Query 027469
Match_columns 223
No_of_seqs 289 out of 1769
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:22:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027469.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027469hhsearch_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 6E-23 1.3E-27 149.7 7.8 67 82-149 1-67 (68)
2 COG0694 Thioredoxin-like prote 99.9 1.1E-22 2.3E-27 157.1 8.0 75 78-153 10-87 (93)
3 PRK11190 Fe/S biogenesis prote 99.8 3.7E-21 8.1E-26 165.3 9.1 77 78-154 107-185 (192)
4 TIGR03341 YhgI_GntY IscR-regul 99.8 1.2E-20 2.6E-25 161.8 10.2 76 78-154 106-183 (190)
5 TIGR03341 YhgI_GntY IscR-regul 99.8 2.5E-21 5.4E-26 166.0 5.8 145 46-222 21-179 (190)
6 PRK11190 Fe/S biogenesis prote 99.8 7.3E-21 1.6E-25 163.5 5.0 145 46-222 22-181 (192)
7 TIGR02000 NifU_proper Fe-S clu 99.7 2.5E-18 5.5E-23 155.8 8.3 69 79-149 221-289 (290)
8 COG0694 Thioredoxin-like prote 99.7 2.7E-18 5.8E-23 132.7 6.7 67 156-222 7-84 (93)
9 PF01106 NifU: NifU-like domai 99.7 5.2E-18 1.1E-22 123.7 7.1 60 163-222 1-68 (68)
10 KOG2358 NifU-like domain-conta 99.6 4.2E-17 9.1E-22 141.2 -0.4 145 7-154 45-202 (213)
11 TIGR02000 NifU_proper Fe-S clu 99.6 1.8E-15 4E-20 137.2 9.8 64 158-222 219-290 (290)
12 KOG2358 NifU-like domain-conta 99.5 1.6E-15 3.5E-20 131.4 1.6 112 77-222 77-198 (213)
13 PF01883 DUF59: Domain of unkn 92.9 0.45 9.7E-06 33.9 6.2 64 80-146 2-69 (72)
14 PF01883 DUF59: Domain of unkn 89.1 1.6 3.6E-05 31.0 6.0 59 162-221 3-72 (72)
15 COG0316 sufA Fe-S cluster asse 88.5 0.1 2.2E-06 41.7 -0.7 57 45-108 25-85 (110)
16 COG2151 PaaD Predicted metal-s 69.3 16 0.00036 29.2 5.9 71 75-148 10-86 (111)
17 PRK10862 SoxR reducing system 66.2 7.6 0.00017 32.4 3.6 25 101-125 7-33 (154)
18 PF04246 RseC_MucC: Positive r 64.7 6.3 0.00014 31.5 2.7 23 102-124 1-25 (135)
19 PRK13623 iron-sulfur cluster i 59.7 2.9 6.2E-05 32.8 -0.1 57 46-107 31-89 (115)
20 COG3449 DNA gyrase inhibitor [ 59.6 75 0.0016 27.0 8.4 106 98-210 1-114 (154)
21 TIGR02945 SUF_assoc FeS assemb 59.0 33 0.00072 25.7 5.7 58 80-138 4-66 (99)
22 PF10646 Germane: Sporulation 56.4 27 0.0006 26.4 4.9 34 188-221 63-106 (117)
23 smart00243 GAS2 Growth-Arrest- 54.3 30 0.00064 26.0 4.5 31 177-207 32-65 (73)
24 TIGR02159 PA_CoA_Oxy4 phenylac 52.8 36 0.00078 28.3 5.4 41 98-139 15-55 (146)
25 PRK09502 iscA iron-sulfur clus 49.1 6.8 0.00015 30.4 0.4 73 46-124 23-104 (107)
26 PF05258 DUF721: Protein of un 48.9 78 0.0017 22.4 6.0 44 178-221 38-89 (89)
27 TIGR02011 IscA iron-sulfur clu 48.0 7.5 0.00016 30.0 0.5 73 46-124 21-102 (105)
28 PRK09504 sufA iron-sulfur clus 45.6 7 0.00015 31.2 0.0 56 46-106 38-95 (122)
29 PF09012 FeoC: FeoC like trans 45.6 26 0.00055 24.8 3.0 27 95-126 39-65 (69)
30 TIGR02945 SUF_assoc FeS assemb 45.0 80 0.0017 23.6 5.8 60 161-221 4-75 (99)
31 PF04852 DUF640: Protein of un 44.2 22 0.00048 29.5 2.7 56 36-101 58-113 (132)
32 PF08777 RRM_3: RNA binding mo 42.8 37 0.0008 26.4 3.7 39 169-208 17-57 (105)
33 PF07315 DUF1462: Protein of u 41.8 24 0.00052 27.6 2.5 26 117-143 11-36 (93)
34 COG1308 EGD2 Transcription fac 37.5 15 0.00032 30.1 0.8 32 69-100 82-113 (122)
35 PF02187 GAS2: Growth-Arrest-S 35.7 54 0.0012 24.6 3.4 28 180-207 37-65 (73)
36 PF07045 DUF1330: Protein of u 35.3 47 0.001 23.3 3.0 24 80-103 2-25 (65)
37 PF02061 Lambda_CIII: Lambda P 34.4 48 0.001 22.5 2.7 27 114-140 6-32 (45)
38 PF12870 Lumazine_bd: Lumazine 34.3 1.5E+02 0.0034 21.2 5.8 34 162-196 49-86 (111)
39 TIGR02554 PrgH type III secret 34.2 3.8E+02 0.0082 26.0 9.8 112 87-222 168-289 (389)
40 PF10262 Rdx: Rdx family; Int 33.9 80 0.0017 22.8 4.1 29 109-142 2-30 (76)
41 CHL00123 rps6 ribosomal protei 32.6 75 0.0016 24.3 4.0 53 158-210 18-84 (97)
42 TIGR01997 sufA_proteo FeS asse 32.4 19 0.00042 27.7 0.6 72 47-124 24-104 (107)
43 COG1901 Uncharacterized conser 31.2 1.6E+02 0.0034 26.1 6.0 112 72-193 26-149 (197)
44 cd00460 RNAP_RPB11_RPB3 RPB11 31.2 84 0.0018 23.4 3.9 36 182-219 2-38 (86)
45 PRK15431 ferrous iron transpor 30.8 35 0.00076 25.9 1.8 26 97-126 43-69 (78)
46 TIGR02159 PA_CoA_Oxy4 phenylac 30.8 1.8E+02 0.0038 24.2 6.1 40 179-220 15-61 (146)
47 TIGR00049 Iron-sulfur cluster 30.8 22 0.00049 26.8 0.7 57 46-107 21-79 (105)
48 COG3086 RseC Positive regulato 29.0 56 0.0012 27.7 2.9 35 101-136 7-43 (150)
49 PF08777 RRM_3: RNA binding mo 27.3 1.3E+02 0.0029 23.3 4.6 28 87-115 16-45 (105)
50 cd04910 ACT_AK-Ectoine_1 ACT d 26.0 2.7E+02 0.0058 20.4 5.9 47 169-215 20-66 (71)
51 COG1298 FlhA Flagellar biosynt 25.8 75 0.0016 32.9 3.6 64 123-188 531-603 (696)
52 TIGR02174 CXXU_selWTH selT/sel 25.0 1E+02 0.0023 22.2 3.4 23 118-142 6-28 (72)
53 PRK15327 type III secretion sy 24.3 3E+02 0.0066 26.7 7.2 116 87-222 173-294 (393)
54 PF01545 Cation_efflux: Cation 24.1 3E+02 0.0064 23.9 6.7 52 169-220 209-275 (284)
55 PF15092 UPF0728: Uncharacteri 23.5 1.1E+02 0.0024 23.7 3.4 32 167-198 27-59 (88)
56 TIGR00532 HMG_CoA_R_NAD hydrox 23.2 3.8E+02 0.0081 26.0 7.7 65 78-142 142-214 (393)
57 TIGR01297 CDF cation diffusion 22.9 1.7E+02 0.0037 25.2 5.0 32 190-221 226-263 (268)
58 TIGR03406 FeS_long_SufT probab 22.8 2.1E+02 0.0046 24.4 5.3 67 77-146 73-148 (174)
59 COG4837 Uncharacterized protei 22.7 64 0.0014 25.7 2.0 25 117-142 18-42 (106)
60 PF13192 Thioredoxin_3: Thiore 22.4 93 0.002 22.1 2.7 24 110-138 3-26 (76)
61 PRK11670 antiporter inner memb 21.8 2.2E+02 0.0048 26.8 5.8 64 158-222 12-86 (369)
62 cd02008 TPP_IOR_alpha Thiamine 21.5 81 0.0018 26.0 2.5 22 115-142 4-25 (178)
63 cd06927 RNAP_L L subunit of Ar 21.5 1.6E+02 0.0035 22.1 3.9 35 181-216 1-36 (83)
64 PRK00321 rdgC recombination as 21.3 4.8E+02 0.01 24.2 7.8 83 102-198 128-211 (303)
65 TIGR03406 FeS_long_SufT probab 20.5 3E+02 0.0065 23.5 5.8 64 157-221 72-151 (174)
66 PRK09509 fieF ferrous iron eff 20.2 2E+02 0.0043 25.8 4.9 27 191-217 247-279 (299)
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=6e-23 Score=149.68 Aligned_cols=67 Identities=49% Similarity=0.944 Sum_probs=61.0
Q ss_pred HHHHHHhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccc
Q 027469 82 VDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQ 149 (223)
Q Consensus 82 v~~~l~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~ 149 (223)
|+.+|++|||+|++||||++++++++++|+|||+|+|+|||++.+||+++||++|++++|+ ++.|..
