Query psy8978
Match_columns 252
No_of_seqs 143 out of 1318
Neff 10.3
Searched_HMMs 46136
Date Sat Aug 17 00:32:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8978.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8978hhsearch_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 6.4E-47 1.4E-51 298.2 24.0 227 11-248 1-232 (232)
2 smart00020 Tryp_SPc Trypsin-li 100.0 5E-44 1.1E-48 281.5 23.2 223 10-245 1-229 (229)
3 KOG3627|consensus 100.0 3.9E-42 8.4E-47 275.3 24.5 234 8-250 10-255 (256)
4 PF00089 Trypsin: Trypsin; In 100.0 3.4E-41 7.3E-46 263.6 24.1 217 11-245 1-220 (220)
5 COG5640 Secreted trypsin-like 100.0 4.3E-32 9.3E-37 213.5 15.0 232 7-251 29-280 (413)
6 PF03761 DUF316: Domain of unk 99.9 1.6E-20 3.4E-25 152.2 18.5 227 1-251 31-281 (282)
7 PF09342 DUF1986: Domain of un 99.7 7.6E-15 1.6E-19 111.0 14.7 117 18-149 12-130 (267)
8 COG3591 V8-like Glu-specific e 99.4 2.7E-12 5.9E-17 99.4 11.9 202 17-250 44-251 (251)
9 TIGR02037 degP_htrA_DO peripla 98.7 2.8E-07 6E-12 79.2 13.2 143 35-226 57-200 (428)
10 TIGR02038 protease_degS peripl 98.6 1.2E-06 2.7E-11 73.1 13.3 156 21-226 54-219 (351)
11 PRK10898 serine endoprotease; 98.6 4.3E-06 9.3E-11 69.9 15.7 155 22-226 55-219 (353)
12 PF13365 Trypsin_2: Trypsin-li 98.6 5.7E-07 1.2E-11 63.0 8.9 21 38-58 1-22 (120)
13 PRK10139 serine endoprotease; 98.4 3.8E-06 8.2E-11 72.4 11.6 143 35-226 89-233 (455)
14 PRK10942 serine endoprotease; 98.4 7.6E-06 1.7E-10 70.9 13.0 142 35-225 110-253 (473)
15 PF02395 Peptidase_S6: Immunog 97.5 0.00031 6.7E-09 63.9 7.8 154 38-229 67-245 (769)
16 PF00863 Peptidase_C4: Peptida 97.2 0.051 1.1E-06 42.4 15.0 156 36-240 31-186 (235)
17 PF00548 Peptidase_C3: 3C cyst 93.4 0.43 9.2E-06 35.7 6.8 29 197-226 143-171 (172)
18 PF05416 Peptidase_C37: Southa 93.3 0.51 1.1E-05 39.8 7.5 30 196-226 498-527 (535)
19 COG0265 DegQ Trypsin-like seri 91.1 5.9 0.00013 33.2 11.8 146 35-228 71-217 (347)
20 PF00947 Pico_P2A: Picornaviru 90.4 0.35 7.6E-06 33.7 3.1 35 199-241 88-122 (127)
21 PF10459 Peptidase_S46: Peptid 77.9 1.5 3.2E-05 40.3 2.0 22 37-58 48-70 (698)
22 TIGR02860 spore_IV_B stage IV 73.1 6.1 0.00013 33.8 4.3 46 196-252 355-402 (402)
23 PF02907 Peptidase_S29: Hepati 73.0 3.2 6.9E-05 29.4 2.2 23 199-225 106-128 (148)
24 PF05579 Peptidase_S32: Equine 69.4 4 8.7E-05 32.5 2.3 23 199-225 206-228 (297)
25 PF05580 Peptidase_S55: SpoIVB 66.8 7.4 0.00016 30.0 3.2 28 195-227 174-201 (218)
26 KOG1421|consensus 60.8 1.4E+02 0.0031 27.7 11.3 85 36-147 84-170 (955)
27 PF00949 Peptidase_S7: Peptida 47.3 16 0.00034 26.0 2.0 26 197-226 93-118 (132)
28 PF10459 Peptidase_S46: Peptid 44.9 26 0.00057 32.5 3.5 35 184-225 619-653 (698)
29 PF08192 Peptidase_S64: Peptid 41.2 2.9E+02 0.0063 25.6 9.1 56 195-251 633-691 (695)
30 COG2967 ApaG Uncharacterized p 38.3 39 0.00084 23.4 2.7 37 17-55 23-59 (126)
31 PF00944 Peptidase_S3: Alphavi 32.5 26 0.00057 24.9 1.2 24 199-226 104-127 (158)
32 PRK05461 apaG CO2+/MG2+ efflux 31.1 70 0.0015 22.6 3.2 34 18-53 25-58 (127)
33 PF04379 DUF525: Protein of un 29.1 51 0.0011 21.7 2.1 36 17-54 7-42 (90)
34 PF12381 Peptidase_C3G: Tungro 21.8 51 0.0011 25.6 1.2 33 196-228 175-207 (231)
35 PF02122 Peptidase_S39: Peptid 21.5 73 0.0016 24.6 2.0 23 197-224 143-165 (203)
36 PF10411 DsbC_N: Disulfide bon 20.4 63 0.0014 19.0 1.2 27 196-222 23-50 (57)
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=6.4e-47 Score=298.25 Aligned_cols=227 Identities=44% Similarity=0.866 Sum_probs=198.9
Q ss_pred EecCeecCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceee
Q psy8978 11 IDKGQASEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTD 90 (252)
Q Consensus 11 i~~g~~~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~ 90 (252)
|+||+++..++|||+|.|+... ..++|+||||+++||||||||+... ....+.|.+|....... ......
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~-~~~~C~GtlIs~~~VLTaAhC~~~~--------~~~~~~v~~g~~~~~~~-~~~~~~ 70 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTG-GRHFCGGSLISPRWVLTAAHCVYSS--------APSNYTVRLGSHDLSSN-EGGGQV 70 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccC-CcEEEEEEEeeCCEEEECHHhcCCC--------CCccEEEEeCcccccCC-CCceEE
Confidence 5799999999999999998764 6789999999999999999999764 35678899998776543 235677
Q ss_pred eeceeEEECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCC-CCCCCceEEEEecCcCCCCCCCCccceEeeeeEe
Q psy8978 91 IPAAAMKVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAG-DFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVW 169 (252)
Q Consensus 91 ~~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~-~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~ 169 (252)
+.+.++++||.|+.....+|||||||++|+.++..++|+||+... ....+..+.++|||...........++...+.++
T Consensus 71 ~~v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~ 150 (232)
T cd00190 71 IKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIV 150 (232)
T ss_pred EEEEEEEECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeE
Confidence 899999999999988888999999999999999999999999985 4677889999999987755455778999999999
Q ss_pred cchhhhhhhc--CCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCC--CCeeeEeCcccHHHH
Q psy8978 170 RLTECRKQFS--QNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWI 245 (252)
Q Consensus 170 ~~~~C~~~~~--~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~--~~~~~t~v~~~~~WI 245 (252)
+...|...+. ..+.+.++|+.........|.||+||||++.. +++++|+||+|++..|.. .|.+|++|..|.+||
T Consensus 151 ~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~-~~~~~lvGI~s~g~~c~~~~~~~~~t~v~~~~~WI 229 (232)
T cd00190 151 SNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCND-NGRGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWI 229 (232)
T ss_pred CHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEe-CCEEEEEEEEehhhccCCCCCCCEEEEcHHhhHHh
Confidence 9999999887 46778999998765467899999999999998 799999999999999985 899999999999999
Q ss_pred HHh
Q psy8978 246 YNT 248 (252)
Q Consensus 246 ~~~ 248 (252)
+++
T Consensus 230 ~~~ 232 (232)
T cd00190 230 QKT 232 (232)
T ss_pred hcC
Confidence 864
No 2
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=100.00 E-value=5e-44 Score=281.51 Aligned_cols=223 Identities=42% Similarity=0.869 Sum_probs=192.6
Q ss_pred EEecCeecCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCccee
Q psy8978 10 KIDKGQASEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVT 89 (252)
Q Consensus 10 ~i~~g~~~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~ 89 (252)
||+||+++..++|||+|.++... ..+.|+||||++++|||||||+... ....+.|.+|....... ....
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~-~~~~C~GtlIs~~~VLTaahC~~~~--------~~~~~~v~~g~~~~~~~--~~~~ 69 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRG-GRHFCGGSLISPRWVLTAAHCVYGS--------DPSNIRVRLGSHDLSSG--EEGQ 69 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcC-CCcEEEEEEecCCEEEECHHHcCCC--------CCcceEEEeCcccCCCC--CCce
Confidence 58999999999999999998763 4789999999999999999999875 24578899998765442 2227
Q ss_pred eeeceeEEECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCC-CCCCCceEEEEecCcCCC-CCCCCccceEeeee
Q psy8978 90 DIPAAAMKVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAG-DFYEDQIGIVTGWGTLSY-GGPRSDVLMEVPIP 167 (252)
Q Consensus 90 ~~~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~-~~~~~~~~~~~G~g~~~~-~~~~~~~~~~~~~~ 167 (252)
.+.+.++++||+|+.....+|+|||+|++|+.++..++|+||+... ....+..+.++|||.... .......++...+.
