Query 020531
Match_columns 325
No_of_seqs 177 out of 1524
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 03:08:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020531.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020531hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 8.3E-35 1.8E-39 255.7 17.5 134 185-325 2-143 (163)
2 PRK10861 signal peptidase I; P 100.0 7.4E-32 1.6E-36 260.7 18.2 94 185-285 64-171 (324)
3 KOG0171 Mitochondrial inner me 99.9 3.4E-28 7.4E-33 213.6 9.8 129 173-325 10-139 (176)
4 PRK13838 conjugal transfer pil 99.9 4E-23 8.7E-28 184.8 15.0 113 204-325 27-156 (176)
5 PRK13884 conjugal transfer pep 99.9 2.4E-21 5.1E-26 173.6 15.7 113 204-325 29-160 (178)
6 TIGR02771 TraF_Ti conjugative 99.9 9E-21 1.9E-25 168.9 14.8 92 233-325 45-153 (171)
7 PF10502 Peptidase_S26: Signal 99.8 2.3E-21 5.1E-26 166.9 -0.0 92 234-325 21-121 (138)
8 KOG1568 Mitochondrial inner me 99.8 4.9E-19 1.1E-23 155.8 8.1 101 198-325 26-132 (174)
9 cd06530 S26_SPase_I The S26 Ty 99.6 9.2E-15 2E-19 114.2 10.0 72 205-325 2-73 (85)
10 COG0681 LepB Signal peptidase 99.6 1.2E-14 2.5E-19 125.4 11.2 98 182-289 8-107 (166)
11 TIGR02754 sod_Ni_protease nick 99.6 1.1E-14 2.4E-19 115.4 9.8 75 207-325 2-76 (90)
12 COG4959 TraF Type IV secretory 99.4 1.8E-12 3.9E-17 113.6 10.0 114 205-325 31-153 (173)
13 TIGR02228 sigpep_I_arch signal 99.3 2.1E-11 4.6E-16 107.6 11.0 53 208-270 36-88 (158)
14 PF00717 Peptidase_S24: Peptid 99.2 5.6E-11 1.2E-15 89.1 6.8 57 207-275 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 98.7 1E-07 2.3E-12 72.8 9.8 58 206-275 3-61 (84)
16 cd06529 S24_LexA-like Peptidas 98.5 5.9E-07 1.3E-11 68.7 7.7 56 206-275 3-58 (81)
17 KOG3342 Signal peptidase I [In 98.0 7.7E-06 1.7E-10 72.2 5.8 86 174-269 16-104 (180)
18 COG2932 Predicted transcriptio 98.0 1.6E-05 3.6E-10 72.5 7.2 58 205-275 125-182 (214)
19 PRK00215 LexA repressor; Valid 97.7 0.00019 4.1E-09 64.9 9.4 56 205-275 120-176 (205)
20 TIGR00498 lexA SOS regulatory 97.6 0.00035 7.7E-09 62.8 8.9 56 204-274 112-168 (199)
21 PRK10276 DNA polymerase V subu 97.5 0.00076 1.7E-08 57.9 9.1 49 205-267 53-102 (139)
22 PRK12423 LexA repressor; Provi 97.4 0.00078 1.7E-08 61.3 8.9 56 205-275 116-172 (202)
23 COG1974 LexA SOS-response tran 94.9 0.23 4.9E-06 45.9 9.7 55 206-274 115-170 (201)
24 COG0681 LepB Signal peptidase 91.9 0.24 5.1E-06 42.5 4.4 29 257-285 137-165 (166)
25 PF12518 DUF3721: Protein of u 69.6 2 4.4E-05 29.0 0.6 9 125-133 23-31 (34)
26 COG1097 RRP4 RNA-binding prote 57.8 19 0.00041 34.4 4.9 64 210-286 106-194 (239)
27 PF05257 CHAP: CHAP domain; I 56.3 26 0.00057 28.8 5.1 38 233-277 61-99 (124)
28 PF06890 Phage_Mu_Gp45: Bacter 48.4 67 0.0015 28.8 6.7 44 223-275 63-109 (162)
29 TIGR02594 conserved hypothetic 44.8 56 0.0012 27.9 5.5 13 233-245 72-84 (129)
30 TIGR00008 infA translation ini 43.7 22 0.00049 27.5 2.6 20 219-241 47-66 (68)
31 COG0361 InfA Translation initi 43.4 23 0.0005 28.0 2.6 22 217-241 47-68 (75)
32 TIGR02228 sigpep_I_arch signal 40.4 2.3E+02 0.005 25.0 8.8 12 234-245 44-55 (158)
33 COG4079 Uncharacterized protei 36.0 60 0.0013 31.4 4.6 30 257-286 249-282 (293)
34 PF11101 DUF2884: Protein of u 33.8 46 0.00099 31.2 3.5 25 263-287 17-42 (229)
35 cd04456 S1_IF1A_like S1_IF1A_l 33.2 41 0.00089 26.5 2.6 21 219-241 41-61 (78)
36 PF01176 eIF-1a: Translation i 32.0 38 0.00083 25.4 2.2 11 235-245 42-52 (65)
37 PF14085 DUF4265: Domain of un 30.7 1.6E+02 0.0034 24.6 5.9 28 220-247 11-38 (117)
38 cd05793 S1_IF1A S1_IF1A: Trans 29.9 48 0.001 26.0 2.5 20 219-241 41-60 (77)
39 KOG0369 Pyruvate carboxylase [ 29.7 18 0.0004 39.6 0.1 34 8-41 586-622 (1176)
40 smart00652 eIF1a eukaryotic tr 28.5 51 0.0011 26.3 2.4 10 219-228 46-55 (83)
41 COG4393 Predicted membrane pro 28.4 3.3E+02 0.0072 27.6 8.5 9 218-226 286-294 (405)
42 PF14345 GDYXXLXY: GDYXXLXY pr 27.5 2.2E+02 0.0048 24.3 6.4 32 216-247 16-47 (144)
43 PRK04012 translation initiatio 27.4 54 0.0012 27.1 2.5 22 219-243 62-83 (100)
44 PRK09919 anti-adapter protein 25.5 63 0.0014 27.6 2.6 21 267-287 40-60 (114)
45 PF04790 Sarcoglycan_1: Sarcog 25.3 6.2E+02 0.013 24.4 10.2 41 184-224 17-58 (264)
46 PF00498 FHA: FHA domain; Int 23.1 2.6E+02 0.0056 20.0 5.3 33 271-313 32-68 (68)
47 PF00278 Orn_DAP_Arg_deC: Pyri 22.3 1.2E+02 0.0027 24.2 3.7 30 215-246 65-94 (116)
48 PF07423 DUF1510: Protein of u 21.6 86 0.0019 29.5 2.9 21 182-202 16-36 (217)
49 cd03695 CysN_NodQ_II CysN_NodQ 21.1 2E+02 0.0042 22.2 4.5 34 233-275 25-66 (81)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=8.3e-35 Score=255.68 Aligned_cols=134 Identities=40% Similarity=0.694 Sum_probs=119.2
Q ss_pred HHHHHHHHHHHHHHHHheeeeEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEE
Q 020531 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRI 264 (325)
Q Consensus 185 l~~i~iai~v~lll~~fv~~~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRV 264 (325)
++.++++++++++++.|+++++.|+|+||+|||++||+++++|..+...++++||+|+|+.|.+ .++.+||||
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~-------~~~~~iKRV 74 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDD-------NKNIYVKRV 74 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCC-------CCceeEEEE
