Query 038446
Match_columns 231
No_of_seqs 218 out of 1784
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:09:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038446hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01106 NifU: NifU-like domai 99.9 8E-23 1.7E-27 149.8 7.1 68 85-152 1-68 (68)
2 COG0694 Thioredoxin-like prote 99.9 1.8E-22 3.9E-27 156.6 8.8 76 82-157 11-89 (93)
3 KOG2358 NifU-like domain-conta 99.8 2.9E-22 6.2E-27 173.9 3.0 161 35-230 24-198 (213)
4 PF01106 NifU: NifU-like domai 99.8 4.9E-21 1.1E-25 140.3 7.0 64 166-230 1-68 (68)
5 TIGR03341 YhgI_GntY IscR-regul 99.8 9.8E-21 2.1E-25 163.2 7.9 78 81-158 106-185 (190)
6 PRK11190 Fe/S biogenesis prote 99.8 1.7E-20 3.6E-25 162.1 7.9 77 82-158 108-187 (192)
7 COG0694 Thioredoxin-like prote 99.8 1.1E-19 2.4E-24 141.0 8.7 67 163-230 11-84 (93)
8 TIGR02000 NifU_proper Fe-S clu 99.8 4E-20 8.6E-25 168.4 5.6 120 105-230 156-290 (290)
9 TIGR02000 NifU_proper Fe-S clu 99.7 3E-18 6.5E-23 156.1 8.3 70 82-152 221-290 (290)
10 TIGR03341 YhgI_GntY IscR-regul 99.7 3.4E-18 7.4E-23 147.4 7.5 68 162-230 106-179 (190)
11 PRK11190 Fe/S biogenesis prote 99.7 4.9E-18 1.1E-22 146.8 7.5 68 162-230 107-181 (192)
12 KOG2358 NifU-like domain-conta 99.4 1.8E-13 3.9E-18 119.3 2.4 74 83-156 126-202 (213)
13 PF01883 DUF59: Domain of unkn 95.7 0.087 1.9E-06 37.9 8.0 65 164-229 2-72 (72)
14 PF01883 DUF59: Domain of unkn 95.4 0.099 2.1E-06 37.6 7.1 67 82-150 1-71 (72)
15 TIGR03406 FeS_long_SufT probab 83.0 21 0.00045 30.8 10.7 70 159-229 71-151 (174)
16 TIGR02945 SUF_assoc FeS assemb 79.8 14 0.00031 27.9 7.8 66 163-229 3-75 (99)
17 TIGR02945 SUF_assoc FeS assemb 79.2 12 0.00026 28.3 7.2 67 82-150 3-74 (99)
18 TIGR03406 FeS_long_SufT probab 66.7 34 0.00073 29.5 7.7 72 77-150 70-150 (174)
19 PRK10862 SoxR reducing system 66.6 7.8 0.00017 32.5 3.7 26 103-128 6-33 (154)
20 PF09012 FeoC: FeoC like trans 61.0 15 0.00033 26.1 3.9 40 79-129 25-65 (69)
21 PF04246 RseC_MucC: Positive r 60.9 8.2 0.00018 31.0 2.8 22 105-126 1-24 (135)
22 TIGR02159 PA_CoA_Oxy4 phenylac 59.1 36 0.00078 28.4 6.4 44 183-228 15-61 (146)
23 PF00403 HMA: Heavy-metal-asso 58.1 12 0.00027 25.4 2.9 50 115-172 2-58 (62)
24 COG2151 PaaD Predicted metal-s 56.8 71 0.0015 25.7 7.5 66 82-149 14-85 (111)
25 PF07315 DUF1462: Protein of u 55.9 6.8 0.00015 30.8 1.4 58 120-179 8-73 (93)
26 PF09580 Spore_YhcN_YlaJ: Spor 55.4 48 0.001 27.5 6.6 46 109-156 98-143 (177)
27 TIGR02159 PA_CoA_Oxy4 phenylac 51.3 1.1E+02 0.0023 25.6 7.9 75 101-179 15-94 (146)
28 PRK11670 antiporter inner memb 51.1 81 0.0017 29.9 8.1 68 161-229 12-85 (369)
29 COG2151 PaaD Predicted metal-s 48.5 1.3E+02 0.0028 24.2 7.7 66 163-229 14-87 (111)
30 PRK09579 multidrug efflux prot 40.4 2.7E+02 0.0059 30.0 10.8 112 111-229 45-176 (1017)
31 PRK11670 antiporter inner memb 40.3 1.1E+02 0.0024 29.0 7.1 68 80-149 12-83 (369)
32 COG1941 FrhG Coenzyme F420-red 40.1 63 0.0014 29.6 5.2 29 112-141 6-34 (247)
33 PF07315 DUF1462: Protein of u 39.7 21 0.00046 28.1 1.9 22 202-224 8-36 (93)
34 PF04246 RseC_MucC: Positive r 39.0 28 0.00061 27.9 2.6 20 187-206 1-22 (135)
35 PRK10862 SoxR reducing system 39.0 38 0.00082 28.4 3.4 22 185-206 6-29 (154)
36 PRK10503 multidrug efflux syst 38.6 3.2E+02 0.0069 29.6 11.0 112 111-229 54-186 (1040)
37 PF02061 Lambda_CIII: Lambda P 38.5 28 0.00061 23.7 2.1 33 116-148 5-37 (45)
38 COG4837 Uncharacterized protei 36.1 22 0.00047 28.4 1.4 26 120-146 15-43 (106)
39 PF13192 Thioredoxin_3: Thiore 35.6 63 0.0014 23.1 3.8 25 195-220 3-27 (76)
40 PF00873 ACR_tran: AcrB/AcrD/A 35.4 81 0.0017 33.6 6.0 112 111-229 43-176 (1021)
41 COG4837 Uncharacterized protei 35.1 36 0.00079 27.2 2.5 29 196-224 6-43 (106)
42 PRK10614 multidrug efflux syst 33.8 4.4E+02 0.0096 28.4 11.2 112 111-229 45-177 (1025)
43 PF04865 Baseplate_J: Baseplat 30.8 1.5E+02 0.0033 25.5 6.1 79 63-146 146-228 (243)
44 PRK10718 RpoE-regulated lipopr 30.4 94 0.002 27.5 4.6 106 76-206 51-169 (191)
45 PF10646 Germane: Sporulation 29.8 2.4E+02 0.0053 21.2 6.7 48 182-229 52-106 (117)
46 TIGR02898 spore_YhcN_YlaJ spor 28.3 2.7E+02 0.0058 23.7 6.9 48 109-156 77-124 (158)
47 CHL00123 rps6 ribosomal protei 28.1 66 0.0014 24.8 3.0 29 79-107 17-45 (97)
48 PF01545 Cation_efflux: Cation 27.9 2.6E+02 0.0057 24.3 7.1 34 195-228 240-275 (284)
49 COG3086 RseC Positive regulato 26.1 64 0.0014 27.5 2.7 35 104-139 7-43 (150)
50 TIGR01297 CDF cation diffusion 25.9 3.6E+02 0.0078 23.4 7.6 63 163-228 194-262 (268)
51 PF06572 DUF1131: Protein of u 23.4 1.2E+02 0.0026 26.3 4.0 125 53-205 11-148 (171)
52 PF15603 Imm45: Immunity prote 22.8 92 0.002 23.8 2.8 32 73-104 49-80 (82)
53 PF01545 Cation_efflux: Cation 21.8 3E+02 0.0065 24.0 6.3 37 112-150 239-275 (284)
54 PF05258 DUF721: Protein of un 21.4 3E+02 0.0066 19.4 5.5 62 163-228 22-88 (89)
55 PF02641 DUF190: Uncharacteriz 21.4 1.5E+02 0.0033 22.7 3.9 27 80-108 72-98 (101)
No 1
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=99.88 E-value=8e-23 Score=149.77 Aligned_cols=68 Identities=53% Similarity=0.906 Sum_probs=64.4
Q ss_pred HHHHHHHhcCccccCCCeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeee
Q 038446 85 VERVLDEVRPGLMADGGNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQI 152 (231)
Q Consensus 85 V~~vL~~IRP~L~~dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v 152 (231)
|+++|++|||+|++||||++|++|++++|||||+|+|++||++.+|++++||++|++++|++.+|.++
T Consensus 1 V~~~l~~IrP~L~~dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~~v 68 (68)
T PF01106_consen 1 VEEVLEEIRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHHCHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHHhChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 68899999999999999999999999999999999999999999999999999999999999998763
No 2
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.8e-22 Score=156.59 Aligned_cols=76 Identities=55% Similarity=0.874 Sum_probs=71.5
Q ss_pred HHHHHHHHH-HhcCccccCCCeEEEEEEe--CcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeeccccc
Q 038446 82 EENVERVLD-EVRPGLMADGGNVALHEID--GLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTET 157 (231)
Q Consensus 82 ~e~V~~vL~-~IRP~L~~dGGdVeLv~Ve--~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~~ 157 (231)
.++|+.+|+ +|||+|++|||||+|++|+ +|+|+++|+|+|+|||++.+|||++||++|++.+|++.+|+++.++..