T Consensus 70 ~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~ 149 (229)
T smart00020 70 VIKVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVP 149 (229)
T ss_pred EEeeEEEEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEE
Confidence 7899999999999988889999999999999999999999999874 466778999999998763 23446788899999
Q ss_pred EecchhhhhhhcC--CCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCC--CCeeeEeCcccHH
Q psy8978 168 VWRLTECRKQFSQ--NIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLR 243 (252)
Q Consensus 168 ~~~~~~C~~~~~~--~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~--~~~~~t~v~~~~~ 243 (252)
+++.+.|...+.. .+.+.++|+.........|.||+|+||++.. + +|+|+||++++..|.. .|.+|++|.+|.+
T Consensus 150 ~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~-~-~~~l~Gi~s~g~~C~~~~~~~~~~~i~~~~~ 227 (229)
T smart00020 150 IVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCND-G-RWVLVGIVSWGSGCARPGKPGVYTRVSSYLD 227 (229)
T ss_pred EeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEEC-C-CEEEEEEEEECCCCCCCCCCCEEEEeccccc
Confidence 9999999988775 5778899998765467899999999999998 5 9999999999999983 8999999999999
Q ss_pred HH
Q psy8978 244 WI 245 (252)
Q Consensus 244 WI 245 (252)
||
T Consensus 228 WI 229 (229)
T smart00020 228 WI 229 (229)
T ss_pred cC
Confidence 98
No 3
>KOG3627|consensus
Probab=100.00 E-value=3.9e-42 Score=275.28 Aligned_cols=234 Identities=41% Similarity=0.823 Sum_probs=193.3
Q ss_pred ccEEecCeecCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcc
Q psy8978 8 TAKIDKGQASEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETK 87 (252)
Q Consensus 8 ~~~i~~g~~~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~ 87 (252)
..||+||.++..++|||++.+.......++|+|+||+++||||||||+.... .. .+.|.+|...........
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~-------~~-~~~V~~G~~~~~~~~~~~ 81 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGAS-------AS-LYTVRLGEHDINLSVSEG 81 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCC-------Cc-ceEEEECccccccccccC
Confidence 4799999999999999999999873226799999999999999999998741 11 677888876544331222
Q ss_pred --eeeeeceeEEECCCCCCCCCC-CCeEEEEeCCcccCCCceeeccCCCCCC---CCCCceEEEEecCcCCCC-CCCCcc
Q psy8978 88 --VTDIPAAAMKVYPRFSEQNYE-NDIALVQLSKKAQYNSFVRPVCLPQAGD---FYEDQIGIVTGWGTLSYG-GPRSDV 160 (252)
Q Consensus 88 --~~~~~v~~~~~hp~y~~~~~~-~Diall~L~~~~~~~~~~~pi~l~~~~~---~~~~~~~~~~G~g~~~~~-~~~~~~ 160 (252)
.....+.++++||+|+..... +|||||+|++++.|++.++|||||.... ......|.+.|||..... ......
T Consensus 82 ~~~~~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~ 161 (256)
T KOG3627|consen 82 EEQLVGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDT 161 (256)
T ss_pred chhhhceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCce
Confidence 244557788899999988877 9999999999999999999999985552 455589999999988754 244778
Q ss_pred ceEeeeeEecchhhhhhhcC--CCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCC-CCC--CCeee
Q psy8978 161 LMEVPIPVWRLTECRKQFSQ--NIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIG-CGK--TPGVY 235 (252)
Q Consensus 161 ~~~~~~~~~~~~~C~~~~~~--~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~-c~~--~~~~~ 235 (252)
++...+.+++...|...+.. .+.+.++|++......+.|.|||||||++.. +++++++||+|||.. |.. .|.+|
T Consensus 162 L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~-~~~~~~~GivS~G~~~C~~~~~P~vy 240 (256)
T KOG3627|consen 162 LQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCED-NGRWVLVGIVSWGSGGCGQPNYPGVY 240 (256)
T ss_pred eEEEEEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEee-CCcEEEEEEEEecCCCCCCCCCCeEE
Confidence 88889999999999998875 4666789998755567789999999999998 558999999999998 987 69999
Q ss_pred EeCcccHHHHHHhhc
Q psy8978 236 VQVNKYLRWIYNTAK 250 (252)
Q Consensus 236 t~v~~~~~WI~~~~~ 250 (252)
|+|+.|.+||++.+.
T Consensus 241 t~V~~y~~WI~~~~~ 255 (256)
T KOG3627|consen 241 TRVSSYLDWIKENIG 255 (256)
T ss_pred eEhHHhHHHHHHHhc
Confidence 999999999999875
No 4
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=100.00 E-value=3.4e-41 Score=263.63 Aligned_cols=217 Identities=40% Similarity=0.831 Sum_probs=187.0
Q ss_pred EecCeecCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceee
Q psy8978 11 IDKGQASEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTD 90 (252)
Q Consensus 11 i~~g~~~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~ 90 (252)
|.||++++.++|||+|.++.... .++|+|+||+++||||||||+.. ...+.+.+|....... ......
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~-~~~C~G~li~~~~vLTaahC~~~----------~~~~~v~~g~~~~~~~-~~~~~~ 68 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNG-RFFCTGTLISPRWVLTAAHCVDG----------ASDIKVRLGTYSIRNS-DGSEQT 68 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTT-EEEEEEEEEETTEEEEEGGGHTS----------GGSEEEEESESBTTST-TTTSEE
T ss_pred CCCCEECCCCCCCeEEEEeeCCC-CeeEeEEeccccccccccccccc----------cccccccccccccccc-cccccc
Confidence 57999999999999999998743 89999999999999999999976 2467788887333322 334678
Q ss_pred eeceeEEECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCC-CCCCCceEEEEecCcCCCCCCCCccceEeeeeEe
Q psy8978 91 IPAAAMKVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAG-DFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVW 169 (252)
Q Consensus 91 ~~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~-~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~ 169 (252)
+.+.+++.||+|+.....+|+|||+|++++.+.+.++|+|++... ....++.+.++||+.....+ ....++...+.++
T Consensus 69 ~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~~~~~~ 147 (220)
T PF00089_consen 69 IKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG-YSSNLQSVTVPVV 147 (220)
T ss_dssp EEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS-BTSBEEEEEEEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc
Confidence 899999999999988889999999999999899999999999955 45778899999999866444 4567888999999
Q ss_pred cchhhhhhhcCCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCC--CCeeeEeCcccHHHH
Q psy8978 170 RLTECRKQFSQNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWI 245 (252)
Q Consensus 170 ~~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~--~~~~~t~v~~~~~WI 245 (252)
+.+.|...+...+.+.++|+... ...+.|.|||||||++.+ + +|+||++++.+|.. .|.+|++|+.|.+||
T Consensus 148 ~~~~c~~~~~~~~~~~~~c~~~~-~~~~~~~g~sG~pl~~~~-~---~lvGI~s~~~~c~~~~~~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 148 SRKTCRSSYNDNLTPNMICAGSS-GSGDACQGDSGGPLICNN-N---YLVGIVSFGENCGSPNYPGVYTRVSSYLDWI 220 (220)
T ss_dssp EHHHHHHHTTTTSTTTEEEEETT-SSSBGGTTTTTSEEEETT-E---EEEEEEEEESSSSBTTSEEEEEEGGGGHHHH
T ss_pred ccccccccccccccccccccccc-ccccccccccccccccce-e---eecceeeecCCCCCCCcCEEEEEHHHhhccC
Confidence 99999998766688899999875 467899999999999987 2 69999999999987 589999999999998
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-32 Score=213.47 Aligned_cols=232 Identities=28% Similarity=0.448 Sum_probs=170.1
Q ss_pred CccEEecCeecCCCCCceEEEEeeccC---CceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceecccc
Q psy8978 7 QTAKIDKGQASEVNDWPWLVALKRQYE---RDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKV 83 (252)
Q Consensus 7 ~~~~i~~g~~~~~~~~P~~v~i~~~~~---~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~ 83 (252)
.+.||+||+.+..++||++|.+..+.+ ...+|+|+++..|||||||||++... ........|.++-.+
T Consensus 29 vs~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s-----~is~d~~~vv~~l~d---- 99 (413)
T COG5640 29 VSSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASS-----PISSDVNRVVVDLND---- 99 (413)
T ss_pred cceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCC-----CccccceEEEecccc----
Confidence 567999999999999999999976543 45789999999999999999998751 012233334444333
Q ss_pred CCcceeeeeceeEEECCCCCCCCCCCCeEEEEeCCcccCC-CceeeccCCC--CCCCCCCceEEEEecCcCCCCC---CC
Q psy8978 84 NETKVTDIPAAAMKVYPRFSEQNYENDIALVQLSKKAQYN-SFVRPVCLPQ--AGDFYEDQIGIVTGWGTLSYGG---PR 157 (252)
Q Consensus 84 ~~~~~~~~~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~-~~~~pi~l~~--~~~~~~~~~~~~~G~g~~~~~~---~~ 157 (252)
....+..++..++.|..|...++.||+|+++|.++.... ..++-.--+. ..+.....+....+|+...... ..
