Query 026830
Match_columns 232
No_of_seqs 241 out of 1851
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 13:18:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026830.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026830hhsearch_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 8.5E-24 1.8E-28 153.8 7.7 68 87-154 1-68 (68)
2 COG0694 Thioredoxin-like prote 99.9 1.2E-23 2.7E-28 161.4 8.5 77 84-160 11-90 (93)
3 KOG2358 NifU-like domain-conta 99.9 1.2E-23 2.6E-28 180.6 4.5 150 8-158 38-202 (213)
4 TIGR03341 YhgI_GntY IscR-regul 99.9 5.3E-22 1.1E-26 170.3 8.5 78 84-161 107-186 (190)
5 PF01106 NifU: NifU-like domai 99.9 6.6E-22 1.4E-26 143.9 7.0 64 168-232 1-68 (68)
6 PRK11190 Fe/S biogenesis prote 99.9 1.2E-21 2.5E-26 168.5 8.2 78 84-161 108-188 (192)
7 COG0694 Thioredoxin-like prote 99.8 8.7E-21 1.9E-25 145.7 8.3 68 164-232 10-84 (93)
8 KOG2358 NifU-like domain-conta 99.8 1E-20 2.2E-25 162.6 2.2 133 65-232 60-198 (213)
9 TIGR02000 NifU_proper Fe-S clu 99.8 3.5E-19 7.5E-24 161.7 9.2 66 165-232 221-290 (290)
10 TIGR02000 NifU_proper Fe-S clu 99.8 7E-19 1.5E-23 159.7 8.7 70 84-154 221-290 (290)
11 TIGR03341 YhgI_GntY IscR-regul 99.8 6E-19 1.3E-23 151.4 7.7 68 164-232 106-179 (190)
12 PRK11190 Fe/S biogenesis prote 99.8 1E-18 2.2E-23 150.3 7.5 68 164-232 107-181 (192)
13 PF08712 Nfu_N: Scaffold prote 98.7 1.2E-09 2.5E-14 83.1 -2.3 52 8-60 26-85 (87)
14 PF01883 DUF59: Domain of unkn 95.6 0.1 2.2E-06 37.3 8.0 64 166-231 2-72 (72)
15 PF01883 DUF59: Domain of unkn 95.4 0.1 2.2E-06 37.4 7.2 66 85-152 2-71 (72)
16 TIGR02945 SUF_assoc FeS assemb 81.9 11 0.00025 28.3 7.9 64 165-230 3-74 (99)
17 TIGR02945 SUF_assoc FeS assemb 80.6 9 0.0002 28.9 6.9 67 84-152 3-74 (99)
18 TIGR03406 FeS_long_SufT probab 75.3 16 0.00034 31.2 7.5 68 162-231 72-151 (174)
19 TIGR03406 FeS_long_SufT probab 70.3 30 0.00066 29.5 8.1 79 81-161 72-161 (174)
20 PF07315 DUF1462: Protein of u 70.1 2.9 6.2E-05 32.4 1.6 57 123-180 9-72 (93)
21 TIGR02159 PA_CoA_Oxy4 phenylac 68.0 20 0.00043 29.7 6.4 45 184-230 14-61 (146)
22 PRK10862 SoxR reducing system 67.8 6.9 0.00015 32.6 3.6 26 105-130 6-33 (154)
23 PF04246 RseC_MucC: Positive r 65.3 6.1 0.00013 31.6 2.8 23 107-129 1-25 (135)
24 COG4837 Uncharacterized protei 65.1 7.9 0.00017 30.3 3.2 36 122-158 15-54 (106)
25 TIGR02159 PA_CoA_Oxy4 phenylac 63.8 43 0.00094 27.7 7.6 75 103-180 15-93 (146)
26 PF09580 Spore_YhcN_YlaJ: Spor 63.2 30 0.00066 28.6 6.7 45 111-157 98-142 (177)
27 COG2151 PaaD Predicted metal-s 62.6 31 0.00067 27.4 6.3 68 84-153 14-87 (111)
28 PF07315 DUF1462: Protein of u 59.6 7 0.00015 30.2 2.0 23 204-226 8-36 (93)
29 PF09012 FeoC: FeoC like trans 59.4 18 0.00039 25.5 4.1 41 81-132 25-66 (69)
30 COG2151 PaaD Predicted metal-s 59.3 39 0.00085 26.8 6.3 65 164-230 13-86 (111)
31 COG4837 Uncharacterized protei 55.6 5.4 0.00012 31.2 0.8 22 205-226 16-43 (106)
32 PF02061 Lambda_CIII: Lambda P 52.0 18 0.00038 24.1 2.7 27 120-146 7-33 (45)
33 PRK11670 antiporter inner memb 51.2 78 0.0017 29.8 8.0 66 163-230 12-84 (369)
34 PF13192 Thioredoxin_3: Thiore 47.5 31 0.00067 24.5 3.7 25 197-222 3-27 (76)
35 PRK11670 antiporter inner memb 38.8 1E+02 0.0023 29.0 6.8 68 82-151 12-83 (369)
36 COG1941 FrhG Coenzyme F420-red 32.1 78 0.0017 28.7 4.4 30 114-144 6-35 (247)
37 smart00243 GAS2 Growth-Arrest- 31.2 1.1E+02 0.0025 22.7 4.4 27 105-138 38-64 (73)
38 PF01545 Cation_efflux: Cation 28.9 1.9E+02 0.0041 25.2 6.5 37 114-152 239-275 (284)
39 TIGR02554 PrgH type III secret 27.3 5.7E+02 0.012 24.7 10.5 108 94-231 170-288 (389)
40 COG3086 RseC Positive regulato 26.7 78 0.0017 26.6 3.3 34 107-141 8-43 (150)
41 CHL00123 rps6 ribosomal protei 26.4 87 0.0019 23.9 3.3 29 81-109 17-45 (97)
42 COG1901 Uncharacterized conser 25.8 1.8E+02 0.004 25.5 5.5 82 111-199 60-149 (197)
43 PF07045 DUF1330: Protein of u 25.3 1E+02 0.0022 21.5 3.3 24 85-108 2-25 (65)
44 TIGR02174 CXXU_selWTH selT/sel 24.9 86 0.0019 22.5 2.9 24 123-148 6-29 (72)
45 PF15092 UPF0728: Uncharacteri 24.0 80 0.0017 24.3 2.7 32 172-204 27-59 (88)
46 PF02591 DUF164: Putative zinc 22.0 83 0.0018 21.3 2.2 18 203-220 23-41 (56)
47 PF02187 GAS2: Growth-Arrest-S 21.7 1.3E+02 0.0027 22.4 3.2 29 104-139 37-65 (73)
48 PF01545 Cation_efflux: Cation 20.8 3.2E+02 0.0069 23.7 6.3 34 197-230 240-275 (284)
49 PF00873 ACR_tran: AcrB/AcrD/A 20.4 1.8E+02 0.0038 31.0 5.3 111 114-231 44-176 (1021)
50 PF10646 Germane: Sporulation 20.2 2.6E+02 0.0057 20.9 5.0 55 175-231 45-106 (117)
51 COG1614 CdhC CO dehydrogenase/ 20.0 2E+02 0.0043 27.7 5.0 89 84-180 81-170 (470)
52 PF11718 CPSF73-100_C: Pre-mRN 20.0 5.9E+02 0.013 22.2 9.0 58 85-144 148-209 (216)
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=99.90 E-value=8.5e-24 Score=153.81 Aligned_cols=68 Identities=56% Similarity=0.949 Sum_probs=64.5
Q ss_pred HHHHHHHhcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeecc
Q 026830 87 IESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESV 154 (232)
Q Consensus 87 v~~~L~~IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v 154 (232)
|+++|++|||+|++||||++|+++++++|+|||+|+|+|||++..||+.+|+++|++++|++..|+++
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=99.90 E-value=1.2e-23 Score=161.42 Aligned_cols=77 Identities=55% Similarity=0.890 Sum_probs=72.6
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEe--CcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeecccccccc
Q 026830 84 AENIESVLD-EIRPYLISDGGNVALHEID--GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETG 160 (232)
Q Consensus 84 ~~~v~~~L~-~IrP~L~~dGGdvelv~i~--~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v~d~e~g 160 (232)
.++|+++|+ +|||+|++||||++|++|+ +|+|++||+|||+|||||++|||++||++|++++|++..|+++.++..+
T Consensus 11 ~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~~~~~~ 90 (93)
T COG0694 11 LERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVTEHARG 90 (93)
T ss_pred HHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEccCcccc
Confidence 679999998 8999999999999999999 6899999999999999999999999999999999999999998876543
