Query 021403
Match_columns 313
No_of_seqs 264 out of 1390
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 02:40:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021403.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021403hhsearch_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 7.5E-28 1.6E-32 210.4 16.6 122 185-313 2-131 (163)
2 PRK10861 signal peptidase I; P 99.9 2.8E-25 6.1E-30 214.0 17.0 95 184-285 63-171 (324)
3 KOG0171 Mitochondrial inner me 99.8 1.9E-20 4.1E-25 164.3 8.7 105 192-313 22-127 (176)
4 PRK13838 conjugal transfer pil 99.7 1.3E-15 2.9E-20 135.7 13.8 102 204-313 27-145 (176)
5 COG0681 LepB Signal peptidase 99.6 9.8E-15 2.1E-19 125.1 10.0 91 182-281 8-100 (166)
6 PRK13884 conjugal transfer pep 99.5 3.8E-13 8.2E-18 120.1 15.1 81 233-313 49-148 (178)
7 TIGR02771 TraF_Ti conjugative 99.5 3.5E-13 7.5E-18 119.7 14.5 104 200-313 21-141 (171)
8 KOG1568 Mitochondrial inner me 99.5 7.6E-14 1.6E-18 122.7 6.1 88 196-290 24-127 (174)
9 TIGR02228 sigpep_I_arch signal 99.4 7.1E-13 1.5E-17 116.4 10.2 53 208-270 36-88 (158)
10 PF10502 Peptidase_S26: Signal 99.3 8.5E-13 1.8E-17 113.1 1.6 80 234-313 21-109 (138)
11 PF00717 Peptidase_S24: Peptid 99.3 1.2E-11 2.7E-16 92.2 7.1 57 207-275 1-57 (70)
12 TIGR02754 sod_Ni_protease nick 99.2 3.3E-11 7.1E-16 95.0 8.8 62 207-275 2-63 (90)
13 cd06530 S26_SPase_I The S26 Ty 99.1 4.9E-10 1.1E-14 86.9 8.6 55 205-266 2-56 (85)
14 cd06462 Peptidase_S24_S26 The 98.6 1.8E-07 4E-12 71.0 8.7 59 205-275 2-61 (84)
15 cd06529 S24_LexA-like Peptidas 98.6 2.2E-07 4.7E-12 70.7 7.8 57 205-275 2-58 (81)
16 COG4959 TraF Type IV secretory 98.3 3.5E-06 7.7E-11 74.1 9.2 80 233-312 52-140 (173)
17 COG2932 Predicted transcriptio 98.2 2.4E-06 5.2E-11 77.5 6.8 59 204-275 124-182 (214)
18 PRK00215 LexA repressor; Valid 97.7 0.00013 2.9E-09 65.4 7.7 57 204-275 119-176 (205)
19 KOG3342 Signal peptidase I [In 97.6 0.00018 4E-09 63.4 6.7 53 205-267 50-102 (180)
20 PRK10276 DNA polymerase V subu 97.6 0.0003 6.4E-09 60.1 7.8 50 204-267 52-102 (139)
21 PRK12423 LexA repressor; Provi 97.6 0.00025 5.4E-09 64.2 7.5 56 205-275 116-172 (202)
22 TIGR00498 lexA SOS regulatory 97.5 0.00038 8.3E-09 62.2 8.0 58 203-275 111-169 (199)
23 COG1974 LexA SOS-response tran 94.4 0.18 3.9E-06 46.3 7.8 58 204-275 113-171 (201)
24 COG0681 LepB Signal peptidase 92.2 0.2 4.4E-06 42.6 4.3 29 257-285 137-165 (166)
25 PF12518 DUF3721: Protein of u 80.3 0.73 1.6E-05 31.0 0.6 9 125-133 23-31 (34)
26 COG1097 RRP4 RNA-binding prote 76.7 4.6 0.0001 38.2 5.0 67 207-286 103-194 (239)
27 TIGR00008 infA translation ini 60.4 8.3 0.00018 29.7 2.5 22 217-241 45-66 (68)
28 COG0361 InfA Translation initi 59.4 9.1 0.0002 30.2 2.6 23 216-241 46-68 (75)
29 PF05257 CHAP: CHAP domain; I 58.8 24 0.00051 28.9 5.2 39 233-278 61-100 (124)
30 PF06890 Phage_Mu_Gp45: Bacter 52.2 54 0.0012 29.3 6.7 41 226-275 66-109 (162)
31 cd04456 S1_IF1A_like S1_IF1A_l 47.7 17 0.00037 28.5 2.5 21 219-241 41-61 (78)
32 TIGR02594 conserved hypothetic 47.6 43 0.00094 28.5 5.2 33 233-275 72-106 (129)
33 PRK12442 translation initiatio 45.5 20 0.00044 29.0 2.7 22 217-241 47-68 (87)
34 KOG0171 Mitochondrial inner me 44.8 41 0.00089 30.5 4.7 105 173-290 10-134 (176)
35 PF04790 Sarcoglycan_1: Sarcog 43.8 2.9E+02 0.0064 26.5 10.7 40 185-224 18-58 (264)
36 cd05793 S1_IF1A S1_IF1A: Trans 43.1 20 0.00044 28.0 2.3 11 219-229 41-51 (77)
37 PF01176 eIF-1a: Translation i 42.4 18 0.0004 27.0 1.9 12 234-245 41-52 (65)
38 smart00652 eIF1a eukaryotic tr 40.1 24 0.00052 28.0 2.3 10 235-244 44-53 (83)
39 PF11101 DUF2884: Protein of u 39.2 34 0.00074 31.8 3.5 25 263-287 17-42 (229)
40 PF14345 GDYXXLXY: GDYXXLXY pr 39.2 1.1E+02 0.0024 26.1 6.4 32 216-247 16-47 (144)
41 PRK04012 translation initiatio 38.7 26 0.00056 28.9 2.4 23 218-243 61-83 (100)
42 PF14085 DUF4265: Domain of un 32.5 1.5E+02 0.0032 24.6 6.0 28 219-246 10-37 (117)
43 PF09285 Elong-fact-P_C: Elong 32.1 72 0.0016 23.7 3.6 30 211-246 19-49 (56)
44 PF10000 ACT_3: ACT domain; I 28.3 29 0.00063 26.8 1.0 18 211-228 12-29 (72)
45 KOG0369 Pyruvate carboxylase [ 27.4 22 0.00048 38.8 0.2 34 8-41 586-622 (1176)
46 COG4079 Uncharacterized protei 26.8 76 0.0017 30.6 3.7 31 256-286 248-282 (293)
47 PF00278 Orn_DAP_Arg_deC: Pyri 26.6 90 0.0019 24.8 3.7 30 215-246 65-94 (116)
48 TIGR02390 RNA_pol_rpoA1 DNA-di 25.6 75 0.0016 35.4 3.9 48 215-275 396-443 (868)
49 smart00663 RPOLA_N RNA polymer 24.5 1.4E+02 0.0031 29.0 5.2 50 213-275 185-234 (295)
50 smart00841 Elong-fact-P_C Elon 24.1 92 0.002 23.1 3.0 31 210-246 18-49 (56)
51 COG3602 Uncharacterized protei 22.4 51 0.0011 28.3 1.4 17 211-227 12-28 (134)
52 PF14118 YfzA: YfzA-like prote 22.2 76 0.0016 26.1 2.4 16 207-222 29-44 (94)
53 PRK15095 FKBP-type peptidyl-pr 21.9 2.2E+02 0.0049 24.8 5.5 36 234-278 92-127 (156)
54 PF04319 NifZ: NifZ domain; I 21.9 1.6E+02 0.0034 23.2 4.0 31 213-243 1-34 (75)
55 COG0234 GroS Co-chaperonin Gro 21.7 3.7E+02 0.008 22.2 6.3 58 220-284 7-80 (96)
56 cd03695 CysN_NodQ_II CysN_NodQ 21.7 1.9E+02 0.0042 22.1 4.5 34 233-275 25-66 (81)
57 TIGR00523 eIF-1A eukaryotic/ar 21.1 90 0.0019 25.6 2.6 9 235-243 58-66 (99)
58 PF15057 DUF4537: Domain of un 21.0 69 0.0015 27.0 2.0 17 210-226 49-65 (124)
59 PRK14977 bifunctional DNA-dire 20.4 1.4E+02 0.003 35.1 4.7 38 233-275 426-463 (1321)
60 PRK09919 anti-adapter protein 20.4 91 0.002 26.5 2.6 21 267-287 40-60 (114)