T Consensus 11 ~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~~~~~ 89 (93)
T COG0694 11 LERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVTEHAR 89 (93)
T ss_pred HHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEccCccc
Confidence 578999998 7999999999999999999 789999999999999999999999999999999999999999877653
No 3
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=2.9e-22 Score=173.91 Aligned_cols=161 Identities=38% Similarity=0.502 Sum_probs=136.2
Q ss_pred cccccCCcC---CCccccccccccc---ccccccccceeecccccCCC--CCCCcHHHHHHHHHHhcCccccCCCeEEEE
Q 038446 35 LSLFKNPIS---DFSGFSSKQSSFL---GFSLNHVRRKHRGLVVSPCC--VLPLTEENVERVLDEVRPGLMADGGNVALH 106 (231)
Q Consensus 35 ~~~~~~~~~---~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~p~~--~~~lt~e~V~~vL~~IRP~L~~dGGdVeLv 106 (231)
+.+.++++. ....|+..++.|+ ...+.+..+.+..++..|+. -.+++++.++.+|+..+|++.+|||++.+-
T Consensus 24 ~f~p~~~i~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~p 103 (213)
T KOG2358|consen 24 LFLPGKQILSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLP 103 (213)
T ss_pred cccCCCcccccccccccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccch
Confidence 334667777 4666777777663 33444555677778888884 458989999999999999999999999999
Q ss_pred EEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccccccchhhHHHHHHHHhccceecccCCCcEE
Q 038446 107 EIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTETGLELNEENIEKVLAEIRPYLAGTGGGILE 186 (231)
Q Consensus 107 ~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~~~~~lt~e~V~~vL~~IRP~L~~hdGGdvE 186 (231)
.|++..+.++++|+|..||.+.+++|+.||. +|||.++. ||||++
T Consensus 104 li~g~~~~~~~~~~~e~d~e~t~~ikeliet----------------------------------RiRp~i~e-dggdi~ 148 (213)
T KOG2358|consen 104 LIDGNIVVLKLQGACESDPESTMTIKELIET----------------------------------RIRPKIQE-DGGDED 148 (213)
T ss_pred hhccchhhhhhcccccCChhHHHHHHHHHHH----------------------------------hhhhhhhc-cCCcee
Confidence 9999999999999999999998888776663 36777888 799999
Q ss_pred EEEEeC--CEEEEEecCCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 038446 187 LIQIDD--YVVRVRLSGPAAGVM----TVRVALTQKLREKIPSIAAVQLI 230 (231)
Q Consensus 187 lV~v~~--~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iPei~~V~~v 230 (231)
++++|+ ++++.||+|+|.+|+ |||++||..|+.++|++|.|+.+
T Consensus 149 y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv 198 (213)
T KOG2358|consen 149 YVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGVIQV 198 (213)
T ss_pred eccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEEEec
Confidence 999998 599999999999995 99999999999999999999875
No 4
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=99.84 E-value=4.9e-21 Score=140.33 Aligned_cols=64 Identities=45% Similarity=0.773 Sum_probs=59.8
Q ss_pred HHHHHHhccceecccCCCcEEEEEEeCCEEEEEecCCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 038446 166 IEKVLAEIRPYLAGTGGGILELIQIDDYVVRVRLSGPAAGVM----TVRVALTQKLREKIPSIAAVQLI 230 (231)
Q Consensus 166 V~~vL~~IRP~L~~hdGGdvElV~v~~~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iPei~~V~~v 230 (231)
|+++|++|||+|++| |||++|+++++++|+|||+|+|++|+ |++++||++|++++|++++|+++
T Consensus 1 V~~~l~~IrP~L~~d-GGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~~v 68 (68)
T PF01106_consen 1 VEEVLEEIRPYLQSD-GGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHHCHHHHHHT-TEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHHhChHHHhc-CCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 678999999999995 99999999999999999999999994 99999999999999999999875
No 5
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=99.83 E-value=9.8e-21 Score=163.20 Aligned_cols=78 Identities=38% Similarity=0.662 Sum_probs=72.8
Q ss_pred cHHHHHHHHH-HhcCccccCCCeEEEEEEe-CcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccccc
Q 038446 81 TEENVERVLD-EVRPGLMADGGNVALHEID-GLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTETG 158 (231)
Q Consensus 81 t~e~V~~vL~-~IRP~L~~dGGdVeLv~Ve-~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~~~ 158 (231)
..++|+.+|+ +|||+|++|||||+|++|+ +++|+|||+|+|++||++.+||+++||++|++.+|++.+|+.+++|..+
T Consensus 106 ~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~~~~~~~ 185 (190)
T TIGR03341 106 LEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDATDHTRG 185 (190)
T ss_pred HHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEecCcccc
Confidence 3678999998 7999999999999999998 4799999999999999999999999999999999999999999888654
No 6
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.82 E-value=1.7e-20 Score=162.12 Aligned_cols=77 Identities=36% Similarity=0.658 Sum_probs=72.5
Q ss_pred HHHHHHHHH-HhcCccccCCCeEEEEEEe-CcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcc-cceeeeeecccccc
Q 038446 82 EENVERVLD-EVRPGLMADGGNVALHEID-GLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIP-EILEVEQILDTETG 158 (231)
Q Consensus 82 ~e~V~~vL~-~IRP~L~~dGGdVeLv~Ve-~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iP-ei~~V~~v~~~~~~ 158 (231)
.++|+.+|+ +|||+|++|||||+|++|+ +++|+|||+|+|++||++.+||+++||.+|++.+| ++.+|+.+++|+.+
T Consensus 108 ~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~~~~~ 187 (192)
T PRK11190 108 MERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTEHQRG 187 (192)
T ss_pred HHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEecccccC
Confidence 678999997 7999999999999999998 57999999999999999999999999999999999 99999999888654
No 7
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.81 E-value=1.1e-19 Score=141.00 Aligned_cols=67 Identities=42% Similarity=0.684 Sum_probs=63.3
Q ss_pred hHHHHHHHH-hccceecccCCCcEEEEEEe--CCEEEEEecCCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 038446 163 EENIEKVLA-EIRPYLAGTGGGILELIQID--DYVVRVRLSGPAAGVM----TVRVALTQKLREKIPSIAAVQLI 230 (231)
Q Consensus 163 ~e~V~~vL~-~IRP~L~~hdGGdvElV~v~--~~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iPei~~V~~v 230 (231)
.++|+++|+ +|||+|++ ||||++|++|+ +|+|++||.|||+||+ |||++||++|++.+|++++|+.+
T Consensus 11 ~e~v~~~l~~~irP~l~~-dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v 84 (93)
T COG0694 11 LERVEEVLDEKIRPQLAM-DGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQV 84 (93)
T ss_pred HHHHHHHHHhccCcceec-cCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEc
Confidence 589999998 99999999 59999999998 7899999999999994 99999999999999999999876
No 8
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=99.80 E-value=4e-20 Score=168.42 Aligned_cols=120 Identities=28% Similarity=0.454 Sum_probs=89.0
Q ss_pred EEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccce---eeeeecccc----cccchh----hHHHHHHHHhc
Q 038446 105 LHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEIL---EVEQILDTE----TGLELN----EENIEKVLAEI 173 (231)
Q Consensus 105 Lv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~---~V~~v~~~~----~~~~lt----~e~V~~vL~~I 173 (231)
..++++...+++.++.|++|-. .++..++..+.+. +... ...+.+++. .+.+|+ .++|+++|++|
T Consensus 156 ~~t~~el~~~t~agt~CG~C~~---~~~~il~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~i 231 (290)
T TIGR02000 156 LTTLEEVTNYTKAGGGCGSCHE---KIEDVLKEVLANK-GATNPANAGGSKPTNKPNSGQKRPLTNVQRIQLIQKVLEEV 231 (290)
T ss_pred CCcHHHHHhhccCCCCCcchHH---HHHHHHHHHHHhc-cccccccccccCcccccccCcchhcChHHHHHHHHHHHHHh
Confidence 3456666778899999999954 3444444444432 1110 112221111 112344 58899999999
Q ss_pred cceecccCCCcEEEEEEeCCEEEEEecCCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 038446 174 RPYLAGTGGGILELIQIDDYVVRVRLSGPAAGVM----TVRVALTQKLREKIPSIAAVQLI 230 (231)
Q Consensus 174 RP~L~~hdGGdvElV~v~~~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iPei~~V~~v 230 (231)
||||++| |||+||++|++++|+|||+|+|+||+ ||++ ||++|++++|++.+|+.|
T Consensus 232 rP~l~~d-GGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 232 RPVLQAD-GGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred CchHhhc-CCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 9999995 99999999999999999999999994 9998 999999999999999875
No 9
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=99.74 E-value=3e-18 Score=156.15 Aligned_cols=70 Identities=49% Similarity=0.818 Sum_probs=66.4
Q ss_pred HHHHHHHHHHhcCccccCCCeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeee
Q 038446 82 EENVERVLDEVRPGLMADGGNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQI 152 (231)
Q Consensus 82 ~e~V~~vL~~IRP~L~~dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v 152 (231)
.++|+.+|++|||+|++|||||+|++|++++|||||+|+|++||++.+||+. ||++|++.+|++..|.++
T Consensus 221 ~~~v~~~l~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 221 IQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred HHHHHHHHHHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 3689999989999999999999999999999999999999999999999998 999999999999988753
No 10
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=99.74 E-value=3.4e-18 Score=147.44 Aligned_cols=68 Identities=34% Similarity=0.523 Sum_probs=63.3