No 3
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.2e-23 Score=180.58 Aligned_cols=150 Identities=29% Similarity=0.418 Sum_probs=124.7
Q ss_pred CCCCCCCCCCCCCCcCCCC---CCcceeeEecCe-eeec------cCCccccchHHHHHHhhhcccchhhhhhhcC-CC-
Q 026830 8 PSYSRPHQTLDSPSCSRPA---SKSTKSFFGERV-SLTR------WRNPVCHSSCRLLLIRKRGAARRNVIKAVAT-PD- 75 (232)
Q Consensus 8 ~s~~~~~~a~~~pla~~lf---~~v~~~~~~~~~-t~t~------w~~~l~~~~~~~i~~~~~~~~~~~~~~~~~~-~~- 75 (232)
.+|+++-++..+|||+++| .+|..+||+++| |+|+ |.- |++.+...+++++....+......++. -+
T Consensus 38 ~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~-L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~ 116 (213)
T KOG2358|consen 38 GDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSV-LDPEIPSLMSDGGNVGLPLIDGNIVVLKLQG 116 (213)
T ss_pred cccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhh-hchhhHHHHhccccccchhhccchhhhhhcc
Confidence 5778888889999999999 699999999999 9999 998 999999999998654444321111111 11
Q ss_pred cccCCCCcHHHHHHHHH-HhcchhhhCCCcEEEEEEeC--cEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEee
Q 026830 76 SAIELPLTAENIESVLD-EIRPYLISDGGNVALHEIDG--NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (232)
Q Consensus 76 ~~~~~~l~~~~v~~~L~-~IrP~L~~dGGdvelv~i~~--~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~ 152 (232)
.-.+.+.+...++..|+ +|||.|+.||||++++++|+ |.|+++|+|+|.+||++..|||+||+..|+.++|+++.|+
T Consensus 117 ~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v~ 196 (213)
T KOG2358|consen 117 ACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGVI 196 (213)
T ss_pred cccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEEE
Confidence 11223445678999998 79999999999999999998 5999999999999999999999999999999999999999
Q ss_pred cccccc
Q 026830 153 SVADEE 158 (232)
Q Consensus 153 ~v~d~e 158 (232)
++.+.+
T Consensus 197 qv~d~e 202 (213)
T KOG2358|consen 197 QVPDAE 202 (213)
T ss_pred eccCcc
Confidence 887754
No 4
>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=99.86 E-value=5.3e-22 Score=170.34 Aligned_cols=78 Identities=40% Similarity=0.685 Sum_probs=74.1
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEe-CcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeeccccccccc
Q 026830 84 AENIESVLD-EIRPYLISDGGNVALHEID-GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETGL 161 (232)
Q Consensus 84 ~~~v~~~L~-~IrP~L~~dGGdvelv~i~-~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v~d~e~g~ 161 (232)
.++|+++|+ +|||+|++||||+||++|+ +++|+|||+|+|+|||++..||+++||++|++++|+++.|+.+++|++|.
T Consensus 107 ~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~~~~~~~~ 186 (190)
T TIGR03341 107 EERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDATDHTRGE 186 (190)
T ss_pred HHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEecCccccC
Confidence 789999998 7999999999999999998 47999999999999999999999999999999999999999999988763
No 5
>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=99.86 E-value=6.6e-22 Score=143.88 Aligned_cols=64 Identities=45% Similarity=0.798 Sum_probs=60.3
Q ss_pred HHHHHhhccccccccCCCcEEEEEeeCCEEEEEEccCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 026830 168 IEKVLEEIRPYLVGAAGGSLELVTIDEPIVKVRITGPAAGVM----TVRVAVTQKLREKIPAIAAVQLL 232 (232)
Q Consensus 168 i~~~L~~iRP~L~~~dGGdielv~v~~gvv~Vrl~GaC~~c~----Tl~~~Ie~~L~~~~P~i~~V~~~ 232 (232)
|+++|++|||+|+ +||||++|+++++++|+|||+|+|++|| |++++||++|++++|++.+|+.|
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 VEEVLEEIRPYLQ-SDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHHCHHHHH-HTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHHhChHHH-hcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 5789999999999 8999999999999999999999999996 99999999999999999999875
No 6
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.85 E-value=1.2e-21 Score=168.50 Aligned_cols=78 Identities=35% Similarity=0.660 Sum_probs=73.9
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEe-CcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCC-cceEeecccccccc
Q 026830 84 AENIESVLD-EIRPYLISDGGNVALHEID-GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIP-EIVAVESVADEETG 160 (232)
Q Consensus 84 ~~~v~~~L~-~IrP~L~~dGGdvelv~i~-~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vp-ei~~V~~v~d~e~g 160 (232)
.++|+.+|+ +|||+|++||||+||++|+ +++|+|||+|+|+|||++..||+++||++|++++| +++.|+.+++|.++
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 789999998 8999999999999999998 57999999999999999999999999999999999 99999999998866
Q ss_pred c
Q 026830 161 L 161 (232)
Q Consensus 161 ~ 161 (232)
.
T Consensus 188 ~ 188 (192)
T PRK11190 188 E 188 (192)
T ss_pred C
Confidence 3
No 7
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=8.7e-21 Score=145.71 Aligned_cols=68 Identities=37% Similarity=0.676 Sum_probs=63.8
Q ss_pred hhhhHHHHHh-hccccccccCCCcEEEEEee--CCEEEEEEccCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 026830 164 NEENIEKVLE-EIRPYLVGAAGGSLELVTID--EPIVKVRITGPAAGVM----TVRVAVTQKLREKIPAIAAVQLL 232 (232)
Q Consensus 164 ~~~~i~~~L~-~iRP~L~~~dGGdielv~v~--~gvv~Vrl~GaC~~c~----Tl~~~Ie~~L~~~~P~i~~V~~~ 232 (232)
..++++++|+ +|||+|+ +||||++|++|+ +|+|+|||.|||+||| |||++||++|++++|++++|+.+
T Consensus 10 ~~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 10 LLERVEEVLDEKIRPQLA-MDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQV 84 (93)
T ss_pred HHHHHHHHHHhccCccee-ccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEc
Confidence 3578999998 8999999 999999999998 7899999999999997 99999999999999999999864
No 8
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=1e-20 Score=162.58 Aligned_cols=133 Identities=40% Similarity=0.570 Sum_probs=120.9
Q ss_pred hhhhhhhcCCCcccCCCCcHHHHHHHHHHhcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhh
Q 026830 65 RNVIKAVATPDSAIELPLTAENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEK 144 (232)
Q Consensus 65 ~~~~~~~~~~~~~~~~~l~~~~v~~~L~~IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~ 144 (232)
+........|+-....+++++....+|+..+|++.+|||+.-+-.|++..+.++++|+|..||.+.+++|+.|+.