T Consensus 1 V~~~l~~IrP~L~~dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~-v~~V~~ 67 (68)
T PF01106_consen 1 VEEVLEEIRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPE-VKRVVP 67 (68)
T ss_dssp HHHHHHHCHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT--SEEEE
T ss_pred CHHHHHHhChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCC-CceEEE
Confidence 5788877999999999999999999999999999999999999999999999999999994 554543
No 2
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.1e-22 Score=157.15 Aligned_cols=75 Identities=47% Similarity=0.845 Sum_probs=68.6
Q ss_pred hHHHHHHHH-HhhhhHHHhcCCceEEEeee--CCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccc
Q 027469 78 TAKNVDLVL-EDVRPYLIADGGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE 153 (223)
Q Consensus 78 ~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~--~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~ 153 (223)
..++++.+| ++|||+|+.|||||++++|+ +|+|+|||.|||+|||||+.|||++||++|++.+| +++.|+++.++
T Consensus 10 ~~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~-ev~~V~~v~~~ 87 (93)
T COG0694 10 LLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIP-EVKEVEQVTEH 87 (93)
T ss_pred HHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCC-ccceEEEccCc
Confidence 457788888 59999999999999999998 78999999999999999999999999999999999 57778887654
No 3
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.84 E-value=3.7e-21 Score=165.27 Aligned_cols=77 Identities=26% Similarity=0.610 Sum_probs=71.2
Q ss_pred hHHHHHHHH-HhhhhHHHhcCCceEEEeee-CCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccch
Q 027469 78 TAKNVDLVL-EDVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154 (223)
Q Consensus 78 ~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~-~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~ 154 (223)
..++|+.+| ++|||+|++|||||||++|+ +++|+|||+|||+|||+|++||+.+||++|++++|++++.|+++++++
T Consensus 107 ~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~~~ 185 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTEHQ 185 (192)
T ss_pred HHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEecccc
Confidence 457799999 59999999999999999997 579999999999999999999999999999999997799899987765
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=99.84 E-value=1.2e-20 Score=161.77 Aligned_cols=76 Identities=29% Similarity=0.675 Sum_probs=70.2
Q ss_pred hHHHHHHHHH-hhhhHHHhcCCceEEEeee-CCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccch
Q 027469 78 TAKNVDLVLE-DVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154 (223)
Q Consensus 78 ~~~~v~~~l~-~IrP~Lq~dGGdVelvdv~-~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~ 154 (223)
..++|+.+|+ +|||+|++|||||||++|+ +++|+|||+|+|+|||++++||+++||++|++++| +++.|+.+++++
T Consensus 106 ~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p-~v~~V~~~~~~~ 183 (190)
T TIGR03341 106 LEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFP-ELKGVRDATDHT 183 (190)
T ss_pred HHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCC-CcceEEEecCcc
Confidence 5688999995 9999999999999999997 57999999999999999999999999999999999 588898888775
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=2.5e-21 Score=165.98 Aligned_cols=145 Identities=17% Similarity=0.307 Sum_probs=116.4
Q ss_pred eeeeEEEEecCCCCCCCCC---CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCC
Q 027469 46 KSGSHETAIRASNPSAPAG---SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSC 121 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~---~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gC 121 (223)
+.++|+++...|.+...++ |.+....+.|..+....+..++ ....|||..- .+|+.++- +
T Consensus 21 ~~~LRv~V~~gGCsG~~Y~l~~~~~~~~~~~D~v~e~~g~~v~Vd~~s~~~L~g~-----~IDyve~~----~------- 84 (190)
T TIGR03341 21 GTGIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEFNGFSAYVDALSAPFLEDA-----VIDFVTDR----M------- 84 (190)
T ss_pred CceEEEEEECCccCCceeeeEEcccCCCCCCCEEEEeCCEEEEEccchhhHhCCC-----EEEEeecC----C-------
Confidence 4579999999999887777 4456666677777778888888 7999999988 88886443 2
Q ss_pred CCchHHHHHHHHHHHHHHhCcccccccccccchhhhhhHHHhhcccc-cchhHHHhcCCcEEEEEEe-CCEEEEEEeCh-
Q 027469 122 PSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEAVNGHLD-ILRPAIKNYGGSVEVLSVE-SGDCIVKYVGP- 198 (223)
Q Consensus 122 pss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~e~l~e~I~~~L~-~IRP~L~~~GGdvelv~v~-~g~v~vrl~G~- 198 (223)
++..++++ | +++. ... +.++++.++|+++|+ +|||+|++||||++|++|+ +++|+|||+|+
T Consensus 85 -g~gF~f~N----------P-na~~-~~~---~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC 148 (190)
T TIGR03341 85 -GGQLTLKA----------P-NAKM-PKV---ADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGC 148 (190)
T ss_pred -CceeEEeC----------C-ccCC-CcC---ccchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecC
Confidence 34455554 5 4442 111 123468999999996 9999999999999999995 68999999999
Q ss_pred -------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 199 -------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 199 -------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
.|||++||++|++++|+|++|+.+
T Consensus 149 ~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~ 179 (190)
T TIGR03341 149 NGCSMVDVTLKDGVEKTLLERFPELKGVRDA 179 (190)
T ss_pred CCCcchHHHHHHHHHHHHHHhCCCcceEEEe
Confidence 899999999999999999999875
No 6
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.82 E-value=7.3e-21 Score=163.50 Aligned_cols=145 Identities=21% Similarity=0.328 Sum_probs=113.4
Q ss_pred eeeeEEEEecCCCCCCCCC---CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCC
Q 027469 46 KSGSHETAIRASNPSAPAG---SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSC 121 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~---~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gC 121 (223)
+.++|+++...|.....++ |.....++.|..+....+..++ ....|||... .+|+.++- +
T Consensus 22 ~~~LRI~V~~gGCsG~~Y~~~~~~~~~~~~~D~v~e~~gv~v~Vd~~S~~~L~G~-----~IDyve~~----~------- 85 (192)
T PRK11190 22 GTQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKFDGFSAYVDELSAPFLEDA-----EIDFVTDQ----L------- 85 (192)
T ss_pred CceEEEEEECCCcCCceeeeEEeecCCCCCCCEEEEeCCEEEEECcchHhHhCCC-----EEEEeecC----C-------
Confidence 4579999999998877666 3244445566666667788888 7999999988 88886543 2
Q ss_pred CCchHHHHHHHHHHHHHHhCcccccccccccchhhhhhHHHhhcccc-cchhHHHhcCCcEEEEEEe-CCEEEEEEeCh-
Q 027469 122 PSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEAVNGHLD-ILRPAIKNYGGSVEVLSVE-SGDCIVKYVGP- 198 (223)
Q Consensus 122 pss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~e~l~e~I~~~L~-~IRP~L~~~GGdvelv~v~-~g~v~vrl~G~- 198 (223)
++..++++ | +++. +... .+..+.++|+++|+ +|||+|++||||++|++|+ +++|+|||+|+
T Consensus 86 -g~gF~f~N----------P-Na~~-~~~~---~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC 149 (192)
T PRK11190 86 -GSQLTLKA----------P-NAKM-RKVA---DDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGC 149 (192)
T ss_pred -CCceEEEC----------C-CCCC-CCCc---ccHHHHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecC
Confidence 34445544 5 4543 1111 23368899999995 9999999999999999995 68999999999
Q ss_pred -------hhHHHHHHHHHHhhCC-CcceEEeC
Q 027469 199 -------DSIASGIRAAIKEKFP-DIENVVFT 222 (223)
Q Consensus 199 -------~Tlk~gIE~~L~e~~P-ei~~V~~v 222 (223)
.|||++||++|++++| +|++|+.+
T Consensus 150 ~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v 181 (192)
T PRK11190 150 NGCSMVDVTLKEGIEKQLLNEFPGELKGVRDL 181 (192)
T ss_pred CCCcchHHHHHHHHHHHHHHhCCHhhceEEEe
Confidence 8999999999999999 99999876
No 7
>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=99.75 E-value=2.5e-18 Score=155.78 Aligned_cols=69 Identities=38% Similarity=0.686 Sum_probs=63.4
Q ss_pred HHHHHHHHHhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccc
Q 027469 79 AKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQ 149 (223)
Q Consensus 79 ~~~v~~~l~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~ 149 (223)
.++|+.+|++|||+|++|||||+|++|++++|+|||+|+|+|||++.+||+. ||++|++++|+ +..|..