Q ss_pred hhHHHHHHHH-hccceecccCCCcEEEEEEe-CCEEEEEecCCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 038446 162 NEENIEKVLA-EIRPYLAGTGGGILELIQID-DYVVRVRLSGPAAGVM----TVRVALTQKLREKIPSIAAVQLI 230 (231)
Q Consensus 162 t~e~V~~vL~-~IRP~L~~hdGGdvElV~v~-~~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iPei~~V~~v 230 (231)
..++|+++|+ +|||+|++| |||+|||+|+ +++|+|||+|+|++|+ |||++||++|++++|++++|+.+
T Consensus 106 ~~~~i~~~l~~~irP~l~~d-GGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~ 179 (190)
T TIGR03341 106 LEERINYVLQSEINPQLASH-GGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDA 179 (190)
T ss_pred HHHHHHHHHHhccCHHHHhc-CCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEe
Confidence 3689999998 899999995 9999999997 5799999999999995 99999999999999999999875
No 11
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.73 E-value=4.9e-18 Score=146.78 Aligned_cols=68 Identities=29% Similarity=0.512 Sum_probs=63.4
Q ss_pred hhHHHHHHHH-hccceecccCCCcEEEEEEe-CCEEEEEecCCCCCch----hHHHHHHHHHHhhCC-CcceEEeC
Q 038446 162 NEENIEKVLA-EIRPYLAGTGGGILELIQID-DYVVRVRLSGPAAGVM----TVRVALTQKLREKIP-SIAAVQLI 230 (231)
Q Consensus 162 t~e~V~~vL~-~IRP~L~~hdGGdvElV~v~-~~vv~VrL~GaC~gC~----Tlk~~Ie~~Lr~~iP-ei~~V~~v 230 (231)
..++|+++|+ +|||+|++| |||+||++|+ +++|+|||+|+|+||+ |||++||++|++++| +|++|+.+
T Consensus 107 ~~~~i~~~l~~~irP~l~~d-GGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v 181 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAGH-GGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDL 181 (192)
T ss_pred HHHHHHHHHHhccChhHHhc-CCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEe
Confidence 3689999997 999999995 9999999997 6899999999999995 999999999999999 99999875
No 12
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.37 E-value=1.8e-13 Score=119.32 Aligned_cols=74 Identities=41% Similarity=0.669 Sum_probs=68.8
Q ss_pred HHHHHHHH-HhcCccccCCCeEEEEEEeC--cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccc
Q 038446 83 ENVERVLD-EVRPGLMADGGNVALHEIDG--LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTE 156 (231)
Q Consensus 83 e~V~~vL~-~IRP~L~~dGGdVeLv~Ve~--~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~ 156 (231)
..++..|+ +|||.++.||||++++++|+ +.|++|++|+|.+||++..||+++||..|+.++|+++.|+++.+.+
T Consensus 126 ~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv~d~e 202 (213)
T KOG2358|consen 126 MTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGVIQVPDAE 202 (213)
T ss_pred HHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEEEeccCcc
Confidence 45777776 69999999999999999998 5999999999999999999999999999999999999999988765
No 13
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=95.73 E-value=0.087 Score=37.86 Aligned_cols=65 Identities=22% Similarity=0.358 Sum_probs=47.8
Q ss_pred HHHHHHHH-hccceeccc--CCCcEEEEEEeCCEEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceEEe
Q 038446 164 ENIEKVLA-EIRPYLAGT--GGGILELIQIDDYVVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAVQL 229 (231)
Q Consensus 164 e~V~~vL~-~IRP~L~~h--dGGdvElV~v~~~vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V~~ 229 (231)
+.|.++|. -.-|++... +-|-+.=+.++++.|+|.+.=+..+|+ .++..|+++|+ .+|+++.|++
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~-~l~gv~~V~V 72 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT-SEEEE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCCCceEeC
Confidence 55667775 355655442 247888899999999999999988885 78899999999 7999998864
No 14
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=95.36 E-value=0.099 Score=37.57 Aligned_cols=67 Identities=25% Similarity=0.387 Sum_probs=51.5
Q ss_pred HHHHHHHHHH-hcCccc---cCCCeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeee
Q 038446 82 EENVERVLDE-VRPGLM---ADGGNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVE 150 (231)
Q Consensus 82 ~e~V~~vL~~-IRP~L~---~dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~ 150 (231)
+++|..+|.. .-|++. -+=|-|.=+.++++.|++.+.-...+|| ....++..|+++|+ .+|++.+|.
T Consensus 1 k~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~gv~~V~ 71 (72)
T PF01883_consen 1 KQAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVK 71 (72)
T ss_dssp HHHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEE
T ss_pred CHHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEe
Confidence 3678888864 556555 3447788899999999999999999999 67889999999999 788877664
No 15
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=83.00 E-value=21 Score=30.76 Aligned_cols=70 Identities=17% Similarity=0.228 Sum_probs=49.5
Q ss_pred cchhhHHHHHHHH-hccceeccc--CCCcEEEEEEeC---C--EEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceE
Q 038446 159 LELNEENIEKVLA-EIRPYLAGT--GGGILELIQIDD---Y--VVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAV 227 (231)
Q Consensus 159 ~~lt~e~V~~vL~-~IRP~L~~h--dGGdvElV~v~~---~--vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V 227 (231)
.+.++++|.++|+ -.-|.+... +-|-|.=+.+++ + .|+|.++=...+|. .++..|+++|.. +|.++.|
T Consensus 71 ~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL~~-l~gV~~V 149 (174)
T TIGR03406 71 GEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVLA-VPNVDEV 149 (174)
T ss_pred ccccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHHHh-CCCceeE
Confidence 3456788999997 466766541 135565567765 5 78888887777773 788888888864 7888876
Q ss_pred Ee
Q 038446 228 QL 229 (231)
Q Consensus 228 ~~ 229 (231)
.+
T Consensus 150 ~V 151 (174)
T TIGR03406 150 EV 151 (174)
T ss_pred EE
Confidence 53
No 16
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=79.82 E-value=14 Score=27.91 Aligned_cols=66 Identities=17% Similarity=0.303 Sum_probs=42.4
Q ss_pred hHHHHHHHH-hccceeccc--CCCcEEEEEEeC-CEEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceEEe
Q 038446 163 EENIEKVLA-EIRPYLAGT--GGGILELIQIDD-YVVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAVQL 229 (231)
Q Consensus 163 ~e~V~~vL~-~IRP~L~~h--dGGdvElV~v~~-~vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V~~ 229 (231)
+++|.++|+ -.-|.+... +-|-+.=+.+++ +.++|.+.-+..+|+ .++..+++.|.. +|+++.|.+
T Consensus 3 ~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~~l~~~i~~al~~-l~gv~~v~v 75 (99)
T TIGR02945 3 KDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEVENAVRA-VPGVGSVTV 75 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHHHHHHHHHHHHh-CCCCceEEE
Confidence 356777776 345555431 124455567775 888887776666663 677888888864 788877653
No 17
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=79.22 E-value=12 Score=28.31 Aligned_cols=67 Identities=18% Similarity=0.298 Sum_probs=46.9
Q ss_pred HHHHHHHHHH-hcCcccc---CCCeEEEEEEeC-cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeee
Q 038446 82 EENVERVLDE-VRPGLMA---DGGNVALHEIDG-LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVE 150 (231)
Q Consensus 82 ~e~V~~vL~~-IRP~L~~---dGGdVeLv~Ve~-~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~ 150 (231)
.++|..+|+. .-|.+.. .=|-|.=+.+++ +.+++.+.-...+||.. ..++..++++|.. +|.+..|.
T Consensus 3 ~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~-~~l~~~i~~al~~-l~gv~~v~ 74 (99)
T TIGR02945 3 KDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVA-GSMPGEVENAVRA-VPGVGSVT 74 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChH-HHHHHHHHHHHHh-CCCCceEE
Confidence 4678888875 5566553 334566667785 88998888877778854 4588888888865 66665554
No 18
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=66.73 E-value=34 Score=29.47 Aligned_cols=72 Identities=21% Similarity=0.192 Sum_probs=51.1
Q ss_pred CCCCcHHHHHHHHHH-hcCcccc---CCCeEEEEEEeC---c--EEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccce
Q 038446 77 VLPLTEENVERVLDE-VRPGLMA---DGGNVALHEIDG---L--VVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEIL 147 (231)
Q Consensus 77 ~~~lt~e~V~~vL~~-IRP~L~~---dGGdVeLv~Ve~---~--~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~ 147 (231)
.-+.++++|..+|+. .-|.+.. +=|-|.=+++++ + .|+|++.-...+|+.. ..++..|+++|.. +|.+.
T Consensus 70 ~~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~-~~L~~dV~~aL~~-l~gV~ 147 (174)
T TIGR03406 70 DGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMG-PVLVEDVEDKVLA-VPNVD 147 (174)
T ss_pred cccccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHH-HHHHHHHHHHHHh-CCCce
Confidence 345667889999975 5566553 335566667776 5 8999998888889864 5677788888864 67766
Q ss_pred eee
Q 038446 148 EVE 150 (231)
Q Consensus 148 ~V~ 150 (231)
+|.
T Consensus 148 ~V~ 150 (174)
T TIGR03406 148 EVE 150 (174)
T ss_pred eEE
Confidence 654
No 19
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=66.64 E-value=7.8 Score=32.50 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=20.8
Q ss_pred EEEEEEeCcEEEEEE--ccCCCCCCCch
Q 038446 103 VALHEIDGLVVVLKL--QGACGSCPSST 128 (231)
Q Consensus 103 VeLv~Ve~~~V~VrL--~GaC~gCpss~ 128 (231)
-.+++++++.++|+. +.+|++|.+..