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=99.96 E-value=7.5e-28 Score=210.40 Aligned_cols=122 Identities=34% Similarity=0.574 Sum_probs=107.0
Q ss_pred HHHHHHHHHHHHHHHHheeeeEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEE
Q 021403 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRI 264 (313)
Q Consensus 185 ~~~l~ial~v~lllr~fv~~~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRV 264 (313)
++.++++++++++++.|++++++|+|+||+|||++||+|+++|..|...++++||+|+|+.|.. .++.+||||
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 4567778888899999999999999999999999999999999988778999999999998752 567899999
Q ss_pred EEeCCCEEEEECCEEEECCEEcCccccccccc--------CCCCCEEecCCeEEEeC
Q 021403 265 VATAGDCVEVHGGKLLVNGVAQDEDFILEPLA--------YEMDPVVMFPILVLFLF 313 (313)
Q Consensus 265 IGlPGDtV~I~dg~vyVNGk~l~E~yi~~~~~--------~~~~~~tVPeGeyFVL~ 313 (313)
+|+|||+|+++++.+||||+.++|+|+.+... ....+++||+|+||||+
T Consensus 75 ig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlG 131 (163)
T TIGR02227 75 IGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLG 131 (163)
T ss_pred EecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEEC
Confidence 99999999999999999999999988654311 22456799999999985
No 2
>PRK10861 signal peptidase I; Provisional
Probab=99.93 E-value=2.8e-25 Score=213.97 Aligned_cols=95 Identities=36% Similarity=0.562 Sum_probs=86.0
Q ss_pred HHHHHHHHHHHHHHHHHheeeeEEECCCCCccCCCCCCEEEEEeeeccC------------CCCCcCcEEEEecCCcccc
Q 021403 184 DAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFF------------KRPEVSDIVIFRAPPILQE 251 (313)
Q Consensus 184 ~~~~l~ial~v~lllr~fv~~~~~I~g~SMePTL~~GD~VlV~K~~y~~------------~~p~rGDIVVF~~P~~~~~ 251 (313)
++..++++++++++++.|+++++.|+|+||+|||++||+|+++|+.|++ .+|+|||||+|+.|.+
T Consensus 63 ~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~--- 139 (324)
T PRK10861 63 TGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPED--- 139 (324)
T ss_pred HHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCC---
Confidence 3466778888899999999999999999999999999999999999864 5799999999999863
Q ss_pred cCCCCCceeEEEEEEeCCCEEEEE--CCEEEECCEE
Q 021403 252 IGFSSGDVFIKRIVATAGDCVEVH--GGKLLVNGVA 285 (313)
Q Consensus 252 ~g~~~~~~~VKRVIGlPGDtV~I~--dg~vyVNGk~ 285 (313)
+++.+||||||+|||+|+++ ++++||||+.
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=99.82 E-value=1.9e-20 Score=164.27 Aligned_cols=105 Identities=41% Similarity=0.589 Sum_probs=89.1
Q ss_pred HHHHHHHHHheeeeEEECCCCCccCCCC-CCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCC
Q 021403 192 LTVSFLFKSFLAEPRSIPSASMNPTLDV-GDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD 270 (313)
Q Consensus 192 l~v~lllr~fv~~~~~I~g~SMePTL~~-GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGD 270 (313)
.+++++...|++++..++|.||+|||++ ||+++.+|++|.++++++||||+++.|.. +.+.+||||+|+|||
T Consensus 22 ~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~-------~~~~~cKRIva~eGD 94 (176)
T KOG0171|consen 22 AAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD-------PKEHICKRIVAMEGD 94 (176)
T ss_pred HHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC-------chhhhhheeeccCCc
Confidence 3444556679999999999999998887 56666699999999999999999999984 678899999999999
Q ss_pred EEEEECCEEEECCEEcCcccccccccCCCCCEEecCCeEEEeC
Q 021403 271 CVEVHGGKLLVNGVAQDEDFILEPLAYEMDPVVMFPILVLFLF 313 (313)
Q Consensus 271 tV~I~dg~vyVNGk~l~E~yi~~~~~~~~~~~tVPeGeyFVL~ 313 (313)
.|++.++.+.+|+.. |.+. .+++||+|++||++
T Consensus 95 ~v~v~~~~~~~n~~~--e~~~--------~~i~VP~GhVfv~G 127 (176)
T KOG0171|consen 95 LVEVHDGPLVVNDLV--EKFS--------TPIRVPEGHVFVEG 127 (176)
T ss_pred eEEEecCCcccchhh--hhcc--------ceeeccCceEEEec
Confidence 999999999888754 4332 66799999999974
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.66 E-value=1.3e-15 Score=135.69 Aligned_cols=102 Identities=19% Similarity=0.191 Sum_probs=73.9
Q ss_pred eeEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCccc-----ccCCC-------CCceeEEEEEEeCCCE
Q 021403 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ-----EIGFS-------SGDVFIKRIVATAGDC 271 (313)
Q Consensus 204 ~~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~-----~~g~~-------~~~~~VKRVIGlPGDt 271 (313)
.-++++-..-.| +.++++.+..++++|||+|+|+.|+... +++|- ....+||||+|+|||+
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 335555444344 7888887666899999999999886421 12221 1246999999999999
Q ss_pred EEEECCEEEECCEEcCcccccccccC-----CCCCEEecCCeEEEeC
Q 021403 272 VEVHGGKLLVNGVAQDEDFILEPLAY-----EMDPVVMFPILVLFLF 313 (313)
Q Consensus 272 V~I~dg~vyVNGk~l~E~yi~~~~~~-----~~~~~tVPeGeyFVL~ 313 (313)
|++++ ++||||+.++|+|+.+.... ...+.+||+|+||||.
T Consensus 100 V~i~~-~v~iNg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlg 145 (176)
T PRK13838 100 VEIGG-SVSIDGRPLPSSSVRRRDGEGRPLTPFPGGVVPPGHLFLHS 145 (176)
T ss_pred EEECC-EEEECCEEccccccccccccCCcCCCCCccCcCCCeEEEEC
Confidence 99984 89999999999887654321 1234589999999984
No 5
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.58 E-value=9.8e-15 Score=125.06 Aligned_cols=91 Identities=35% Similarity=0.609 Sum_probs=79.9
Q ss_pred hhHHHHHHHHHHHHHHH--HHheeeeEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCce
Q 021403 182 SDDAKAAFTALTVSFLF--KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDV 259 (313)
Q Consensus 182 ~~~~~~l~ial~v~lll--r~fv~~~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~ 259 (313)
.+++..++.++++++++ +.|+++++.|+|+||+|||+.||+|+++|..|....+..+|++ ..|. .....