T Consensus 221 ~~~v~~~l~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~-~~~V~~ 289 (290)
T TIGR02000 221 IQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGE-FVVVEA 289 (290)
T ss_pred HHHHHHHHHHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCC-ceEEEe
Confidence 4778999999999999999999999999999999999999999999999998 99999999995 544543
No 8
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.74 E-value=2.7e-18 Score=132.70 Aligned_cols=67 Identities=27% Similarity=0.518 Sum_probs=62.8
Q ss_pred hhhhHHHhhcccc-cchhHHHhcCCcEEEEEEe--CCEEEEEEeCh--------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 156 RETTVEAVNGHLD-ILRPAIKNYGGSVEVLSVE--SGDCIVKYVGP--------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 156 ~e~l~e~I~~~L~-~IRP~L~~~GGdvelv~v~--~g~v~vrl~G~--------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
+.++.++|+++|+ +|||+|++|||||+|++|+ +|+|+|||+|| .|||+|||++|++.||++++|+.+
T Consensus 7 ~~~~~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 7 DAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQV 84 (93)
T ss_pred cHHHHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEc
Confidence 4478899999995 9999999999999999997 88999999999 899999999999999999999875
No 9
>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=99.74 E-value=5.2e-18 Score=123.69 Aligned_cols=60 Identities=32% Similarity=0.607 Sum_probs=55.9
Q ss_pred hhcccccchhHHHhcCCcEEEEEEeCCEEEEEEeCh--------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 163 VNGHLDILRPAIKNYGGSVEVLSVESGDCIVKYVGP--------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 163 I~~~L~~IRP~L~~~GGdvelv~v~~g~v~vrl~G~--------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
|+++|++|||+|++||||++|+++++++|+|||+|+ .||+++||++|++++|++++|+.|
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 567888899999999999999999999999999999 899999999999999999999875
No 10
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.62 E-value=4.2e-17 Score=141.20 Aligned_cols=145 Identities=28% Similarity=0.303 Sum_probs=109.0
Q ss_pred ccceeeeecccccCCCCCCccccCccceeeeccCccceeeeeeE---EEEec----CCCCCCCCCCCCCc----CCcchh
Q 027469 7 TAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSH---ETAIR----ASNPSAPAGSSPGL----YSAHQF 75 (223)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r---~~~~~----~gtp~a~~~~~p~~----~~~~~~ 75 (223)
++.||.+.++ +.++++++.+....+.|+....++..+.-+-++ ..... -|-|-+.. ..... ..+++.
T Consensus 45 s~~~s~La~s-~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g-~~~~~~~~~~~e~d~ 122 (213)
T KOG2358|consen 45 SAFFSPLAKS-ILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDG-NIVVLKLQGACESDP 122 (213)
T ss_pred chhhcHHHHH-HHhhcCCcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccchhhcc-chhhhhhcccccCCh
Confidence 4556777776 778888999999999999998888844433321 11111 11111111 11111 235667
Q ss_pred hhhHHHHHHHHHhhhhHHHhcCCceEEEeeeC--CEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccc
Q 027469 76 DLTAKNVDLVLEDVRPYLIADGGNIDVVSVED--GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE 153 (223)
Q Consensus 76 ~l~~~~v~~~l~~IrP~Lq~dGGdVelvdv~~--g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~ 153 (223)
+......+.+..+|||.+++||||++++++|+ |.|++||+|+|.+||++..||+.+||++|+.++| ++|+++++.|+
T Consensus 123 e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~-eVK~v~qv~d~ 201 (213)
T KOG2358|consen 123 ESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVP-EVKGVIQVPDA 201 (213)
T ss_pred hHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcc-eeeEEEeccCc
Confidence 77766666666999999999999999999998 5899999999999999999999999999999999 79999999776
Q ss_pred h
Q 027469 154 E 154 (223)
Q Consensus 154 ~ 154 (223)
+
T Consensus 202 e 202 (213)
T KOG2358|consen 202 E 202 (213)
T ss_pred c
Confidence 5
No 11
>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=99.61 E-value=1.8e-15 Score=137.18 Aligned_cols=64 Identities=20% Similarity=0.381 Sum_probs=60.4
Q ss_pred hhHHHhhcccccchhHHHhcCCcEEEEEEeCCEEEEEEeCh--------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 158 TTVEAVNGHLDILRPAIKNYGGSVEVLSVESGDCIVKYVGP--------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 158 ~l~e~I~~~L~~IRP~L~~~GGdvelv~v~~g~v~vrl~G~--------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
...++|+++|++|||+|++|||||+|++|++++|+|||+|+ +||++ ||++|++++|++..|+.|
T Consensus 219 ~~~~~v~~~l~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 219 QRIQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred HHHHHHHHHHHHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 45689999999999999999999999999999999999999 89998 999999999999999875
No 12
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.54 E-value=1.6e-15 Score=131.42 Aligned_cols=112 Identities=35% Similarity=0.558 Sum_probs=101.1
Q ss_pred hhHHHHHHHHHhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccchhh
Q 027469 77 LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVR 156 (223)
Q Consensus 77 l~~~~v~~~l~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~ 156 (223)
+..+....+|...+|++-+|||.+-+--+++..+.+++.|+|..||.+.+|+|++||
T Consensus 77 ~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelie----------------------- 133 (213)
T KOG2358|consen 77 LTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIE----------------------- 133 (213)
T ss_pred cchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHH-----------------------
Confidence 445567888999999999999999999999999999999999999999999886331
Q ss_pred hhhHHHhhcccccchhHHHhcCCcEEEEEEeC--CEEEEEEeCh--------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 157 ETTVEAVNGHLDILRPAIKNYGGSVEVLSVES--GDCIVKYVGP--------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 157 e~l~e~I~~~L~~IRP~L~~~GGdvelv~v~~--g~v~vrl~G~--------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
.+|||.++.||||++++++|+ |+|+++++|+ .|||+|||..|+.++|++|.|+++
T Consensus 134 -----------tRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv 198 (213)
T KOG2358|consen 134 -----------TRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGVIQV 198 (213)
T ss_pred -----------HhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEEEec
Confidence 468899999999999999987 5999999999 799999999999999999999875
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=92.87 E-value=0.45 Score=33.92 Aligned_cols=64 Identities=30% Similarity=0.400 Sum_probs=46.6
Q ss_pred HHHHHHH-HhhhhHHHhc---CCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCccccc
Q 027469 80 KNVDLVL-EDVRPYLIAD---GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKD 146 (223)
Q Consensus 80 ~~v~~~l-~~IrP~Lq~d---GGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~ 146 (223)
+.|..+| .-.-|++..+ =|-|+=+.+++|.|+|.+.-...+|+ ....|++.|+++|+ .+| ++++
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~-gv~~ 69 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALP-GVKS 69 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TST-T-SE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCC-CCce
Confidence 4566777 5556766543 36788899999999999999999999 77788899999999 576 3543
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=89.05 E-value=1.6 Score=30.96 Aligned_cols=59 Identities=29% Similarity=0.455 Sum_probs=40.0
Q ss_pred Hhhccc-ccchhHHHhc---CCcEEEEEEeCCEEEEEEeCh-------hhHHHHHHHHHHhhCCCcceEEe
Q 027469 162 AVNGHL-DILRPAIKNY---GGSVEVLSVESGDCIVKYVGP-------DSIASGIRAAIKEKFPDIENVVF 221 (223)
Q Consensus 162 ~I~~~L-~~IRP~L~~~---GGdvelv~v~~g~v~vrl~G~-------~Tlk~gIE~~L~e~~Pei~~V~~ 221 (223)
+|.++| .-.-|.+..+ =|-|.=+.+++|.|.+.+.=+ ..++.-|+++|+ .+|+++.|..