T Consensus 60 ~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikeliet----- 134 (213)
T KOG2358|consen 60 GGVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIET----- 134 (213)
T ss_pred CCcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHHH-----
Confidence 366677777888877899999999999999999999999999999999999999999999999999888765543
Q ss_pred CCcceEeecccccccccchhhhhHHHHHhhccccccccCCCcEEEEEeeC--CEEEEEEccCCCCch----hHHHHHHHH
Q 026830 145 IPEIVAVESVADEETGLELNEENIEKVLEEIRPYLVGAAGGSLELVTIDE--PIVKVRITGPAAGVM----TVRVAVTQK 218 (232)
Q Consensus 145 vpei~~V~~v~d~e~g~e~~~~~i~~~L~~iRP~L~~~dGGdielv~v~~--gvv~Vrl~GaC~~c~----Tl~~~Ie~~ 218 (232)
+|||.++ .||||++++++|+ |+|++||+|+|.+|| |+++|||++
T Consensus 135 -----------------------------RiRp~i~-edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~m 184 (213)
T KOG2358|consen 135 -----------------------------RIRPKIQ-EDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENM 184 (213)
T ss_pred -----------------------------hhhhhhh-ccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHH
Confidence 6789999 8999999999998 599999999999997 999999999
Q ss_pred HHhhCCCcceEEeC
Q 026830 219 LREKIPAIAAVQLL 232 (232)
Q Consensus 219 L~~~~P~i~~V~~~ 232 (232)
|+.++|+||.|+.+
T Consensus 185 L~~y~~eVK~v~qv 198 (213)
T KOG2358|consen 185 LEIYVPEVKGVIQV 198 (213)
T ss_pred HHhhcceeeEEEec
Confidence 99999999999864
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=99.78 E-value=3.5e-19 Score=161.72 Aligned_cols=66 Identities=41% Similarity=0.646 Sum_probs=63.1
Q ss_pred hhhHHHHHhhccccccccCCCcEEEEEeeCCEEEEEEccCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 026830 165 EENIEKVLEEIRPYLVGAAGGSLELVTIDEPIVKVRITGPAAGVM----TVRVAVTQKLREKIPAIAAVQLL 232 (232)
Q Consensus 165 ~~~i~~~L~~iRP~L~~~dGGdielv~v~~gvv~Vrl~GaC~~c~----Tl~~~Ie~~L~~~~P~i~~V~~~ 232 (232)
.++|+++|++|||||+ +||||+||++|++++|+|||+|+|+||| ||+. ||++|++++|++.+|+.|
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 IQLIQKVLEEVRPVLQ-ADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred HHHHHHHHHHhCchHh-hcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 5789999999999999 9999999999999999999999999997 9998 999999999999999875
No 10
>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=99.77 E-value=7e-19 Score=159.75 Aligned_cols=70 Identities=47% Similarity=0.816 Sum_probs=66.8
Q ss_pred HHHHHHHHHHhcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeecc
Q 026830 84 AENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESV 154 (232)
Q Consensus 84 ~~~v~~~L~~IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v 154 (232)
.++|+++|++|||+|++||||++|++|++++|+|||+|+|+|||++.+||+. ||++|++++|++..|+++
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 4789999999999999999999999999999999999999999999999998 999999999999998753
No 11
>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=99.77 E-value=6e-19 Score=151.45 Aligned_cols=68 Identities=32% Similarity=0.520 Sum_probs=63.6
Q ss_pred hhhhHHHHHh-hccccccccCCCcEEEEEee-CCEEEEEEccCCCCch----hHHHHHHHHHHhhCCCcceEEeC
Q 026830 164 NEENIEKVLE-EIRPYLVGAAGGSLELVTID-EPIVKVRITGPAAGVM----TVRVAVTQKLREKIPAIAAVQLL 232 (232)
Q Consensus 164 ~~~~i~~~L~-~iRP~L~~~dGGdielv~v~-~gvv~Vrl~GaC~~c~----Tl~~~Ie~~L~~~~P~i~~V~~~ 232 (232)
..++|+++|+ +|||+|+ +||||+||++|+ +++|+|||+|+|+||| ||+++||++|++++|++++|+.+
T Consensus 106 ~~~~i~~~l~~~irP~l~-~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~ 179 (190)
T TIGR03341 106 LEERINYVLQSEINPQLA-SHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDA 179 (190)
T ss_pred HHHHHHHHHHhccCHHHH-hcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEe
Confidence 4688999998 8999999 999999999997 5799999999999997 99999999999999999999864
No 12
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.76 E-value=1e-18 Score=150.33 Aligned_cols=68 Identities=26% Similarity=0.475 Sum_probs=63.5
Q ss_pred hhhhHHHHHh-hccccccccCCCcEEEEEee-CCEEEEEEccCCCCch----hHHHHHHHHHHhhCC-CcceEEeC
Q 026830 164 NEENIEKVLE-EIRPYLVGAAGGSLELVTID-EPIVKVRITGPAAGVM----TVRVAVTQKLREKIP-AIAAVQLL 232 (232)
Q Consensus 164 ~~~~i~~~L~-~iRP~L~~~dGGdielv~v~-~gvv~Vrl~GaC~~c~----Tl~~~Ie~~L~~~~P-~i~~V~~~ 232 (232)
..++|+++|+ +|||+|+ +||||+||++|+ +++|+|||+|+|+||| ||+++||++|++++| +|++|+.+
T Consensus 107 ~~~~i~~~l~~~irP~l~-~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v 181 (192)
T PRK11190 107 LMERVEYVLQSQINPQLA-GHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDL 181 (192)
T ss_pred HHHHHHHHHHhccChhHH-hcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEe
Confidence 4788999997 8999999 999999999997 5899999999999997 999999999999999 99999864
No 13
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 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 domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=98.69 E-value=1.2e-09 Score=83.11 Aligned_cols=52 Identities=13% Similarity=0.286 Sum_probs=43.7
Q ss_pred CCCCCCCCCCCCCCcCCCC--CCcceeeEecCe-eeec-----cCCccccchHHHHHHhhh
Q 026830 8 PSYSRPHQTLDSPSCSRPA--SKSTKSFFGERV-SLTR-----WRNPVCHSSCRLLLIRKR 60 (232)
Q Consensus 8 ~s~~~~~~a~~~pla~~lf--~~v~~~~~~~~~-t~t~-----w~~~l~~~~~~~i~~~~~ 60 (232)
.+|.+.++|.+||||++|| +||++|||++|| |||| |+. |++.|...|+++++
T Consensus 26 ~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~~~~W~~-l~~~I~~~I~~~l~ 85 (87)
T PF08712_consen 26 FEFKSAEEASDSPLAQALFAIPGVKSVFIGDDFITVTKNPDADWED-LKPEIREVIMEFLE 85 (87)
T ss_dssp -EEESSS-TTS-HHHHHHHTSTTEEEEEEETTEEEEEE-TTS-HHH-HHHHHHHHTH----
T ss_pred EEeCChHHcccCHHHHHhcCCCCEeEEEEECCEEEEeeCCCCCHHH-HHHHHHHHHhhhcc
Confidence 4799999999999999999 999999999999 9999 998 99999999998864
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=95.64 E-value=0.1 Score=37.34 Aligned_cols=64 Identities=19% Similarity=0.360 Sum_probs=49.5
Q ss_pred hhHHHHHhh-ccccccccC---CCcEEEEEeeCCEEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceEEe
Q 026830 166 ENIEKVLEE-IRPYLVGAA---GGSLELVTIDEPIVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAVQL 231 (232)
Q Consensus 166 ~~i~~~L~~-iRP~L~~~d---GGdielv~v~~gvv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V~~ 231 (232)
++|.++|.. .-|++. .+ =|-+.=+.+++|.|+|.|.-+..+|+ .++..|+++|+ .+|++++|+.
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 QAVRDALKQVKDPELG-KDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHTT-BETTTS-SBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT-SEEEE
T ss_pred HHHHHHHhCCCCCCCC-CCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCCCceEeC
Confidence 567778874 566665 44 37788899999999999999999997 78889999999 9999998864
No 15
>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=0.1 Score=37.36 Aligned_cols=66 Identities=24% Similarity=0.391 Sum_probs=51.3
Q ss_pred HHHHHHHHH-hcchhhhC---CCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEee
Q 026830 85 ENIESVLDE-IRPYLISD---GGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (232)
Q Consensus 85 ~~v~~~L~~-IrP~L~~d---GGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~ 152 (232)
++|.++|.. .-|.+..+ =|-|.=+.+++|.|++.|.-...+|+ ....++..|+++|+ .+|++..|.