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~--~~~~-------~~~~~ 78 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDII--VLPA-------VVEGD 78 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceee--ecCC-------CCCcc
Confidence 45667777788888888 8999999999999999999999999999999988889999988 3332 26788
Q ss_pred eEEEEEEeCCCEEEEECCEEEE
Q 021403 260 FIKRIVATAGDCVEVHGGKLLV 281 (313)
Q Consensus 260 ~VKRVIGlPGDtV~I~dg~vyV 281 (313)
++||+++++||.|.++++..++
T Consensus 79 ~~kr~~~~~GD~i~~~~~~~~~ 100 (166)
T COG0681 79 LIKRVIGLRGDIVVFKDDRLYV 100 (166)
T ss_pred eEEEeccCCCCEEEEECCEEEe
Confidence 9999999999999999999887
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.51 E-value=3.8e-13 Score=120.11 Aligned_cols=81 Identities=22% Similarity=0.258 Sum_probs=59.2
Q ss_pred CCCCcCcEEEEecCCcc-----cccCCC------C-CceeEEEEEEeCCCEEEEECCEEEECCEEcCcccccc--cc---
Q 021403 233 KRPEVSDIVIFRAPPIL-----QEIGFS------S-GDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILE--PL--- 295 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~-----~~~g~~------~-~~~~VKRVIGlPGDtV~I~dg~vyVNGk~l~E~yi~~--~~--- 295 (313)
..+++||+|+|+.|+.. .+++|- . ...+||||+|+|||+|+++++.+||||+.+.+..... ..
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 57999999999987632 123331 1 1479999999999999999999999999986543221 11
Q ss_pred --cCCCCCEEecCCeEEEeC
Q 021403 296 --AYEMDPVVMFPILVLFLF 313 (313)
Q Consensus 296 --~~~~~~~tVPeGeyFVL~ 313 (313)
.+....++||+|+||||.
T Consensus 129 l~~~~~~~~~lp~g~~fvlg 148 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMS 148 (178)
T ss_pred ccccCCCceEECCCEEEEEC
Confidence 122234699999999984
No 7
>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=99.51 E-value=3.5e-13 Score=119.66 Aligned_cols=104 Identities=23% Similarity=0.255 Sum_probs=69.0
Q ss_pred HheeeeEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCccc-----ccCC-CCC------ceeEEEEEEe
Q 021403 200 SFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQ-----EIGF-SSG------DVFIKRIVAT 267 (313)
Q Consensus 200 ~fv~~~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~-----~~g~-~~~------~~~VKRVIGl 267 (313)
.|......-.++||-..+ +. +.+ .++++|||+|+|+.|+... .+++ ..+ ..+||||+|+
T Consensus 21 ~~~~~~~~N~T~S~P~g~----Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVigl 91 (171)
T TIGR02771 21 LYCVGARINTTKSLPLGL----YW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGL 91 (171)
T ss_pred cceeeEEEECCCCCcceE----EE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEe
Confidence 344333444566666543 22 222 2689999999999875321 1122 111 3799999999
Q ss_pred CCCEEEEECCEEEECCEEcCccccccccc-----CCCCCEEecCCeEEEeC
Q 021403 268 AGDCVEVHGGKLLVNGVAQDEDFILEPLA-----YEMDPVVMFPILVLFLF 313 (313)
Q Consensus 268 PGDtV~I~dg~vyVNGk~l~E~yi~~~~~-----~~~~~~tVPeGeyFVL~ 313 (313)
|||+|+++++.++|||+.+++.+...... ....+.+||+| ||+|.
T Consensus 92 pGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lg 141 (171)
T TIGR02771 92 PGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVH 141 (171)
T ss_pred CCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEEC
Confidence 99999999999999999988765432211 12346899999 88773
No 8
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.46 E-value=7.6e-14 Score=122.68 Aligned_cols=88 Identities=27% Similarity=0.416 Sum_probs=71.8
Q ss_pred HHHHHheeeeEEECCCCCccCCCCC------CEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCC
Q 021403 196 FLFKSFLAEPRSIPSASMNPTLDVG------DRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAG 269 (313)
Q Consensus 196 lllr~fv~~~~~I~g~SMePTL~~G------D~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPG 269 (313)
+-+...+.....|.|.||+|||+++ |+|+++|+....+...|||||+|+.|.+ +++++||||+|+||
T Consensus 24 ~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~aleg 96 (174)
T KOG1568|consen 24 LTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAALEG 96 (174)
T ss_pred eeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeecccc
Confidence 3445567788999999999999984 9999999976556789999999999984 88999999999999
Q ss_pred CEEEE----------ECCEEEECCEEcCccc
Q 021403 270 DCVEV----------HGGKLLVNGVAQDEDF 290 (313)
Q Consensus 270 DtV~I----------~dg~vyVNGk~l~E~y 290 (313)
|.+.- ..|++||.|....+.|
T Consensus 97 d~~~t~~~k~~~v~vpkghcWVegDn~~hs~ 127 (174)
T KOG1568|consen 97 DIMVTEDEKEEPVVVPKGHCWVEGDNQKHSY 127 (174)
T ss_pred cEeccCCCCCCceecCCCcEEEecCCccccc
Confidence 98865 2577777776554443
No 9
>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=99.43 E-value=7.1e-13 Score=116.38 Aligned_cols=53 Identities=25% Similarity=0.467 Sum_probs=46.2
Q ss_pred ECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCC
Q 021403 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD 270 (313)
Q Consensus 208 I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGD 270 (313)
|.|+||+|||++||.+++++..+ .++++||+|+|+.|. ..+.++|||+++.++
T Consensus 36 V~g~SM~Ptl~~GD~vlv~~~~~--~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~ 88 (158)
T TIGR02228 36 VLSGSMEPTFNTGDLILVTGADP--NDIQVGDVITYKSPG--------FNTPVTHRVIEINNS 88 (158)
T ss_pred EcCCCCcCCccCCCEEEEEeccc--CCCCCCCEEEEEECC--------CCccEEEEEEEEECC
Confidence 99999999999999999998543 689999999999875 237899999999754
No 10
>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=99.28 E-value=8.5e-13 Score=113.15 Aligned_cols=80 Identities=28% Similarity=0.368 Sum_probs=9.9
Q ss_pred CCCcCcEEEEecCCccc----ccCC-CCCceeEEEEEEeCCCEEEEECCEEEECCEEcCcccccccccC----CCCCEEe
Q 021403 234 RPEVSDIVIFRAPPILQ----EIGF-SSGDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILEPLAY----EMDPVVM 304 (313)
Q Consensus 234 ~p~rGDIVVF~~P~~~~----~~g~-~~~~~~VKRVIGlPGDtV~I~dg~vyVNGk~l~E~yi~~~~~~----~~~~~tV 304 (313)
.++|||+|+|+.|.... +++| ..+..++|||+|+|||+|+++++.++|||+++.+.+..+.... ...+.+|
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 48999999999986322 3344 3456999999999999999999999999988887665433222 2246799
Q ss_pred cCCeEEEeC
Q 021403 305 FPILVLFLF 313 (313)
Q Consensus 305 PeGeyFVL~ 313 (313)
|+|+||||.