T Consensus 3 ~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 3 AVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPGVKSVKV 72 (72)
T ss_dssp HHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT-SEEEE
T ss_pred HHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCCCceEeC
Confidence 344455 2444555444 477888889999988888766 568889999999 7999998863
No 15
>COG0316 sufA Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]
Probab=88.52 E-value=0.1 Score=41.69 Aligned_cols=57 Identities=12% Similarity=0.148 Sum_probs=46.5
Q ss_pred eeeeeEEEEecCCCCCCCCC---CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeCC
Q 027469 45 QKSGSHETAIRASNPSAPAG---SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVEDG 108 (223)
Q Consensus 45 ~~~~~r~~~~~~gtp~a~~~---~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~g 108 (223)
.++++|++|.++|.+..+++ |+ ..+++|..+..+.+..++ ...-|||... .+|+.++
T Consensus 25 ~~~~lRv~V~~gGCsG~~Y~~~~~~--~~~~~D~v~e~~g~~v~vD~~S~~~L~G~-----~IDyv~~ 85 (110)
T COG0316 25 ENLGLRVGVKGGGCSGFQYGLEFDD--EINEDDTVFEQDGVKVVVDPKSLPYLEGT-----EIDYVED 85 (110)
T ss_pred CCceEEEEEeCCCCCCcEeEEEEcC--CCCCCCEEEEeCCEEEEEChhhhhhhcCC-----EEEEEEc
Confidence 36789999999999999998 44 556778888888899998 7999999766 6777433
No 16
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=69.27 E-value=16 Score=29.21 Aligned_cols=71 Identities=24% Similarity=0.393 Sum_probs=47.8
Q ss_pred hhhhHHHHHHHH-HhhhhHHHhc---CCceEEEeee--CCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCccccccc
Q 027469 75 FDLTAKNVDLVL-EDVRPYLIAD---GGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIR 148 (223)
Q Consensus 75 ~~l~~~~v~~~l-~~IrP~Lq~d---GGdVelvdv~--~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~ 148 (223)
.+...+.+-.+| .-+-|.|--+ =|=|.=++++ ++.++|+|+..-.|||++.. +...++++|++.- .+++++
T Consensus 10 ~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~-i~~~v~~al~~~~--~v~~v~ 86 (111)
T COG2151 10 IKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEV-IADQVEAALEEIP--GVEDVE 86 (111)
T ss_pred hhhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHH-HHHHHHHHHHhcC--CcceEE
Confidence 344456677777 5667777554 2333335565 44899999999999999876 4568899988833 355443
No 17
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=66.21 E-value=7.6 Score=32.37 Aligned_cols=25 Identities=32% Similarity=0.696 Sum_probs=19.7
Q ss_pred EEEeeeCCEEEEEEc--cccCCCCCch
Q 027469 101 DVVSVEDGVVSVKLQ--GACGSCPSST 125 (223)
Q Consensus 101 elvdv~~g~V~Vrl~--GaC~gCpss~ 125 (223)
.+++++++.++|+.. .+|++|.+..
T Consensus 7 ~Vv~v~~~~a~Ve~~r~saCg~C~a~~ 33 (154)
T PRK10862 7 TVVSWQNGIALLRCEVKAGCSSCASRA 33 (154)
T ss_pred EEEEEECCEEEEEEecCCCCcCcCCCC
Confidence 578999998777754 8999998744
No 18
>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=64.66 E-value=6.3 Score=31.52 Aligned_cols=23 Identities=52% Similarity=0.962 Sum_probs=17.7
Q ss_pred EEeeeCCEEEEEE--ccccCCCCCc
Q 027469 102 VVSVEDGVVSVKL--QGACGSCPSS 124 (223)
Q Consensus 102 lvdv~~g~V~Vrl--~GaC~gCpss 124 (223)
+++++++.++|+. ..+|++|.++
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~~ 25 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSAS 25 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCCC
Confidence 4678899888877 4889888843
No 19
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=59.74 E-value=2.9 Score=32.77 Aligned_cols=57 Identities=12% Similarity=0.087 Sum_probs=36.3
Q ss_pred eeeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeC
Q 027469 46 KSGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVED 107 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~ 107 (223)
+.++|+++...|......+ .-.....+.|.....+.+..++ ....+||... .+|+.+
T Consensus 31 ~~~LRi~v~~~GCsG~~y~l~l~~~~~~~D~v~e~~gv~v~id~~s~~~l~g~-----~IDy~~ 89 (115)
T PRK13623 31 DLKLRVYITGGGCSGFQYGFTFDEQVNEDDTTIEKQGVTLVVDPMSLQYLVGA-----EVDYTE 89 (115)
T ss_pred ceEEEEEEeCCCCCCcEEEEEECCCCCCCCEEEEcCCEEEEEcHHHHHHhCCC-----EEEeec
Confidence 4569999998876444332 1111223456666667788887 7888998765 677743
No 20
>COG3449 DNA gyrase inhibitor [DNA replication, recombination, and repair]
Probab=59.64 E-value=75 Score=26.97 Aligned_cols=106 Identities=12% Similarity=0.235 Sum_probs=69.3
Q ss_pred CceEEEeee-CCEEEEEEccccCCCCCchHHHHHHHHHHHHHH----hCcccccccccccchhhhhhHHHhhccc-ccch
Q 027469 98 GNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK----FGDAIKDIRQVYDEEVRETTVEAVNGHL-DILR 171 (223)
Q Consensus 98 GdVelvdv~-~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~----lp~~vk~V~~V~~~~~~e~l~e~I~~~L-~~IR 171 (223)
.||+++++. -.++++|..| ...|+++.+++.++=+ +.++....-.+..++++....++-++=+ --+.
T Consensus 1 mdv~I~e~p~~~VA~~rh~G-------~~~~~~~~~~~l~~W~~~~~l~p~~S~~~gI~~ddP~~Tp~e~~R~D~cv~v~ 73 (154)
T COG3449 1 MDVEIIELPPIPVAYLRHVG-------DPATLKQTFEQLIAWRRENGLLPEQSETLGIYQDDPDTTPAEKCRYDACVVVP 73 (154)
T ss_pred CCceEEecCCceEEEEEeeC-------cHHHHHHHHHHHHHHHHHcCCCCCCceEEEEecCCCCCCCHHHceeeEEEEcC
Confidence 478999995 4789999976 6678887777765432 1111122223444455555556666555 4566
Q ss_pred hHHHhcCCcEEEEEEeCC-EEEEEEeCh-hhHHHHHHHHHH
Q 027469 172 PAIKNYGGSVEVLSVESG-DCIVKYVGP-DSIASGIRAAIK 210 (223)
Q Consensus 172 P~L~~~GGdvelv~v~~g-~v~vrl~G~-~Tlk~gIE~~L~ 210 (223)
+-++..-|.|.+-++.+| ++++|+.|. ..+......--.
T Consensus 74 ~~~~~n~~~v~~~~i~GG~YAV~r~~~~~d~~~~aw~~if~ 114 (154)
T COG3449 74 EPIPENSEGVQLGEIPGGLYAVARFRGTADDLAKAWGYIFG 114 (154)
T ss_pred CccCCCCCceeEeeecCCceEEEEEeccHHHHHHHHHHHHh
Confidence 778888899999999765 899999998 445444444333
No 21
>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=59.01 E-value=33 Score=25.71 Aligned_cols=58 Identities=22% Similarity=0.343 Sum_probs=40.9
Q ss_pred HHHHHHH-HhhhhHHHhc---CCceEEEeeeC-CEEEEEEccccCCCCCchHHHHHHHHHHHHH
Q 027469 80 KNVDLVL-EDVRPYLIAD---GGNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKE 138 (223)
Q Consensus 80 ~~v~~~l-~~IrP~Lq~d---GGdVelvdv~~-g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e 138 (223)
+.|..+| .-.-|.+..+ =|-|.=+.+++ +.++|.+.-...+|+... .|+..++++|..