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C~a~~ 33 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSCASRA 33 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCcCCCC
Confidence 367889999888887 68999998643
No 20
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=60.98 E-value=15 Score=26.15 Aligned_cols=40 Identities=23% Similarity=0.535 Sum_probs=24.0
Q ss_pred CCcHHHHHHHHHH-hcCccccCCCeEEEEEEeCcEEEEEEccCCCCCCCchH
Q 038446 79 PLTEENVERVLDE-VRPGLMADGGNVALHEIDGLVVVLKLQGACGSCPSSTM 129 (231)
Q Consensus 79 ~lt~e~V~~vL~~-IRP~L~~dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~ 129 (231)
.++.+.|+..|+. + +-|-|+-++..... +|.|++|+....
T Consensus 25 ~~s~~~ve~mL~~l~------~kG~I~~~~~~~~~-----~~~C~~C~~~~~ 65 (69)
T PF09012_consen 25 GISPEAVEAMLEQLI------RKGYIRKVDMSSCC-----GGSCSSCGPASK 65 (69)
T ss_dssp T--HHHHHHHHHHHH------CCTSCEEEEEE--S-----SSSSSS-SS---
T ss_pred CcCHHHHHHHHHHHH------HCCcEEEecCCCCC-----CCCCCCCCCccc
Confidence 4556778888875 4 56778876666544 899999998654
No 21
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=60.95 E-value=8.2 Score=31.02 Aligned_cols=22 Identities=27% Similarity=0.750 Sum_probs=17.9
Q ss_pred EEEEeCcEEEEEE--ccCCCCCCC
Q 038446 105 LHEIDGLVVVLKL--QGACGSCPS 126 (231)
Q Consensus 105 Lv~Ve~~~V~VrL--~GaC~gCps 126 (231)
+++++++.++|+. ..+|++|.+
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~ 24 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSA 24 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCC
Confidence 3678999888888 778999984
No 22
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=59.12 E-value=36 Score=28.44 Aligned_cols=44 Identities=18% Similarity=0.364 Sum_probs=34.7
Q ss_pred CcEEEEEEeCCEEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceEE
Q 038446 183 GILELIQIDDYVVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAVQ 228 (231)
Q Consensus 183 GdvElV~v~~~vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V~ 228 (231)
|-|.=|+++++.|.|.|+=.-.+|+ .|++.|+++|++. .+..|+
T Consensus 15 G~Vr~V~v~gd~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~--Gv~~V~ 61 (146)
T TIGR02159 15 GMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRAL--GVEVVE 61 (146)
T ss_pred CCeeEEEEECCEEEEEEEeCCCCCchHHHHHHHHHHHHHhc--CCCeEE
Confidence 6677778888899999998888885 7888899999874 555544
No 23
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=58.14 E-value=12 Score=25.39 Aligned_cols=50 Identities=22% Similarity=0.398 Sum_probs=30.4
Q ss_pred EEE-ccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccc------cccchhhHHHHHHHHh
Q 038446 115 LKL-QGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTE------TGLELNEENIEKVLAE 172 (231)
Q Consensus 115 VrL-~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~------~~~~lt~e~V~~vL~~ 172 (231)
++. +-.|.+|.. .|+++|.. +|.+..|....... +....+.+.|.+.|++
T Consensus 2 ~~v~~m~C~~C~~-------~v~~~l~~-~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 2 FKVPGMTCEGCAK-------KVEKALSK-LPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp EEEESTTSHHHHH-------HHHHHHHT-STTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred EEECCcccHHHHH-------HHHHHHhc-CCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 344 557888877 88988886 68887765432211 1122345667776654
No 24
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=56.79 E-value=71 Score=25.69 Aligned_cols=66 Identities=26% Similarity=0.393 Sum_probs=44.2
Q ss_pred HHHHHHHHHH-hcCccccC---CCeEEEEEEeC--cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceee
Q 038446 82 EENVERVLDE-VRPGLMAD---GGNVALHEIDG--LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEV 149 (231)
Q Consensus 82 ~e~V~~vL~~-IRP~L~~d---GGdVeLv~Ve~--~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V 149 (231)
.++|..+|.. +-|.|--+ =|=|.=+++++ +.++|++..-=.+||.+. -+...|+.+|++ +|.+.+|
T Consensus 14 ~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~-~i~~~v~~al~~-~~~v~~v 85 (111)
T COG2151 14 LEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAE-VIADQVEAALEE-IPGVEDV 85 (111)
T ss_pred HHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccH-HHHHHHHHHHHh-cCCcceE
Confidence 5677777764 66766544 23233356664 489999999889999975 345678888876 5545443
No 25
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=55.93 E-value=6.8 Score=30.79 Aligned_cols=58 Identities=28% Similarity=0.474 Sum_probs=30.8
Q ss_pred CCCCC---CCchHhHHHHHHHHHhhhcccc-eeee--eecccccccchhhHHHHHHHH--hccceecc
Q 038446 120 ACGSC---PSSTMTLKMGIETRLRDKIPEI-LEVE--QILDTETGLELNEENIEKVLA--EIRPYLAG 179 (231)
Q Consensus 120 aC~gC---pss~~TLk~~IE~~L~e~iPei-~~V~--~v~~~~~~~~lt~e~V~~vL~--~IRP~L~~ 179 (231)
-|.+| |+|-.|. .+++.+|.+++|+. -++. ++..+.+. +-..+-++++++ ..=|.+-.
T Consensus 8 ~CASCVn~PsSkeTy-eWL~aal~RKyp~~~f~~~YiDi~~p~~~-~~~~~~a~~I~ede~fYPlV~i 73 (93)
T PF07315_consen 8 ICASCVNAPSSKETY-EWLEAALKRKYPDQPFEFTYIDIENPPEN-DHDQQFAERILEDELFYPLVVI 73 (93)
T ss_dssp --GGGSSS--HHHHH-HHHHHHHHHH-TTS-EEEEEEETTT-----HHHHHHHHHHHTTSS-SSEEEE
T ss_pred cchhhcCCCCchhHH-HHHHHHHhCcCCCCceEEEEEecCCCCcc-HHHHHHHHHHHhcccccceEEE
Confidence 36666 7776665 89999999999985 3332 22222211 223455677775 36777766
No 26
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=55.39 E-value=48 Score=27.47 Aligned_cols=46 Identities=15% Similarity=0.099 Sum_probs=33.2
Q ss_pred eCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccc
Q 038446 109 DGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTE 156 (231)
Q Consensus 109 e~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~ 156 (231)
.+..+||-+.-. .. ..-...++..|++++++..|.+..|....++.
T Consensus 98 ~~~~a~Vav~~~-~~-~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D~~ 143 (177)
T PF09580_consen 98 TDDNAYVAVDLD-FN-RFNTKKIKKKVEKAVKSADPRIYNVYVSTDPD 143 (177)
T ss_pred ECCEEEEEEEec-cc-ccchhHHHHHHHHHHHHhCCCccEEEEEcCHH
Confidence 455555555433 22 46678899999999999999999988666544
No 27
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=51.34 E-value=1.1e+02 Score=25.63 Aligned_cols=75 Identities=25% Similarity=0.319 Sum_probs=47.3
Q ss_pred CeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceee--eeecccc-cccchhhHHHHHHH-H-hccc
Q 038446 101 GNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEV--EQILDTE-TGLELNEENIEKVL-A-EIRP 175 (231)
Q Consensus 101 GdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V--~~v~~~~-~~~~lt~e~V~~vL-~-~IRP 175 (231)
|-|.=++++++.|.|.+.-.-.+||.. ..+++.|+++|++. .+.+| ....++. +.+-+++ .-++-| + -|.|
T Consensus 15 G~Vr~V~v~gd~V~VtIt~Ty~gcpa~-e~L~~~I~~aL~~~--Gv~~V~V~i~~~p~Wt~d~it~-~gr~~l~~~giap 90 (146)
T TIGR02159 15 GMVREVDVDGGGVVVKFTPTYSGCPAL-EVIRQDIRDAVRAL--GVEVVEVSTSLDPPWTTDWITE-DAREKLREYGIAP 90 (146)
T ss_pred CCeeEEEEECCEEEEEEEeCCCCCchH-HHHHHHHHHHHHhc--CCCeEEEeEeeCCCCChHHCCH-HHHHHHHhcCccC
Confidence 667777888889999998889999974 57888899998874 34333 3222221 1223443 334445 4 4666
Q ss_pred eecc
Q 038446 176 YLAG 179 (231)
Q Consensus 176 ~L~~ 179 (231)
=...
T Consensus 91 p~~~ 94 (146)
T TIGR02159 91 PAGH 94 (146)
T ss_pred CCcc
Confidence 5544
No 28
>PRK11670 antiporter inner membrane protein; Provisional
Probab=51.06 E-value=81 Score=29.87 Aligned_cols=68 Identities=16% Similarity=0.133 Sum_probs=47.7
Q ss_pred hhhHHHHHHHHh-ccceeccc--CCCcEEEEEEeCCEEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceEEe
Q 038446 161 LNEENIEKVLAE-IRPYLAGT--GGGILELIQIDDYVVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAVQL 229 (231)
Q Consensus 161 lt~e~V~~vL~~-IRP~L~~h--dGGdvElV~v~~~vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V~~ 229 (231)
++.+.|.++|.. .-|.+... .-|-+.=+.++++.+.+.+.-+-..|+ .++..+++.|++ +|+++.|..