T Consensus 101 p~g~~~v~g 109 (138)
T PF10502_consen 101 PEGEYFVLG 109 (138)
T ss_dssp -TTEEEEE-
T ss_pred CCCEEEEec
Confidence 999999984
No 11
>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=99.27 E-value=1.2e-11 Score=92.19 Aligned_cols=57 Identities=28% Similarity=0.540 Sum_probs=47.1
Q ss_pred EECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 207 ~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
+|.|+||+|+|++||+|++++. ..++.||+|+|..+.. ...++||+++.+|+.+.+.
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 5899999999999999999987 4899999999998641 1389999999999999987
No 12
>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=99.25 E-value=3.3e-11 Score=94.97 Aligned_cols=62 Identities=29% Similarity=0.480 Sum_probs=50.8
Q ss_pred EECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 207 ~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
.|.|+||+|||++||+|+++++......+++||+|+|+.|.. +++.++||+++++++.+.+.
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~-------~~~~~vkRv~~~~~~~~~l~ 63 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQ-------PYGLIIKRLAAVDDNGLFLL 63 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCC-------CcceEEEEeeEEcCCeEEEe
Confidence 689999999999999999998654335567899999998752 46899999999987766554
No 13
>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=99.09 E-value=4.9e-10 Score=86.95 Aligned_cols=55 Identities=42% Similarity=0.810 Sum_probs=47.7
Q ss_pred eEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEE
Q 021403 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVA 266 (313)
Q Consensus 205 ~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIG 266 (313)
.+.|.|+||+||+++||++++++....+..+++||+|+|+.+.. .++.++|||++
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 57899999999999999999999864444799999999998751 35799999999
No 14
>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=98.64 E-value=1.8e-07 Score=70.99 Aligned_cols=59 Identities=34% Similarity=0.598 Sum_probs=49.5
Q ss_pred eEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCC-CEEEEE
Q 021403 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAG-DCVEVH 275 (313)
Q Consensus 205 ~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPG-DtV~I~ 275 (313)
.+.+.|+||+|++++||.+++++.. ..++.||+|+++.+ .+..++||+...++ +++.+.
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~~~~~~l~ 61 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPGEGHYFLL 61 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECCCCEEEEE
Confidence 4689999999999999999999864 24899999999984 23799999999987 565554
No 15
>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=98.59 E-value=2.2e-07 Score=70.68 Aligned_cols=57 Identities=28% Similarity=0.488 Sum_probs=49.4
Q ss_pred eEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 205 ~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
.++|.|+||+|++++||.+++++. ..++.||++++..+ ++.++||+...+++.+.+.
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~----~~~~~g~i~~~~~~----------~~~~ikr~~~~~~~~~~L~ 58 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPS----DTPRDGDIVVARLD----------GELTVKRLQRRGGGRLRLI 58 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCC----CCCCCCCEEEEEEC----------CEEEEEEEEECCCCcEEEE
Confidence 368999999999999999999986 35999999999973 4789999999997766665
No 16
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.31 E-value=3.5e-06 Score=74.14 Aligned_cols=80 Identities=18% Similarity=0.265 Sum_probs=59.6
Q ss_pred CCCCcCcEEEEecCCcc----cccCC-CCCceeEEEEEEeCCCEEEEECCEEEECCEEcCcccccccccCC----CCCEE
Q 021403 233 KRPEVSDIVIFRAPPIL----QEIGF-SSGDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDFILEPLAYE----MDPVV 303 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~----~~~g~-~~~~~~VKRVIGlPGDtV~I~dg~vyVNGk~l~E~yi~~~~~~~----~~~~t 303 (313)
..+.+||+|+++.|+.. ..+|| .....++|||.|+|||+|++.++.+-|||+.+......+..... .+.-.
T Consensus 52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~ 131 (173)
T COG4959 52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY 131 (173)
T ss_pred CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence 34599999999999742 24677 45678899999999999999999999999987654433332222 22235
Q ss_pred ecCCeEEEe
Q 021403 304 MFPILVLFL 312 (313)
Q Consensus 304 VPeGeyFVL 312 (313)
+-++|+|+|
T Consensus 132 l~~~el~lL 140 (173)
T COG4959 132 LAPSELLLL 140 (173)
T ss_pred ecCCeEEEE
Confidence 788888887
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.24 E-value=2.4e-06 Score=77.54 Aligned_cols=59 Identities=20% Similarity=0.385 Sum_probs=49.5
Q ss_pred eeEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 204 ~~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
....|.|+||+|++++||.++|+.- .+..+||.|++..- .++.+|||+...+|-.+.+.
T Consensus 124 ~~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l~ 182 (214)
T COG2932 124 FALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVETD---------GGELYVKKLQREPGGLLRLV 182 (214)
T ss_pred EEEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEEE
Confidence 3479999999999999999999976 47788997777652 46899999999998888554
No 18
>PRK00215 LexA repressor; Validated
Probab=97.69 E-value=0.00013 Score=65.43 Aligned_cols=57 Identities=18% Similarity=0.222 Sum_probs=45.3
Q ss_pred eeEEECCCCCc-cCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 204 ~~~~I~g~SMe-PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
..++|.|+||. |++.+||+|++++. ..++.||+|++.. +++.++||+.-. ++.+.+.
T Consensus 119 ~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~----------~~~~~vKrl~~~-~~~~~L~ 176 (205)
T PRK00215 119 FLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI----------DDEATVKRFRRE-GGHIRLE 176 (205)
T ss_pred EEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEEE
Confidence 45889999995 79999999999975 4678999999986 347899999865 4444443
No 19
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.58 E-value=0.00018 Score=63.42 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=42.9
Q ss_pred eEEECCCCCccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEe
Q 021403 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267 (313)
Q Consensus 205 ~~~I~g~SMePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGl 267 (313)
.+.|-++||||.++.||.++..... ....+.||||+|+.+. .+-.+|+||+-+
T Consensus 50 iVVVLSgSMePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg--------R~IPiVHRviK~ 102 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG--------REIPIVHRVIKQ 102 (180)
T ss_pred EEEEEcCCcCcccccccEEEEecCC--CCcceeccEEEEEECC--------ccCchhHHHHHH
Confidence 5788899999999999999987543 2356889999999875 456789998854
No 20
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=97.57 E-value=0.0003 Score=60.12 Aligned_cols=50 Identities=20% Similarity=0.260 Sum_probs=41.6
Q ss_pred eeEEECCCCCc-cCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEe
Q 021403 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267 (313)
Q Consensus 204 ~~~~I~g~SMe-PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGl 267 (313)
...+|.|+||. |++++||++++++- .+++.||+|++.. +++..+||+.-.