T Consensus 4 ~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~-~l~~~i~~al~~ 66 (99)
T TIGR02945 4 DAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAG-SMPGEVENAVRA 66 (99)
T ss_pred HHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHH-HHHHHHHHHHHh
Confidence 5677777 4556666542 34555567775 899999988888888544 477888888876
No 22
>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=56.43 E-value=27 Score=26.38 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=27.2
Q ss_pred CCEEEEEEeCh----------hhHHHHHHHHHHhhCCCcceEEe
Q 027469 188 SGDCIVKYVGP----------DSIASGIRAAIKEKFPDIENVVF 221 (223)
Q Consensus 188 ~g~v~vrl~G~----------~Tlk~gIE~~L~e~~Pei~~V~~ 221 (223)
+++++|.|... .-+...|-.+|.+.|++|++|.+
T Consensus 63 ~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i 106 (117)
T PF10646_consen 63 GNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVKKVQI 106 (117)
T ss_pred CCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCccEEEE
Confidence 44899988875 23457888899999999999986
No 23
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=54.26 E-value=30 Score=26.02 Aligned_cols=31 Identities=13% Similarity=0.350 Sum_probs=23.9
Q ss_pred cCCc--EEEEEEeCCEEEEEEeCh-hhHHHHHHH
Q 027469 177 YGGS--VEVLSVESGDCIVKYVGP-DSIASGIRA 207 (223)
Q Consensus 177 ~GGd--velv~v~~g~v~vrl~G~-~Tlk~gIE~ 207 (223)
.|.+ +-++.+-++.|.||.+|+ +||++.+.+
T Consensus 32 ~Gd~~~~~~vRil~~~VMVRVGGGW~tL~~fL~k 65 (73)
T smart00243 32 FGDSQILRLVRILRSTVMVRVGGGWETLDEYLLK 65 (73)
T ss_pred EcCCceEEEEEEeCCeEEEEECCcHHHHHHHHHh
Confidence 4544 456788778999999999 999877654
No 24
>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=52.83 E-value=36 Score=28.27 Aligned_cols=41 Identities=24% Similarity=0.448 Sum_probs=34.2
Q ss_pred CceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHH
Q 027469 98 GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK 139 (223)
Q Consensus 98 GdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~ 139 (223)
|-|.=++++++.|.|.+.-.-.+||.. ..|++.|+++|++.
T Consensus 15 G~Vr~V~v~gd~V~VtIt~Ty~gcpa~-e~L~~~I~~aL~~~ 55 (146)
T TIGR02159 15 GMVREVDVDGGGVVVKFTPTYSGCPAL-EVIRQDIRDAVRAL 55 (146)
T ss_pred CCeeEEEEECCEEEEEEEeCCCCCchH-HHHHHHHHHHHHhc
Confidence 667778888899999999999999964 46888899999873
No 25
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=49.12 E-value=6.8 Score=30.37 Aligned_cols=73 Identities=12% Similarity=0.131 Sum_probs=43.9
Q ss_pred eeeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeCC----EEEEE---Ecc
Q 027469 46 KSGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVEDG----VVSVK---LQG 116 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~g----~V~Vr---l~G 116 (223)
+.++|+++...|..--.=. .-.+...+.|..+..+.+..++ ....|||... .+|+.++ ...++ ..+
T Consensus 23 ~~~LRi~v~~~GCsG~~Y~l~~~~~~~~~D~~~~~~g~~v~id~~s~~~l~g~-----~IDy~~~~~~~~F~f~NPna~~ 97 (107)
T PRK09502 23 GFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKVVVDGKSLQFLDGT-----QLDFVKEGLNEGFKFTNPNVKD 97 (107)
T ss_pred CceEEEEEECCCcCCeeeEeeecCCCCCCCEEEEcCCeEEEEeHHHHhHhCCC-----EEEEeeCCCCceEEEECCCCCC
Confidence 4579999998875521100 1123344566667777888888 7889999877 6776422 22222 235
Q ss_pred ccCCCCCc
Q 027469 117 ACGSCPSS 124 (223)
Q Consensus 117 aC~gCpss 124 (223)
.|+ |..|
T Consensus 98 ~Cg-CG~S 104 (107)
T PRK09502 98 ECG-CGES 104 (107)
T ss_pred ccC-CCCC
Confidence 566 7654
No 26
>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=48.86 E-value=78 Score=22.41 Aligned_cols=44 Identities=16% Similarity=0.342 Sum_probs=34.9
Q ss_pred CCcEEEEEEeCCEEEEEEeCh------hhHHHHHHHHHHhhC--CCcceEEe
Q 027469 178 GGSVEVLSVESGDCIVKYVGP------DSIASGIRAAIKEKF--PDIENVVF 221 (223)
Q Consensus 178 GGdvelv~v~~g~v~vrl~G~------~Tlk~gIE~~L~e~~--Pei~~V~~ 221 (223)
.+.+.++++++|+++|.-.-+ .=++.-|-++|.+++ +.|+++++
T Consensus 38 ~~~~~~~~i~~g~L~i~v~~~~~~~~L~~~~~~il~~l~~~~g~~~i~~I~~ 89 (89)
T PF05258_consen 38 AQHTRPVSIKDGTLVIEVDSSAWAQELRYMKPQILKKLNEFLGFPAIKDIRF 89 (89)
T ss_pred HccEEEEEEECCEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCCccEeeC
Confidence 456999999999999999988 234578888888888 56777763
No 27
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=47.95 E-value=7.5 Score=29.96 Aligned_cols=73 Identities=14% Similarity=0.154 Sum_probs=43.3
Q ss_pred eeeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeCC----EEEEE---Ecc
Q 027469 46 KSGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVEDG----VVSVK---LQG 116 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~g----~V~Vr---l~G 116 (223)
+.++|+++...|..--.=. .-.+...+.|..+..+.+..++ ....+||..- .+|+.++ ...++ ..+
T Consensus 21 ~~~lRi~v~~~GCsG~~y~l~l~~~~~~~D~v~~~~g~~v~id~~s~~~l~g~-----~IDy~~~~~~~~F~~~nPna~~ 95 (105)
T TIGR02011 21 GFGLRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVKIVIDGKSLQYLDGT-----QLDFVKEGLNEGFKFTNPNVKD 95 (105)
T ss_pred CceEEEEEeCCCCCCEEEEeeecCCCCCCCEEEEcCCEEEEEcHHHhHHhCCC-----EEEEecCCCcceEEEECCCCCc
Confidence 3578999988765521000 1112234456666667788888 7889999776 6777432 23332 246
Q ss_pred ccCCCCCc
Q 027469 117 ACGSCPSS 124 (223)
Q Consensus 117 aC~gCpss 124 (223)
+|+ |..|
T Consensus 96 ~Cg-Cg~S 102 (105)
T TIGR02011 96 ECG-CGES 102 (105)
T ss_pred cCC-CCCC
Confidence 676 7765
No 28
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=45.62 E-value=7 Score=31.24 Aligned_cols=56 Identities=9% Similarity=0.021 Sum_probs=33.2
Q ss_pred eeeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeee
Q 027469 46 KSGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVE 106 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~ 106 (223)
..++|+++..+|..--.=. .-.....+.|..+..+.+..++ ....+||..- .+|+.
T Consensus 38 ~~~LRi~v~~gGCsG~~Y~~~l~~e~~~~D~v~e~~g~~v~Id~~s~~~L~g~-----~IDy~ 95 (122)
T PRK09504 38 MKGVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEHDGAKLFVPLQAMPFIDGT-----EVDYV 95 (122)
T ss_pred CceEEEEEECCCCCceEEEeeecCCCCCCCEEEEeCCEEEEEcHHHHHhhCCc-----EEEee
Confidence 3579999987764310000 1012223456666667777777 7888999765 66664
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=45.57 E-value=26 Score=24.84 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=17.1
Q ss_pred hcCCceEEEeeeCCEEEEEEccccCCCCCchH
Q 027469 95 ADGGNIDVVSVEDGVVSVKLQGACGSCPSSTT 126 (223)
Q Consensus 95 ~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~ 126 (223)
.+-|.|+-++....- .|.|.+|+....