Confidence 4566778888899999999999999999999999999999999988888999999999998754 467899999
Q ss_pred EEeCCCEEEEeCCEEEECCeecCccccccCCC--------CCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 265 VATAGDCVEVHGGKLLVNGVAQDEDFILEPLA--------YEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 265 IGlPGDtV~Ik~g~lyVNGk~l~e~yi~~p~~--------~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
+|+|||+|+++++.+||||+.++|.|..+... ....+.+||+|||||||||+++|+|||||
T Consensus 75 ig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~ 143 (163)
T TIGR02227 75 IGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYF 143 (163)
T ss_pred EecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCc
Confidence 99999999999999999999999988654311 22346899999999999999999999998
No 2
>PRK10861 signal peptidase I; Provisional
Probab=99.98 E-value=7.4e-32 Score=260.75 Aligned_cols=94 Identities=36% Similarity=0.568 Sum_probs=85.6
Q ss_pred HHHHHHHHHHHHHHHHheeeeEEECCCCCCCCCCCCCEEEEEeccccC------------CCCccccEEEEecCCccccc
Q 020531 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFF------------KRPEVSDIVIFRAPPILQEI 252 (325)
Q Consensus 185 l~~i~iai~v~lll~~fv~~~~~I~g~SM~PTL~~GD~VlV~K~s~~~------------~~pkrGDIVVF~~P~~~~~~ 252 (325)
+..++++++++++++.|+++++.|+++||+|||..||+|+|+|++|++ .+|+|||||+|+.|.+
T Consensus 64 ~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~---- 139 (324)
T PRK10861 64 GASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPED---- 139 (324)
T ss_pred HHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCC----
Confidence 456777888899999999999999999999999999999999999874 5789999999998875
Q ss_pred ccCCCCeEEEEEEEeCCCEEEEe--CCEEEECCee
Q 020531 253 GFSSGDVFIKRIVATAGDCVEVH--GGKLLVNGVA 285 (325)
Q Consensus 253 ~y~~g~~~IKRVIGlPGDtV~Ik--~g~lyVNGk~ 285 (325)
+++.+||||||+|||+|+++ ++.|||||+.
T Consensus 140 ---~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~ 171 (324)
T PRK10861 140 ---PKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGC 171 (324)
T ss_pred ---CCCcEEEEeeecCCcEEEEEeCCCEEEEcCcc
Confidence 56789999999999999998 8999999974
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=3.4e-28 Score=213.65 Aligned_cols=129 Identities=53% Similarity=0.786 Sum_probs=108.1
Q ss_pred hhHHHHHhhhhHHHHHHHHHHHHHHHHHheeeeEEECCCCCCCCCCC-CCEEEEEeccccCCCCccccEEEEecCCcccc
Q 020531 173 WLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDV-GDRILAEKVSYFFKRPEVSDIVIFRAPPILQE 251 (325)
Q Consensus 173 wl~~~~~~l~~~l~~i~iai~v~lll~~fv~~~~~I~g~SM~PTL~~-GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~ 251 (325)
|..++ +++...+++|++++.. |++++..++|.||+||++. ||+++.+|++++++++++||||+++.|.+
T Consensus 10 l~~~~--~~~~~~~~~f~h~t~~-----yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~--- 79 (176)
T KOG0171|consen 10 LVGKS--FCSEIAYAAFTHVTHE-----YLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD--- 79 (176)
T ss_pred ccchh--hHHHHHHHHHHHHHHH-----HhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC---
Confidence 44544 4565666666555544 7789999999999998887 56666799999999999999999999987
Q ss_pred cccCCCCeEEEEEEEeCCCEEEEeCCEEEECCeecCccccccCCCCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 252 IGFSSGDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 252 ~~y~~g~~~IKRVIGlPGDtV~Ik~g~lyVNGk~l~e~yi~~p~~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
..+.++|||+|+|||.|++.++.+.+|+.. |.+. .+++||+||+||+|||+++|+|||+|
T Consensus 80 ----~~~~~cKRIva~eGD~v~v~~~~~~~n~~~--e~~~--------~~i~VP~GhVfv~GDN~~nS~DSr~y 139 (176)
T KOG0171|consen 80 ----PKEHICKRIVAMEGDLVEVHDGPLVVNDLV--EKFS--------TPIRVPEGHVFVEGDNRNNSLDSRNY 139 (176)
T ss_pred ----chhhhhheeeccCCceEEEecCCcccchhh--hhcc--------ceeeccCceEEEecCCCCCccccccc
Confidence 577899999999999999999999888655 3333 57899999999999999999999998
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.90 E-value=4e-23 Score=184.81 Aligned_cols=113 Identities=22% Similarity=0.284 Sum_probs=86.7
Q ss_pred eeEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCccc-----ccccC-C------CCeEEEEEEEeCCCE
Q 020531 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ-----EIGFS-S------GDVFIKRIVATAGDC 271 (325)
Q Consensus 204 ~~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~-----~~~y~-~------g~~~IKRVIGlPGDt 271 (325)
.-+.++.....| +.++++.+..+++++||+|+|+.|++.+ +++|. . ...++|||+|+|||+
T Consensus 27 ~~~~~N~T~S~p-------ig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~ 99 (176)
T PRK13838 27 GGYRINLTPSEP-------LGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQR 99 (176)
T ss_pred CceEEECCCCCE-------EEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcE
Confidence 446666665555 8888887666899999999999887532 13331 1 246999999999999
Q ss_pred EEEeCCEEEECCeecCccccccCCCC-----CCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 272 VEVHGGKLLVNGVAQDEDFILEPLAY-----EMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 272 V~Ik~g~lyVNGk~l~e~yi~~p~~~-----~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
|++++ .+||||+.++|.|+...... .....+||+|+||||||| ++|+|||||
T Consensus 100 V~i~~-~v~iNg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~-~~S~DSRy~ 156 (176)