T Consensus 12 ~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 85 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQCSAELLR-ITGAKAIDW 85 (369)
T ss_pred chHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHHHHHHHHHHHHHHh-cCCCceEEE
Confidence 345778888874 55655541 125555567888998888887766775 688888998886 788877653
No 29
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=48.54 E-value=1.3e+02 Score=24.23 Aligned_cols=66 Identities=26% Similarity=0.401 Sum_probs=41.4
Q ss_pred hHHHHHHHH-hccceeccc--CCCcEEEEEEe--CCEEEEEecCCCCCch---hHHHHHHHHHHhhCCCcceEEe
Q 038446 163 EENIEKVLA-EIRPYLAGT--GGGILELIQID--DYVVRVRLSGPAAGVM---TVRVALTQKLREKIPSIAAVQL 229 (231)
Q Consensus 163 ~e~V~~vL~-~IRP~L~~h--dGGdvElV~v~--~~vv~VrL~GaC~gC~---Tlk~~Ie~~Lr~~iPei~~V~~ 229 (231)
.++|.++|. -+-|.|--. |=|=+.=++++ ++.++|+++..-.||+ -+.+.++++|++ +|.++.|+.
T Consensus 14 ~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~~-~~~v~~v~V 87 (111)
T COG2151 14 LEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALEE-IPGVEDVEV 87 (111)
T ss_pred HHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHHHHHHHHHHHHh-cCCcceEEE
Confidence 455555565 355554431 12333344565 4589999999999997 566777777776 666766653
No 30
>PRK09579 multidrug efflux protein; Reviewed
Probab=40.36 E-value=2.7e+02 Score=29.96 Aligned_cols=112 Identities=13% Similarity=0.150 Sum_probs=59.8
Q ss_pred cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhccc---ceeeeeecccc---------c--ccchhhHHHHHHHHhccce
Q 038446 111 LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPE---ILEVEQILDTE---------T--GLELNEENIEKVLAEIRPY 176 (231)
Q Consensus 111 ~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPe---i~~V~~v~~~~---------~--~~~lt~e~V~~vL~~IRP~ 176 (231)
..|.+.+.|+ +...++..|-.-|.+.+.. ++++....... . ..+....++++.++.+|+.
T Consensus 45 v~V~t~~pGa------spe~vE~~Vt~plE~~L~~v~gi~~i~S~S~~G~s~I~v~f~~g~d~~~a~~~v~~~v~~v~~~ 118 (1017)
T PRK09579 45 ITVTTAYPGA------NAETIQGYITQPLQQSLASAEGIDYMTSVSRQNFSIISIYARIGADSDRLFTELLAKANEVKNQ 118 (1017)
T ss_pred EEEEEecCCC------CHHHHHHHHHHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCCHHHHHHHHHHHHHHHHHh
Confidence 4677778886 5556666665555555544 44444322111 1 1222356778888888766
Q ss_pred ecccCCCcEEEEEE--e-CCEEEEEecCCCCCchhHHHHHHHHHHhhC---CCcceEEe
Q 038446 177 LAGTGGGILELIQI--D-DYVVRVRLSGPAAGVMTVRVALTQKLREKI---PSIAAVQL 229 (231)
Q Consensus 177 L~~hdGGdvElV~v--~-~~vv~VrL~GaC~gC~Tlk~~Ie~~Lr~~i---Pei~~V~~ 229 (231)
|=. +-..-.+... . ..+.++-+.+.-..-.+++..+++.|+.++ |++.+|..
T Consensus 119 LP~-~~~~P~i~~~~~~~~~v~~~~~~~~~~~~~~L~~~~~~~i~~~L~~i~GV~~V~~ 176 (1017)
T PRK09579 119 LPQ-DAEDPVLSKEAADASALMYISFYSEEMSNPQITDYLSRVIQPKLATLPGMAEAEI 176 (1017)
T ss_pred CCC-CCCCCeEEeCCCCCcceEEEEEECCCCCHHHHHHHHHHHHHHHhhcCCCceEEEe
Confidence 653 2222223332 1 235666776642222467666666665554 77777754
No 31
>PRK11670 antiporter inner membrane protein; Provisional
Probab=40.28 E-value=1.1e+02 Score=29.00 Aligned_cols=68 Identities=13% Similarity=-0.014 Sum_probs=48.9
Q ss_pred CcHHHHHHHHHH-hcCcccc---CCCeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceee
Q 038446 80 LTEENVERVLDE-VRPGLMA---DGGNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEV 149 (231)
Q Consensus 80 lt~e~V~~vL~~-IRP~L~~---dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V 149 (231)
.++++|..+|.. .-|.+.. .=|-|.=+.++++.+++.+.-.-..||. ...++..++++|.. +|.+.+|
T Consensus 12 ~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~ 83 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSA-FEELKEQCSAELLR-ITGAKAI 83 (369)
T ss_pred chHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchH-HHHHHHHHHHHHHh-cCCCceE
Confidence 456889999986 5666664 3355666788888888888766667775 45688899999986 5665544
No 32
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=40.06 E-value=63 Score=29.60 Aligned_cols=29 Identities=31% Similarity=0.496 Sum_probs=22.5
Q ss_pred EEEEEEccCCCCCCCchHhHHHHHHHHHhh
Q 038446 112 VVVLKLQGACGSCPSSTMTLKMGIETRLRD 141 (231)
Q Consensus 112 ~V~VrL~GaC~gCpss~~TLk~~IE~~L~e 141 (231)
..++.|+| |+||..|-..|.++.-+.+..
T Consensus 6 va~~~L~g-C~GC~~slldl~E~L~dll~~ 34 (247)
T COG1941 6 VATVWLTG-CSGCHMSLLDLYEKLLDLLED 34 (247)
T ss_pred EEEEEecc-ccchHHHHHhHHHHHHHhhhh
Confidence 44566655 999999998888888887773
No 33
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=39.71 E-value=21 Score=28.07 Aligned_cols=22 Identities=27% Similarity=0.264 Sum_probs=16.2
Q ss_pred CCCCch-------hHHHHHHHHHHhhCCCc
Q 038446 202 PAAGVM-------TVRVALTQKLREKIPSI 224 (231)
Q Consensus 202 aC~gC~-------Tlk~~Ie~~Lr~~iPei 224 (231)
-|++|. |. ++++.+|+.|+|+.
T Consensus 8 ~CASCVn~PsSkeTy-eWL~aal~RKyp~~ 36 (93)
T PF07315_consen 8 ICASCVNAPSSKETY-EWLEAALKRKYPDQ 36 (93)
T ss_dssp --GGGSSS--HHHHH-HHHHHHHHHH-TTS
T ss_pred cchhhcCCCCchhHH-HHHHHHHhCcCCCC
Confidence 388883 55 89999999999985
No 34
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=39.01 E-value=28 Score=27.89 Aligned_cols=20 Identities=5% Similarity=0.270 Sum_probs=15.2
Q ss_pred EEEEeCCEEEEEec--CCCCCc
Q 038446 187 LIQIDDYVVRVRLS--GPAAGV 206 (231)
Q Consensus 187 lV~v~~~vv~VrL~--GaC~gC 206 (231)
+++++++.++|+.. .+|++|
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C 22 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSC 22 (135)
T ss_pred CEEEeCCEEEEEEccCCcCccc
Confidence 47889998888774 667776
No 35
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=38.95 E-value=38 Score=28.37 Aligned_cols=22 Identities=5% Similarity=0.126 Sum_probs=17.1
Q ss_pred EEEEEEeCCEEEEEec--CCCCCc
Q 038446 185 LELIQIDDYVVRVRLS--GPAAGV 206 (231)
Q Consensus 185 vElV~v~~~vv~VrL~--GaC~gC 206 (231)
-.+++++++.++|+.. .+|++|
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C 29 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSC 29 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCc
Confidence 4688999998887655 678877
No 36
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=38.64 E-value=3.2e+02 Score=29.57 Aligned_cols=112 Identities=13% Similarity=0.206 Sum_probs=61.5
Q ss_pred cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhc---ccceeeeeecccc---------ccc--chhhHHHHHHHHhccce
Q 038446 111 LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKI---PEILEVEQILDTE---------TGL--ELNEENIEKVLAEIRPY 176 (231)
Q Consensus 111 ~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~i---Pei~~V~~v~~~~---------~~~--~lt~e~V~~vL~~IRP~ 176 (231)
-.|.+.+.|+ +...+...|-.-|.+.+ ++++.+....... .+. +....++++.++.+++.
T Consensus 54 v~V~t~~pGa------s~~~vE~~Vt~piE~~l~~v~gv~~i~S~S~~G~s~i~v~f~~g~d~~~a~~ev~~~i~~~~~~ 127 (1040)
T PRK10503 54 IQVVTLYPGA------SPDVMTSAVTAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLTLPLDVAEQEVQAAINAATNL 127 (1040)
T ss_pred EEEEEEcCCC------CHHHHHHHHHHHHHHHhcCCCCccEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHHHHHh
Confidence 3566778886 45555555555555554 4454444322111 111 12247788888888887
Q ss_pred ecccCCCc-EEEEEEeC---CEEEEEecCCCCCchhHHHHHHHHHHhhC---CCcceEEe
Q 038446 177 LAGTGGGI-LELIQIDD---YVVRVRLSGPAAGVMTVRVALTQKLREKI---PSIAAVQL 229 (231)
Q Consensus 177 L~~hdGGd-vElV~v~~---~vv~VrL~GaC~gC~Tlk~~Ie~~Lr~~i---Pei~~V~~ 229 (231)
|-. |.-. -.+.++++ .++++.+.+.-..=..|+...++.|+.++ |++.+|..