T Consensus 39 ~~kG~I~~~~~~~~~-----~~~C~~C~~~~~ 65 (69)
T PF09012_consen 39 IRKGYIRKVDMSSCC-----GGSCSSCGPASK 65 (69)
T ss_dssp HCCTSCEEEEEE--S-----SSSSSS-SS---
T ss_pred HHCCcEEEecCCCCC-----CCCCCCCCCccc
Confidence 458999888776544 899999998765
No 30
>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=44.97 E-value=80 Score=23.60 Aligned_cols=60 Identities=20% Similarity=0.336 Sum_probs=33.9
Q ss_pred HHhhcccc-cchhHHHhc---CCcEEEEEEeC-CEEEEEEeCh-------hhHHHHHHHHHHhhCCCcceEEe
Q 027469 161 EAVNGHLD-ILRPAIKNY---GGSVEVLSVES-GDCIVKYVGP-------DSIASGIRAAIKEKFPDIENVVF 221 (223)
Q Consensus 161 e~I~~~L~-~IRP~L~~~---GGdvelv~v~~-g~v~vrl~G~-------~Tlk~gIE~~L~e~~Pei~~V~~ 221 (223)
++|.++|+ -.-|.+... =|-|.=+.+++ +.+.+.+.-+ ..++..++..|.. +|+++.|.+
T Consensus 4 ~~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 4 DAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEVENAVRA-VPGVGSVTV 75 (99)
T ss_pred HHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHHHHHHHHHHHHh-CCCCceEEE
Confidence 33444442 333444332 24444456664 7666666654 4677777777754 687777653
No 31
>PF04852 DUF640: Protein of unknown function (DUF640); InterPro: IPR006936 This conserved region is found in plant proteins including the resistance protein-like protein (O49468 from SWISSPROT).
Probab=44.17 E-value=22 Score=29.50 Aligned_cols=56 Identities=14% Similarity=0.168 Sum_probs=38.0
Q ss_pred eeccCccceeeeeeEEEEecCCCCCCCCCCCCCcCCcchhhhhHHHHHHHHHhhhhHHHhcCCceE
Q 027469 36 SIKPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNID 101 (223)
Q Consensus 36 ~~~~~~~~~~~~~~r~~~~~~gtp~a~~~~~p~~~~~~~~~l~~~~v~~~l~~IrP~Lq~dGGdVe 101 (223)
+-+|+.++.-+.+ -.|.-.| +|.++|.|+-- ...--++.+|.++|-...+|||+=|
T Consensus 58 ~d~~GkTkVh~~~-C~~~g~~-~~p~~C~CPlr--------qAwGSlDalIGrLraafee~Gg~pe 113 (132)
T PF04852_consen 58 LDQFGKTKVHGQG-CPFFGHP-SPPAPCPCPLR--------QAWGSLDALIGRLRAAFEEHGGHPE 113 (132)
T ss_pred HhccCCeeecCCC-CCCCCCC-CCCCCCCCcHH--------HHhccHHHHHHHHHHHHHHhCCCCC
Confidence 3466766653222 2344444 45679999863 4445579999999999999999877
No 32
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=42.82 E-value=37 Score=26.44 Aligned_cols=39 Identities=13% Similarity=0.365 Sum_probs=21.2
Q ss_pred cchhHHHhcCCcEEEEEEe--CCEEEEEEeChhhHHHHHHHH
Q 027469 169 ILRPAIKNYGGSVEVLSVE--SGDCIVKYVGPDSIASGIRAA 208 (223)
Q Consensus 169 ~IRP~L~~~GGdvelv~v~--~g~v~vrl~G~~Tlk~gIE~~ 208 (223)
.|+-.++.+| +|..|++. +...+|||..+.+-+.++++.
T Consensus 17 ~iK~~f~~~g-~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~ 57 (105)
T PF08777_consen 17 DIKEAFSQFG-EVAYVDFSRGDTEGYVRFKTPEAAQKALEKL 57 (105)
T ss_dssp HHHHHT-SS---EEEEE--TT-SEEEEEESS---HHHHHHHH
T ss_pred HHHHHHHhcC-CcceEEecCCCCEEEEEECCcchHHHHHHHH
Confidence 3444455555 99999994 458999999996555555543
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=41.84 E-value=24 Score=27.63 Aligned_cols=26 Identities=38% Similarity=0.561 Sum_probs=18.6
Q ss_pred ccCCCCCchHHHHHHHHHHHHHHhCcc
Q 027469 117 ACGSCPSSTTTMSMGIERVLKEKFGDA 143 (223)
Q Consensus 117 aC~gCpss~~Tlk~~IE~~L~e~lp~~ 143 (223)
+|.+=|+|..|. .+++.+|..++|+.
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~ 36 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQ 36 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCC
Confidence 466668888888 59999999999964
No 34
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=37.49 E-value=15 Score=30.12 Aligned_cols=32 Identities=19% Similarity=0.259 Sum_probs=27.7
Q ss_pred cCCcchhhhhHHHHHHHHHhhhhHHHhcCCce
Q 027469 69 LYSAHQFDLTAKNVDLVLEDVRPYLIADGGNI 100 (223)
Q Consensus 69 ~~~~~~~~l~~~~v~~~l~~IrP~Lq~dGGdV 100 (223)
.++++|++|..+....--++.|-.|.++|||+
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDl 113 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDL 113 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcH
Confidence 57888999988877776789999999999996
No 35
>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=35.66 E-value=54 Score=24.59 Aligned_cols=28 Identities=11% Similarity=0.205 Sum_probs=22.8
Q ss_pred cEEEEEEeCCEEEEEEeCh-hhHHHHHHH
Q 027469 180 SVEVLSVESGDCIVKYVGP-DSIASGIRA 207 (223)
Q Consensus 180 dvelv~v~~g~v~vrl~G~-~Tlk~gIE~ 207 (223)
.+-++.+-.+.|.||.+|+ .||.+.+.+
T Consensus 37 ~l~~~ril~~~vMVRVGGGW~tL~~~L~k 65 (73)
T PF02187_consen 37 KLFFVRILRSHVMVRVGGGWDTLEEYLDK 65 (73)
T ss_dssp EEEEEEETTTEEEEEETTEEEEHHHHHHH
T ss_pred eEEEEEEeCCEEEEEeCCcHHHHHHHhhc
Confidence 3667888778999999999 899877654
No 36
>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=35.34 E-value=47 Score=23.29 Aligned_cols=24 Identities=25% Similarity=0.225 Sum_probs=19.9
Q ss_pred HHHHHHHHhhhhHHHhcCCceEEE
Q 027469 80 KNVDLVLEDVRPYLIADGGNIDVV 103 (223)
Q Consensus 80 ~~v~~~l~~IrP~Lq~dGGdVelv 103 (223)
+.++.+.+.+.|.|+.+||.+-..
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 467888899999999999998766
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=34.36 E-value=48 Score=22.52 Aligned_cols=27 Identities=19% Similarity=0.303 Sum_probs=21.8
Q ss_pred EccccCCCCCchHHHHHHHHHHHHHHh
Q 027469 114 LQGACGSCPSSTTTMSMGIERVLKEKF 140 (223)
Q Consensus 114 l~GaC~gCpss~~Tlk~~IE~~L~e~l 140 (223)
-+++|.|||--...|...|-+.|++-.
T Consensus 6 AG~~~~G~~ql~ESLLdrItRklr~gw 32 (45)
T PF02061_consen 6 AGWPRMGCPQLSESLLDRITRKLRDGW 32 (45)
T ss_pred cCccccCCchhhHHHHHHHHHHHHHHH
Confidence 468999999877888888888888743
No 38
>PF12870 Lumazine_bd: Lumazine-binding domain; InterPro: IPR024267 This entry represents a lumazine-binding domain found in a family of putative lipoproteins from bacteria. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength.; PDB: 3K7C_C.
Probab=34.25 E-value=1.5e+02 Score=21.24 Aligned_cols=34 Identities=18% Similarity=0.252 Sum_probs=20.1
Q ss_pred HhhcccccchhHHHhcCCcEEEEEEe----CCEEEEEEe
Q 027469 162 AVNGHLDILRPAIKNYGGSVEVLSVE----SGDCIVKYV 196 (223)
Q Consensus 162 ~I~~~L~~IRP~L~~~GGdvelv~v~----~g~v~vrl~ 196 (223)
....+....+...... +.+..++|. ++.+.|.+.