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~gv~~V~ 71 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVK 71 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEe
Confidence 567777874 56666533 37788899999999999999999998 77889999999999 799887764
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=81.87 E-value=11 Score=28.30 Aligned_cols=64 Identities=17% Similarity=0.308 Sum_probs=43.9
Q ss_pred hhhHHHHHhh-ccccccccCC---CcEEEEEeeC-CEEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceEE
Q 026830 165 EENIEKVLEE-IRPYLVGAAG---GSLELVTIDE-PIVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAVQ 230 (232)
Q Consensus 165 ~~~i~~~L~~-iRP~L~~~dG---Gdielv~v~~-gvv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V~ 230 (232)
+++|.++|+. .-|.+. .+- |-+.=+.+++ +.++|.|.-+-.+|+ .++..+++.|. .+|.+..|.
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 KDAVIEALKTVYDPEIP-VNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEVENAVR-AVPGVGSVT 74 (99)
T ss_pred HHHHHHHHcCCCCCCCC-CCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHHHHHHHHHHHH-hCCCCceEE
Confidence 4568888875 456654 433 3344456675 888888887777775 67778888885 478887765
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=80.64 E-value=9 Score=28.86 Aligned_cols=67 Identities=16% Similarity=0.294 Sum_probs=47.3
Q ss_pred HHHHHHHHHH-hcchhhhC---CCcEEEEEEeC-cEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEee
Q 026830 84 AENIESVLDE-IRPYLISD---GGNVALHEIDG-NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (232)
Q Consensus 84 ~~~v~~~L~~-IrP~L~~d---GGdvelv~i~~-~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~ 152 (232)
.++|.++|+. .-|.+..+ =|-|.=+.+++ +.++|.+.-...+||.. ..++..++.+|.. +|++..|.
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 45666542 24555567775 88999998877788754 5588899999965 77776664
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=75.31 E-value=16 Score=31.24 Aligned_cols=68 Identities=21% Similarity=0.265 Sum_probs=49.5
Q ss_pred chhhhhHHHHHhh-ccccccccC---CCcEEEEEeeC---C--EEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceE
Q 026830 162 ELNEENIEKVLEE-IRPYLVGAA---GGSLELVTIDE---P--IVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAV 229 (232)
Q Consensus 162 e~~~~~i~~~L~~-iRP~L~~~d---GGdielv~v~~---g--vv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V 229 (232)
+.++++|.++|+. .-|.+. .+ =|-+.=+.+++ + .|+|.|+=+..+|+ .++..|+++|. .+|.+++|
T Consensus 72 ~~~ee~V~eaL~tV~DPei~-~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL~-~l~gV~~V 149 (174)
T TIGR03406 72 EDNEDQVWEQLRTVYDPEIP-VNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVL-AVPNVDEV 149 (174)
T ss_pred cccHHHHHHHHcCCCCCCCC-CChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHHH-hCCCceeE
Confidence 4556789999985 567765 43 34455556765 5 89999998888886 77788888886 57888876
Q ss_pred Ee
Q 026830 230 QL 231 (232)
Q Consensus 230 ~~ 231 (232)
..
T Consensus 150 ~V 151 (174)
T TIGR03406 150 EV 151 (174)
T ss_pred EE
Confidence 53
No 19
>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=70.27 E-value=30 Score=29.48 Aligned_cols=79 Identities=16% Similarity=0.207 Sum_probs=55.1
Q ss_pred CCcHHHHHHHHHH-hcchhhh---CCCcEEEEEEeC---c--EEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEe
Q 026830 81 PLTAENIESVLDE-IRPYLIS---DGGNVALHEIDG---N--VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (232)
Q Consensus 81 ~l~~~~v~~~L~~-IrP~L~~---dGGdvelv~i~~---~--~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V 151 (232)
+.++++|.++|.. .-|.+.. +=|-|.=+.+++ + .|+|.|.-...+|++. ..|+..|+.+|.. +|.+.+|
T Consensus 72 ~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~-~~L~~dV~~aL~~-l~gV~~V 149 (174)
T TIGR03406 72 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMG-PVLVEDVEDKVLA-VPNVDEV 149 (174)
T ss_pred cccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHH-HHHHHHHHHHHHh-CCCceeE
Confidence 5557889999985 5676654 235566667776 5 8999999888889754 6677888888875 7887766
Q ss_pred ec--cccccccc
Q 026830 152 ES--VADEETGL 161 (232)
Q Consensus 152 ~~--v~d~e~g~ 161 (232)
.. ..+..+..
T Consensus 150 ~V~l~~dp~W~~ 161 (174)
T TIGR03406 150 EVELVFDPPWSR 161 (174)
T ss_pred EEEEEecCCCCh
Confidence 43 33334443
No 20
>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=70.10 E-value=2.9 Score=32.35 Aligned_cols=57 Identities=30% Similarity=0.443 Sum_probs=30.8
Q ss_pred CCCC---CCchHhHHHHHHHHHHhhCCcc-eEeeccccccccc-chhhhhHHHHHh--hcccccc
Q 026830 123 CGSC---PSSVMTMKMGIERRLMEKIPEI-VAVESVADEETGL-ELNEENIEKVLE--EIRPYLV 180 (232)
Q Consensus 123 C~gC---p~s~~Tlk~~Ie~~L~~~vpei-~~V~~v~d~e~g~-e~~~~~i~~~L~--~iRP~L~ 180 (232)
|.+| |+|-.|. .+++.+|..++|+. -.+.=++.+.... +...+-++++++ ..=|.+-
T Consensus 9 CASCVn~PsSkeTy-eWL~aal~RKyp~~~f~~~YiDi~~p~~~~~~~~~a~~I~ede~fYPlV~ 72 (93)
T PF07315_consen 9 CASCVNAPSSKETY-EWLEAALKRKYPDQPFEFTYIDIENPPENDHDQQFAERILEDELFYPLVV 72 (93)
T ss_dssp -GGGSSS--HHHHH-HHHHHHHHHH-TTS-EEEEEEETTT----HHHHHHHHHHHTTSS-SSEEE
T ss_pred chhhcCCCCchhHH-HHHHHHHhCcCCCCceEEEEEecCCCCccHHHHHHHHHHHhcccccceEE
Confidence 6666 8888887 89999999999985 3443233222111 223344566665 3667665
No 21
>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=68.03 E-value=20 Score=29.72 Aligned_cols=45 Identities=22% Similarity=0.298 Sum_probs=35.0
Q ss_pred CCcEEEEEeeCCEEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceEE
Q 026830 184 GGSLELVTIDEPIVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAVQ 230 (232)
Q Consensus 184 GGdielv~v~~gvv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V~ 230 (232)
=|-+.=+.++++.|.|.|+-.-++|+ .+++.|+++|++. .+..|.
T Consensus 14 LG~Vr~V~v~gd~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~--Gv~~V~ 61 (146)
T TIGR02159 14 LGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRAL--GVEVVE 61 (146)
T ss_pred cCCeeEEEEECCEEEEEEEeCCCCCchHHHHHHHHHHHHHhc--CCCeEE
Confidence 35666677888899999998888997 7778899999874 555554
No 22
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=67.79 E-value=6.9 Score=32.57 Aligned_cols=26 Identities=19% Similarity=0.482 Sum_probs=20.7
Q ss_pred EEEEEEeCcEEEEEEc--ccCCCCCCch
Q 026830 105 VALHEIDGNVVRLKLQ--GACGSCPSSV 130 (232)
Q Consensus 105 velv~i~~~~v~Vrl~--GaC~gCp~s~ 130 (232)
-.+++++++.++|+.. .+|++|.+..