T PRK13838 100 VEIGG-SVSIDGRPLPSSSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSF-AGSYDSRYF 156 (176)
T ss_pred EEECC-EEEECCEEccccccccccccCCcCCCCCccCcCCCeEEEECCC-CCCCccccc
Confidence 99985 89999999999886543211 123468999999999998 589999998
No 5
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.87 E-value=2.4e-21 Score=173.60 Aligned_cols=113 Identities=25% Similarity=0.373 Sum_probs=81.8
Q ss_pred eeEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCccc-----ccccC-----CC--CeEEEEEEEeCCCE
Q 020531 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ-----EIGFS-----SG--DVFIKRIVATAGDC 271 (325)
Q Consensus 204 ~~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~-----~~~y~-----~g--~~~IKRVIGlPGDt 271 (325)
..+.++.....| .|=+. +. ...+++||+|+|++|+... +++|. ++ ..++|||+|+|||+
T Consensus 29 ~~~~~N~T~S~P---~glY~-~~-----~~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~ 99 (178)
T PRK13884 29 AGARVNTTKSIP---VGLYW-TS-----SAPVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDA 99 (178)
T ss_pred CcEEEECCCCCc---ceEEE-Ee-----CCCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcE
Confidence 556666655555 33333 22 2579999999999886421 34442 11 37999999999999
Q ss_pred EEEeCCEEEECCeecCccccc--c----CCC-CCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 272 VEVHGGKLLVNGVAQDEDFIL--E----PLA-YEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 272 V~Ik~g~lyVNGk~l~e~yi~--~----p~~-~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
|+++++.+||||+.+.+.+.. + +.. +....++||+|+|||||||+++|+|||||
T Consensus 100 V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYf 160 (178)
T PRK13884 100 VSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSATSFDGRYF 160 (178)
T ss_pred EEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCCCCCccccc
Confidence 999999999999998654321 1 121 22234699999999999999999999998
No 6
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.85 E-value=9e-21 Score=168.90 Aligned_cols=92 Identities=32% Similarity=0.439 Sum_probs=72.4
Q ss_pred CCCccccEEEEecCCccc-----cccc-CCC------CeEEEEEEEeCCCEEEEeCCEEEECCeecCccccccCC-----
Q 020531 233 KRPEVSDIVIFRAPPILQ-----EIGF-SSG------DVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILEPL----- 295 (325)
Q Consensus 233 ~~pkrGDIVVF~~P~~~~-----~~~y-~~g------~~~IKRVIGlPGDtV~Ik~g~lyVNGk~l~e~yi~~p~----- 295 (325)
++++|||+|+|+.|++.+ +++| ..+ ..+||||+|+|||+|+++++.++|||+.+++.+.....
T Consensus 45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~ 124 (171)
T TIGR02771 45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP 124 (171)
T ss_pred CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence 589999999999886432 1222 112 37999999999999999999999999998876543211
Q ss_pred CCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 296 AYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 296 ~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
.....+.+||+| ||+||||+++|+|||||
T Consensus 125 l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~ 153 (171)
T TIGR02771 125 LPPFPEGVIPPG-FFVVHDTSPTSFDSRYF 153 (171)
T ss_pred cccCCCcEECCC-EEEECCCCCCCCccccc
Confidence 112247899999 99999999999999998
No 7
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 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 a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.81 E-value=2.3e-21 Score=166.87 Aligned_cols=92 Identities=42% Similarity=0.668 Sum_probs=20.1
Q ss_pred CCccccEEEEecCCccc----ccccC-CCCeEEEEEEEeCCCEEEEeCCEEEECCeecCcccccc----CCCCCCCcEEe
Q 020531 234 RPEVSDIVIFRAPPILQ----EIGFS-SGDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILE----PLAYEMDPVVV 304 (325)
Q Consensus 234 ~pkrGDIVVF~~P~~~~----~~~y~-~g~~~IKRVIGlPGDtV~Ik~g~lyVNGk~l~e~yi~~----p~~~~~~~~~V 304 (325)
.+++||+|+|+.|.... +++|. .+..++|||+|+|||+|++++++++|||+++.+.+..+ +......+.+|
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v 100 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV 100 (138)
T ss_dssp --------------------------------------------------------------------S-T----TEEE-
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence 48999999999987533 34443 45699999999999999999999999998887765443 33333357999
Q ss_pred cCCcEEEEcCCCCCCCCCCCC
Q 020531 305 PEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 305 P~g~yFVLGDNr~nS~DSRyf 325 (325)
|+|+|||||||+.+|+|||||
T Consensus 101 p~g~~~v~gd~~~~S~DSRy~ 121 (138)
T PF10502_consen 101 PEGEYFVLGDNRPNSFDSRYF 121 (138)
T ss_dssp -TTEEEEE-SBTTS--SHHHH
T ss_pred CCCEEEEecCCCCCccccCEe
Confidence 999999999999999999997
No 8
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.77 E-value=4.9e-19 Score=155.78 Aligned_cols=101 Identities=33% Similarity=0.535 Sum_probs=86.1
Q ss_pred HHHheeeeEEECCCCCCCCCCCC------CEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCE
Q 020531 198 FKSFLAEPRSIPSASMNPTLDVG------DRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDC 271 (325)
Q Consensus 198 l~~fv~~~~~I~g~SM~PTL~~G------D~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDt 271 (325)
+..-+.....|.|.||.|||+++ |+|+++|+.-..+...+||||+|+.|.+ +++++||||+|+|||.