T Consensus 49 ~~~~~~~~~~~~~~~~-~~~~~~~v~~~~~g~~A~V~v~ 86 (111)
T PF12870_consen 49 FEKQFASEMKKKYKKI-GSIKIVEVEENTIGDTATVTVK 86 (111)
T ss_dssp HHHHHHHHHHHHHHHT-TSEEEEEEEEEEESSEEEEEEE
T ss_pred HHHHHHHHHHHhhhcc-CceEEEEEEEeccCCEEEEEEE
Confidence 4444445666665555 677888884 565555543
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=34.25 E-value=3.8e+02 Score=25.96 Aligned_cols=112 Identities=11% Similarity=0.161 Sum_probs=72.7
Q ss_pred HhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccchhhhhhHHHhhcc
Q 027469 87 EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEAVNGH 166 (223)
Q Consensus 87 ~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~e~l~e~I~~~ 166 (223)
..+.-.|+.+.+-+.++-=.||.+||-. +.+-.+.=..+..+++..++.++ |..+. ...++|+..
T Consensus 168 ~~L~~lL~g~~~p~~il~grDg~iyVla--------~~qrd~~W~~Q~Llk~~~~e~v~-v~~i~------~~~~~i~~~ 232 (389)
T TIGR02554 168 AELNGLLGGAPVRFAVLPGRDGRIYVAA--------ASQRDAEWARQALLRAALPEKIE-VAVIG------AERQRVSRW 232 (389)
T ss_pred HHHHHHhcCCCCCeEEEeCCCCcEEEEE--------ccccHhHHHHHHHhhcCCCCCeE-EechH------HHHHHHHHH
Confidence 4555667778888888777788999977 77777765666666765664443 22221 233455554
Q ss_pred cccchhHHHhcCCcEEEEEEe--C---CEEEEEEeCh-----hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 167 LDILRPAIKNYGGSVEVLSVE--S---GDCIVKYVGP-----DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 167 L~~IRP~L~~~GGdvelv~v~--~---g~v~vrl~G~-----~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
|..++..+-++.++ + -++ -+.+. ..-++.+.++|++.+|=.+.|.+.
T Consensus 233 -------L~~~~P~l~~~kv~l~~P~~Pvl--~l~~q~~~~~~~~~~~l~~~l~~~~pya~~v~I~ 289 (389)
T TIGR02554 233 -------LDEAGPQLAFYRLRLDAPRHPEL--WLSRQRNAAPAAARARLIGELRRLMPYARDVRII 289 (389)
T ss_pred -------HHhhCCcceEEEEEcCCCCCCEE--EEecccCCCCHHHHHHHHHHHHHhCCccceeEEE
Confidence 55566666666663 2 344 46775 345568899999999988887763
No 40
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=33.92 E-value=80 Score=22.78 Aligned_cols=29 Identities=24% Similarity=0.536 Sum_probs=22.8
Q ss_pred EEEEEEccccCCCCCchHHHHHHHHHHHHHHhCc
Q 027469 109 VVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGD 142 (223)
Q Consensus 109 ~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~ 142 (223)
.|.|.| |.+|.....-+ .+++.|...+|.
T Consensus 2 ~V~IeY---C~~C~~~~~a~--~l~~~l~~~fp~ 30 (76)
T PF10262_consen 2 KVTIEY---CTSCGYRPRAL--ELAQELLQTFPD 30 (76)
T ss_dssp EEEEEE---ETTTTCHHHHH--HHHHHHHHHSTT
T ss_pred EEEEEE---CCCCCCHHHHH--HHHHHHHHHCCC
Confidence 366777 99998766644 889999999996
No 41
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=32.57 E-value=75 Score=24.33 Aligned_cols=53 Identities=11% Similarity=0.192 Sum_probs=38.1
Q ss_pred hhHHHhhcccccchhHHHhcCCcEEEEEE--------------eCCEEEEEEeChhhHHHHHHHHHH
Q 027469 158 TTVEAVNGHLDILRPAIKNYGGSVEVLSV--------------ESGDCIVKYVGPDSIASGIRAAIK 210 (223)
Q Consensus 158 ~l~e~I~~~L~~IRP~L~~~GGdvelv~v--------------~~g~v~vrl~G~~Tlk~gIE~~L~ 210 (223)
...+.++.+++.+.-.|+..||.+.-++- ++-++.+.|.+.-..-..+++.|+
T Consensus 18 l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~~~G~Yv~~~f~~~~~~i~eler~lr 84 (97)
T CHL00123 18 LNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQMNYSGNGKLVNSLEKALK 84 (97)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCCCEEEEEEEEEEECHHHHHHHHHHhC
Confidence 34577888899999999999998865542 123688999988444456666653
No 42
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=32.37 E-value=19 Score=27.73 Aligned_cols=72 Identities=10% Similarity=0.111 Sum_probs=40.3
Q ss_pred eeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeC---C-EEEEE---Eccc
Q 027469 47 SGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVED---G-VVSVK---LQGA 117 (223)
Q Consensus 47 ~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~---g-~V~Vr---l~Ga 117 (223)
.++|+++...|...-.=. .--....+.|..+..+.+..++ ....+||..- .+|+.+ + ...+. ..+.
T Consensus 24 ~~lRi~v~~~GC~G~~y~~~l~~~~~~~D~v~~~~g~~v~id~~s~~~l~g~-----~IDy~~~~~~~~F~~~NPn~~~~ 98 (107)
T TIGR01997 24 VGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAKVFVAPEAVLFILGT-----QVDFVRTTLRQGFKFNNPNATSA 98 (107)
T ss_pred cEEEEEEECCCCCCcEEEeeecCCCCCCCEEEecCCEEEEEcHHHHhhhCCC-----EEEEEEcCCcceEEEECCCCCCc
Confidence 478998887653211000 0011223455666666777777 7889999877 777742 2 22221 2456
Q ss_pred cCCCCCc
Q 027469 118 CGSCPSS 124 (223)
Q Consensus 118 C~gCpss 124 (223)
|+ |.+|
T Consensus 99 Cg-CG~S 104 (107)
T TIGR01997 99 CG-CGES 104 (107)
T ss_pred cC-CCCC
Confidence 76 8765
No 43
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=31.22 E-value=1.6e+02 Score=26.13 Aligned_cols=112 Identities=18% Similarity=0.275 Sum_probs=60.8
Q ss_pred cchhhhhHHHHHHHH---HhhhhHHHhcCCceEEEee----eCCEEEEEEccccCC--CCCchHHHHHHHHHHHHHHhCc
Q 027469 72 AHQFDLTAKNVDLVL---EDVRPYLIADGGNIDVVSV----EDGVVSVKLQGACGS--CPSSTTTMSMGIERVLKEKFGD 142 (223)
Q Consensus 72 ~~~~~l~~~~v~~~l---~~IrP~Lq~dGGdVelvdv----~~g~V~Vrl~GaC~g--Cpss~~Tlk~~IE~~L~e~lp~ 142 (223)
...+++...-+..++ ..+|+ ||++-=+ .+.-..|++.|.|.. =|. -.++-..|.++|...+..