T Consensus 100 -~Sq~~rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~~pr~ki~~~~~sdt~l~sv~~~s~~~n~t~~~~~~~~v~~~~ 178 (413)
T COG5640 100 -SSQAERGHVRTIYVHEFYSPGNLGNDIAVLELARAASLPRVKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSS 178 (413)
T ss_pred -cccccCcceEEEeeecccccccccCcceeeccccccccchhheeeccCcccceecccccccccceeeeeeeecCCCCCC
Confidence 345577899999999999999999999999999865422 1111111111 1123444555666776654331 11
Q ss_pred --CccceEeeeeEecchhhhhhhcC------CCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCC-C
Q psy8978 158 --SDVLMEVPIPVWRLTECRKQFSQ------NIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIG-C 228 (252)
Q Consensus 158 --~~~~~~~~~~~~~~~~C~~~~~~------~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~-c 228 (252)
...+++..+.+.+.+.|...++. ...-.-+|++.. ..+.|+||||||++.+. +....++||+|||.+ |
T Consensus 179 p~gt~l~e~~v~fv~~stc~~~~g~an~~dg~~~lT~~cag~~--~~daCqGDSGGPi~~~g-~~G~vQ~GVvSwG~~~C 255 (413)
T COG5640 179 PKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP--PKDACQGDSGGPIFHKG-EEGRVQRGVVSWGDGGC 255 (413)
T ss_pred CccceeeeeeeeeechHHhhhhccccccCCCCCCccceecCCC--CcccccCCCCCceEEeC-CCccEEEeEEEecCCCC
Confidence 24788889999999999888751 111234999865 47889999999999998 555599999999996 9
Q ss_pred CC--CCeeeEeCcccHHHHHHhhcc
Q psy8978 229 GK--TPGVYVQVNKYLRWIYNTAKV 251 (252)
Q Consensus 229 ~~--~~~~~t~v~~~~~WI~~~~~~ 251 (252)
.. .|.+||+|+.|.+||...++-
T Consensus 256 g~t~~~gVyT~vsny~~WI~a~~~~ 280 (413)
T COG5640 256 GGTLIPGVYTNVSNYQDWIAAMTNG 280 (413)
T ss_pred CCCCcceeEEehhHHHHHHHHHhcC
Confidence 87 889999999999999998763
No 6
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=99.87 E-value=1.6e-20 Score=152.23 Aligned_cols=227 Identities=25% Similarity=0.449 Sum_probs=147.5
Q ss_pred CCCC-CCCccEEecCeecCCCCCceEEEEeeccCC--ceeeEeEEeeCCEEEecccCcccccccceeeec------Cc--
Q psy8978 1 CGRN-GKQTAKIDKGQASEVNDWPWLVALKRQYER--DNFCGGVLINERWVLTAAHCIKQKIDNALVLRR------TS-- 69 (252)
Q Consensus 1 cg~~-~~~~~~i~~g~~~~~~~~P~~v~i~~~~~~--~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~------~~-- 69 (252)
||+. .....++.+|..+..++.||+|.+...... ...++||||||||||||+||+............ ..
T Consensus 31 CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~~~~~W~~~~~~~~~~C~~~~ 110 (282)
T PF03761_consen 31 CGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMNDKSKWLNGEEFDNKKCEGNN 110 (282)
T ss_pred cCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEecccccccCcccccceeeCCC
Confidence 8954 344456799999999999999999876522 356799999999999999999753221100000 00
Q ss_pred -cEEE---Eecceec---cccCCcceeeeeceeEEECCCC----CCCCCCCCeEEEEeCCcccCCCceeeccCCCCC-CC
Q psy8978 70 -DLIV---RLGEYDF---SKVNETKVTDIPAAAMKVYPRF----SEQNYENDIALVQLSKKAQYNSFVRPVCLPQAG-DF 137 (252)
Q Consensus 70 -~~~v---~~g~~~~---~~~~~~~~~~~~v~~~~~hp~y----~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~-~~ 137 (252)
.+.| .+..... ............+.++++.-.. ......++++||+|+++ ++....|+||++.. ..
T Consensus 111 ~~l~vP~~~l~~~~v~~~~~~~~~~~~~~~v~ka~il~~C~~~~~~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~~~ 188 (282)
T PF03761_consen 111 NHLIVPEEVLSKIDVRCCNCFSNGKCFSIKVKKAYILNGCKKIKKNFNRPYSPMILELEED--FSKNVSPPCLADSSTNW 188 (282)
T ss_pred ceEEeCHHHhccEEEEeecccccCCcccceeEEEEEEecCCCcccccccccceEEEEEccc--ccccCCCEEeCCCcccc
Confidence 1111 0000000 1111122334566666664333 23345689999999999 66888999999987 45
Q ss_pred CCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEE
Q psy8978 138 YEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWT 217 (252)
Q Consensus 138 ~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~ 217 (252)
..++.+.++|+ .....+....+.+.....| ...++ .....|.+|+||||+... +|+|.
T Consensus 189 ~~~~~~~~yg~-------~~~~~~~~~~~~i~~~~~~---------~~~~~-----~~~~~~~~d~Gg~lv~~~-~gr~t 246 (282)
T PF03761_consen 189 EKGDEVDVYGF-------NSTGKLKHRKLKITNCTKC---------AYSIC-----TKQYSCKGDRGGPLVKNI-NGRWT 246 (282)
T ss_pred ccCceEEEeec-------CCCCeEEEEEEEEEEeecc---------ceeEe-----cccccCCCCccCeEEEEE-CCCEE
Confidence 56677777777 1123344444444332221 11222 245679999999999999 99999
Q ss_pred EEEEEEEcC-CCCCCCeeeEeCcccHHHHHHhhcc
Q psy8978 218 IIGVVSWGI-GCGKTPGVYVQVNKYLRWIYNTAKV 251 (252)
Q Consensus 218 lvGi~s~~~-~c~~~~~~~t~v~~~~~WI~~~~~~ 251 (252)
|+||.+.+. .|......|.+|..|.+=|.+.+++
T Consensus 247 lIGv~~~~~~~~~~~~~~f~~v~~~~~~IC~ltGI 281 (282)
T PF03761_consen 247 LIGVGASGNYECNKNNSYFFNVSWYQDEICELTGI 281 (282)
T ss_pred EEEEEccCCCcccccccEEEEHHHhhhhhccceec
Confidence 999998776 4544578899999999988877653
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=99.65 E-value=7.6e-15 Score=110.96 Aligned_cols=117 Identities=23% Similarity=0.476 Sum_probs=89.0
Q ss_pred CCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccc-cCCcceeeeeceeE
Q psy8978 18 EVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSK-VNETKVTDIPAAAM 96 (252)
Q Consensus 18 ~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~-~~~~~~~~~~v~~~ 96 (252)
....|||.|.|+.+ +.+.|+|+||.++|||++..|+.+.. .....+.+.+|...... ......|.+.|..+
T Consensus 12 e~y~WPWlA~IYvd--G~~~CsgvLlD~~WlLvsssCl~~I~------L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~ 83 (267)
T PF09342_consen 12 EDYHWPWLADIYVD--GRYWCSGVLLDPHWLLVSSSCLRGIS------LSHHYVSALLGGGKTYLSVDGPHEQISRVDCF 83 (267)
T ss_pred ccccCcceeeEEEc--CeEEEEEEEeccceEEEeccccCCcc------cccceEEEEecCcceecccCCChheEEEeeee
Confidence 45679999999999 89999999999999999999997731 13356778888665332 22334455555544
Q ss_pred EECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCC-CCCCCceEEEEecC
Q psy8978 97 KVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAG-DFYEDQIGIVTGWG 149 (252)
Q Consensus 97 ~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~-~~~~~~~~~~~G~g 149 (252)
..-| ..+++||+|++|+.|+.+++|..||... ....+..|.++|-.
T Consensus 84 ~~V~-------~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d 130 (267)
T PF09342_consen 84 KDVP-------ESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHD 130 (267)
T ss_pred eecc-------ccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEcc
Confidence 4333 4789999999999999999999999844 46666799999854
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=99.43 E-value=2.7e-12 Score=99.44 Aligned_cols=202 Identities=21% Similarity=0.263 Sum_probs=112.8
Q ss_pred cCCCCCceEEEEeecc-CCceeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeecee
Q psy8978 17 SEVNDWPWLVALKRQY-ERDNFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAA 95 (252)
Q Consensus 17 ~~~~~~P~~v~i~~~~-~~~~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~ 95 (252)
....+|||-+...+.. +++.-|++++|+|+.||||+||+++..- ....+.+.. .....+......+....