T Consensus 52 f~l~V~GdSM~~~~I~~GD~liVd~~----~~~~~Gdivv~~~----------~g~~~vKrl~~~ 102 (139)
T PRK10276 52 YFVKASGDSMIDAGISDGDLLIVDSA----ITASHGDIVIAAV----------DGEFTVKKLQLR 102 (139)
T ss_pred EEEEEecCCCCCCCCCCCCEEEEECC----CCCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence 34899999998 68999999999975 3678999999875 456889999853
No 21
>PRK12423 LexA repressor; Provisional
Probab=97.56 E-value=0.00025 Score=64.21 Aligned_cols=56 Identities=25% Similarity=0.325 Sum_probs=45.4
Q ss_pred eEEECCCCCc-cCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 205 ~~~I~g~SMe-PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
..+|.|+||. |+|.+||.|++++. .+++.||+|++.. +++.++||+.-. ++.+.+.
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 4799999997 79999999999975 4788999999986 357899999855 4555554
No 22
>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=97.50 E-value=0.00038 Score=62.23 Aligned_cols=58 Identities=24% Similarity=0.275 Sum_probs=46.2
Q ss_pred eeeEEECCCCCc-cCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 203 AEPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 203 ~~~~~I~g~SMe-PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
...++|.|+||. |++.+||++++++. ..++.||+|++.. +++.++||+.-. |+.+.+.
T Consensus 111 ~f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L~ 169 (199)
T TIGR00498 111 VFLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVELK 169 (199)
T ss_pred EEEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEEE
Confidence 355899999996 68999999999975 4789999999986 457899998754 4444443
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=94.40 E-value=0.18 Score=46.34 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=45.5
Q ss_pred eeEEECCCCCcc-CCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 204 EPRSIPSASMNP-TLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 204 ~~~~I~g~SMeP-TL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
...+|.|+||.. .+.+||.|+|++- ...+.||||+...+ +++..+||..- .|+.|...
T Consensus 113 f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~-~g~~i~L~ 171 (201)
T COG1974 113 FFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYR-DGNQILLK 171 (201)
T ss_pred EEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEE-eCCEEEEE
Confidence 347999999965 7888999999976 58899999999974 35588999874 45555543
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=92.17 E-value=0.2 Score=42.58 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=24.2
Q ss_pred CceeEEEEEEeCCCEEEEECCEEEECCEE
Q 021403 257 GDVFIKRIVATAGDCVEVHGGKLLVNGVA 285 (313)
Q Consensus 257 ~~~~VKRVIGlPGDtV~I~dg~vyVNGk~ 285 (313)
...++||++++|||.+...+..+++||++
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 46789999999999999986558888864
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=80.35 E-value=0.73 Score=31.05 Aligned_cols=9 Identities=56% Similarity=1.782 Sum_probs=7.9
Q ss_pred cCccccCCC
Q 021403 125 GSKWLPCNE 133 (313)
Q Consensus 125 ~~~w~~c~~ 133 (313)
++||+||++
T Consensus 23 g~~WMPC~~ 31 (34)
T PF12518_consen 23 GDKWMPCSN 31 (34)
T ss_pred cCccccCcc
Confidence 689999985
No 26
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=76.66 E-value=4.6 Score=38.23 Aligned_cols=67 Identities=22% Similarity=0.392 Sum_probs=42.8
Q ss_pred EECCCCCccCCCCCCEEEEEeeecc-------------CCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEE-
Q 021403 207 SIPSASMNPTLDVGDRILAEKVSYF-------------FKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCV- 272 (313)
Q Consensus 207 ~I~g~SMePTL~~GD~VlV~K~~y~-------------~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV- 272 (313)
.-....|.|.|+.||.|+..-.... +++++.|-+|-..+ ..+-|++|.-|--+
T Consensus 103 ~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p-------------~kVpRvig~~~sm~~ 169 (239)
T COG1097 103 ENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP-------------SKVPRVIGKKGSMLN 169 (239)
T ss_pred cccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch-------------hhcceEecCCCcHHH
Confidence 3347889999999999987654432 34555565555543 23455555544333
Q ss_pred ----------EE-ECCEEEECCEEc
Q 021403 273 ----------EV-HGGKLLVNGVAQ 286 (313)
Q Consensus 273 ----------~I-~dg~vyVNGk~l 286 (313)
-+ .||.+||+++..
T Consensus 170 ~l~~~~~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 170 MLKEKTGCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred HhhhhcCeEEEEecCCEEEecCCCc
Confidence 11 389999999765
No 27
>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=60.38 E-value=8.3 Score=29.75 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=11.8
Q ss_pred CCCCCEEEEEeeeccCCCCCcCcEE
Q 021403 217 LDVGDRILAEKVSYFFKRPEVSDIV 241 (313)
Q Consensus 217 L~~GD~VlV~K~~y~~~~p~rGDIV 241 (313)
+.+||+|.|....| ++.+||||
T Consensus 45 I~~GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 45 ILPGDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred ECCCCEEEEEECcc---cCCcEeEE
Confidence 34566666655543 35555554
No 28
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=59.45 E-value=9.1 Score=30.15 Aligned_cols=23 Identities=30% Similarity=0.365 Sum_probs=16.6
Q ss_pred CCCCCCEEEEEeeeccCCCCCcCcEE
Q 021403 216 TLDVGDRILAEKVSYFFKRPEVSDIV 241 (313)
Q Consensus 216 TL~~GD~VlV~K~~y~~~~p~rGDIV 241 (313)
-+.+||+|+|..+.| +..+|||+
T Consensus 46 ~I~~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 46 RILPGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred EeCCCCEEEEEeccc---ccccccEE
Confidence 566788888887764 47777765
No 29
>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=58.79 E-value=24 Score=28.92 Aligned_cols=39 Identities=18% Similarity=0.336 Sum_probs=24.0
Q ss_pred CCCCcCcEEEEecCCcccccCCCCCceeEEEEEEe-CCCEEEEECCE
Q 021403 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT-AGDCVEVHGGK 278 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGl-PGDtV~I~dg~ 278 (313)
..|+.||||+|.... ....=.|--|.++ .+++|.+.++.
T Consensus 61 ~~P~~Gdivv~~~~~-------~~~~GHVaIV~~v~~~~~i~v~e~N 100 (124)
T PF05257_consen 61 STPQPGDIVVWDSGS-------GGGYGHVAIVESVNDGGTITVIEQN 100 (124)
T ss_dssp S---TTEEEEEEECT-------TTTT-EEEEEEEE-TTSEEEEEECS
T ss_pred cccccceEEEeccCC-------CCCCCeEEEEEEECCCCEEEEEECC
Confidence 689999999995221 1222356668888 88899887543
No 30
>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=52.17 E-value=54 Score=29.30 Aligned_cols=41 Identities=20% Similarity=0.345 Sum_probs=28.7
Q ss_pred EeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEE---EEEeCCCEEEEE
Q 021403 226 EKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKR---IVATAGDCVEVH 275 (313)
Q Consensus 226 ~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKR---VIGlPGDtV~I~ 275 (313)
+.-.|+.+.++.||+.+|... ....++|| +|.+.++++++.