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C~a~~ 33 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSCASRA 33 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCcCCCC
Confidence 3578899998888875 7999998753
No 23
>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=65.25 E-value=6.1 Score=31.63 Aligned_cols=23 Identities=35% Similarity=0.869 Sum_probs=18.3
Q ss_pred EEEEeCcEEEEEEc--ccCCCCCCc
Q 026830 107 LHEIDGNVVRLKLQ--GACGSCPSS 129 (232)
Q Consensus 107 lv~i~~~~v~Vrl~--GaC~gCp~s 129 (232)
+++++++.++|+.. .+|++|.++
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~~ 25 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSAS 25 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCCC
Confidence 46789999988884 789999743
No 24
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.12 E-value=7.9 Score=30.31 Aligned_cols=36 Identities=28% Similarity=0.368 Sum_probs=25.5
Q ss_pred cCCCC---CCchHhHHHHHHHHHHhhCCcce-Eeecccccc
Q 026830 122 ACGSC---PSSVMTMKMGIERRLMEKIPEIV-AVESVADEE 158 (232)
Q Consensus 122 aC~gC---p~s~~Tlk~~Ie~~L~~~vpei~-~V~~v~d~e 158 (232)
-|.+| |+|-.|. ++.+.+|+.++|+.- .+.=++.+.
T Consensus 15 iCASCV~aPtsKdt~-eWLeaalkRKyp~~~F~~~YiDI~n 54 (106)
T COG4837 15 ICASCVNAPTSKDTY-EWLEAALKRKYPNQPFKYTYIDITN 54 (106)
T ss_pred hhHHhcCCCcchhHH-HHHHHHHhccCCCCCcEEEEEEcCC
Confidence 36666 8887777 899999999999854 333333333
No 25
>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=63.75 E-value=43 Score=27.70 Aligned_cols=75 Identities=23% Similarity=0.291 Sum_probs=49.2
Q ss_pred CcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEee--cccccccccchhhhhHHHHH-h-hcccc
Q 026830 103 GNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE--SVADEETGLELNEENIEKVL-E-EIRPY 178 (232)
Q Consensus 103 Gdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~--~v~d~e~g~e~~~~~i~~~L-~-~iRP~ 178 (232)
|-|.=+.++++.|.|.|.-.-.+||.. ..|++.|+++|++. ++..|. ..-+..+...-.-+.-++-| + -|.|=
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~~~giapp 91 (146)
T TIGR02159 15 GMVREVDVDGGGVVVKFTPTYSGCPAL-EVIRQDIRDAVRAL--GVEVVEVSTSLDPPWTTDWITEDAREKLREYGIAPP 91 (146)
T ss_pred CCeeEEEEECCEEEEEEEeCCCCCchH-HHHHHHHHHHHHhc--CCCeEEEeEeeCCCCChHHCCHHHHHHHHhcCccCC
Confidence 667777888889999999988999865 57889999999884 455443 23333343322223344445 3 37776
Q ss_pred cc
Q 026830 179 LV 180 (232)
Q Consensus 179 L~ 180 (232)
..
T Consensus 92 ~~ 93 (146)
T TIGR02159 92 AG 93 (146)
T ss_pred Cc
Confidence 55
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=63.22 E-value=30 Score=28.57 Aligned_cols=45 Identities=13% Similarity=0.090 Sum_probs=34.5
Q ss_pred eCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeeccccc
Q 026830 111 DGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADE 157 (232)
Q Consensus 111 ~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v~d~ 157 (232)
.++.++|-+.-. .. ......++..|+++++...|.+..|...++.
T Consensus 98 ~~~~a~Vav~~~-~~-~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D~ 142 (177)
T PF09580_consen 98 TDDNAYVAVDLD-FN-RFNTKKIKKKVEKAVKSADPRIYNVYVSTDP 142 (177)
T ss_pred ECCEEEEEEEec-cc-ccchhHHHHHHHHHHHHhCCCccEEEEEcCH
Confidence 456777766644 33 5677899999999999999999998766554
No 27
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=62.62 E-value=31 Score=27.44 Aligned_cols=68 Identities=31% Similarity=0.393 Sum_probs=46.8
Q ss_pred HHHHHHHHHH-hcchhhhC---CCcEEEEEEeC--cEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeec
Q 026830 84 AENIESVLDE-IRPYLISD---GGNVALHEIDG--NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVES 153 (232)
Q Consensus 84 ~~~v~~~L~~-IrP~L~~d---GGdvelv~i~~--~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~ 153 (232)
.++|..+|.. +-|.|--| =|=+.=+.+++ +.++|+++..=.|||++..=. ..++.+|.+ +|.+..++.
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 LEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIA-DQVEAALEE-IPGVEDVEV 87 (111)
T ss_pred HHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHHHH-HHHHHHHHh-cCCcceEEE
Confidence 5677777764 67777433 23333445653 489999999889999986544 788888887 565666643
No 28
>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=59.61 E-value=7 Score=30.23 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=15.5
Q ss_pred CCCCc---hhHH---HHHHHHHHhhCCCc
Q 026830 204 PAAGV---MTVR---VAVTQKLREKIPAI 226 (232)
Q Consensus 204 aC~~c---~Tl~---~~Ie~~L~~~~P~i 226 (232)
-|++| ||-| .+++.+|++++|+.
T Consensus 8 ~CASCVn~PsSkeTyeWL~aal~RKyp~~ 36 (93)
T PF07315_consen 8 ICASCVNAPSSKETYEWLEAALKRKYPDQ 36 (93)
T ss_dssp --GGGSSS--HHHHHHHHHHHHHHH-TTS
T ss_pred cchhhcCCCCchhHHHHHHHHHhCcCCCC
Confidence 38888 4333 79999999999985
No 29
>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=59.41 E-value=18 Score=25.54 Aligned_cols=41 Identities=24% Similarity=0.564 Sum_probs=24.6
Q ss_pred CCcHHHHHHHHHH-hcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHh
Q 026830 81 PLTAENIESVLDE-IRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMT 132 (232)
Q Consensus 81 ~l~~~~v~~~L~~-IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~T 132 (232)
.++.+.|+.+|+. +| -|-|+-++....- .|.|.+|+....+
T Consensus 25 ~~s~~~ve~mL~~l~~------kG~I~~~~~~~~~-----~~~C~~C~~~~~~ 66 (69)
T PF09012_consen 25 GISPEAVEAMLEQLIR------KGYIRKVDMSSCC-----GGSCSSCGPASKE 66 (69)
T ss_dssp T--HHHHHHHHHHHHC------CTSCEEEEEE--S-----SSSSSS-SS----
T ss_pred CcCHHHHHHHHHHHHH------CCcEEEecCCCCC-----CCCCCCCCCcccc
Confidence 5557788888885 43 5888877776544 8999999987653
No 30
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=59.32 E-value=39 Score=26.85 Aligned_cols=65 Identities=28% Similarity=0.359 Sum_probs=42.6
Q ss_pred hhhhHHHHHhh-ccccccccCCCc---EEEEEee--CCEEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceEE
Q 026830 164 NEENIEKVLEE-IRPYLVGAAGGS---LELVTID--EPIVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAVQ 230 (232)
Q Consensus 164 ~~~~i~~~L~~-iRP~L~~~dGGd---ielv~v~--~gvv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V~ 230 (232)
..++|.++|.. +-|.|- -|==| +.=+.++ ++.++|+|+..-.||| -+.+.++++|+ .+|.++.|+
T Consensus 13 ~~~~i~~aL~~V~DPEi~-idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~-~~~~v~~v~ 86 (111)
T COG2151 13 TLEDILEALKTVIDPEIG-IDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALE-EIPGVEDVE 86 (111)
T ss_pred hHHHHHHHhhcCCCcccc-eeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHHHHHHHHHHHH-hcCCcceEE
Confidence 34556666663 566664 44222 2223555 4589999999999998 56678888877 566677665
No 31
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.60 E-value=5.4 Score=31.19 Aligned_cols=22 Identities=23% Similarity=0.240 Sum_probs=18.2
Q ss_pred CCCc---hhHH---HHHHHHHHhhCCCc
Q 026830 205 AAGV---MTVR---VAVTQKLREKIPAI 226 (232)
Q Consensus 205 C~~c---~Tl~---~~Ie~~L~~~~P~i 226 (232)
|++| ||-| .++|.+|++++|+.