T Consensus 128 LP~-~~~~~p~~~~~~~~~~pv~~~~l~~~~~~~~~L~~~~~~~l~~~L~~i~gV~~V~~ 186 (1040)
T PRK10503 128 LPS-DLPNPPVYSKVNPADPPIMTLAVTSTAMPMTQVEDMVETRVAQKISQVSGVGLVTL 186 (1040)
T ss_pred CCC-ccCCCCEEEEeCCCCCceEEEEEEcCCCCHHHHHHHHHHHHHHHhcCCCCceEEEe
Confidence 775 3211 22224433 27888887641112357666666666655 77777764
No 37
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=38.48 E-value=28 Score=23.74 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=26.3
Q ss_pred EEccCCCCCCCchHhHHHHHHHHHhhhccccee
Q 038446 116 KLQGACGSCPSSTMTLKMGIETRLRDKIPEILE 148 (231)
Q Consensus 116 rL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~ 148 (231)
-.+++|.|||.-+..|...|-..|++...-+.+
T Consensus 5 ~AG~~~~G~~ql~ESLLdrItRklr~gwKRl~~ 37 (45)
T PF02061_consen 5 IAGWPRMGCPQLSESLLDRITRKLRDGWKRLWD 37 (45)
T ss_pred ecCccccCCchhhHHHHHHHHHHHHHHHHHHHH
Confidence 358899999988888999999999887654433
No 38
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.06 E-value=22 Score=28.42 Aligned_cols=26 Identities=38% Similarity=0.663 Sum_probs=20.8
Q ss_pred CCCCC---CCchHhHHHHHHHHHhhhcccc
Q 038446 120 ACGSC---PSSTMTLKMGIETRLRDKIPEI 146 (231)
Q Consensus 120 aC~gC---pss~~TLk~~IE~~L~e~iPei 146 (231)
-|.+| |+|-.|. .+.|.+|++++|+.
T Consensus 15 iCASCV~aPtsKdt~-eWLeaalkRKyp~~ 43 (106)
T COG4837 15 ICASCVNAPTSKDTY-EWLEAALKRKYPNQ 43 (106)
T ss_pred hhHHhcCCCcchhHH-HHHHHHHhccCCCC
Confidence 47777 6776665 79999999999985
No 39
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=35.56 E-value=63 Score=23.07 Aligned_cols=25 Identities=16% Similarity=0.105 Sum_probs=20.3
Q ss_pred EEEEecCCCCCchhHHHHHHHHHHhh
Q 038446 195 VRVRLSGPAAGVMTVRVALTQKLREK 220 (231)
Q Consensus 195 v~VrL~GaC~gC~Tlk~~Ie~~Lr~~ 220 (231)
+++ ++-.|..|+.+...+++.+.+.
T Consensus 3 I~v-~~~~C~~C~~~~~~~~~~~~~~ 27 (76)
T PF13192_consen 3 IKV-FSPGCPYCPELVQLLKEAAEEL 27 (76)
T ss_dssp EEE-ECSSCTTHHHHHHHHHHHHHHT
T ss_pred EEE-eCCCCCCcHHHHHHHHHHHHhc
Confidence 567 7777999998888888888776
No 40
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=35.41 E-value=81 Score=33.55 Aligned_cols=112 Identities=15% Similarity=0.294 Sum_probs=63.8
Q ss_pred cEEEEEEccCCCCCCCchHhHHHHHHHHHhhhc---ccceeeeeecccc---------cc--cchhhHHHHHHHHhccce
Q 038446 111 LVVVLKLQGACGSCPSSTMTLKMGIETRLRDKI---PEILEVEQILDTE---------TG--LELNEENIEKVLAEIRPY 176 (231)
Q Consensus 111 ~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~i---Pei~~V~~v~~~~---------~~--~~lt~e~V~~vL~~IRP~ 176 (231)
-.|.+.+.|+ +...+...|-.-|.+.+ +.+++++...... .+ .+....++++.++.+++.
T Consensus 43 i~V~~~~pga------s~~~ve~~vt~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~~~d~~~a~~~v~~~i~~~~~~ 116 (1021)
T PF00873_consen 43 ISVTTSYPGA------SPEEVEQLVTKPLEEALSSVEGVKEIRSTSREGSSSITVEFDDGTDIDEALQEVREKIDQIRSD 116 (1021)
T ss_dssp EEEEEE-TTS-------HHHHHHHTHHHHHHTHCSSTTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGG
T ss_pred eEEEEecCcC------CHHHHHHHHHHHHHHHHcCCCCeEEEEEEecCCcEEEEEEeccccCHHHHHHHHHHHHHhhhhh
Confidence 3677778886 55555555555555554 5555554433221 11 122257888889888887
Q ss_pred ecccCCCcEEEEEE--e-CCEEEEEecCCCC--CchhHHHHHHHHHHhhC---CCcceEEe
Q 038446 177 LAGTGGGILELIQI--D-DYVVRVRLSGPAA--GVMTVRVALTQKLREKI---PSIAAVQL 229 (231)
Q Consensus 177 L~~hdGGdvElV~v--~-~~vv~VrL~GaC~--gC~Tlk~~Ie~~Lr~~i---Pei~~V~~ 229 (231)
|=. +=..-.+... . ..++.+.+.+.-. .-..|+..+++.|+.++ |+|.+|..
T Consensus 117 LP~-~~~~p~i~~~~~~~~~i~~~~l~~~~~~~~~~~l~~~~~~~l~~~L~~i~gV~~v~~ 176 (1021)
T PF00873_consen 117 LPP-GVEEPQIFKFDPSDSPIMILALTSDDGTLDLKELRDYAEEQLKPRLERIPGVARVDI 176 (1021)
T ss_dssp S-H-HHHHHEEEEEEEECCEEEEEEEEESSSSS-HHHHHHHHHHCTHHHHHTSTTEEEEEE
T ss_pred Ccc-cccCCceeeccCCCceeEEEEeccCCCCCCHHHHHHHHHHHHHHhccceeEEEEEEe
Confidence 765 2223334433 2 4578889988822 22467777776666654 77777764
No 41
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.09 E-value=36 Score=27.15 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=20.7
Q ss_pred EEEecCC---CCCch------hHHHHHHHHHHhhCCCc
Q 038446 196 RVRLSGP---AAGVM------TVRVALTQKLREKIPSI 224 (231)
Q Consensus 196 ~VrL~Ga---C~gC~------Tlk~~Ie~~Lr~~iPei 224 (231)
.+-.-|+ |++|. ...+++|.+|+.++|+.
T Consensus 6 ~l~VyGae~iCASCV~aPtsKdt~eWLeaalkRKyp~~ 43 (106)
T COG4837 6 KLVVYGAEVICASCVNAPTSKDTYEWLEAALKRKYPNQ 43 (106)
T ss_pred EEEEecchhhhHHhcCCCcchhHHHHHHHHHhccCCCC
Confidence 3444455 88883 23389999999999975
No 42
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=33.76 E-value=4.4e+02 Score=28.36 Aligned_cols=112 Identities=14% Similarity=0.182 Sum_probs=57.9
Q ss_pred cEEEEEEccCCCCCCCchHhHHHHHHHHHhhh---cccceeeeeecccc---------cc--cchhhHHHHHHHHhccce
Q 038446 111 LVVVLKLQGACGSCPSSTMTLKMGIETRLRDK---IPEILEVEQILDTE---------TG--LELNEENIEKVLAEIRPY 176 (231)
Q Consensus 111 ~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~---iPei~~V~~v~~~~---------~~--~~lt~e~V~~vL~~IRP~ 176 (231)
..|.+.+.|+ +...+...|-..|.+. +|+++.+....... .+ ......++++.++.+++.
T Consensus 45 v~V~~~~pGa------s~~~ve~~vt~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~~d~~~a~~~v~~~v~~~~~~ 118 (1025)
T PRK10614 45 IMVSASLPGA------SPETMASSVATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFDRDINGAARDVQAAINAAQSL 118 (1025)
T ss_pred EEEEEEcCCC------CHHHHHHHHHHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHHHHhh
Confidence 3566667775 4555555554444444 45555554322111 11 122356778888888776
Q ss_pred ecccCC-CcEEEEEEeC---CEEEEEecCCCCCchhHHHHHHHHHHhhC---CCcceEEe
Q 038446 177 LAGTGG-GILELIQIDD---YVVRVRLSGPAAGVMTVRVALTQKLREKI---PSIAAVQL 229 (231)
Q Consensus 177 L~~hdG-GdvElV~v~~---~vv~VrL~GaC~gC~Tlk~~Ie~~Lr~~i---Pei~~V~~ 229 (231)
|-. +. ....+-.++. .++.+.+.+.-..-..|+...++.|+.++ |.+.+|..
T Consensus 119 LP~-~~~~~p~~~~~~~~~~pv~~~~~~~~~~~~~~L~~~~~~~l~~~L~~i~GV~~V~~ 177 (1025)
T PRK10614 119 LPS-GMPSRPTYRKANPSDAPIMILTLTSDTYSQGQLYDFASTQLAQTISQIDGVGDVDV 177 (1025)
T ss_pred CCC-ccCCCCEEEecCCCccceeEEEEEcCCCCHHHHHHHHHHHHHHHhcCCCCceEEEe
Confidence 654 22 1233333332 26666776642122356665555555554 77777754
No 43
>PF04865 Baseplate_J: Baseplate J-like protein; InterPro: IPR006949 The temperate bacteriophage P2 has four defined tail genes: V, J, W and I. Their order is the late gene promoter, VWJI, followed by the tail fibre genes H and G and then a transcription terminator. BAP V protein is the small spike at the tip of the tail and basal plate assembly protein J lies at the edge of the baseplate []. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred.