T Consensus 66 ~d~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 66 EDRRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred CCccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 334556667899999999863 34556665 667777877775
No 31
>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=47.66 E-value=17 Score=28.50 Aligned_cols=21 Identities=19% Similarity=0.357 Sum_probs=8.9
Q ss_pred CCCEEEEEeeeccCCCCCcCcEE
Q 021403 219 VGDRILAEKVSYFFKRPEVSDIV 241 (313)
Q Consensus 219 ~GD~VlV~K~~y~~~~p~rGDIV 241 (313)
.||+|+++...| .+..+|||+
T Consensus 41 ~GD~VlV~~~~~--~~~~kg~Iv 61 (78)
T cd04456 41 RGDFLIVDPIEE--GEDVKADII 61 (78)
T ss_pred CCCEEEEEeccc--CCCceEEEE
Confidence 344444444432 233444444
No 32
>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=47.62 E-value=43 Score=28.48 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=20.7
Q ss_pred CCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCC--EEEEE
Q 021403 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD--CVEVH 275 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGD--tV~I~ 275 (313)
.+|++||||+|+.. +.-.|--+++...| +|.+-
T Consensus 72 ~~p~~GDiv~f~~~----------~~~HVGi~~g~~~~~g~i~~l 106 (129)
T TIGR02594 72 SKPAYGCIAVKRRG----------GGGHVGFVVGKDKQTGTIIVL 106 (129)
T ss_pred CCCCccEEEEEECC----------CCCEEEEEEeEcCCCCEEEEe
Confidence 47899999999753 22345556665443 55444
No 33
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=45.53 E-value=20 Score=28.99 Aligned_cols=22 Identities=27% Similarity=0.330 Sum_probs=12.2
Q ss_pred CCCCCEEEEEeeeccCCCCCcCcEE
Q 021403 217 LDVGDRILAEKVSYFFKRPEVSDIV 241 (313)
Q Consensus 217 L~~GD~VlV~K~~y~~~~p~rGDIV 241 (313)
+.+||+|.|+-+.| ++.+|+||
T Consensus 47 Il~GD~V~VE~spY---DltkGRIi 68 (87)
T PRK12442 47 ILAGDRVTLELSPY---DLTKGRIN 68 (87)
T ss_pred ecCCCEEEEEECcc---cCCceeEE
Confidence 34566666666554 35566553
No 34
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=44.80 E-value=41 Score=30.50 Aligned_cols=105 Identities=22% Similarity=0.296 Sum_probs=56.3
Q ss_pred hhHHHHhhhhhHHHHHHHHHHHHHHHHHhee-----eeEEECCCCC---------ccCCCCCCEEEEEeeeccCC-CC--
Q 021403 173 WLSKLLNVCSDDAKAAFTALTVSFLFKSFLA-----EPRSIPSASM---------NPTLDVGDRILAEKVSYFFK-RP-- 235 (313)
Q Consensus 173 wl~~~l~~~~~~~~~l~ial~v~lllr~fv~-----~~~~I~g~SM---------ePTL~~GD~VlV~K~~y~~~-~p-- 235 (313)
|..++ +|.+...+.|+.++.-++...-.. .+..-+++-- .-+.+.||+|+..+-.--.. -.
T Consensus 10 l~~~~--~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKR 87 (176)
T KOG0171|consen 10 LVGKS--FCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKR 87 (176)
T ss_pred ccchh--hHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhhe
Confidence 44444 667788888888887766532111 1222222211 11236899998765321100 11
Q ss_pred ---CcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEECCEEEECCEEcCccc
Q 021403 236 ---EVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVHGGKLLVNGVAQDEDF 290 (313)
Q Consensus 236 ---~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~dg~vyVNGk~l~E~y 290 (313)
..||.|.+..... ..+.++++-. ..+.+-.|+|||.|......+
T Consensus 88 Iva~eGD~v~v~~~~~-------~~n~~~e~~~----~~i~VP~GhVfv~GDN~~nS~ 134 (176)
T KOG0171|consen 88 IVAMEGDLVEVHDGPL-------VVNDLVEKFS----TPIRVPEGHVFVEGDNRNNSL 134 (176)
T ss_pred eeccCCceEEEecCCc-------ccchhhhhcc----ceeeccCceEEEecCCCCCcc
Confidence 2399777765321 1111222222 447777999999997766544
No 35
>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=43.82 E-value=2.9e+02 Score=26.47 Aligned_cols=40 Identities=10% Similarity=0.094 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHheeeeEEECCCCCcc-CCCCCCEEE
Q 021403 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNP-TLDVGDRIL 224 (313)
Q Consensus 185 ~~~l~ial~v~lllr~fv~~~~~I~g~SMeP-TL~~GD~Vl 224 (313)
+..+++..++-+++..|++...++..+-|.+ .+.+++.++
T Consensus 18 vllL~il~iiNL~LTiwIl~Vl~~~~~Gm~~l~~~~~g~~~ 58 (264)
T PF04790_consen 18 VLLLFILAIINLALTIWILKVLRFSSNGMGSLEFIPDGLRL 58 (264)
T ss_pred HHHHHHHHHHHHHHHhhhheeeecccCccccEEEecCCeEE
Confidence 4555566666777888999999999999988 555555554
No 36
>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=43.09 E-value=20 Score=27.98 Aligned_cols=11 Identities=27% Similarity=0.350 Sum_probs=5.0
Q ss_pred CCCEEEEEeee
Q 021403 219 VGDRILAEKVS 229 (313)
Q Consensus 219 ~GD~VlV~K~~ 229 (313)
+||+|+++...
T Consensus 41 ~GD~V~Ve~~~ 51 (77)
T cd05793 41 EGDIVLVAPWD 51 (77)
T ss_pred CCCEEEEEecc
Confidence 34444444443
No 37
>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=42.37 E-value=18 Score=27.02 Aligned_cols=12 Identities=17% Similarity=0.227 Sum_probs=5.9
Q ss_pred CCCcCcEEEEec
Q 021403 234 RPEVSDIVIFRA 245 (313)
Q Consensus 234 ~p~rGDIVVF~~ 245 (313)
-+++||+|+...
T Consensus 41 wI~~GD~V~V~~ 52 (65)
T PF01176_consen 41 WIKRGDFVLVEP 52 (65)
T ss_dssp ---TTEEEEEEE
T ss_pred ecCCCCEEEEEe
Confidence 356677776664
No 38
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=40.06 E-value=24 Score=27.95 Aligned_cols=10 Identities=30% Similarity=0.365 Sum_probs=5.1
Q ss_pred CCcCcEEEEe
Q 021403 235 PEVSDIVIFR 244 (313)
Q Consensus 235 p~rGDIVVF~ 244 (313)
+++||+|+..
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 3445555554
No 39
>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=39.18 E-value=34 Score=31.83 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=20.8
Q ss_pred EEEEeCCCEEEE-ECCEEEECCEEcC
Q 021403 263 RIVATAGDCVEV-HGGKLLVNGVAQD 287 (313)
Q Consensus 263 RVIGlPGDtV~I-~dg~vyVNGk~l~ 287 (313)
+|++..|+.+.| .+|.+||||+.+.
T Consensus 17 ~v~~~~~~~~~I~~~g~L~i~G~~v~ 42 (229)
T PF11101_consen 17 EVVQASGEKLRIDPDGNLFINGKKVS 42 (229)
T ss_pred EEEeCCCceEEEcCCCcEEECCEEcc
Confidence 367788889999 4899999999875
No 40
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=39.18 E-value=1.1e+02 Score=26.08 Aligned_cols=32 Identities=13% Similarity=0.015 Sum_probs=26.9
Q ss_pred CCCCCCEEEEEeeeccCCCCCcCcEEEEecCC
Q 021403 216 TLDVGDRILAEKVSYFFKRPEVSDIVIFRAPP 247 (313)
Q Consensus 216 TL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~ 247 (313)
++..|..|.+.-..+..+++=+||.|.++...