T Consensus 16 CASCV~aPtsKdt~eWLeaalkRKyp~~ 43 (106)
T COG4837 16 CASCVNAPTSKDTYEWLEAALKRKYPNQ 43 (106)
T ss_pred hHHhcCCCcchhHHHHHHHHHhccCCCC
Confidence 8888 4444 79999999999975
No 32
>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=52.05 E-value=18 Score=24.13 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=22.9
Q ss_pred cccCCCCCCchHhHHHHHHHHHHhhCC
Q 026830 120 QGACGSCPSSVMTMKMGIERRLMEKIP 146 (232)
Q Consensus 120 ~GaC~gCp~s~~Tlk~~Ie~~L~~~vp 146 (232)
+++|.|||.-+..|...|-..|++...
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~gwK 33 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDGWK 33 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHHHH
Confidence 579999998888898999999987543
No 33
>PRK11670 antiporter inner membrane protein; Provisional
Probab=51.25 E-value=78 Score=29.83 Aligned_cols=66 Identities=14% Similarity=0.146 Sum_probs=48.1
Q ss_pred hhhhhHHHHHhh-ccccccccCC---CcEEEEEeeCCEEEEEEccCCCCch---hHHHHHHHHHHhhCCCcceEE
Q 026830 163 LNEENIEKVLEE-IRPYLVGAAG---GSLELVTIDEPIVKVRITGPAAGVM---TVRVAVTQKLREKIPAIAAVQ 230 (232)
Q Consensus 163 ~~~~~i~~~L~~-iRP~L~~~dG---Gdielv~v~~gvv~Vrl~GaC~~c~---Tl~~~Ie~~L~~~~P~i~~V~ 230 (232)
.++++|.++|.. .-|.+. .+= |-+.=+.++++.+.+.+.-+-..|+ .++..+++.|+. +|++++|.
T Consensus 12 ~~~~~v~~~l~~v~~p~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 84 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLK-HNLTTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQCSAELLR-ITGAKAID 84 (369)
T ss_pred chHHHHHHHHhcCCCCCCC-CChhhhCCeeEEEEeCCEEEEEEEECCCCchHHHHHHHHHHHHHHh-cCCCceEE
Confidence 455778888875 556665 543 4454457788999999987777786 677889999984 78887665
No 34
>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=47.46 E-value=31 Score=24.54 Aligned_cols=25 Identities=12% Similarity=0.060 Sum_probs=20.2
Q ss_pred EEEEEccCCCCchhHHHHHHHHHHhh
Q 026830 197 VKVRITGPAAGVMTVRVAVTQKLREK 222 (232)
Q Consensus 197 v~Vrl~GaC~~c~Tl~~~Ie~~L~~~ 222 (232)
+++ ++-.|..|+.+...+++.+.+.
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 7777999998888888887765
No 35
>PRK11670 antiporter inner membrane protein; Provisional
Probab=38.84 E-value=1e+02 Score=28.95 Aligned_cols=68 Identities=12% Similarity=0.061 Sum_probs=48.8
Q ss_pred CcHHHHHHHHHH-hcchhhhC---CCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEe
Q 026830 82 LTAENIESVLDE-IRPYLISD---GGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (232)
Q Consensus 82 l~~~~v~~~L~~-IrP~L~~d---GGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V 151 (232)
.++++|.++|.. .-|.+..+ -|-+.=+.++++.+++.+.-.-.+||.. ..++..++++|+. +|++..|
T Consensus 12 ~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~ 83 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAF-EELKEQCSAELLR-ITGAKAI 83 (369)
T ss_pred chHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHH-HHHHHHHHHHHHh-cCCCceE
Confidence 446889999985 56666552 3556556788888888888766677744 5588899999986 6666544
No 36
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=32.09 E-value=78 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.375 Sum_probs=23.5
Q ss_pred EEEEEEcccCCCCCCchHhHHHHHHHHHHhh
Q 026830 114 VVRLKLQGACGSCPSSVMTMKMGIERRLMEK 144 (232)
Q Consensus 114 ~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~ 144 (232)
..+++|. +|+||..|-..|.+.+-..|...
T Consensus 6 va~~~L~-gC~GC~~slldl~E~L~dll~~~ 35 (247)
T COG1941 6 VATVWLT-GCSGCHMSLLDLYEKLLDLLEDA 35 (247)
T ss_pred EEEEEec-cccchHHHHHhHHHHHHHhhhhh
Confidence 4455555 69999999999999888888744
No 37
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=31.18 E-value=1.1e+02 Score=22.67 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=21.9
Q ss_pred EEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHH
Q 026830 105 VALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIE 138 (232)
Q Consensus 105 velv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie 138 (232)
+-++.+-.+.|-||.+|+ |+||++.+.
T Consensus 38 ~~~vRil~~~VMVRVGGG-------W~tL~~fL~ 64 (73)
T smart00243 38 LRLVRILRSTVMVRVGGG-------WETLDEYLL 64 (73)
T ss_pred EEEEEEeCCeEEEEECCc-------HHHHHHHHH
Confidence 456777778999999998 999977654
No 38
>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=28.93 E-value=1.9e+02 Score=25.20 Aligned_cols=37 Identities=24% Similarity=0.383 Sum_probs=24.6
Q ss_pred EEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEee
Q 026830 114 VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (232)
Q Consensus 114 ~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~ 152 (232)
.+++.+.+.+ .......+++.|++.|++++|++..|.
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 3444444553 112245578999999999999998643
No 39
>TIGR02554 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex.
Probab=27.35 E-value=5.7e+02 Score=24.66 Aligned_cols=108 Identities=17% Similarity=0.243 Sum_probs=68.2
Q ss_pred hcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeecccccccccchhhhhHHHHHh
Q 026830 94 IRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETGLELNEENIEKVLE 173 (232)
Q Consensus 94 IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v~d~e~g~e~~~~~i~~~L~ 173 (232)
+.-.|+...+-+.++-=.+|.+||--. ....+.=..+..+|+..++-..|..+.+ -+++|+..|.
