (425)
.||||-|++-+.| .++||+--|
T Consensus 105 ~GDSGRpi~DNsG--rVVaIVLGG 126 (158)
T PF00944_consen 105 PGDSGRPIFDNSG--RVVAIVLGG 126 (158)
T ss_dssp TTSTTEEEESTTS--BEEEEEEEE
T ss_pred CCCCCCccCcCCC--CEEEEEecC
Confidence 6999999987655 567777554
No 31
>KOG1421|consensus
Probab=22.22 E-value=4.3e+02 Score=29.02 Aligned_cols=72 Identities=19% Similarity=0.250 Sum_probs=38.0
Q ss_pred eeeeEEeeCC--eEEeccccceeccccceeeEEEEeCcccccccCccceEEEEEEEEEecCCCCCCCCCCceEEEEeCCC
Q psy10445 213 FCGGSLIDTQ--HVLTAAHCVAHMSSWDVAKLSVNLGDHNIKQKNEVKHVERKVKRLVRHKAFDMRTLYNDVAILTLDKP 290 (425)
Q Consensus 213 ~CgGtLIs~~--~VLTAAHCv~~~~~~~~~~~~V~lG~~~~~~~~~~~~~~~~V~~ii~Hp~y~~~~~~nDIALLkL~~~ 290 (425)
--.|.+++++ ++||+-|-+.... -.-.+.+-.+ +.+-+.|.|.. --||++++|.+..
T Consensus 85 ~atgfvvd~~~gyiLtnrhvv~pgP----~va~avf~n~---------------ee~ei~pvyrD--pVhdfGf~r~dps 143 (955)
T KOG1421|consen 85 EATGFVVDKKLGYILTNRHVVAPGP----FVASAVFDNH---------------EEIEIYPVYRD--PVHDFGFFRYDPS 143 (955)
T ss_pred ceeEEEEecccceEEEeccccCCCC----ceeEEEeccc---------------ccCCcccccCC--chhhcceeecChh
Confidence 3567777765 8999999875322 1111211110 11122344432 2368888887654
Q ss_pred cccCCCeeeeecCCC
Q psy10445 291 VKYSDTIRAICLPRG 305 (425)
Q Consensus 291 v~~~~~v~PIcLp~~ 305 (425)
-.--..|.-+||..+
T Consensus 144 ~ir~s~vt~i~lap~ 158 (955)
T KOG1421|consen 144 TIRFSIVTEICLAPE 158 (955)
T ss_pred hcceeeeeccccCcc
Confidence 322236777888654
No 32
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=21.03 E-value=44 Score=19.31 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=11.2
Q ss_pred CCchHHHHHHHhhh
Q psy10445 411 VTYFMPWITKNLKK 424 (425)
Q Consensus 411 V~~y~~WI~~~i~~ 424 (425)
+..|..||.+++++
T Consensus 9 IgdfvKlI~~TV~K 22 (25)
T PF05372_consen 9 IGDFVKLIIETVKK 22 (25)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 45688999998875
Done!