T Consensus 44 ~dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~~~------G~~~~~~~p---~g~~~~~~~~~~~~~~~ 114 (251)
T COG3591 44 TDTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSPDY------GEDDIAAAP---PGVNSDGGPFYGITKIE 114 (251)
T ss_pred ccCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecCCC------ChhhhhhcC---CcccCCCCCCCceeeEE
Confidence 4678899999887665 3445566699999999999999988621 112222222 11111122222333333
Q ss_pred EEECCC--CCCCCCCCCeEEEEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchh
Q psy8978 96 MKVYPR--FSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTE 173 (252)
Q Consensus 96 ~~~hp~--y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~ 173 (252)
....|. ++......|+..+.|+....+........++.......++...+.||-..... ...+.+ .
T Consensus 115 ~~~~~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~---~~~~~e---------~ 182 (251)
T COG3591 115 IRVYPGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPN---IGTMWE---------S 182 (251)
T ss_pred EEecCCceeccCCceeeccHHHhccCCCccccccccccccccccccCceeEEEeccCCCCc---ceeEee---------e
Confidence 333443 23344556777777774454555555444555444455556888888533311 111111 1
Q ss_pred hhhhhcCCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCC--CCeeeEeC-cccHHHHHHhhc
Q psy8978 174 CRKQFSQNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQV-NKYLRWIYNTAK 250 (252)
Q Consensus 174 C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~--~~~~~t~v-~~~~~WI~~~~~ 250 (252)
|..... + +..+= ....++++|+||+|++... + +++|+.+.++.-.. .....+++ ..+++||++.++
T Consensus 183 t~~v~~--~-~~~~l----~y~~dT~pG~SGSpv~~~~-~---~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~~~ 251 (251)
T COG3591 183 TGKVNS--I-KGNKL----FYDADTLPGSSGSPVLISK-D---EVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQNIK 251 (251)
T ss_pred cceeEE--E-ecceE----EEEecccCCCCCCceEecC-c---eEEEEEecCCCcccccccCcceEecHHHHHHHHHhhC
Confidence 111110 0 00000 1245789999999999876 3 89999998875332 22334454 557899988764
No 9
>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=98.73 E-value=2.8e-07 Score=79.21 Aligned_cols=143 Identities=17% Similarity=0.254 Sum_probs=83.5
Q ss_pred ceeeEeEEeeCC-EEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeEE
Q psy8978 35 DNFCGGVLINER-WVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIAL 113 (252)
Q Consensus 35 ~~~C~GtlI~~~-~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Dial 113 (252)
...++|.+|+++ +|||++|++.+. ..+.|.+.+. ..+...-+..++ ..|+||
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~~----------~~i~V~~~~~----------~~~~a~vv~~d~-------~~DlAl 109 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDGA----------DEITVTLSDG----------REFKAKLVGKDP-------RTDIAV 109 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCCC----------CeEEEEeCCC----------CEEEEEEEEecC-------CCCEEE
Confidence 457999999986 999999999764 3455554421 123333223333 479999
Q ss_pred EEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeCC
Q psy8978 114 VQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGYK 193 (252)
Q Consensus 114 l~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~~ 193 (252)
|+++.+ ..+.++.|.+......++.+.++|+..... ..+....+....... ........++=.
T Consensus 110 lkv~~~----~~~~~~~l~~~~~~~~G~~v~aiG~p~g~~-----~~~t~G~vs~~~~~~----~~~~~~~~~i~t---- 172 (428)
T TIGR02037 110 LKIDAK----KNLPVIKLGDSDKLRVGDWVLAIGNPFGLG-----QTVTSGIVSALGRSG----LGIGDYENFIQT---- 172 (428)
T ss_pred EEecCC----CCceEEEccCCCCCCCCCEEEEEECCCcCC-----CcEEEEEEEecccCc----cCCCCccceEEE----
Confidence 999864 235577777665578899999999854321 111111111111100 000000111111
Q ss_pred CCccCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 194 GGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 194 ~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
+....+|.|||||+.... .++||.+...
T Consensus 173 -da~i~~GnSGGpl~n~~G----~viGI~~~~~ 200 (428)
T TIGR02037 173 -DAAINPGNSGGPLVNLRG----EVIGINTAIY 200 (428)
T ss_pred -CCCCCCCCCCCceECCCC----eEEEEEeEEE
Confidence 334567999999995442 8999987643
No 10
>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=98.61 E-value=1.2e-06 Score=73.08 Aligned_cols=156 Identities=15% Similarity=0.198 Sum_probs=88.4
Q ss_pred CCceEEEEeecc---------CCceeeEeEEeeCC-EEEecccCcccccccceeeecCccEEEEecceeccccCCcceee
Q psy8978 21 DWPWLVALKRQY---------ERDNFCGGVLINER-WVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTD 90 (252)
Q Consensus 21 ~~P~~v~i~~~~---------~~~~~C~GtlI~~~-~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~ 90 (252)
--|-+|.|.... .....++|.+|+++ +|||++|.+... ..+.|.+.+. ..
T Consensus 54 ~~psVV~I~~~~~~~~~~~~~~~~~~GSG~vi~~~G~IlTn~HVV~~~----------~~i~V~~~dg----------~~ 113 (351)
T TIGR02038 54 AAPAVVNIYNRSISQNSLNQLSIQGLGSGVIMSKEGYILTNYHVIKKA----------DQIVVALQDG----------RK 113 (351)
T ss_pred cCCcEEEEEeEeccccccccccccceEEEEEEeCCeEEEecccEeCCC----------CEEEEEECCC----------CE
Confidence 348888886531 11346999999977 999999999753 3455554321 22
Q ss_pred eeceeEEECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEec
Q psy8978 91 IPAAAMKVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWR 170 (252)
Q Consensus 91 ~~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~ 170 (252)
+...-+..+| ..|+||||++.+- ..++.+........++.+.++|+..... .......+....
T Consensus 114 ~~a~vv~~d~-------~~DlAvlkv~~~~-----~~~~~l~~s~~~~~G~~V~aiG~P~~~~-----~s~t~GiIs~~~ 176 (351)
T TIGR02038 114 FEAELVGSDP-------LTDLAVLKIEGDN-----LPTIPVNLDRPPHVGDVVLAIGNPYNLG-----QTITQGIISATG 176 (351)
T ss_pred EEEEEEEecC-------CCCEEEEEecCCC-----CceEeccCcCccCCCCEEEEEeCCCCCC-----CcEEEEEEEecc
Confidence 3333333333 5799999998542 2344454444578899999999854321 111111121111
Q ss_pred chhhhhhhcCCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 171 LTECRKQFSQNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 171 ~~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
... +........+=. +....+|.|||||+..+. .++||.+...
T Consensus 177 r~~----~~~~~~~~~iqt-----da~i~~GnSGGpl~n~~G----~vIGI~~~~~ 219 (351)
T TIGR02038 177 RNG----LSSVGRQNFIQT-----DAAINAGNSGGALINTNG----ELVGINTASF 219 (351)
T ss_pred Ccc----cCCCCcceEEEE-----CCccCCCCCcceEECCCC----eEEEEEeeee
Confidence 100 000000111111 345678999999995442 8999987543
No 11
>PRK10898 serine endoprotease; Provisional
Probab=98.58 E-value=4.3e-06 Score=69.87 Aligned_cols=155 Identities=16% Similarity=0.175 Sum_probs=86.5
Q ss_pred CceEEEEeeccC---------CceeeEeEEeeCC-EEEecccCcccccccceeeecCccEEEEecceeccccCCcceeee
Q psy8978 22 WPWLVALKRQYE---------RDNFCGGVLINER-WVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDI 91 (252)
Q Consensus 22 ~P~~v~i~~~~~---------~~~~C~GtlI~~~-~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~ 91 (252)
-|-+|.|..... .....+|.+|+++ +|||++|-+.+. ..+.|.+.+. ..+
T Consensus 55 ~psvV~v~~~~~~~~~~~~~~~~~~GSGfvi~~~G~IlTn~HVv~~a----------~~i~V~~~dg----------~~~ 114 (353)
T PRK10898 55 APAVVNVYNRSLNSTSHNQLEIRTLGSGVIMDQRGYILTNKHVINDA----------DQIIVALQDG----------RVF 114 (353)
T ss_pred CCcEEEEEeEeccccCcccccccceeeEEEEeCCeEEEecccEeCCC----------CEEEEEeCCC----------CEE
Confidence 477888865321 1257999999976 999999999753 3455655421 123
Q ss_pred eceeEEECCCCCCCCCCCCeEEEEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecc
Q psy8978 92 PAAAMKVYPRFSEQNYENDIALVQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRL 171 (252)
Q Consensus 92 ~v~~~~~hp~y~~~~~~~Diall~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~ 171 (252)
...-+...| ..|+||||++.+ . ..++.+.+......++.+.++|+...... ......+.-..+
T Consensus 115 ~a~vv~~d~-------~~DlAvl~v~~~-~----l~~~~l~~~~~~~~G~~V~aiG~P~g~~~-----~~t~Giis~~~r 177 (353)
T PRK10898 115 EALLVGSDS-------LTDLAVLKINAT-N----LPVIPINPKRVPHIGDVVLAIGNPYNLGQ-----TITQGIISATGR 177 (353)
T ss_pred EEEEEEEcC-------CCCEEEEEEcCC-C----CCeeeccCcCcCCCCCEEEEEeCCCCcCC-----CcceeEEEeccc
Confidence 333233333 489999999854 1 23444544444677899999998533211 111111111000
Q ss_pred hhhhhhhcCCCCCCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 172 TECRKQFSQNIFDSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 172 ~~C~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
. .....-....+= -+....+|.|||||+..+. .++||.+...