T Consensus 170 L~~lL~g~~~p~~il~grDg~iyVla~--------~qrd~~W~~Q~Llk~~~~e~v~v~~i~~-------~~~~i~~~L~ 234 (389)
T TIGR02554 170 LNGLLGGAPVRFAVLPGRDGRIYVAAA--------SQRDAEWARQALLRAALPEKIEVAVIGA-------ERQRVSRWLD 234 (389)
T ss_pred HHHHhcCCCCCeEEEeCCCCcEEEEEc--------cccHhHHHHHHHhhcCCCCCeEEechHH-------HHHHHHHHHH
Confidence 556677777888888777788888543 2344533445555555666555543322 2457888888
Q ss_pred hccccccccCCCcEEEEEeeCCEEEEEEccCCCCc-----------hhHHHHHHHHHHhhCCCcceEEe
Q 026830 174 EIRPYLVGAAGGSLELVTIDEPIVKVRITGPAAGV-----------MTVRVAVTQKLREKIPAIAAVQL 231 (232)
Q Consensus 174 ~iRP~L~~~dGGdielv~v~~gvv~Vrl~GaC~~c-----------~Tl~~~Ie~~L~~~~P~i~~V~~ 231 (232)
+..|.|. .++|+|.-+|.-- ...+..+.+.|++.+|=.+.|++
T Consensus 235 ~~~P~l~---------------~~kv~l~~P~~Pvl~l~~q~~~~~~~~~~~l~~~l~~~~pya~~v~I 288 (389)
T TIGR02554 235 EAGPQLA---------------FYRLRLDAPRHPELWLSRQRNAAPAAARARLIGELRRLMPYARDVRI 288 (389)
T ss_pred hhCCcce---------------EEEEEcCCCCCCEEEEecccCCCCHHHHHHHHHHHHHhCCccceeEE
Confidence 8888875 2344444444421 14446889999999998777764
No 40
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=26.74 E-value=78 Score=26.61 Aligned_cols=34 Identities=24% Similarity=0.436 Sum_probs=25.1
Q ss_pred EEEEeCcEEEEEE--cccCCCCCCchHhHHHHHHHHH
Q 026830 107 LHEIDGNVVRLKL--QGACGSCPSSVMTMKMGIERRL 141 (232)
Q Consensus 107 lv~i~~~~v~Vrl--~GaC~gCp~s~~Tlk~~Ie~~L 141 (232)
+++.++|.+.|+= +-+|++|++...-- ..+...|
T Consensus 8 vv~~q~G~a~V~c~~~S~CgsC~a~~~CG-s~~l~kL 43 (150)
T COG3086 8 VVSWQNGQAKVSCQRQSACGSCAARAGCG-SGLLSKL 43 (150)
T ss_pred EEEccCCeEEEEeeccCccccchhhcccc-hHHHHHh
Confidence 4778888777776 47999998875544 5666666
No 41
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=26.41 E-value=87 Score=23.89 Aligned_cols=29 Identities=14% Similarity=0.203 Sum_probs=24.8
Q ss_pred CCcHHHHHHHHHHhcchhhhCCCcEEEEE
Q 026830 81 PLTAENIESVLDEIRPYLISDGGNVALHE 109 (232)
Q Consensus 81 ~l~~~~v~~~L~~IrP~L~~dGGdvelv~ 109 (232)
.+++++++.+++.+.-.|...||.+.-++
T Consensus 17 ~l~e~~~~~~~~~~~~~i~~~gg~i~~~~ 45 (97)
T CHL00123 17 DLNEEELLKWIENYKKLLRKRGAKNISVQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 56789999999999999999999875544
No 42
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=25.82 E-value=1.8e+02 Score=25.46 Aligned_cols=82 Identities=17% Similarity=0.243 Sum_probs=48.2
Q ss_pred eCcEEEEEEcccCCC--CCCchHhHHHHHHHHHHhhCCc-ceEeecccccccccchhhhhHHHHHhhc-----ccccccc
Q 026830 111 DGNVVRLKLQGACGS--CPSSVMTMKMGIERRLMEKIPE-IVAVESVADEETGLELNEENIEKVLEEI-----RPYLVGA 182 (232)
Q Consensus 111 ~~~~v~Vrl~GaC~g--Cp~s~~Tlk~~Ie~~L~~~vpe-i~~V~~v~d~e~g~e~~~~~i~~~L~~i-----RP~L~~~ 182 (232)
.+.-.+|++.|.|.. -|.- .++-.-|.++|...+.+ -++. + ..|.--+..-.+.+|+++ .=||. .
T Consensus 60 p~ppktI~~~g~~~~~~~pdE-rs~a~~i~kAL~~~~~~~~~~~--~---~pGi~V~~~~~e~ll~~l~~~~~ly~L~-E 132 (197)
T COG1901 60 PDPPKTIRVEGSELRYLNPDE-RSLAILIKKALDAELGKEQTRE--V---TPGIYVRNGGFEALLAELAEGRSLYYLH-E 132 (197)
T ss_pred CCCCEEEEEEcccccccCcch-HHHHHHHHHHHHhhccccceee--c---CCCEEEecCCHHHHHHHHhccCcEEEEc-c
Confidence 456889999999887 3333 34446788888884432 1111 1 111111112233444333 34787 8
Q ss_pred CCCcEEEEEeeCCEEEE
Q 026830 183 AGGSLELVTIDEPIVKV 199 (232)
Q Consensus 183 dGGdielv~v~~gvv~V 199 (232)
||+||+=++...+-++|
T Consensus 133 ~G~DI~~v~~~~np~FI 149 (197)
T COG1901 133 DGRDISEVDLIPNPVFI 149 (197)
T ss_pred CCccHhhcccCCCceEE
Confidence 99999999988888777
No 43
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=25.29 E-value=1e+02 Score=21.47 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=19.1
Q ss_pred HHHHHHHHHhcchhhhCCCcEEEE
Q 026830 85 ENIESVLDEIRPYLISDGGNVALH 108 (232)
Q Consensus 85 ~~v~~~L~~IrP~L~~dGGdvelv 108 (232)
+..+++.+.+.|.|+.|||.+-..
T Consensus 2 ~~~~~Y~~~~~~~l~~~GG~~l~~ 25 (65)
T PF07045_consen 2 EAYQEYREAVPPILEKYGGRVLAR 25 (65)
T ss_dssp HHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEE
Confidence 567788889999999999986665
No 44
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=24.88 E-value=86 Score=22.47 Aligned_cols=24 Identities=29% Similarity=0.731 Sum_probs=19.4
Q ss_pred CCCCCCchHhHHHHHHHHHHhhCCcc
Q 026830 123 CGSCPSSVMTMKMGIERRLMEKIPEI 148 (232)
Q Consensus 123 C~gCp~s~~Tlk~~Ie~~L~~~vpei 148 (232)
|.+|. +..--..+.+.|...+|+.
T Consensus 6 C~~C~--y~~Ra~~l~q~L~~~Fp~~ 29 (72)
T TIGR02174 6 CGSCG--YKPRAAWLKQELLEEFPDL 29 (72)
T ss_pred CCCCC--ChHHHHHHHHHHHHHCCCC
Confidence 77787 5555578999999999985
No 45
>PF15092 UPF0728: Uncharacterised protein family UPF0728
Probab=24.00 E-value=80 Score=24.25 Aligned_cols=32 Identities=25% Similarity=0.481 Sum_probs=25.8
Q ss_pred HhhccccccccCCCcEEEEEeeC-CEEEEEEccC
Q 026830 172 LEEIRPYLVGAAGGSLELVTIDE-PIVKVRITGP 204 (232)
Q Consensus 172 L~~iRP~L~~~dGGdielv~v~~-gvv~Vrl~Ga 204 (232)
|+-++-.|+ .||-.++|..+++ +.|.+-+.|-
T Consensus 27 L~GLqa~L~-~dGh~v~L~~~~d~n~vel~vnge 59 (88)
T PF15092_consen 27 LEGLQAVLA-KDGHEVILEKIEDWNVVELVVNGE 59 (88)
T ss_pred HHHHHHHHH-hCCcEEEEEEeccccEEEEEECCe
Confidence 456677788 8999999999987 8888777664
No 46
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.00 E-value=83 Score=21.33 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=10.6
Q ss_pred cCCCCch-hHHHHHHHHHH
Q 026830 203 GPAAGVM-TVRVAVTQKLR 220 (232)
Q Consensus 203 GaC~~c~-Tl~~~Ie~~L~ 220 (232)
|.|+||- ++....-+.|+
T Consensus 23 ~~C~gC~~~l~~~~~~~i~ 41 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIR 41 (56)
T ss_pred CccCCCCEEcCHHHHHHHH
Confidence 6899994 55444444443
No 47
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=21.66 E-value=1.3e+02 Score=22.39 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=23.4
Q ss_pred cEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHH
Q 026830 104 NVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIER 139 (232)
Q Consensus 104 dvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~ 139 (232)
.+-++.+-.+.|-||.+|+ |.||.+.+.+
T Consensus 37 ~l~~~ril~~~vMVRVGGG-------W~tL~~~L~k 65 (73)
T PF02187_consen 37 KLFFVRILRSHVMVRVGGG-------WDTLEEYLDK 65 (73)
T ss_dssp EEEEEEETTTEEEEEETTE-------EEEHHHHHHH
T ss_pred eEEEEEEeCCEEEEEeCCc-------HHHHHHHhhc
Confidence 3667777788999999998 9999877643
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=20.77 E-value=3.2e+02 Score=23.74 Aligned_cols=34 Identities=26% Similarity=0.444 Sum_probs=23.2
Q ss_pred EEEEEccCCCCc--hhHHHHHHHHHHhhCCCcceEE
Q 026830 197 VKVRITGPAAGV--MTVRVAVTQKLREKIPAIAAVQ 230 (232)
Q Consensus 197 v~Vrl~GaC~~c--~Tl~~~Ie~~L~~~~P~i~~V~ 230 (232)
++|++.+.++.- ..+++.|++.|++++|++.+|.