T Consensus 26 ~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~alegd~ 98 (174)
T KOG1568|consen 26 FSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAALEGDI 98 (174)
T ss_pred eeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeecccccE
Confidence 33446677899999999999984 8999999876555688999999999987 7899999999999999
Q ss_pred EEEeCCEEEECCeecCccccccCCCCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 272 VEVHGGKLLVNGVAQDEDFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 272 V~Ik~g~lyVNGk~l~e~yi~~p~~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
+.-.+ +..+.+.||+|||||.|||...|+|||.|
T Consensus 99 ~~t~~--------------------~k~~~v~vpkghcWVegDn~~hs~DSntF 132 (174)
T KOG1568|consen 99 MVTED--------------------EKEEPVVVPKGHCWVEGDNQKHSYDSNTF 132 (174)
T ss_pred eccCC--------------------CCCCceecCCCcEEEecCCcccccccCcc
Confidence 98522 22356899999999999999999999987
No 9
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.59 E-value=9.2e-15 Score=114.24 Aligned_cols=72 Identities=50% Similarity=0.920 Sum_probs=63.5
Q ss_pred eEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEeCCEEEECCe
Q 020531 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVHGGKLLVNGV 284 (325)
Q Consensus 205 ~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik~g~lyVNGk 284 (325)
.+.|.|+||+|++..||++++++....+.++++||+|+|+.+.. .++.++|||++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~-------~~~~~vkRv~~------------------ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-------PGKPIIKRVIG------------------ 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCC-------CCCEEEEEEEE------------------
Confidence 57899999999999999999998865445799999999998752 35789999998
Q ss_pred ecCccccccCCCCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 285 AQDEDFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 285 ~l~e~yi~~p~~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
||++|||+.+|+|||+|
T Consensus 57 ------------------------~~~~gDn~~ns~d~~~~ 73 (85)
T cd06530 57 ------------------------YFVLGDNRNNSLDSRYW 73 (85)
T ss_pred ------------------------EEEeeCCCCCCCccCCc
Confidence 99999999999999986
No 10
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.58 E-value=1.2e-14 Score=125.39 Aligned_cols=98 Identities=33% Similarity=0.542 Sum_probs=81.7
Q ss_pred hhHHHHHHHHHHHHHHH--HHheeeeEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCe
Q 020531 182 SDDAKAAFTALTVSFLF--KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDV 259 (325)
Q Consensus 182 ~~~l~~i~iai~v~lll--~~fv~~~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~ 259 (325)
.+++..++.++++++++ +.|+++++.|+|+||+|||+.||+|+++|.++...+++.+|++ ..|.. ....
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~--~~~~~-------~~~~ 78 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDII--VLPAV-------VEGD 78 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceee--ecCCC-------CCcc
Confidence 34566677777777777 8999999999999999999999999999999998899999988 32322 5678
Q ss_pred EEEEEEEeCCCEEEEeCCEEEECCeecCcc
Q 020531 260 FIKRIVATAGDCVEVHGGKLLVNGVAQDED 289 (325)
Q Consensus 260 ~IKRVIGlPGDtV~Ik~g~lyVNGk~l~e~ 289 (325)
++||+++++||.|.++++.+|+ +..+.+.
T Consensus 79 ~~kr~~~~~GD~i~~~~~~~~~-~~~~~~~ 107 (166)
T COG0681 79 LIKRVIGLRGDIVVFKDDRLYV-VPIIPRV 107 (166)
T ss_pred eEEEeccCCCCEEEEECCEEEe-ecccCcc
Confidence 9999999999999999999997 3334333
No 11
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.58 E-value=1.1e-14 Score=115.39 Aligned_cols=75 Identities=35% Similarity=0.565 Sum_probs=62.9
Q ss_pred EECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEeCCEEEECCeec
Q 020531 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVHGGKLLVNGVAQ 286 (325)
Q Consensus 207 ~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik~g~lyVNGk~l 286 (325)
.|.|+||+|||++||+|++++.......+++||+|+|+.|.. +++.++|||++++
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~-------~~~~~vkRv~~~~------------------ 56 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQ-------PYGLIIKRLAAVD------------------ 56 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCC-------CcceEEEEeeEEc------------------
Confidence 588999999999999999998644335567899999998753 4678999999873
Q ss_pred CccccccCCCCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 287 DEDFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 287 ~e~yi~~p~~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
++++|++|||+.+|+|||+|
T Consensus 57 -------------------~~~~~l~~dN~~~~~d~~~~ 76 (90)
T TIGR02754 57 -------------------DNGLFLLGDNPKASTDSRQL 76 (90)
T ss_pred -------------------CCeEEEeCCCCCCCCccccc
Confidence 45689999999999999985
No 12
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.39 E-value=1.8e-12 Score=113.61 Aligned_cols=114 Identities=20% Similarity=0.270 Sum_probs=86.0
Q ss_pred eEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCccc----ccccC-CCCeEEEEEEEeCCCEEEEeCCEE
Q 020531 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ----EIGFS-SGDVFIKRIVATAGDCVEVHGGKL 279 (325)
Q Consensus 205 ~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~----~~~y~-~g~~~IKRVIGlPGDtV~Ik~g~l 279 (325)
..+++.+-..| .| ...++|.+ ..+.+||+|++++|+... +++|. ...+++|||.|+|||+|.+.++.+
T Consensus 31 ~l~~N~S~S~p---lG-lyrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I 103 (173)
T COG4959 31 GLRVNASASAP---LG-LYRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGI 103 (173)
T ss_pred ceEeccCCCcc---ee-EEEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceE
Confidence 35565555555 22 23444432 345999999999997533 57774 467899999999999999999999
Q ss_pred EECCeecCc----cccccCCCCCCCcEEecCCcEEEEcCCCCCCCCCCCC
Q 020531 280 LVNGVAQDE----DFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325 (325)
Q Consensus 280 yVNGk~l~e----~yi~~p~~~~~~~~~VP~g~yFVLGDNr~nS~DSRyf 325 (325)
.|||+.+.- |-..+++......-.+.++|+|+|+|..+.|||||||
T Consensus 104 ~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYf 153 (173)
T COG4959 104 AIDGKPVAASLPVDRVGRALPRWQGCRYLAPSELLLLTDRSSTSFDSRYF 153 (173)
T ss_pred EECCEEeeeeccccccCCcCCcccCCceecCCeEEEEeccCCccccccee
Confidence 999998753 3334455555566679999999999999999999998
No 13
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.29 E-value=2.1e-11 Score=107.64 Aligned_cols=53 Identities=25% Similarity=0.486 Sum_probs=46.0
Q ss_pred ECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCC
Q 020531 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD 270 (325)
Q Consensus 208 I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGD 270 (325)
|.|+||+||+++||++++++.. ..++++||+|+|+.|.. .+.++|||+++.++
T Consensus 36 V~g~SM~Ptl~~GD~vlv~~~~--~~~~~~GDIVvf~~~~~--------~~~iihRVi~v~~~ 88 (158)
T TIGR02228 36 VLSGSMEPTFNTGDLILVTGAD--PNDIQVGDVITYKSPGF--------NTPVTHRVIEINNS 88 (158)
T ss_pred EcCCCCcCCccCCCEEEEEecc--cCCCCCCCEEEEEECCC--------CccEEEEEEEEECC
Confidence 9999999999999999999953 36899999999998652 37899999999754
No 14
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 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) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.18 E-value=5.6e-11 Score=89.15 Aligned_cols=57 Identities=28% Similarity=0.540 Sum_probs=47.1
Q ss_pred EECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEe
Q 020531 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (325)
Q Consensus 207 ~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik 275 (325)
+|.|+||+|+|++||+|++++. .+++.||+|+|..+.. +..++||+++.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~----~~~~~gdivv~~~~~~--------~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS----SEPKDGDIVVVKIDGD--------EELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET----S---TTSEEEEEETTE--------ESEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeCCCEEEEEEc----CCCccCeEEEEEECCc--------eeeEEEEEEEeCCCEEEEe
Confidence 4789999999999999999987 4899999999998542 1389999999999999987
No 15
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=98.73 E-value=1e-07 Score=72.78 Aligned_cols=58 Identities=34% Similarity=0.595 Sum_probs=48.1
Q ss_pred EEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCC-CEEEEe
Q 020531 206 RSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAG-DCVEVH 275 (325)
Q Consensus 206 ~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPG-DtV~Ik 275 (325)
+.|.|+||+|++..||++++++.. ..++.||+|+++.+. +..++||+...++ +.+.+.