T Consensus 178 ~----~~~~~~~~~~iq-----tda~i~~GnSGGPl~n~~G----~vvGI~~~~~ 219 (353)
T PRK10898 178 I----GLSPTGRQNFLQ-----TDASINHGNSGGALVNSLG----ELMGINTLSF 219 (353)
T ss_pred c----ccCCccccceEE-----eccccCCCCCcceEECCCC----eEEEEEEEEe
Confidence 0 000000001111 1345577999999995432 8999988654
No 12
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=98.57 E-value=5.7e-07 Score=63.00 Aligned_cols=21 Identities=38% Similarity=0.594 Sum_probs=19.5
Q ss_pred eEeEEeeCC-EEEecccCcccc
Q psy8978 38 CGGVLINER-WVLTAAHCIKQK 58 (252)
Q Consensus 38 C~GtlI~~~-~VLTaa~C~~~~ 58 (252)
|+|++|+++ +|||++||+...
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~ 22 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDW 22 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCC
T ss_pred CEEEEEcCCceEEEchhheecc
Confidence 799999999 999999999864
No 13
>PRK10139 serine endoprotease; Provisional
Probab=98.41 E-value=3.8e-06 Score=72.45 Aligned_cols=143 Identities=18% Similarity=0.287 Sum_probs=83.5
Q ss_pred ceeeEeEEeeC--CEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeE
Q psy8978 35 DNFCGGVLINE--RWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIA 112 (252)
Q Consensus 35 ~~~C~GtlI~~--~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Dia 112 (252)
....+|.+|++ -+|||.+|.+.+. ..+.|.+.+. ..+..+-+...| ..|+|
T Consensus 89 ~~~GSG~ii~~~~g~IlTn~HVv~~a----------~~i~V~~~dg----------~~~~a~vvg~D~-------~~DlA 141 (455)
T PRK10139 89 EGLGSGVIIDAAKGYVLTNNHVINQA----------QKISIQLNDG----------REFDAKLIGSDD-------QSDIA 141 (455)
T ss_pred cceEEEEEEECCCCEEEeChHHhCCC----------CEEEEEECCC----------CEEEEEEEEEcC-------CCCEE
Confidence 35799999974 5999999999754 4566665421 223333333333 57999
Q ss_pred EEEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeC
Q psy8978 113 LVQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGY 192 (252)
Q Consensus 113 ll~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~ 192 (252)
|||++.+- ...++.|.+......++.+.++|+..... ......-+....+.. ... ... ...+=.
T Consensus 142 vlkv~~~~----~l~~~~lg~s~~~~~G~~V~aiG~P~g~~-----~tvt~GivS~~~r~~--~~~-~~~-~~~iqt--- 205 (455)
T PRK10139 142 LLQIQNPS----KLTQIAIADSDKLRVGDFAVAVGNPFGLG-----QTATSGIISALGRSG--LNL-EGL-ENFIQT--- 205 (455)
T ss_pred EEEecCCC----CCceeEecCccccCCCCEEEEEecCCCCC-----CceEEEEEccccccc--cCC-CCc-ceEEEE---
Confidence 99998542 23466776666677899999999743211 111111111111100 000 000 111111
Q ss_pred CCCccCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 193 KGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 193 ~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
+....+|.|||||+.... .|+||.+...
T Consensus 206 --da~in~GnSGGpl~n~~G----~vIGi~~~~~ 233 (455)
T PRK10139 206 --DASINRGNSGGALLNLNG----ELIGINTAIL 233 (455)
T ss_pred --CCccCCCCCcceEECCCC----eEEEEEEEEE
Confidence 345678999999996542 8999998643
No 14
>PRK10942 serine endoprotease; Provisional
Probab=98.39 E-value=7.6e-06 Score=70.93 Aligned_cols=142 Identities=17% Similarity=0.254 Sum_probs=81.2
Q ss_pred ceeeEeEEeeC--CEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeE
Q psy8978 35 DNFCGGVLINE--RWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIA 112 (252)
Q Consensus 35 ~~~C~GtlI~~--~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Dia 112 (252)
....+|.+|++ -+|||.+|.+.+. ..+.|.+.+. ..+...-+..+| ..|+|
T Consensus 110 ~~~GSG~ii~~~~G~IlTn~HVv~~a----------~~i~V~~~dg----------~~~~a~vv~~D~-------~~DlA 162 (473)
T PRK10942 110 MALGSGVIIDADKGYVVTNNHVVDNA----------TKIKVQLSDG----------RKFDAKVVGKDP-------RSDIA 162 (473)
T ss_pred cceEEEEEEECCCCEEEeChhhcCCC----------CEEEEEECCC----------CEEEEEEEEecC-------CCCEE
Confidence 35799999985 4999999999753 4566665421 223333333333 57999
Q ss_pred EEEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeC
Q psy8978 113 LVQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGY 192 (252)
Q Consensus 113 ll~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~ 192 (252)
|||++.+- ...++.|.+......++.+.++|+..... .......+.-..... ....-...++=.
T Consensus 163 vlki~~~~----~l~~~~lg~s~~l~~G~~V~aiG~P~g~~-----~tvt~GiVs~~~r~~----~~~~~~~~~iqt--- 226 (473)
T PRK10942 163 LIQLQNPK----NLTAIKMADSDALRVGDYTVAIGNPYGLG-----ETVTSGIVSALGRSG----LNVENYENFIQT--- 226 (473)
T ss_pred EEEecCCC----CCceeEecCccccCCCCEEEEEcCCCCCC-----cceeEEEEEEeeccc----CCcccccceEEe---
Confidence 99997432 23466676665678889999998642210 111111111111100 000000111111
Q ss_pred CCCccCccCCCCCceEEEcCCCcEEEEEEEEEc
Q psy8978 193 KGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWG 225 (252)
Q Consensus 193 ~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~ 225 (252)
+....+|.|||||+.... .|+||.+..
T Consensus 227 --da~i~~GnSGGpL~n~~G----eviGI~t~~ 253 (473)
T PRK10942 227 --DAAINRGNSGGALVNLNG----ELIGINTAI 253 (473)
T ss_pred --ccccCCCCCcCccCCCCC----eEEEEEEEE
Confidence 344567999999995542 899998754
No 15
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=97.55 E-value=0.00031 Score=63.94 Aligned_cols=154 Identities=22% Similarity=0.224 Sum_probs=72.2
Q ss_pred eEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeEEEEeC
Q psy8978 38 CGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIALVQLS 117 (252)
Q Consensus 38 C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Diall~L~ 117 (252)
-.+|||+|++|+|++|-.... -.|.+|... ...|.+.+--.|+. .|+.+-||+
T Consensus 67 G~aTLigpqYiVSV~HN~~gy------------~~v~FG~~g--------~~~Y~iV~RNn~~~-------~Df~~pRLn 119 (769)
T PF02395_consen 67 GVATLIGPQYIVSVKHNGKGY------------NSVSFGNEG--------QNTYKIVDRNNYPS-------GDFHMPRLN 119 (769)
T ss_dssp SS-EEEETTEEEBETTG-TSC------------CEECESCSS--------TCEEEEEEEEBETT-------STEBEEEES
T ss_pred ceEEEecCCeEEEEEccCCCc------------CceeecccC--------CceEEEEEccCCCC-------cccceeecC
Confidence 449999999999999998332 245666432 14566666555553 699999999
Q ss_pred CcccCCCceeeccCCCCC-------CCCCCceEEEEecCcCCCCCCCCcc---------ceEeeeeEecchhhhhhhcCC
Q psy8978 118 KKAQYNSFVRPVCLPQAG-------DFYEDQIGIVTGWGTLSYGGPRSDV---------LMEVPIPVWRLTECRKQFSQN 181 (252)
Q Consensus 118 ~~~~~~~~~~pi~l~~~~-------~~~~~~~~~~~G~g~~~~~~~~~~~---------~~~~~~~~~~~~~C~~~~~~~ 181 (252)
+-+ ..+.|+...... ........+-+|=|.+......... .............