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 57789999988888888899999999998754
No 41
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=38.72 E-value=26 Score=28.88 Aligned_cols=23 Identities=22% Similarity=0.380 Sum_probs=12.4
Q ss_pred CCCCEEEEEeeeccCCCCCcCcEEEE
Q 021403 218 DVGDRILAEKVSYFFKRPEVSDIVIF 243 (313)
Q Consensus 218 ~~GD~VlV~K~~y~~~~p~rGDIVVF 243 (313)
..||+|+|..+.| +..+||||--
T Consensus 61 ~~GD~VlVe~~~~---~~~kg~Iv~r 83 (100)
T PRK04012 61 REGDVVIVAPWDF---QDEKADIIWR 83 (100)
T ss_pred cCCCEEEEEeccc---CCCEEEEEEE
Confidence 3566666665554 2455665443
No 42
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=32.49 E-value=1.5e+02 Score=24.65 Aligned_cols=28 Identities=14% Similarity=0.208 Sum_probs=22.5
Q ss_pred CCCEEEEEeeeccCCCCCcCcEEEEecC
Q 021403 219 VGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (313)
Q Consensus 219 ~GD~VlV~K~~y~~~~p~rGDIVVF~~P 246 (313)
.+|..-+...++.-..+..||+|.++..
T Consensus 10 ~~~~y~l~n~Pf~a~glA~gDvV~~~~~ 37 (117)
T PF14085_consen 10 GDDTYRLDNIPFFAYGLALGDVVRAEPD 37 (117)
T ss_pred CCCEEEEEecccccCCCCCCCEEEEEeC
Confidence 3567777777766789999999999975
No 43
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=32.13 E-value=72 Score=23.68 Aligned_cols=30 Identities=27% Similarity=0.335 Sum_probs=17.5
Q ss_pred CCCcc-CCCCCCEEEEEeeeccCCCCCcCcEEEEecC
Q 021403 211 ASMNP-TLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (313)
Q Consensus 211 ~SMeP-TL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P 246 (313)
.++.| +|..|-.|.|-.+ ++.||.|..+..
T Consensus 19 ~~~K~A~letG~~i~VP~F------I~~Gd~I~VdT~ 49 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVPLF------IEEGDKIKVDTR 49 (56)
T ss_dssp TTEEEEEETTS-EEEEETT--------TT-EEEEETT
T ss_pred CCccEEEEcCCCEEEccce------ecCCCEEEEECC
Confidence 44566 5566777766433 789999999873
No 44
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=28.30 E-value=29 Score=26.82 Aligned_cols=18 Identities=33% Similarity=0.578 Sum_probs=12.2
Q ss_pred CCCccCCCCCCEEEEEee
Q 021403 211 ASMNPTLDVGDRILAEKV 228 (313)
Q Consensus 211 ~SMePTL~~GD~VlV~K~ 228 (313)
.+|+|.|++|++|++.--
T Consensus 12 ~~m~P~L~~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-
T ss_pred hhCCcEeCCCCEEEEEec
Confidence 489999999999998754
No 45
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=27.36 E-value=22 Score=38.83 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=28.5
Q ss_pred EechHHHHHhhhhhCcccccCC---CCcchhhhcccc
Q 021403 8 NFSGYVAQNLAHSAGIRFGFST---TSTRSFHECLFR 41 (313)
Q Consensus 8 ~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 41 (313)
.-+-|||+++|+.+.+-+--|. +.-||||||-|+
T Consensus 586 ~IaPyvah~f~~lfslE~WGGATFDVamRFLhEcPWe 622 (1176)
T KOG0369|consen 586 KIAPYVAHAFAGLFSLENWGGATFDVAMRFLHECPWE 622 (1176)
T ss_pred hcchHHHHHhhhhhhhhhcCCchhhHHHHHHhcChHH
Confidence 3467999999999999887764 488999999875
No 46
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.83 E-value=76 Score=30.59 Aligned_cols=31 Identities=23% Similarity=0.426 Sum_probs=24.6
Q ss_pred CCceeEEEEEE----eCCCEEEEECCEEEECCEEc
Q 021403 256 SGDVFIKRIVA----TAGDCVEVHGGKLLVNGVAQ 286 (313)
Q Consensus 256 ~~~~~VKRVIG----lPGDtV~I~dg~vyVNGk~l 286 (313)
+++..+++|-+ .|||.|.++||...|+|+.+
T Consensus 248 Pg~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~ 282 (293)
T COG4079 248 PGEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDL 282 (293)
T ss_pred CCceEEEEEccCCccCCCCEEEEecCceEeccccc
Confidence 44566677665 39999999999999999764
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=26.56 E-value=90 Score=24.82 Aligned_cols=30 Identities=37% Similarity=0.464 Sum_probs=20.2
Q ss_pred cCCCCCCEEEEEeeeccCCCCCcCcEEEEecC
Q 021403 215 PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (313)
Q Consensus 215 PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P 246 (313)
||...+|++.-+..- ..+++.||+++|..-
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 677789998643322 138999999999764
No 48
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=25.59 E-value=75 Score=35.40 Aligned_cols=48 Identities=19% Similarity=0.290 Sum_probs=34.7
Q ss_pred cCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 215 PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 215 PTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
-.|+.||+|. +.+..||+|+|+.++.+. .-...-.||.=+||.|+.+.
T Consensus 396 ~~l~~g~~v~--------rhl~dgd~vl~NRqPsLH-----r~si~a~~~~v~~~~t~r~n 443 (868)
T TIGR02390 396 ERLEPGWVVE--------RHLIDGDIVLFNRQPSLH-----RMSMMGHKVKVLPGKTFRLN 443 (868)
T ss_pred hhcccCCEEE--------EehhcCccceeccCCccc-----cccceeEEEEEecCceEeec
Confidence 3466676543 467889999998765443 34567888888999999874
No 49
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=24.49 E-value=1.4e+02 Score=29.00 Aligned_cols=50 Identities=20% Similarity=0.414 Sum_probs=34.9
Q ss_pred CccCCCCCCEEEEEeeeccCCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 213 MNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 213 MePTL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
+.-.|+.||.|. +.+..||+|+|+.++.+. .....-.||.=++|.++.+.
T Consensus 185 ~~~~l~~g~~v~--------r~l~dgd~Vl~NRqPsLH-----r~si~a~~v~v~~~~tir~n 234 (295)
T smart00663 185 IAKHLKIGDIVE--------RHVIDGDVVLFNRQPTLH-----RMSIQAHRVRVLEGKTIRLN 234 (295)
T ss_pred HHhcCccccEeh--------eehhcCCEEEEecCCccc-----cccceeEEEEEecCceEEec
Confidence 344556676532 567889999998765443 34466778888899888874
No 50
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=24.14 E-value=92 Score=23.11 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=20.6
Q ss_pred CCCCcc-CCCCCCEEEEEeeeccCCCCCcCcEEEEecC
Q 021403 210 SASMNP-TLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (313)
Q Consensus 210 g~SMeP-TL~~GD~VlV~K~~y~~~~p~rGDIVVF~~P 246 (313)
++++.| +|..|-.|.|-.+ ++.||.|..+..