T Consensus 3 ~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~~---------~~~~ikrl~~~~~~~~~~l~ 61 (84)
T cd06462 3 LRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLPG---------GELTVKRVIGLPGEGHYFLL 61 (84)
T ss_pred eEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcCC---------CcEEEEEEEEECCCCEEEEE
Confidence 578999999999999999999863 248999999999742 3799999999987 555554
No 16
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.48 E-value=5.9e-07 Score=68.67 Aligned_cols=56 Identities=29% Similarity=0.495 Sum_probs=48.7
Q ss_pred EEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEe
Q 020531 206 RSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (325)
Q Consensus 206 ~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik 275 (325)
+.|.|+||+|+++.||++++++. ..++.||+++++.+ ++.++||+...+++.+.++
T Consensus 3 ~~v~g~sM~p~i~~gd~lii~~~----~~~~~g~i~~~~~~----------~~~~ikr~~~~~~~~~~L~ 58 (81)
T cd06529 3 LRVKGDSMEPTIPDGDLVLVDPS----DTPRDGDIVVARLD----------GELTVKRLQRRGGGRLRLI 58 (81)
T ss_pred EEEECCCcCCccCCCCEEEEcCC----CCCCCCCEEEEEEC----------CEEEEEEEEECCCCcEEEE
Confidence 57899999999999999999986 45999999999973 4689999999997777765
No 17
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.05 E-value=7.7e-06 Score=72.23 Aligned_cols=86 Identities=19% Similarity=0.201 Sum_probs=57.0
Q ss_pred hHHHHHhhhhHHHHHHHHHHHHHHHHHhe---eeeEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCccc
Q 020531 174 LSKLLNVCSDDAKAAFTALTVSFLFKSFL---AEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ 250 (325)
Q Consensus 174 l~~~~~~l~~~l~~i~iai~v~lll~~fv---~~~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~ 250 (325)
+|+.++.+.+++.++.-|..++-.+...- -..+.|-++||+|.++.||.++...... ..++.||||+|+.+.
T Consensus 16 ~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~RGDlLfL~N~~~--~p~~vGdivVf~veg--- 90 (180)
T KOG3342|consen 16 IRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNRNE--DPIRVGDIVVFKVEG--- 90 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCcccccccEEEEecCCC--CcceeccEEEEEECC---
Confidence 34444444555555555555444432211 1246788999999999999999875431 346789999999864
Q ss_pred ccccCCCCeEEEEEEEeCC
Q 020531 251 EIGFSSGDVFIKRIVATAG 269 (325)
Q Consensus 251 ~~~y~~g~~~IKRVIGlPG 269 (325)
+..++++||+-+-+
T Consensus 91 -----R~IPiVHRviK~he 104 (180)
T KOG3342|consen 91 -----REIPIVHRVIKQHE 104 (180)
T ss_pred -----ccCchhHHHHHHhc
Confidence 45688999986533
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=97.99 E-value=1.6e-05 Score=72.51 Aligned_cols=58 Identities=21% Similarity=0.414 Sum_probs=48.3
Q ss_pred eEEECCCCCCCCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEe
Q 020531 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (325)
Q Consensus 205 ~~~I~g~SM~PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik 275 (325)
...|.|+||+|++++||.++|+.- .+..+||.|++... .++.+|||+.-.+|-.+.+.
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l~ 182 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVETD---------GGELYVKKLQREPGGLLRLV 182 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEEE
Confidence 357899999999999999999886 46788997766652 36899999999999988653
No 19
>PRK00215 LexA repressor; Validated
Probab=97.73 E-value=0.00019 Score=64.86 Aligned_cols=56 Identities=18% Similarity=0.249 Sum_probs=44.2
Q ss_pred eEEECCCCCC-CCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEe
Q 020531 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (325)
Q Consensus 205 ~~~I~g~SM~-PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik 275 (325)
.++|.|+||. |++.+||+|++++. .+++.||+|++.. +++..+||+.-. ++.+.+.
T Consensus 120 ~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~----------~~~~~vKrl~~~-~~~~~L~ 176 (205)
T PRK00215 120 LLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI----------DDEATVKRFRRE-GGHIRLE 176 (205)
T ss_pred EEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEEE
Confidence 4679999995 79999999999974 4678999999986 346899999865 4444443
No 20
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=97.58 E-value=0.00035 Score=62.82 Aligned_cols=56 Identities=25% Similarity=0.281 Sum_probs=44.9
Q ss_pred eeEEECCCCCC-CCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEE
Q 020531 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (325)
Q Consensus 204 ~~~~I~g~SM~-PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~I 274 (325)
..+.|.|+||. |.+.+||++++++. .+++.||+|++.. +++..+||+.-. |+.+.+
T Consensus 112 f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L 168 (199)
T TIGR00498 112 FLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL 168 (199)
T ss_pred EEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence 35689999996 58999999999875 4789999999987 367899998754 445544
No 21
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=97.47 E-value=0.00076 Score=57.93 Aligned_cols=49 Identities=20% Similarity=0.284 Sum_probs=40.7
Q ss_pred eEEECCCCCC-CCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEe
Q 020531 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267 (325)
Q Consensus 205 ~~~I~g~SM~-PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGl 267 (325)
..+|.|+||. |++.+||++++++- .+++.||+|++.. +++..+||+.-.
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~----~~~~~Gdivv~~~----------~g~~~vKrl~~~ 102 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSA----ITASHGDIVIAAV----------DGEFTVKKLQLR 102 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECC----CCCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence 3689999998 68999999999975 3678999999875 356889999854
No 22
>PRK12423 LexA repressor; Provisional
Probab=97.42 E-value=0.00078 Score=61.33 Aligned_cols=56 Identities=25% Similarity=0.325 Sum_probs=44.8
Q ss_pred eEEECCCCCC-CCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEEe
Q 020531 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (325)
Q Consensus 205 ~~~I~g~SM~-PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~Ik 275 (325)
...|.|+||. |+|.+||+|+|++. .+++.||+|++.. +++..+||+.-. ++.+.+.