Probab=30.83 E-value=1.5e+02 Score=25.51 Aligned_cols=79 Identities=15% Similarity=0.117 Sum_probs=45.5
Q ss_pred ccceeecccccCCCCCCCc--HHHHHHHH--HHhcCccccCCCeEEEEEEeCcEEEEEEccCCCCCCCchHhHHHHHHHH
Q 038446 63 VRRKHRGLVVSPCCVLPLT--EENVERVL--DEVRPGLMADGGNVALHEIDGLVVVLKLQGACGSCPSSTMTLKMGIETR 138 (231)
Q Consensus 63 ~~~~~~~~~~~p~~~~~lt--~e~V~~vL--~~IRP~L~~dGGdVeLv~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~ 138 (231)
.++.+. +++.+....|-. -++|+..| +.+||. |-++.+.......+.|.+..-...=+......+..|+++
T Consensus 146 ~~G~V~-v~v~~~~g~~~~~l~~~V~~~i~~~~~~p~----~~~v~v~~~~~~~v~v~~~l~~~~~~~~~~~~~~~i~~a 220 (243)
T PF04865_consen 146 GPGTVD-VYVLGANGAPSQELLAAVQAYINAEDVRPL----GDRVTVKAPTYVPVDVTATLTVYPGYDTAEVIQAAIKAA 220 (243)
T ss_pred CCCEEE-EEEccCCCCCCHHHHHHHHHHhhhhccCCC----ceEEEEECCEEEEEEEEEEEEECCCCChHHHHHHHHHHH
Confidence 345544 444444333322 36788888 678774 557777776666666666543331122234555588888
Q ss_pred Hhhhcccc
Q 038446 139 LRDKIPEI 146 (231)
Q Consensus 139 L~e~iPei 146 (231)
|++++.+.
T Consensus 221 l~~y~~~~ 228 (243)
T PF04865_consen 221 LRAYFNSL 228 (243)
T ss_pred HHHHHHhh
Confidence 88887653
No 44
>PRK10718 RpoE-regulated lipoprotein; Provisional
Probab=30.37 E-value=94 Score=27.47 Aligned_cols=106 Identities=18% Similarity=0.316 Sum_probs=68.6
Q ss_pred CCCCCcHHHHHHHHH---HhcCccccCCCeEEE--EEEeCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeee
Q 038446 76 CVLPLTEENVERVLD---EVRPGLMADGGNVAL--HEIDGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVE 150 (231)
Q Consensus 76 ~~~~lt~e~V~~vL~---~IRP~L~~dGGdVeL--v~Ve~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~ 150 (231)
...|+.++.|+..|+ .+|+..+.++|++-- -.++++.|.+-+.|. .+ . |.+|.
T Consensus 51 a~Tp~~~~aI~~~L~g~y~lrsGm~t~~G~iv~~~qa~~~d~v~lvi~G~-~G------------------~---V~rI~ 108 (191)
T PRK10718 51 ASTPLQEQAIADALDGDYRLRSGMKTANGNVVRFFQAMKGDQVAMVINGQ-QG------------------T---VSRID 108 (191)
T ss_pred ccCccCHHHHHhhcCCCceEeccccCCCCCEEEeeeeecCCceEEEEECC-CC------------------c---EEEEE
Confidence 456888999999996 499999999997544 225678888888875 11 1 22222
Q ss_pred eecc-------cccccchhhHHH-HHHHHhccceecccCCCcEEEEEEeCCEEEEEecCCCCCc
Q 038446 151 QILD-------TETGLELNEENI-EKVLAEIRPYLAGTGGGILELIQIDDYVVRVRLSGPAAGV 206 (231)
Q Consensus 151 ~v~~-------~~~~~~lt~e~V-~~vL~~IRP~L~~hdGGdvElV~v~~~vv~VrL~GaC~gC 206 (231)
.... ..-+.+. ..+ .++...=||--.. |.+.||=+.=....|.+.|.|.=.|-
T Consensus 109 V~d~~i~t~~G~~IGtpF--s~ly~kAfg~C~~g~~~-~~~~V~C~ap~s~~VsYvF~g~W~GP 169 (191)
T PRK10718 109 VLDSDIPTAWGVKIGTPF--SDLYSKAFGNCQKASGD-DNRSVECKAPGSQHISYVFSGEWSGP 169 (191)
T ss_pred EeCCCCCCCCccccCccH--HHHhhhhhhhcccCCCC-CcCCeEEeCCCCCeEEEEecCCcCCC
Confidence 1111 1112222 233 3355666666666 67888888888888999999887764
No 45
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=29.77 E-value=2.4e+02 Score=21.18 Aligned_cols=48 Identities=23% Similarity=0.396 Sum_probs=33.2
Q ss_pred CCcEEEEEEe-CCEEEEEecCCC---CC-c--hhHHHHHHHHHHhhCCCcceEEe
Q 038446 182 GGILELIQID-DYVVRVRLSGPA---AG-V--MTVRVALTQKLREKIPSIAAVQL 229 (231)
Q Consensus 182 GGdvElV~v~-~~vv~VrL~GaC---~g-C--~Tlk~~Ie~~Lr~~iPei~~V~~ 229 (231)
|-.+.=+.++ +++++|.|..+= .+ | .-+...|...|.+.++++++|.+
T Consensus 52 ~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i 106 (117)
T PF10646_consen 52 GTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVKKVQI 106 (117)
T ss_pred ccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCccEEEE
Confidence 3444444556 459999998743 22 2 34557888899999999999975
No 46
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=28.28 E-value=2.7e+02 Score=23.65 Aligned_cols=48 Identities=19% Similarity=0.106 Sum_probs=32.0
Q ss_pred eCcEEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeeeeecccc
Q 038446 109 DGLVVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTE 156 (231)
Q Consensus 109 e~~~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~~v~~~~ 156 (231)
-++.++|-+.-.=.-=.+-...+|..|+++++...|.+..|....+++
T Consensus 77 tg~~A~Vgv~~~~~~~~~~~~~iK~~Va~~Vk~~dp~~~~VyVsaDpd 124 (158)
T TIGR02898 77 TGNYAYVGVDLTNGLEGSVTDELKEKVAETVKSTDNRIANVYVSADPD 124 (158)
T ss_pred ECCEEEEEEEcCCCcchhhHHHHHHHHHHHHHhhCCCcceEEEEcCHH
Confidence 455555555321111124467899999999999999999998765544
No 47
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=28.11 E-value=66 Score=24.78 Aligned_cols=29 Identities=17% Similarity=0.210 Sum_probs=24.7
Q ss_pred CCcHHHHHHHHHHhcCccccCCCeEEEEE
Q 038446 79 PLTEENVERVLDEVRPGLMADGGNVALHE 107 (231)
Q Consensus 79 ~lt~e~V~~vL~~IRP~L~~dGGdVeLv~ 107 (231)
.+++++++.+++.+.-.+...||.+.-++
T Consensus 17 ~l~e~~~~~~~~~~~~~i~~~gg~i~~~~ 45 (97)
T CHL00123 17 DLNEEELLKWIENYKKLLRKRGAKNISVQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 56789999999999999999999875544
No 48
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=27.90 E-value=2.6e+02 Score=24.33 Aligned_cols=34 Identities=26% Similarity=0.432 Sum_probs=23.8
Q ss_pred EEEEecCCCCCc--hhHHHHHHHHHHhhCCCcceEE
Q 038446 195 VRVRLSGPAAGV--MTVRVALTQKLREKIPSIAAVQ 228 (231)
Q Consensus 195 v~VrL~GaC~gC--~Tlk~~Ie~~Lr~~iPei~~V~ 228 (231)
++|+..+.+..- ..+++.|++.+++++|++.+|.
T Consensus 240 i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~i~~v~ 275 (284)
T PF01545_consen 240 IHVQVDPDMSVEEAHEIRERIEKRLREKFPGIYDVT 275 (284)
T ss_dssp EEEEETTTSBHHHHHHHHHHHHHHHHHHSTTCEEEE
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHHHHHhCCCcEEEE
Confidence 444544555321 2578999999999999998643
No 49
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=26.07 E-value=64 Score=27.47 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=25.5
Q ss_pred EEEEEeCcEEEEEE--ccCCCCCCCchHhHHHHHHHHH
Q 038446 104 ALHEIDGLVVVLKL--QGACGSCPSSTMTLKMGIETRL 139 (231)
Q Consensus 104 eLv~Ve~~~V~VrL--~GaC~gCpss~~TLk~~IE~~L 139 (231)
.+++.++|.++|+= +-+|++|++.. .-...+...|
T Consensus 7 ~vv~~q~G~a~V~c~~~S~CgsC~a~~-~CGs~~l~kL 43 (150)
T COG3086 7 TVVSWQNGQAKVSCQRQSACGSCAARA-GCGSGLLSKL 43 (150)
T ss_pred EEEEccCCeEEEEeeccCccccchhhc-ccchHHHHHh
Confidence 35788888888876 78999999854 3345666666
No 50
>TIGR01297 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
Probab=25.88 E-value=3.6e+02 Score=23.36 Aligned_cols=63 Identities=21% Similarity=0.243 Sum_probs=36.5
Q ss_pred hHHHHHHHHhccceecccCCCcEEEEEEeCC----EEEEEecCCCCCc--hhHHHHHHHHHHhhCCCcceEE
Q 038446 163 EENIEKVLAEIRPYLAGTGGGILELIQIDDY----VVRVRLSGPAAGV--MTVRVALTQKLREKIPSIAAVQ 228 (231)
Q Consensus 163 ~e~V~~vL~~IRP~L~~hdGGdvElV~v~~~----vv~VrL~GaC~gC--~Tlk~~Ie~~Lr~~iPei~~V~ 228 (231)
.+++.+.+..+ |.+.. =-++......++ .+.|.+.+.+.-. ..+...+|+.+++++|+++.|.