T Consensus 120 K~V---TEvaP~~~t~~~~~~~~y~d~~rY~~f~R~GsG~Q~i~~~~g~~~~~~~~ay~yltgGt~~~~~~~-------- 188 (769)
T PF02395_consen 120 KFV---TEVAPAEMTTAGSDSNTYNDKERYPAFVRVGSGTQYIKDRNGNGTTILGGAYNYLTGGTVYNLPGY-------- 188 (769)
T ss_dssp S------SS----BBSSTTSTTGGGHTTTC-EEEEEESSSEEEEECCEEEEEEEEETTSCEEEEEESSEEEE--------
T ss_pred ceE---EEEeccccccccccccccccchhchheeecCCceEEEEcCCCCeeEEEEeccceecCCcccccccc--------
Confidence 755 345565554431 1122222333443333211111000 0000000000000
Q ss_pred CCCCeeEeee--------CCCCccCccCCCCCceEEEcC-CCcEEEEEEEEEcCCCC
Q psy8978 182 IFDSNLCAGG--------YKGGTDSCQGDSGGPLLLQRP-DKQWTIIGVVSWGIGCG 229 (252)
Q Consensus 182 ~~~~~~C~~~--------~~~~~~~c~gdsG~Pl~~~~~-~~~~~lvGi~s~~~~c~ 229 (252)
....++-... ..-....-.|||||||+.-+. ..+|.|+|+++.+.+..
T Consensus 189 ~n~~~~~~~~~~~~~~~~~pL~n~~~~GDSGSPlF~YD~~~kKWvl~Gv~~~~~~~~ 245 (769)
T PF02395_consen 189 GNGSMILSGDLKKFNSYNGPLPNYGSPGDSGSPLFAYDKEKKKWVLVGVLSGGNGYN 245 (769)
T ss_dssp ECTCEEEEESTTTCCCCCSSSBEB--TT-TT-EEEEEETTTTEEEEEEEEEEECCCC
T ss_pred ccceEEEecccccccccCCccccccccCcCCCceEEEEccCCeEEEEEEEccccccC
Confidence 0011111100 011123567999999998764 88999999999876543
No 16
>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=97.17 E-value=0.051 Score=42.43 Aligned_cols=156 Identities=18% Similarity=0.208 Sum_probs=67.5
Q ss_pred eeeEeEEeeCCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeEEEE
Q psy8978 36 NFCGGVLINERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIALVQ 115 (252)
Q Consensus 36 ~~C~GtlI~~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Diall~ 115 (252)
....=-+.--.|+||.+|-+... ...+.+....-.+.. ....+.-+||- ...|+.||+
T Consensus 31 ~~~l~gigyG~~iItn~HLf~~n---------ng~L~i~s~hG~f~v--------~nt~~lkv~~i-----~~~Diviir 88 (235)
T PF00863_consen 31 TRSLYGIGYGSYIITNAHLFKRN---------NGELTIKSQHGEFTV--------PNTTQLKVHPI-----EGRDIVIIR 88 (235)
T ss_dssp EEEEEEEEETTEEEEEGGGGSST---------TCEEEEEETTEEEEE--------CEGGGSEEEE------TCSSEEEEE
T ss_pred eEEEEEEeECCEEEEChhhhccC---------CCeEEEEeCceEEEc--------CCccccceEEe-----CCccEEEEe
Confidence 33444456678999999999764 122444333221111 11112222221 157999999
Q ss_pred eCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeCCCC
Q psy8978 116 LSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGYKGG 195 (252)
Q Consensus 116 L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~~~~ 195 (252)
|.+.++ .. |-.+--. .+..++.+.++|.-.+.... .......-.+.+ . ....+... .
T Consensus 89 mPkDfp--Pf--~~kl~FR-~P~~~e~v~mVg~~fq~k~~---~s~vSesS~i~p--~---------~~~~fWkH----w 145 (235)
T PF00863_consen 89 MPKDFP--PF--PQKLKFR-APKEGERVCMVGSNFQEKSI---SSTVSESSWIYP--E---------ENSHFWKH----W 145 (235)
T ss_dssp --TTS--------S---B-----TT-EEEEEEEECSSCCC---EEEEEEEEEEEE--E---------TTTTEEEE-----
T ss_pred CCcccC--Cc--chhhhcc-CCCCCCEEEEEEEEEEcCCe---eEEECCceEEee--c---------CCCCeeEE----E
Confidence 998764 11 1111111 36677888888864333111 100011111111 0 01111111 1
Q ss_pred ccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCCCCeeeEeCcc
Q psy8978 196 TDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGKTPGVYVQVNK 240 (252)
Q Consensus 196 ~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~~~~~~t~v~~ 240 (252)
-.+=.|+=|.||+... +| .+|||+|.+..-. .-..|+.+..
T Consensus 146 IsTk~G~CG~PlVs~~-Dg--~IVGiHsl~~~~~-~~N~F~~f~~ 186 (235)
T PF00863_consen 146 ISTKDGDCGLPLVSTK-DG--KIVGIHSLTSNTS-SRNYFTPFPD 186 (235)
T ss_dssp C---TT-TT-EEEETT-T----EEEEEEEEETTT-SSEEEEE--T
T ss_pred ecCCCCccCCcEEEcC-CC--cEEEEEcCccCCC-CeEEEEcCCH
Confidence 2234588899999865 44 8999999876433 4456776643
No 17
>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=93.39 E-value=0.43 Score=35.71 Aligned_cols=29 Identities=31% Similarity=0.365 Sum_probs=23.2
Q ss_pred cCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 197 DSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 197 ~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
.+..|+=||||+.+. ++...++||+..|.
T Consensus 143 ~t~~G~CG~~l~~~~-~~~~~i~GiHvaG~ 171 (172)
T PF00548_consen 143 PTKPGMCGSPLVSRI-GGQGKIIGIHVAGN 171 (172)
T ss_dssp EEETTGTTEEEEESC-GGTTEEEEEEEEEE
T ss_pred CCCCCccCCeEEEee-ccCccEEEEEeccC
Confidence 345799999999976 56669999998764
No 18
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=93.25 E-value=0.51 Score=39.84 Aligned_cols=30 Identities=30% Similarity=0.657 Sum_probs=23.2
Q ss_pred ccCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 196 TDSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 196 ~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
-.+-+||-|.|.+... ++.|+++|++....
T Consensus 498 LGT~PGDCGcPYvyKr-gNd~VV~GVH~AAt 527 (535)
T PF05416_consen 498 LGTIPGDCGCPYVYKR-GNDWVVIGVHAAAT 527 (535)
T ss_dssp TS--TTGTT-EEEEEE-TTEEEEEEEEEEE-
T ss_pred cCCCCCCCCCceeeec-CCcEEEEEEEehhc
Confidence 4567899999999999 99999999998654
No 19
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=91.11 E-value=5.9 Score=33.23 Aligned_cols=146 Identities=15% Similarity=0.247 Sum_probs=74.9
Q ss_pred ceeeEeEEee-CCEEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeEE
Q psy8978 35 DNFCGGVLIN-ERWVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIAL 113 (252)
Q Consensus 35 ~~~C~GtlI~-~~~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Dial 113 (252)
...++|.+++ .-+|+|-.|-+... ..+.+.+. ....+...-+-. ....|+|+
T Consensus 71 ~~~gSg~i~~~~g~ivTn~hVi~~a----------~~i~v~l~----------dg~~~~a~~vg~-------d~~~dlav 123 (347)
T COG0265 71 EGLGSGFIISSDGYIVTNNHVIAGA----------EEITVTLA----------DGREVPAKLVGK-------DPISDLAV 123 (347)
T ss_pred cccccEEEEcCCeEEEecceecCCc----------ceEEEEeC----------CCCEEEEEEEec-------CCccCEEE
Confidence 3679999998 77999999998753 34444441 112222222222 22579999
Q ss_pred EEeCCcccCCCceeeccCCCCCCCCCCceEEEEecCcCCCCCCCCccceEeeeeEecchhhhhhhcCCCCCCeeEeeeCC
Q psy8978 114 VQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTGWGTLSYGGPRSDVLMEVPIPVWRLTECRKQFSQNIFDSNLCAGGYK 193 (252)
Q Consensus 114 l~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~C~~~~~ 193 (252)
+|.+..-. ...+.+........++.....|-.... .......-+....+. +-..... ....+ .
T Consensus 124 lki~~~~~----~~~~~~~~s~~l~vg~~v~aiGnp~g~-----~~tvt~Givs~~~r~-~v~~~~~--~~~~I-----q 186 (347)
T COG0265 124 LKIDGAGG----LPVIALGDSDKLRVGDVVVAIGNPFGL-----GQTVTSGIVSALGRT-GVGSAGG--YVNFI-----Q 186 (347)
T ss_pred EEeccCCC----CceeeccCCCCcccCCEEEEecCCCCc-----ccceeccEEeccccc-cccCccc--ccchh-----h
Confidence 99986532 222334444434445556666532221 111111111111111 1000000 00111 1
Q ss_pred CCccCccCCCCCceEEEcCCCcEEEEEEEEEcCCC
Q psy8978 194 GGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGC 228 (252)
Q Consensus 194 ~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c 228 (252)
.....++|.||+|++.... .++||.+.....