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~-~~~~~L~ 172 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS-GDRIRLL 172 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEEE
Confidence 3589999997 79999999999975 4788999999986 356899999855 4555553
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=94.85 E-value=0.23 Score=45.89 Aligned_cols=55 Identities=20% Similarity=0.288 Sum_probs=42.8
Q ss_pred EEECCCCCC-CCCCCCCEEEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEEEE
Q 020531 206 RSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (325)
Q Consensus 206 ~~I~g~SM~-PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV~I 274 (325)
.+|.|+||. +.+.+||.|+|++. .+.+.||||+-..++ ++.-+||..-. |+.|.+
T Consensus 115 L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~g---------~e~TvKrl~~~-g~~i~L 170 (201)
T COG1974 115 LRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALIDG---------EEATVKRLYRD-GNQILL 170 (201)
T ss_pred EEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcCC---------CcEEEEEEEEe-CCEEEE
Confidence 578999997 57778999999986 689999999998742 44789998743 444444
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=91.91 E-value=0.24 Score=42.45 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=24.0
Q ss_pred CCeEEEEEEEeCCCEEEEeCCEEEECCee
Q 020531 257 GDVFIKRIVATAGDCVEVHGGKLLVNGVA 285 (325)
Q Consensus 257 g~~~IKRVIGlPGDtV~Ik~g~lyVNGk~ 285 (325)
...++||++++|||.+...+..+++||+.
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 36699999999999999986448888764
No 25
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=69.57 E-value=2 Score=29.03 Aligned_cols=9 Identities=56% Similarity=1.782 Sum_probs=7.7
Q ss_pred ccccccCCC
Q 020531 125 GSKWLPCNE 133 (325)
Q Consensus 125 ~~~~~~~~~ 133 (325)
+.||+||.+
T Consensus 23 g~~WMPC~~ 31 (34)
T PF12518_consen 23 GDKWMPCSN 31 (34)
T ss_pred cCccccCcc
Confidence 689999984
No 26
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=57.85 E-value=19 Score=34.40 Aligned_cols=64 Identities=23% Similarity=0.418 Sum_probs=39.7
Q ss_pred CCCCCCCCCCCCEEEEEeccc-------------cCCCCccccEEEEecCCcccccccCCCCeEEEEEEEeCCCEE----
Q 020531 210 SASMNPTLDVGDRILAEKVSY-------------FFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCV---- 272 (325)
Q Consensus 210 g~SM~PTL~~GD~VlV~K~s~-------------~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGlPGDtV---- 272 (325)
+..|.|.|+.||+|...-... ++.+++.|-+|-..+ ..+-|+++.-|-.+
T Consensus 106 ~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p-------------~kVpRvig~~~sm~~~l~ 172 (239)
T COG1097 106 EKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP-------------SKVPRVIGKKGSMLNMLK 172 (239)
T ss_pred ccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch-------------hhcceEecCCCcHHHHhh
Confidence 789999999999887654432 123445555555433 23455665544433
Q ss_pred -------EE-eCCEEEECCeec
Q 020531 273 -------EV-HGGKLLVNGVAQ 286 (325)
Q Consensus 273 -------~I-k~g~lyVNGk~l 286 (325)
.+ .||.+||++...
T Consensus 173 ~~~~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 173 EKTGCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred hhcCeEEEEecCCEEEecCCCc
Confidence 22 488888888765
No 27
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=56.30 E-value=26 Score=28.80 Aligned_cols=38 Identities=18% Similarity=0.295 Sum_probs=24.1
Q ss_pred CCCccccEEEEecCCcccccccCCCCeEEEEEEEe-CCCEEEEeCC
Q 020531 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT-AGDCVEVHGG 277 (325)
Q Consensus 233 ~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVIGl-PGDtV~Ik~g 277 (325)
..|++||||+|..... ...=.|--|.+. .+++|++.+.
T Consensus 61 ~~P~~Gdivv~~~~~~-------~~~GHVaIV~~v~~~~~i~v~e~ 99 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSG-------GGYGHVAIVESVNDGGTITVIEQ 99 (124)
T ss_dssp S---TTEEEEEEECTT-------TTT-EEEEEEEE-TTSEEEEEEC
T ss_pred cccccceEEEeccCCC-------CCCCeEEEEEEECCCCEEEEEEC
Confidence 6899999999962211 233478888888 8889988643
No 28
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=48.39 E-value=67 Score=28.81 Aligned_cols=44 Identities=20% Similarity=0.344 Sum_probs=30.1
Q ss_pred EEEEeccccCCCCccccEEEEecCCcccccccCCCCeEEEE---EEEeCCCEEEEe
Q 020531 223 ILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKR---IVATAGDCVEVH 275 (325)
Q Consensus 223 VlV~K~s~~~~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKR---VIGlPGDtV~Ik 275 (325)
|-++...|+.+..+.||+++|... ...+++|| +|...++++++.
T Consensus 63 ia~~d~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 63 IAVEDRRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred EEeCCccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 445555666777899999999853 23455655 666777777775
No 29
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=44.82 E-value=56 Score=27.93 Aligned_cols=13 Identities=23% Similarity=0.373 Sum_probs=11.2
Q ss_pred CCCccccEEEEec
Q 020531 233 KRPEVSDIVIFRA 245 (325)
Q Consensus 233 ~~pkrGDIVVF~~ 245 (325)
.+|++||||+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 4789999999975
No 30
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=43.71 E-value=22 Score=27.51 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=9.0
Q ss_pred CCCEEEEEeccccCCCCccccEE
Q 020531 219 VGDRILAEKVSYFFKRPEVSDIV 241 (325)
Q Consensus 219 ~GD~VlV~K~s~~~~~pkrGDIV 241 (325)
+||+|.|+-..| ++.+||||
T Consensus 47 ~GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 47 PGDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred CCCEEEEEECcc---cCCcEeEE
Confidence 355555544432 34444443
No 31
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=43.42 E-value=23 Score=28.03 Aligned_cols=22 Identities=32% Similarity=0.385 Sum_probs=12.1
Q ss_pred CCCCCEEEEEeccccCCCCccccEE
Q 020531 217 LDVGDRILAEKVSYFFKRPEVSDIV 241 (325)
Q Consensus 217 L~~GD~VlV~K~s~~~~~pkrGDIV 241 (325)
+.+||+|+|+-..| +.++|||+
T Consensus 47 I~~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 47 ILPGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred eCCCCEEEEEeccc---ccccccEE
Confidence 44566666665543 35566654
No 32
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=40.38 E-value=2.3e+02 Score=25.03 Aligned_cols=12 Identities=8% Similarity=0.310 Sum_probs=9.9
Q ss_pred CCccccEEEEec
Q 020531 234 RPEVSDIVIFRA 245 (325)
Q Consensus 234 ~pkrGDIVVF~~ 245 (325)
.++.||+|+.+.