T Consensus 194 ~~~i~~~i~~~-~~v~~--v~~~~~~~~G~~~~~v~~~v~v~~~~~~~~ah~i~~~i~~~i~~~~~~v~~v~ 262 (268)
T TIGR01297 194 LEEIKKAILSI-PGVKG--VHDLHIWRIGPGKLFLDVHVVVDPDLDLKQAHDIALEIEREILKRHPGIEHVT 262 (268)
T ss_pred HHHHHHHHhcC-CCccc--ceEeEEEEcCCCCEEEEEEEEECCCCChhHHHHHHHHHHHHHHHhcCCCCeEE
Confidence 34555555433 22221 123444444442 4566666766543 3566789999999999997764
No 51
>PF06572 DUF1131: Protein of unknown function (DUF1131); InterPro: IPR010938 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2QZB_B.
Probab=23.43 E-value=1.2e+02 Score=26.33 Aligned_cols=125 Identities=21% Similarity=0.338 Sum_probs=55.6
Q ss_pred ccccccccccccceeecccccCCCCCCCcHHHHHHHHH---HhcCccccCCCeEE-EE-EEeCcEEEEEEccCCCCCCCc
Q 038446 53 SSFLGFSLNHVRRKHRGLVVSPCCVLPLTEENVERVLD---EVRPGLMADGGNVA-LH-EIDGLVVVLKLQGACGSCPSS 127 (231)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~p~~~~~lt~e~V~~vL~---~IRP~L~~dGGdVe-Lv-~Ve~~~V~VrL~GaC~gCpss 127 (231)
++||+..+.-+.--|.++ ....||.++.|+..|+ .+|..++.++|++. +. .++++.|.+-+.|.=.
T Consensus 11 ~nwfgssl~vs~~GVG~I----ta~Tp~~~~aI~~aL~g~y~lrsGm~t~nG~~v~~~qA~~~d~v~lvI~G~~~----- 81 (171)
T PF06572_consen 11 WNWFGSSLEVSEQGVGGI----TASTPMDEDAIKDALDGDYRLRSGMQTANGNIVSFFQAMKDDQVKLVISGDPK----- 81 (171)
T ss_dssp ---------EETTEETTE----ETTSBSSHHHHHHH--SS-EEEEEEEEETTEEEEEEEEEETTEEEEEEEE--------
T ss_pred ccccCCceEEccCccccc----ccCCcCCHHHHHHhcCCCcEEecceecCCCCeEEeeeeecCCeEEEEEecCCC-----
Confidence 455665444443333332 2446899999999997 48999999999744 33 3467888888887510
Q ss_pred hHhHHHHHHHHHhhhcccceeeeeecccc-------cccchhhHHH-HHHHHhccceecccCCCcEEEEEEeCCEEEEEe
Q 038446 128 TMTLKMGIETRLRDKIPEILEVEQILDTE-------TGLELNEENI-EKVLAEIRPYLAGTGGGILELIQIDDYVVRVRL 199 (231)
Q Consensus 128 ~~TLk~~IE~~L~e~iPei~~V~~v~~~~-------~~~~lt~e~V-~~vL~~IRP~L~~hdGGdvElV~v~~~vv~VrL 199 (231)
..|.+|+....+- -+.+ ...+ .++...=||--.. +.+.++-+.=+...|...|
T Consensus 82 ----------------G~V~rI~V~d~~i~t~~G~kIGt~--Fs~ly~kAfg~C~~g~~~-~~~~V~C~ap~s~~VsYvF 142 (171)
T PF06572_consen 82 ----------------GTVSRIEVMDPDIKTPWGVKIGTP--FSDLYSKAFGNCRPGEGD-DAGMVECVAPQSQHVSYVF 142 (171)
T ss_dssp -----------------BEEEEEE--TTS-BTTS--TT-B--HHHH-S--TTTEEE---------EEEE-TT-SSEEEEE
T ss_pred ----------------CcEEEEEEeccccCCccccccCcc--HHHHHhhhhhhccccCCC-cccceEEecCCCCcEEEEe
Confidence 1233333221110 1222 2223 2445556666665 5677777666666677778
Q ss_pred cCCCCC
Q 038446 200 SGPAAG 205 (231)
Q Consensus 200 ~GaC~g 205 (231)
+|.=.|
T Consensus 143 ~g~W~G 148 (171)
T PF06572_consen 143 SGGWSG 148 (171)
T ss_dssp E----S
T ss_pred cCCccC
Confidence 776554
No 52
>PF15603 Imm45: Immunity protein 45
Probab=22.83 E-value=92 Score=23.80 Aligned_cols=32 Identities=16% Similarity=0.280 Sum_probs=26.5
Q ss_pred cCCCCCCCcHHHHHHHHHHhcCccccCCCeEE
Q 038446 73 SPCCVLPLTEENVERVLDEVRPGLMADGGNVA 104 (231)
Q Consensus 73 ~p~~~~~lt~e~V~~vL~~IRP~L~~dGGdVe 104 (231)
+|....|+|..+++++++.|.-++..+|=.|.
T Consensus 49 ~P~e~~~it~~e~q~II~aI~~~~~~~~~~v~ 80 (82)
T PF15603_consen 49 PPHENEPITIAERQKIIEAIEKYFSERGMTVD 80 (82)
T ss_pred CCCCCcccCHHHHHHHHHHHHHHHhcCceEEE
Confidence 67788899999999999999988877764443
No 53
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=21.81 E-value=3e+02 Score=23.97 Aligned_cols=37 Identities=24% Similarity=0.430 Sum_probs=25.6
Q ss_pred EEEEEEccCCCCCCCchHhHHHHHHHHHhhhcccceeee
Q 038446 112 VVVLKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVE 150 (231)
Q Consensus 112 ~V~VrL~GaC~gCpss~~TLk~~IE~~L~e~iPei~~V~ 150 (231)
.+++...+.+ .......+.+.|++.|++++|++.+|.
T Consensus 239 ~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~~i~~v~ 275 (284)
T PF01545_consen 239 EIHVQVDPDM--SVEEAHEIRERIEKRLREKFPGIYDVT 275 (284)
T ss_dssp EEEEEETTTS--BHHHHHHHHHHHHHHHHHHSTTCEEEE
T ss_pred EEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCCCcEEEE
Confidence 4555555554 223345578999999999999998744
No 54
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=21.41 E-value=3e+02 Score=19.37 Aligned_cols=62 Identities=18% Similarity=0.283 Sum_probs=40.7
Q ss_pred hHHHHHHHHh-ccceecccCCCcEEEEEEeCCEEEEEecCCCCCc--hhHHHHHHHHHHhhC--CCcceEE
Q 038446 163 EENIEKVLAE-IRPYLAGTGGGILELIQIDDYVVRVRLSGPAAGV--MTVRVALTQKLREKI--PSIAAVQ 228 (231)
Q Consensus 163 ~e~V~~vL~~-IRP~L~~hdGGdvElV~v~~~vv~VrL~GaC~gC--~Tlk~~Ie~~Lr~~i--Pei~~V~ 228 (231)
...+.+..++ +-|.+..| ..++++++|+++|.-..+--.= .-++.-|-++|++.+ +.|++++
T Consensus 22 ~~~l~~~w~~ivg~~l~~~----~~~~~i~~g~L~i~v~~~~~~~~L~~~~~~il~~l~~~~g~~~i~~I~ 88 (89)
T PF05258_consen 22 LARLQQNWKQIVGPELAQH----TRPVSIKDGTLVIEVDSSAWAQELRYMKPQILKKLNEFLGFPAIKDIR 88 (89)
T ss_pred HHHHHHHHHHHhCHHHHcc----EEEEEEECCEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCCccEee
Confidence 3455555554 44566665 8999999999999765443211 145667788888888 5577665
No 55
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=21.38 E-value=1.5e+02 Score=22.72 Aligned_cols=27 Identities=30% Similarity=0.455 Sum_probs=20.1
Q ss_pred CcHHHHHHHHHHhcCccccCCCeEEEEEE
Q 038446 80 LTEENVERVLDEVRPGLMADGGNVALHEI 108 (231)
Q Consensus 80 lt~e~V~~vL~~IRP~L~~dGGdVeLv~V 108 (231)
.++|+++.+|+++++.+.. |-|.+-++
T Consensus 72 d~~eki~~~l~~l~~~~~~--glit~~~v 98 (101)
T PF02641_consen 72 DTEEKIEAFLPELKELVKD--GLITLEDV 98 (101)
T ss_dssp EEHHHHHHHHHHHCTT-SS--SEEEEEEE
T ss_pred cCHHHHHHHHHHHHHHcCC--CEEEEEEE
Confidence 4488999999999998864 66665544
Done!