T Consensus 187 tdAain~gnsGgpl~n~~g----~~iGint~~~~~ 217 (347)
T COG0265 187 TDAAINPGNSGGPLVNIDG----EVVGINTAIIAP 217 (347)
T ss_pred cccccCCCCCCCceEcCCC----cEEEEEEEEecC
Confidence 1346789999999996542 899998876653
No 20
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=90.44 E-value=0.35 Score=33.70 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=28.1
Q ss_pred ccCCCCCceEEEcCCCcEEEEEEEEEcCCCCCCCeeeEeCccc
Q psy8978 199 CQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGKTPGVYVQVNKY 241 (252)
Q Consensus 199 c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~~~~~~t~v~~~ 241 (252)
-+||-||+|.|+. =++||++.|-. ...-|++|..+
T Consensus 88 ~PGdCGg~L~C~H-----GViGi~Tagg~---g~VaF~dir~~ 122 (127)
T PF00947_consen 88 EPGDCGGILRCKH-----GVIGIVTAGGE---GHVAFADIRDL 122 (127)
T ss_dssp STT-TCSEEEETT-----CEEEEEEEEET---TEEEEEECCCG
T ss_pred CCCCCCceeEeCC-----CeEEEEEeCCC---ceEEEEechhh
Confidence 3699999999999 79999998754 56678999874
No 21
>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=77.88 E-value=1.5 Score=40.34 Aligned_cols=22 Identities=32% Similarity=0.532 Sum_probs=19.8
Q ss_pred eeEeEEeeCC-EEEecccCcccc
Q psy8978 37 FCGGVLINER-WVLTAAHCIKQK 58 (252)
Q Consensus 37 ~C~GtlI~~~-~VLTaa~C~~~~ 58 (252)
-|||++||++ .|||--||..+.
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~~ 70 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYGA 70 (698)
T ss_pred ceeEEEEcCCceEEecchhhhhH
Confidence 3999999987 999999999764
No 22
>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=73.05 E-value=6.1 Score=33.77 Aligned_cols=46 Identities=28% Similarity=0.548 Sum_probs=34.4
Q ss_pred ccCccCCCCCceEEEcCCCcEEEEEEEEEcCCCCC--CCeeeEeCcccHHHHHHhhccC
Q psy8978 196 TDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWIYNTAKVI 252 (252)
Q Consensus 196 ~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c~~--~~~~~t~v~~~~~WI~~~~~~~ 252 (252)
...-+|-||||++.+. +|+|-+++-.-.++ .+.+ |.+|..+..+++
T Consensus 355 gGivqGMSGSPi~q~g-----kliGAvtHVfvndpt~GYGi------~ie~Ml~~~~~~ 402 (402)
T TIGR02860 355 GGIVQGMSGSPIIQNG-----KVIGAVTHVFVNDPTSGYGV------YIEWMLKEAGIL 402 (402)
T ss_pred CCEEecccCCCEEECC-----EEEEEEEEEEecCCCcceee------hHHHHHHHhccC
Confidence 4678899999999999 99999988763332 3334 688888776653
No 23
>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=73.01 E-value=3.2 Score=29.35 Aligned_cols=23 Identities=30% Similarity=0.586 Sum_probs=16.7
Q ss_pred ccCCCCCceEEEcCCCcEEEEEEEEEc
Q psy8978 199 CQGDSGGPLLLQRPDKQWTIIGVVSWG 225 (252)
Q Consensus 199 c~gdsG~Pl~~~~~~~~~~lvGi~s~~ 225 (252)
-.|.||+|++|... +++||....
T Consensus 106 lkGSSGgPiLC~~G----H~vG~f~aa 128 (148)
T PF02907_consen 106 LKGSSGGPILCPSG----HAVGMFRAA 128 (148)
T ss_dssp HTT-TT-EEEETTS----EEEEEEEEE
T ss_pred EecCCCCcccCCCC----CEEEEEEEE
Confidence 46889999999864 899998643
No 24
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=69.38 E-value=4 Score=32.51 Aligned_cols=23 Identities=35% Similarity=0.590 Sum_probs=16.6
Q ss_pred ccCCCCCceEEEcCCCcEEEEEEEEEc
Q psy8978 199 CQGDSGGPLLLQRPDKQWTIIGVVSWG 225 (252)
Q Consensus 199 c~gdsG~Pl~~~~~~~~~~lvGi~s~~ 225 (252)
-.||||+|++..+. .|+||++..
T Consensus 206 ~~GDSGSPVVt~dg----~liGVHTGS 228 (297)
T PF05579_consen 206 GPGDSGSPVVTEDG----DLIGVHTGS 228 (297)
T ss_dssp -GGCTT-EEEETTC-----EEEEEEEE
T ss_pred CCCCCCCccCcCCC----CEEEEEecC
Confidence 35999999998763 799999754
No 25
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=66.82 E-value=7.4 Score=30.05 Aligned_cols=28 Identities=29% Similarity=0.420 Sum_probs=24.0
Q ss_pred CccCccCCCCCceEEEcCCCcEEEEEEEEEcCC
Q psy8978 195 GTDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIG 227 (252)
Q Consensus 195 ~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~ 227 (252)
....-+|-||||++.+. +|+|-+++..-
T Consensus 174 TGGIvqGMSGSPI~qdG-----KLiGAVthvf~ 201 (218)
T PF05580_consen 174 TGGIVQGMSGSPIIQDG-----KLIGAVTHVFV 201 (218)
T ss_pred hCCEEecccCCCEEECC-----EEEEEEEEEEe
Confidence 34578899999999988 99999998863
No 26
>KOG1421|consensus
Probab=60.80 E-value=1.4e+02 Score=27.69 Aligned_cols=85 Identities=16% Similarity=0.269 Sum_probs=45.2
Q ss_pred eeeEeEEeeCC--EEEecccCcccccccceeeecCccEEEEecceeccccCCcceeeeeceeEEECCCCCCCCCCCCeEE
Q psy8978 36 NFCGGVLINER--WVLTAAHCIKQKIDNALVLRRTSDLIVRLGEYDFSKVNETKVTDIPAAAMKVYPRFSEQNYENDIAL 113 (252)
Q Consensus 36 ~~C~GtlI~~~--~VLTaa~C~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~Dial 113 (252)
.-.+|.++.+. ++||+.|-+..- ++...+-.. ......+ .|-| +...+|+++
T Consensus 84 ~~atgfvvd~~~gyiLtnrhvv~pg-----------P~va~avf~--------n~ee~ei-----~pvy--rDpVhdfGf 137 (955)
T KOG1421|consen 84 SEATGFVVDKKLGYILTNRHVVAPG-----------PFVASAVFD--------NHEEIEI-----YPVY--RDPVHDFGF 137 (955)
T ss_pred cceeEEEEecccceEEEeccccCCC-----------CceeEEEec--------ccccCCc-----cccc--CCchhhcce
Confidence 34788888765 799999998643 121111100 0111222 2222 223578999
Q ss_pred EEeCCcccCCCceeeccCCCCCCCCCCceEEEEe
Q psy8978 114 VQLSKKAQYNSFVRPVCLPQAGDFYEDQIGIVTG 147 (252)
Q Consensus 114 l~L~~~~~~~~~~~pi~l~~~~~~~~~~~~~~~G 147 (252)
++-+..-.--..++.+||..+. -..+...+++|
T Consensus 138 ~r~dps~ir~s~vt~i~lap~~-akvgseirvvg 170 (955)
T KOG1421|consen 138 FRYDPSTIRFSIVTEICLAPEL-AKVGSEIRVVG 170 (955)
T ss_pred eecChhhcceeeeeccccCccc-cccCCceEEec
Confidence 9887543323456777876654 33344444443
No 27
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=47.32 E-value=16 Score=26.04 Aligned_cols=26 Identities=35% Similarity=0.618 Sum_probs=17.1
Q ss_pred cCccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 197 DSCQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 197 ~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
+.-.|.||+|++..+. .++||.-.+.