T Consensus 44 tl~~GD~vlv~~ 55 (158)
T TIGR02228 44 TFNTGDLILVTG 55 (158)
T ss_pred CccCCCEEEEEe
Confidence 568999999875
No 33
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.02 E-value=60 Score=31.43 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=23.8
Q ss_pred CCeEEEEEEE----eCCCEEEEeCCEEEECCeec
Q 020531 257 GDVFIKRIVA----TAGDCVEVHGGKLLVNGVAQ 286 (325)
Q Consensus 257 g~~~IKRVIG----lPGDtV~Ik~g~lyVNGk~l 286 (325)
+..++++|-+ .|||.|.++||.+-|+|+.+
T Consensus 249 g~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~ 282 (293)
T COG4079 249 GEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDL 282 (293)
T ss_pred CceEEEEEccCCccCCCCEEEEecCceEeccccc
Confidence 4455666654 49999999999999999865
No 34
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=33.83 E-value=46 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=21.0
Q ss_pred EEEEeCCCEEEE-eCCEEEECCeecC
Q 020531 263 RIVATAGDCVEV-HGGKLLVNGVAQD 287 (325)
Q Consensus 263 RVIGlPGDtV~I-k~g~lyVNGk~l~ 287 (325)
+|++..|+.+.| .+|.|||||+.+.
T Consensus 17 ~v~~~~~~~~~I~~~g~L~i~G~~v~ 42 (229)
T PF11101_consen 17 EVVQASGEKLRIDPDGNLFINGKKVS 42 (229)
T ss_pred EEEeCCCceEEEcCCCcEEECCEEcc
Confidence 567778889999 5899999999874
No 35
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=33.17 E-value=41 Score=26.48 Aligned_cols=21 Identities=19% Similarity=0.357 Sum_probs=9.0
Q ss_pred CCCEEEEEeccccCCCCccccEE
Q 020531 219 VGDRILAEKVSYFFKRPEVSDIV 241 (325)
Q Consensus 219 ~GD~VlV~K~s~~~~~pkrGDIV 241 (325)
.||+|+++...| .+..+||||
T Consensus 41 ~GD~VlV~~~~~--~~~~kg~Iv 61 (78)
T cd04456 41 RGDFLIVDPIEE--GEDVKADII 61 (78)
T ss_pred CCCEEEEEeccc--CCCceEEEE
Confidence 355555544332 233444444
No 36
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=31.99 E-value=38 Score=25.39 Aligned_cols=11 Identities=18% Similarity=0.296 Sum_probs=5.7
Q ss_pred CccccEEEEec
Q 020531 235 PEVSDIVIFRA 245 (325)
Q Consensus 235 pkrGDIVVF~~ 245 (325)
+++||+|+...
T Consensus 42 I~~GD~V~V~~ 52 (65)
T PF01176_consen 42 IKRGDFVLVEP 52 (65)
T ss_dssp --TTEEEEEEE
T ss_pred cCCCCEEEEEe
Confidence 45666666654
No 37
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=30.66 E-value=1.6e+02 Score=24.63 Aligned_cols=28 Identities=14% Similarity=0.239 Sum_probs=23.3
Q ss_pred CCEEEEEeccccCCCCccccEEEEecCC
Q 020531 220 GDRILAEKVSYFFKRPEVSDIVIFRAPP 247 (325)
Q Consensus 220 GD~VlV~K~s~~~~~pkrGDIVVF~~P~ 247 (325)
+|...+....+....+..||+|.++..+
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~ 38 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD 38 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC
Confidence 5677888888888899999999998753
No 38
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=29.94 E-value=48 Score=26.03 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=9.6
Q ss_pred CCCEEEEEeccccCCCCccccEE
Q 020531 219 VGDRILAEKVSYFFKRPEVSDIV 241 (325)
Q Consensus 219 ~GD~VlV~K~s~~~~~pkrGDIV 241 (325)
.||+|+|+...| +..+|||+
T Consensus 41 ~GD~V~Ve~~~~---d~~kg~Iv 60 (77)
T cd05793 41 EGDIVLVAPWDF---QDDKADII 60 (77)
T ss_pred CCCEEEEEeccc---cCCEEEEE
Confidence 455555554432 34455544
No 39
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=29.72 E-value=18 Score=39.58 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=28.4
Q ss_pred EechHhHHHhhhhhCceeccCC---CCcchhhhcccc
Q 020531 8 NFSGYVAQNLAHSAGIRFGFST---TSTRSFHECLFR 41 (325)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 41 (325)
.-+-||||+++.-+.+-+-.+| -.-||||||-|+
T Consensus 586 ~IaPyvah~f~~lfslE~WGGATFDVamRFLhEcPWe 622 (1176)
T KOG0369|consen 586 KIAPYVAHAFAGLFSLENWGGATFDVAMRFLHECPWE 622 (1176)
T ss_pred hcchHHHHHhhhhhhhhhcCCchhhHHHHHHhcChHH
Confidence 3468999999999999887766 457999999885
No 40
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=28.51 E-value=51 Score=26.25 Aligned_cols=10 Identities=30% Similarity=0.454 Sum_probs=4.7
Q ss_pred CCCEEEEEec
Q 020531 219 VGDRILAEKV 228 (325)
Q Consensus 219 ~GD~VlV~K~ 228 (325)
.||+|+|+..
T Consensus 46 ~GD~VlVe~~ 55 (83)
T smart00652 46 RGDIVLVDPW 55 (83)
T ss_pred CCCEEEEEec
Confidence 3455555443
No 41
>COG4393 Predicted membrane protein [Function unknown]
Probab=28.37 E-value=3.3e+02 Score=27.65 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=4.5
Q ss_pred CCCCEEEEE
Q 020531 218 DVGDRILAE 226 (325)
Q Consensus 218 ~~GD~VlV~ 226 (325)
++|..+.+.
T Consensus 286 d~~n~v~ip 294 (405)
T COG4393 286 DEGNMVVIP 294 (405)
T ss_pred CCCCEEEEE
Confidence 445555543
No 42
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=27.51 E-value=2.2e+02 Score=24.32 Aligned_cols=32 Identities=13% Similarity=0.015 Sum_probs=25.5
Q ss_pred CCCCCCEEEEEeccccCCCCccccEEEEecCC
Q 020531 216 TLDVGDRILAEKVSYFFKRPEVSDIVIFRAPP 247 (325)
Q Consensus 216 TL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P~ 247 (325)
++..|..|.+.-..+..+++=+||.|.++.+.