T Consensus 18 ~~~~K~A~letG~~i~VP~F------I~~Gd~I~V~T~ 49 (56)
T smart00841 18 SGGTKPATLETGAVVQVPLF------INEGDKIKVDTR 49 (56)
T ss_pred CCCcceEEECCCCEEEcCCc------ccCCCEEEEECC
Confidence 345555 5666777666433 688999888864
No 51
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.41 E-value=51 Score=28.32 Aligned_cols=17 Identities=41% Similarity=0.536 Sum_probs=14.5
Q ss_pred CCCccCCCCCCEEEEEe
Q 021403 211 ASMNPTLDVGDRILAEK 227 (313)
Q Consensus 211 ~SMePTL~~GD~VlV~K 227 (313)
.||.|.|.+||+|+..-
T Consensus 12 ~smtPeL~~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLDGDYVFCTV 28 (134)
T ss_pred HhcCccccCCceEEEEe
Confidence 38999999999998653
No 52
>PF14118 YfzA: YfzA-like protein
Probab=22.22 E-value=76 Score=26.12 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=13.0
Q ss_pred EECCCCCccCCCCCCE
Q 021403 207 SIPSASMNPTLDVGDR 222 (313)
Q Consensus 207 ~I~g~SMePTL~~GD~ 222 (313)
.+++.++.|.+++||.
T Consensus 29 ~~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFNEGDF 44 (94)
T ss_pred HhhccccccccCCCch
Confidence 3568899999999875
No 53
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=21.93 E-value=2.2e+02 Score=24.79 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=27.6
Q ss_pred CCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEECCE
Q 021403 234 RPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVHGGK 278 (313)
Q Consensus 234 ~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~dg~ 278 (313)
.++.|..+.+..+ +++.+.-||+.+.+|+|.++-||
T Consensus 92 ~~~~G~~~~~~~~---------~G~~~~~~V~~i~~~~v~vD~NH 127 (156)
T PRK15095 92 EPEIGAIMLFTAM---------DGSEMPGVIREINGDSITVDFNH 127 (156)
T ss_pred CCCCCCEEEEECC---------CCCEEEEEEEEEcCCEEEEECCC
Confidence 5788888888764 35567888999999999998443
No 54
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=21.87 E-value=1.6e+02 Score=23.23 Aligned_cols=31 Identities=23% Similarity=0.343 Sum_probs=21.1
Q ss_pred CccCCCCCCEEEEEeeeccC---CCCCcCcEEEE
Q 021403 213 MNPTLDVGDRILAEKVSYFF---KRPEVSDIVIF 243 (313)
Q Consensus 213 MePTL~~GD~VlV~K~~y~~---~~p~rGDIVVF 243 (313)
|+|.++.||.|.+.+.-++- ..-..|++++-
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~ 34 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLVR 34 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEEc
Confidence 89999999999988765432 23344555553
No 55
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=3.7e+02 Score=22.22 Aligned_cols=58 Identities=21% Similarity=0.337 Sum_probs=31.3
Q ss_pred CCEEEEEeeecc-------------CCCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE---CCEEEECC
Q 021403 220 GDRILAEKVSYF-------------FKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH---GGKLLVNG 283 (313)
Q Consensus 220 GD~VlV~K~~y~-------------~~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~---dg~vyVNG 283 (313)
||+|++.+..-. -.++++|.||..-.-.. ..+...+.-- =.-||+|.+. +..+-+||
T Consensus 7 ~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~------~~~g~~~~~~-VkvGD~Vlf~ky~G~evk~dg 79 (96)
T COG0234 7 GDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRR------DENGELVPLD-VKVGDRVLFGKYAGTEVKIDG 79 (96)
T ss_pred CCEEEEEEchhhccccCcEEecCccccCCcceEEEEEcccee------cCCCCEeccc-cccCCEEEECccCCcEEEECC
Confidence 788988876321 13677888887754211 0111122222 2358888886 33455665
Q ss_pred E
Q 021403 284 V 284 (313)
Q Consensus 284 k 284 (313)
+
T Consensus 80 e 80 (96)
T COG0234 80 E 80 (96)
T ss_pred E
Confidence 4
No 56
>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=21.72 E-value=1.9e+02 Score=22.10 Aligned_cols=34 Identities=26% Similarity=0.282 Sum_probs=23.4
Q ss_pred CCCCcCcEEEEecCCcccccCCCCCceeEEEEE--------EeCCCEEEEE
Q 021403 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIV--------ATAGDCVEVH 275 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVI--------GlPGDtV~I~ 275 (313)
..++.||-|.+.+. ....-||.+. +.+||.|.+.
T Consensus 25 G~v~~Gd~v~~~P~---------~~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 25 GSIRVGDEVVVLPS---------GKTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred ceEECCCEEEEcCC---------CCeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 57788888888653 2345566666 7788888774
No 57
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=21.06 E-value=90 Score=25.64 Aligned_cols=9 Identities=33% Similarity=0.431 Sum_probs=4.6
Q ss_pred CCcCcEEEE
Q 021403 235 PEVSDIVIF 243 (313)
Q Consensus 235 p~rGDIVVF 243 (313)
+++||+|+.
T Consensus 58 I~~GD~VlV 66 (99)
T TIGR00523 58 IREGDVVIV 66 (99)
T ss_pred ecCCCEEEE
Confidence 344555555
No 58
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=21.04 E-value=69 Score=27.04 Aligned_cols=17 Identities=47% Similarity=0.771 Sum_probs=11.5
Q ss_pred CCCCccCCCCCCEEEEE
Q 021403 210 SASMNPTLDVGDRILAE 226 (313)
Q Consensus 210 g~SMePTL~~GD~VlV~ 226 (313)
++.|.+.|+.||.||+.
T Consensus 49 ~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 49 SDAMRHSLQVGDKVLAP 65 (124)
T ss_pred cCcccCcCCCCCEEEEe
Confidence 35667777777777765
No 59
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=20.40 E-value=1.4e+02 Score=35.11 Aligned_cols=38 Identities=26% Similarity=0.461 Sum_probs=29.2
Q ss_pred CCCCcCcEEEEecCCcccccCCCCCceeEEEEEEeCCCEEEEE
Q 021403 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVH 275 (313)
Q Consensus 233 ~~p~rGDIVVF~~P~~~~~~g~~~~~~~VKRVIGlPGDtV~I~ 275 (313)
+.+..||+|+|+.++.+. .-...-+||.=+||.|+.+.
T Consensus 426 Rhl~dGD~VL~NRQPSLH-----k~Simah~vkvl~~kT~Rln 463 (1321)
T PRK14977 426 RHLADGDIVIFNRQPSLH-----KLSILAHRVKVLPGATFRLH 463 (1321)
T ss_pred EEeecCcEEEeccCCccc-----cccceEEEEEEecCceEEec
Confidence 457889999998766443 33567888888999999874
No 60
>PRK09919 anti-adapter protein IraM; Provisional
Probab=20.40 E-value=91 Score=26.51 Aligned_cols=21 Identities=14% Similarity=0.185 Sum_probs=18.7
Q ss_pred eCCCEEEEECCEEEECCEEcC
Q 021403 267 TAGDCVEVHGGKLLVNGVAQD 287 (313)
Q Consensus 267 lPGDtV~I~dg~vyVNGk~l~ 287 (313)
.|||.+...+..|.|||++..
T Consensus 40 ~pG~~i~~~~~gvliNdk~~p 60 (114)
T PRK09919 40 PPGSIITPVKSGVLLNDKPYP 60 (114)
T ss_pred CCCCEEEEcCCeEEECCcEeE
Confidence 599999999999999998754
Done!