T Consensus 93 d~~~GsSGSpi~n~~g----~ivGlYg~g~ 118 (132)
T PF00949_consen 93 DFPKGSSGSPIFNQNG----EIVGLYGNGV 118 (132)
T ss_dssp -S-TTGTT-EEEETTS----CEEEEEEEEE
T ss_pred ccCCCCCCCceEcCCC----cEEEEEccce
Confidence 3456889999995542 7888887654
No 28
>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=44.89 E-value=26 Score=32.48 Aligned_cols=35 Identities=23% Similarity=0.315 Sum_probs=24.5
Q ss_pred CCeeEeeeCCCCccCccCCCCCceEEEcCCCcEEEEEEEEEc
Q psy8978 184 DSNLCAGGYKGGTDSCQGDSGGPLLLQRPDKQWTIIGVVSWG 225 (252)
Q Consensus 184 ~~~~C~~~~~~~~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~ 225 (252)
+.-+|--. +.++..|.||||++..+ -.|||++=-|
T Consensus 619 ~~pv~Fls---tnDitGGNSGSPvlN~~----GeLVGl~FDg 653 (698)
T PF10459_consen 619 SVPVNFLS---TNDITGGNSGSPVLNAK----GELVGLAFDG 653 (698)
T ss_pred CeeeEEEe---ccCcCCCCCCCccCCCC----ceEEEEeecC
Confidence 33455432 56789999999999543 3999997544
No 29
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=41.24 E-value=2.9e+02 Score=25.64 Aligned_cols=56 Identities=18% Similarity=0.318 Sum_probs=38.1
Q ss_pred CccCccCCCCCceEEEcC--CCcEEEEEEEEEcCCCCC-CCeeeEeCcccHHHHHHhhcc
Q psy8978 195 GTDSCQGDSGGPLLLQRP--DKQWTIIGVVSWGIGCGK-TPGVYVQVNKYLRWIYNTAKV 251 (252)
Q Consensus 195 ~~~~c~gdsG~Pl~~~~~--~~~~~lvGi~s~~~~c~~-~~~~~t~v~~~~~WI~~~~~~ 251 (252)
....-.||||+=++.... .-..-++|++. ..++.. --.+||.+..-++=+++++++
T Consensus 633 ~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlh-sydge~kqfglftPi~~il~rl~~vT~I 691 (695)
T PF08192_consen 633 PAFASGGDSGSWVLTKLEDNNKGLGVVGMLH-SYDGEQKQFGLFTPINEILDRLEEVTGI 691 (695)
T ss_pred ccccCCCCcccEEEecccccccCceeeEEee-ecCCccceeeccCcHHHHHHHHHHhhcc
Confidence 344567999999988642 22346888775 444443 457788888888888877764
No 30
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=38.29 E-value=39 Score=23.44 Aligned_cols=37 Identities=11% Similarity=0.157 Sum_probs=25.2
Q ss_pred cCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccCc
Q psy8978 17 SEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHCI 55 (252)
Q Consensus 17 ~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C~ 55 (252)
.+.++|=|.-.|...+ ..--.--|+++.|.+|.+.=-
T Consensus 23 P~~~RyvfaYtitI~N--~g~~~vqLlsR~W~ITd~~g~ 59 (126)
T COG2967 23 PEEERYVFAYTVTIRN--LGEVPVQLLSRYWLITDGNGR 59 (126)
T ss_pred cccceEEEEEEEEEec--CCCccceeeeeEEEEecCCCc
Confidence 3445677776666653 223567899999999988543
No 31
>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=32.47 E-value=26 Score=24.89 Aligned_cols=24 Identities=29% Similarity=0.509 Sum_probs=16.9
Q ss_pred ccCCCCCceEEEcCCCcEEEEEEEEEcC
Q psy8978 199 CQGDSGGPLLLQRPDKQWTIIGVVSWGI 226 (252)
Q Consensus 199 c~gdsG~Pl~~~~~~~~~~lvGi~s~~~ 226 (252)
-+||||-|++.+. | .+|||+-.|-
T Consensus 104 ~~GDSGRpi~DNs--G--rVVaIVLGG~ 127 (158)
T PF00944_consen 104 KPGDSGRPIFDNS--G--RVVAIVLGGA 127 (158)
T ss_dssp STTSTTEEEESTT--S--BEEEEEEEEE
T ss_pred CCCCCCCccCcCC--C--CEEEEEecCC
Confidence 4699999999443 2 6778776553
No 32
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=31.11 E-value=70 Score=22.58 Aligned_cols=34 Identities=15% Similarity=0.292 Sum_probs=25.1
Q ss_pred CCCCCceEEEEeeccCCceeeEeEEeeCCEEEeccc
Q psy8978 18 EVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAH 53 (252)
Q Consensus 18 ~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~ 53 (252)
..++|-|.-.|...+.+. =+.-|+++.|++|.+.
T Consensus 25 ~~~~y~f~Y~ItI~N~~~--~~vQL~~R~W~I~d~~ 58 (127)
T PRK05461 25 EEGRYVFAYTITIENLGR--VPVQLLSRHWLITDAN 58 (127)
T ss_pred cCCEEEEEEEEEEEECCC--CCEEEEeeeEEEEECC
Confidence 566777777777765333 3678999999999884
No 33
>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO). F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.
Probab=29.12 E-value=51 Score=21.68 Aligned_cols=36 Identities=17% Similarity=0.356 Sum_probs=24.2
Q ss_pred cCCCCCceEEEEeeccCCceeeEeEEeeCCEEEecccC
Q psy8978 17 SEVNDWPWLVALKRQYERDNFCGGVLINERWVLTAAHC 54 (252)
Q Consensus 17 ~~~~~~P~~v~i~~~~~~~~~C~GtlI~~~~VLTaa~C 54 (252)
...++|=|.-.|.+.+.+. .+--|+++.|++|.+.=
T Consensus 7 p~~~~y~f~Y~I~I~N~~~--~~vqL~sR~W~I~d~~g 42 (90)
T PF04379_consen 7 PSQNRYVFAYRIRIENHSD--ESVQLLSRHWIITDADG 42 (90)
T ss_dssp GGGTBEEEEEEEEEEE-SS--S-EEEEEEEEEEEETTS
T ss_pred CCCCeEEEEEEEEEEECCC--CCEEEEccEEEEEeCCC
Confidence 3456677777777664222 37889999999998754
No 34
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase; InterPro: IPR024387 This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Probab=21.83 E-value=51 Score=25.62 Aligned_cols=33 Identities=21% Similarity=0.402 Sum_probs=26.2
Q ss_pred ccCccCCCCCceEEEcCCCcEEEEEEEEEcCCC
Q psy8978 196 TDSCQGDSGGPLLLQRPDKQWTIIGVVSWGIGC 228 (252)
Q Consensus 196 ~~~c~gdsG~Pl~~~~~~~~~~lvGi~s~~~~c 228 (252)
...-.||=|+|++..+..-..+++||+..|..+
T Consensus 175 ~~t~~GdCGs~i~~~~t~~~RKIvGiHVAG~~~ 207 (231)
T PF12381_consen 175 MPTMNGDCGSPIVRNNTQMVRKIVGIHVAGSAN 207 (231)
T ss_pred CCCcCCCccceeeEcchhhhhhhheeeeccccc
Confidence 345679999999998766667999999888743
No 35
>PF02122 Peptidase_S39: Peptidase S39; InterPro: IPR000382 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. ORF2 of Potato leafroll virus (PLrV) encodes a polyprotein which is translated following a -1 frameshift. The polyprotein has a putative linear arrangement of membrane achor-VPg-peptidase-polmerase domains. The serine peptidase domain which is found in this group of sequences belongs to MEROPS peptidase family S39 (clan PA(S)). It is likely that the peptidase domain is involved in the cleavage of the polyprotein []. The nucleotide sequence for the RNA of PLrV has been determined [, ]. The sequence contains six large open reading frames (ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which overlap in different reading frames; it is suggested that the third ORF in the 5' block is translated by frameshift readthrough near the end of the 70K protein, yielding a 118K polypeptide []. Segments of the predicted amino acid sequences of these ORFs resemble those of known viral RNA polymerases, ATP-binding proteins and viral genome-linked proteins. The nucleotide sequence of the genomic RNA of Beet western yellows virus (BWYV) has been determined []. The sequence contains six long ORFs. A cluster of three of these ORFs, including the coat protein cistron, display extensive amino acid sequence similarity to corresponding ORFs of a second luteovirus: Barley yellow dwarf virus [].; GO: 0004252 serine-type endopeptidase activity, 0022415 viral reproductive process, 0016021 integral to membrane; PDB: 1ZYO_A.
Probab=21.46 E-value=73 Score=24.57 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=14.4
Q ss_pred cCccCCCCCceEEEcCCCcEEEEEEEEE
Q psy8978 197 DSCQGDSGGPLLLQRPDKQWTIIGVVSW 224 (252)
Q Consensus 197 ~~c~gdsG~Pl~~~~~~~~~~lvGi~s~ 224 (252)
.+..|.||.|++... .++|++..
T Consensus 143 ~T~~G~SGtp~y~g~-----~vvGvH~G 165 (203)
T PF02122_consen 143 NTSPGWSGTPYYSGK-----NVVGVHTG 165 (203)
T ss_dssp ---TT-TT-EEE-SS------EEEEEEE
T ss_pred CCCCCCCCCCeEECC-----CceEeecC
Confidence 457799999999776 99999986
No 36
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=20.43 E-value=63 Score=19.00 Aligned_cols=27 Identities=22% Similarity=0.298 Sum_probs=19.7
Q ss_pred ccCccCCC-CCceEEEcCCCcEEEEEEE
Q psy8978 196 TDSCQGDS-GGPLLLQRPDKQWTIIGVV 222 (252)
Q Consensus 196 ~~~c~gds-G~Pl~~~~~~~~~~lvGi~ 222 (252)
...|.-.. |++++.-+++|++.+.|=+
T Consensus 23 ~GlyeV~~~~~~i~Y~~~dg~yli~G~l 50 (57)
T PF10411_consen 23 PGLYEVVLKGGGILYVDEDGRYLIQGQL 50 (57)
T ss_dssp TTEEEEEE-TTEEEEEETTSSEEEES-E
T ss_pred CCeEEEEECCCeEEEEcCCCCEEEEeEE
Confidence 34566666 7788877779999998854
Done!