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 444444554211 1567999999999999998753
No 49
>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=20.37 E-value=1.8e+02 Score=30.98 Aligned_cols=111 Identities=18% Similarity=0.320 Sum_probs=62.5
Q ss_pred EEEEEEcccCCCCCCch---HhHHHHHHHHHHhhCCcceEeeccccccc-----------ccchhhhhHHHHHhhccccc
Q 026830 114 VVRLKLQGACGSCPSSV---MTMKMGIERRLMEKIPEIVAVESVADEET-----------GLELNEENIEKVLEEIRPYL 179 (232)
Q Consensus 114 ~v~Vrl~GaC~gCp~s~---~Tlk~~Ie~~L~~~vpei~~V~~v~d~e~-----------g~e~~~~~i~~~L~~iRP~L 179 (232)
.|.+.+.|+ +.. ..+-.-+|++|+. +++++.+........ .......++++.++.+++.|
T Consensus 44 ~V~~~~pga-----s~~~ve~~vt~plE~~l~~-v~gv~~i~S~s~~g~s~i~v~f~~~~d~~~a~~~v~~~i~~~~~~L 117 (1021)
T PF00873_consen 44 SVTTSYPGA-----SPEEVEQLVTKPLEEALSS-VEGVKEIRSTSREGSSSITVEFDDGTDIDEALQEVREKIDQIRSDL 117 (1021)
T ss_dssp EEEEE-TTS------HHHHHHHTHHHHHHTHCS-STTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGGS
T ss_pred EEEEecCcC-----CHHHHHHHHHHHHHHHHcC-CCCeEEEEEEecCCcEEEEEEeccccCHHHHHHHHHHHHHhhhhhC
Confidence 566777777 321 2233456666654 677777765443321 12334567888888888877
Q ss_pred cccCCCcEEEEEe--e-CCEEEEEEccCCCC--chhHHHHHHHHHHh---hCCCcceEEe
Q 026830 180 VGAAGGSLELVTI--D-EPIVKVRITGPAAG--VMTVRVAVTQKLRE---KIPAIAAVQL 231 (232)
Q Consensus 180 ~~~dGGdielv~v--~-~gvv~Vrl~GaC~~--c~Tl~~~Ie~~L~~---~~P~i~~V~~ 231 (232)
= .+=..-.+... . ..+..+.+.+.-++ =..|+..++..|+. ++|+|.+|..
T Consensus 118 P-~~~~~p~i~~~~~~~~~i~~~~l~~~~~~~~~~~l~~~~~~~l~~~L~~i~gV~~v~~ 176 (1021)
T PF00873_consen 118 P-PGVEEPQIFKFDPSDSPIMILALTSDDGTLDLKELRDYAEEQLKPRLERIPGVARVDI 176 (1021)
T ss_dssp --HHHHHHEEEEEEEECCEEEEEEEEESSSSS-HHHHHHHHHHCTHHHHHTSTTEEEEEE
T ss_pred c-ccccCCceeeccCCCceeEEEEeccCCCCCCHHHHHHHHHHHHHHhccceeEEEEEEe
Confidence 5 22223344443 2 36788888888222 13666666655554 4588888764
No 50
>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=20.24 E-value=2.6e+02 Score=20.88 Aligned_cols=55 Identities=25% Similarity=0.435 Sum_probs=36.2
Q ss_pred ccccccccCCCcEEEEEeeC-CEEEEEEccCC---CC-c--hhHHHHHHHHHHhhCCCcceEEe
Q 026830 175 IRPYLVGAAGGSLELVTIDE-PIVKVRITGPA---AG-V--MTVRVAVTQKLREKIPAIAAVQL 231 (232)
Q Consensus 175 iRP~L~~~dGGdielv~v~~-gvv~Vrl~GaC---~~-c--~Tl~~~Ie~~L~~~~P~i~~V~~ 231 (232)
.+|.+- .|-.+.=+.+++ ++++|.|..+= .+ | .-+...|-..|.+.++++++|.+
T Consensus 45 ~~~~~p--~~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i 106 (117)
T PF10646_consen 45 LRSALP--PGTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVKKVQI 106 (117)
T ss_pred eeecCC--CccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCccEEEE
Confidence 344443 444444455564 49999998643 12 2 24557888899999999999975
No 51
>COG1614 CdhC CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]
Probab=20.05 E-value=2e+02 Score=27.69 Aligned_cols=89 Identities=19% Similarity=0.231 Sum_probs=54.1
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhhCCcceEeecccccccccc
Q 026830 84 AENIESVLD-EIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETGLE 162 (232)
Q Consensus 84 ~~~v~~~L~-~IrP~L~~dGGdvelv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~vpei~~V~~v~d~e~g~e 162 (232)
+++++.+|+ +|-.++.---|-..|-.- ..+|+|.+-.-..=..+-..+...+....++.||-|.++...--++
T Consensus 81 EedlE~VlERRiHef~NYieG~MHLNQR--dqvW~Rv~k~~~~kg~rl~hig~a~~~Lfk~efp~Iek~~vt~~Td---- 154 (470)
T COG1614 81 EEDLEGVLERRIHEFCNYIEGFMHLNQR--DQVWIRVSKNAFNKGFRLEHIGKAVMMLFKEEFPFIEKIEVTIITD---- 154 (470)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcccc--ceEEEEechhhhhhccchHHHHHHHHHHHHhhCCceeeEEEEEEcC----
Confidence 667777776 465555544454444322 4688888754322234445666788888899999887765432211
Q ss_pred hhhhhHHHHHhhcccccc
Q 026830 163 LNEENIEKVLEEIRPYLV 180 (232)
Q Consensus 163 ~~~~~i~~~L~~iRP~L~ 180 (232)
.+.+++.|+..|+...
T Consensus 155 --~~~Vee~LE~Ar~iy~ 170 (470)
T COG1614 155 --EAKVEEFLETAREIYK 170 (470)
T ss_pred --HHHHHHHHHHHHHHHH
Confidence 4456667776666554
No 52
>PF11718 CPSF73-100_C: Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; InterPro: IPR021718 This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
Probab=20.04 E-value=5.9e+02 Score=22.18 Aligned_cols=58 Identities=17% Similarity=0.232 Sum_probs=38.3
Q ss_pred HHHHHHHH-Hhcchhh--hCCCcE-EEEEEeCcEEEEEEcccCCCCCCchHhHHHHHHHHHHhh
Q 026830 85 ENIESVLD-EIRPYLI--SDGGNV-ALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEK 144 (232)
Q Consensus 85 ~~v~~~L~-~IrP~L~--~dGGdv-elv~i~~~~v~Vrl~GaC~gCp~s~~Tlk~~Ie~~L~~~ 144 (232)
+++..+|+ .--+... ..+|.. -.+.+++..+.|.|..--..|. +..|+..|+.+|+.-
T Consensus 148 ~~l~~~L~~qFG~~~~~~~~~~~~~~~v~vd~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~ 209 (216)
T PF11718_consen 148 ERLIELLEAQFGDVEVPDIEKPKEPLSVTVDGKVAHIDLSTLEVECE--DEPLKQRVETALKRL 209 (216)
T ss_pred HHHHHHHHHHcCCCccccccccceeEEEEeCCcEEEEecCCCceecC--CHHHHHHHHHHHHHH
Confidence 34555554 2333311 233444 4567778888898887777887 888999999988764
Done!