T Consensus 16 ~l~~G~~v~L~~~PvDPRdllrGdYv~L~Y~i 47 (144)
T PF14345_consen 16 ILAQGKEVTLKTAPVDPRDLLRGDYVALNYDI 47 (144)
T ss_pred HHhCCCEEEEEecccCcccccccceEEEEccc
Confidence 45678888888877778888899999987653
No 43
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=27.36 E-value=54 Score=27.12 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=12.7
Q ss_pred CCCEEEEEeccccCCCCccccEEEE
Q 020531 219 VGDRILAEKVSYFFKRPEVSDIVIF 243 (325)
Q Consensus 219 ~GD~VlV~K~s~~~~~pkrGDIVVF 243 (325)
.||+|+|+...| +..+||||--
T Consensus 62 ~GD~VlVe~~~~---~~~kg~Iv~r 83 (100)
T PRK04012 62 EGDVVIVAPWDF---QDEKADIIWR 83 (100)
T ss_pred CCCEEEEEeccc---CCCEEEEEEE
Confidence 567776666543 2556666543
No 44
>PRK09919 anti-adapter protein IraM; Provisional
Probab=25.50 E-value=63 Score=27.58 Aligned_cols=21 Identities=14% Similarity=0.185 Sum_probs=18.9
Q ss_pred eCCCEEEEeCCEEEECCeecC
Q 020531 267 TAGDCVEVHGGKLLVNGVAQD 287 (325)
Q Consensus 267 lPGDtV~Ik~g~lyVNGk~l~ 287 (325)
.|||.+...+..+.|||++..
T Consensus 40 ~pG~~i~~~~~gvliNdk~~p 60 (114)
T PRK09919 40 PPGSIITPVKSGVLLNDKPYP 60 (114)
T ss_pred CCCCEEEEcCCeEEECCcEeE
Confidence 599999999999999999753
No 45
>PF04790 Sarcoglycan_1: Sarcoglycan complex subunit protein; InterPro: IPR006875 The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma and delta members [, ].; GO: 0007010 cytoskeleton organization, 0016012 sarcoglycan complex, 0016021 integral to membrane
Probab=25.33 E-value=6.2e+02 Score=24.39 Aligned_cols=41 Identities=10% Similarity=0.055 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHheeeeEEECCCCCCC-CCCCCCEEE
Q 020531 184 DAKAAFTALTVSFLFKSFLAEPRSIPSASMNP-TLDVGDRIL 224 (325)
Q Consensus 184 ~l~~i~iai~v~lll~~fv~~~~~I~g~SM~P-TL~~GD~Vl 224 (325)
++..+++.+++-+.+..++.....+...-|.+ .+.+++.++
T Consensus 17 ~vllL~il~iiNL~LTiwIl~Vl~~~~~Gm~~l~~~~~g~~~ 58 (264)
T PF04790_consen 17 FVLLLFILAIINLALTIWILKVLRFSSNGMGSLEFIPDGLRL 58 (264)
T ss_pred HHHHHHHHHHHHHHHHhhhheeeecccCccccEEEecCCeEE
Confidence 35556666677777778888888888888887 333344333
No 46
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=23.15 E-value=2.6e+02 Score=20.00 Aligned_cols=33 Identities=21% Similarity=0.380 Sum_probs=20.6
Q ss_pred EEEEe----CCEEEECCeecCccccccCCCCCCCcEEecCCcEEEEc
Q 020531 271 CVEVH----GGKLLVNGVAQDEDFILEPLAYEMDPVVVPEGYVFVLG 313 (325)
Q Consensus 271 tV~Ik----~g~lyVNGk~l~e~yi~~p~~~~~~~~~VP~g~yFVLG 313 (325)
.+.++ .+.++|||+++... .+..+.+|..+.+|
T Consensus 32 ~~~i~d~~s~ngt~vng~~l~~~----------~~~~L~~gd~i~~G 68 (68)
T PF00498_consen 32 QFYIEDLGSTNGTFVNGQRLGPG----------EPVPLKDGDIIRFG 68 (68)
T ss_dssp EEEEEESSSSS-EEETTEEESST----------SEEEE-TTEEEEET
T ss_pred eEEEEeCCCCCcEEECCEEcCCC----------CEEECCCCCEEEcC
Confidence 55554 37789999887541 34667777777665
No 47
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=22.26 E-value=1.2e+02 Score=24.16 Aligned_cols=30 Identities=37% Similarity=0.464 Sum_probs=19.8
Q ss_pred CCCCCCCEEEEEeccccCCCCccccEEEEecC
Q 020531 215 PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (325)
Q Consensus 215 PTL~~GD~VlV~K~s~~~~~pkrGDIVVF~~P 246 (325)
||...+|++.-+..- .++++.||.++|..-
T Consensus 65 ptC~~~D~i~~~~~l--P~~l~~GD~l~f~~~ 94 (116)
T PF00278_consen 65 PTCDSGDVIARDVML--PKELEVGDWLVFENM 94 (116)
T ss_dssp SSSSTTSEEEEEEEE--ESTTTTT-EEEESS-
T ss_pred CCcCCCceEeeeccC--CCCCCCCCEEEEecC
Confidence 688889977643321 138899999999753
No 48
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=21.59 E-value=86 Score=29.49 Aligned_cols=21 Identities=14% Similarity=0.221 Sum_probs=12.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhe
Q 020531 182 SDDAKAAFTALTVSFLFKSFL 202 (325)
Q Consensus 182 ~~~l~~i~iai~v~lll~~fv 202 (325)
++++++|+++++++++...|+
T Consensus 16 LNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 16 LNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HHHHHHHHHHHHHHHhhhhee
Confidence 456666666666666655554
No 49
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=21.11 E-value=2e+02 Score=22.19 Aligned_cols=34 Identities=26% Similarity=0.262 Sum_probs=23.3
Q ss_pred CCCccccEEEEecCCcccccccCCCCeEEEEEE--------EeCCCEEEEe
Q 020531 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIV--------ATAGDCVEVH 275 (325)
Q Consensus 233 ~~pkrGDIVVF~~P~~~~~~~y~~g~~~IKRVI--------GlPGDtV~Ik 275 (325)
..++.||-|.+.+.. ...-||.+. +.+||.|.+.
T Consensus 25 G~v~~Gd~v~~~P~~---------~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 25 GSIRVGDEVVVLPSG---------KTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred ceEECCCEEEEcCCC---------CeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 467788888886532 235566665 8889998874
Done!