T Consensus 26 sGR~DvlcRc~~~alf~sh~~R~-------dV~v~lvL~G~p~ppktI~~~g~~~~~~~pd-Ers~a~~i~kAL~~~~~~ 97 (197)
T COG1901 26 SGRLDVLCRCVSSALFLSHGIRR-------DVVVYLVLLGPPDPPKTIRVEGSELRYLNPD-ERSLAILIKKALDAELGK 97 (197)
T ss_pred CcchhHHHHHHhHHHHHhccccC-------ceEEEEEEecCCCCCEEEEEEcccccccCcc-hHHHHHHHHHHHHhhccc
Confidence 346677766666665 24444 4444333 346788999999987 333 344445788888884432
Q ss_pred ccccccccccc-hhhhhhHHHhhccccc--chhHHHhcCCcEEEEEEeCCEEEE
Q 027469 143 AIKDIRQVYDE-EVRETTVEAVNGHLDI--LRPAIKNYGGSVEVLSVESGDCIV 193 (223)
Q Consensus 143 ~vk~V~~V~~~-~~~e~l~e~I~~~L~~--IRP~L~~~GGdvelv~v~~g~v~v 193 (223)
+-+ +.+..- -......|.+-..+.+ =.=||..+|+|++=++..++-++|
T Consensus 98 ~~~--~~~~pGi~V~~~~~e~ll~~l~~~~~ly~L~E~G~DI~~v~~~~np~FI 149 (197)
T COG1901 98 EQT--REVTPGIYVRNGGFEALLAELAEGRSLYYLHEDGRDISEVDLIPNPVFI 149 (197)
T ss_pred cce--eecCCCEEEecCCHHHHHHHHhccCcEEEEccCCccHhhcccCCCceEE
Confidence 211 111000 0001222323333322 223788999999988886555554
No 44
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=31.18 E-value=84 Score=23.40 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=30.2
Q ss_pred EEEEEeCCEEEEEEeCh-hhHHHHHHHHHHhhCCCcceE
Q 027469 182 EVLSVESGDCIVKYVGP-DSIASGIRAAIKEKFPDIENV 219 (223)
Q Consensus 182 elv~v~~g~v~vrl~G~-~Tlk~gIE~~L~e~~Pei~~V 219 (223)
++++-+++.+.+.|.|- .|+-+.+...|.+ |.|+.+
T Consensus 2 ki~~~~~~~~~~~~~~edhTl~n~L~~~l~~--~pV~~a 38 (86)
T cd00460 2 KILEKEKNYVDFVLENEDHTLGNSLRRILLK--SPVEFA 38 (86)
T ss_pred ceecCCCCEEEEEEeCCCchHHHHHHHHHhC--CCceEE
Confidence 46666788999999999 8999999999998 666654
No 45
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=30.84 E-value=35 Score=25.86 Aligned_cols=26 Identities=35% Similarity=0.709 Sum_probs=19.1
Q ss_pred CCceEEEe-eeCCEEEEEEccccCCCCCchH
Q 027469 97 GGNIDVVS-VEDGVVSVKLQGACGSCPSSTT 126 (223)
Q Consensus 97 GGdVelvd-v~~g~V~Vrl~GaC~gCpss~~ 126 (223)
=|-|+-++ -..+- ++|+|.+||-+..
T Consensus 43 kGkverv~~~~~gC----~sGsCk~C~e~~~ 69 (78)
T PRK15431 43 MGKAVRIQEEPDGC----LSGSCKSCPEGKA 69 (78)
T ss_pred CCCeEeeccCCCCC----CCCCCCCCCCCcc
Confidence 57787776 33466 6899999998654
No 46
>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=30.77 E-value=1.8e+02 Score=24.16 Aligned_cols=40 Identities=30% Similarity=0.517 Sum_probs=28.2
Q ss_pred CcEEEEEEeCCEEEEEEeCh-------hhHHHHHHHHHHhhCCCcceEE
Q 027469 179 GSVEVLSVESGDCIVKYVGP-------DSIASGIRAAIKEKFPDIENVV 220 (223)
Q Consensus 179 Gdvelv~v~~g~v~vrl~G~-------~Tlk~gIE~~L~e~~Pei~~V~ 220 (223)
|-|.=|+++++.|.|.+.=+ ..|++.|+++|++. .+..|.
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 56666777777777766655 57888999999874 565554
No 47
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=30.76 E-value=22 Score=26.83 Aligned_cols=57 Identities=12% Similarity=0.092 Sum_probs=34.0
Q ss_pred eeeeEEEEecCCCCCCCCC-CCCCcCCcchhhhhHHHHHHHH-HhhhhHHHhcCCceEEEeeeC
Q 027469 46 KSGSHETAIRASNPSAPAG-SSPGLYSAHQFDLTAKNVDLVL-EDVRPYLIADGGNIDVVSVED 107 (223)
Q Consensus 46 ~~~~r~~~~~~gtp~a~~~-~~p~~~~~~~~~l~~~~v~~~l-~~IrP~Lq~dGGdVelvdv~~ 107 (223)
+.++|+++...|.....-+ .-.....+.|.....+.+..++ ....+||..- .||+.+
T Consensus 21 ~~~lRi~~~~~Gc~G~~~~l~l~~~~~~~D~~~~~~gi~~~id~~~~~~l~~~-----~IDy~~ 79 (105)
T TIGR00049 21 NLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKVVVDPKSLPYLDGS-----EIDYVE 79 (105)
T ss_pred ceEEEEEEecCCCCCeEEEEeecCCCCCCCEEEEcCCEEEEEeHHHHhhhCCC-----EEEEee
Confidence 4679999998876432222 1111112345555556677777 6788999854 677743
No 48
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=28.96 E-value=56 Score=27.69 Aligned_cols=35 Identities=40% Similarity=0.596 Sum_probs=24.8
Q ss_pred EEEeeeCCEEEEEE--ccccCCCCCchHHHHHHHHHHH
Q 027469 101 DVVSVEDGVVSVKL--QGACGSCPSSTTTMSMGIERVL 136 (223)
Q Consensus 101 elvdv~~g~V~Vrl--~GaC~gCpss~~Tlk~~IE~~L 136 (223)
.+++.++|.+.|+- +-+|++|++...--. .+...|
T Consensus 7 ~vv~~q~G~a~V~c~~~S~CgsC~a~~~CGs-~~l~kL 43 (150)
T COG3086 7 TVVSWQNGQAKVSCQRQSACGSCAARAGCGS-GLLSKL 43 (150)
T ss_pred EEEEccCCeEEEEeeccCccccchhhcccch-HHHHHh
Confidence 46888999877765 489999998776554 333333
No 49
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=27.30 E-value=1.3e+02 Score=23.26 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=17.4
Q ss_pred HhhhhHHHhcCCceEEEeeeC--CEEEEEEc
Q 027469 87 EDVRPYLIADGGNIDVVSVED--GVVSVKLQ 115 (223)
Q Consensus 87 ~~IrP~Lq~dGGdVelvdv~~--g~V~Vrl~ 115 (223)
+.++-.++.+| +|.+||+.. ..-+|||.
T Consensus 16 e~iK~~f~~~g-~V~yVD~~~G~~~g~VRf~ 45 (105)
T PF08777_consen 16 EDIKEAFSQFG-EVAYVDFSRGDTEGYVRFK 45 (105)
T ss_dssp HHHHHHT-SS---EEEEE--TT-SEEEEEES
T ss_pred HHHHHHHHhcC-CcceEEecCCCCEEEEEEC
Confidence 45566667665 999999974 47999995
No 50
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=25.99 E-value=2.7e+02 Score=20.42 Aligned_cols=47 Identities=9% Similarity=0.192 Sum_probs=36.5
Q ss_pred cchhHHHhcCCcEEEEEEeCCEEEEEEeChhhHHHHHHHHHHhhCCC
Q 027469 169 ILRPAIKNYGGSVEVLSVESGDCIVKYVGPDSIASGIRAAIKEKFPD 215 (223)
Q Consensus 169 ~IRP~L~~~GGdvelv~v~~g~v~vrl~G~~Tlk~gIE~~L~e~~Pe 215 (223)
+|=-.|++|+-++-..+..-+.+..-+.|..-.-.-+.+.|.++||+
T Consensus 20 ~i~~~l~~~~v~ii~K~~nANtit~yl~~~~k~~~r~~~~Le~~~p~ 66 (71)
T cd04910 20 EILELLQRFKVSIIAKDTNANTITHYLAGSLKTIKRLTEDLENRFPN 66 (71)
T ss_pred HHHHHHHHcCCeEEEEecCCCeEEEEEEcCHHHHHHHHHHHHHhCcc
Confidence 55556888888888887767899999998853345788889999984
No 51
>COG1298 FlhA Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=25.79 E-value=75 Score=32.94 Aligned_cols=64 Identities=20% Similarity=0.388 Sum_probs=48.0
Q ss_pred CchHHHHHHHHHHHHHHhCcccccccccccc--------hhhhhhHHHhhccc-ccchhHHHhcCCcEEEEEEeC
Q 027469 123 SSTTTMSMGIERVLKEKFGDAIKDIRQVYDE--------EVRETTVEAVNGHL-DILRPAIKNYGGSVEVLSVES 188 (223)
Q Consensus 123 ss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~--------~~~e~l~e~I~~~L-~~IRP~L~~~GGdvelv~v~~ 188 (223)
.+-.+++...+..|+|++| +++.+.+.+. .+.+.+.|.|+..| ..|=-++....|.++++.+++
T Consensus 531 is~s~iqkVLq~LL~E~Vs--IRdl~tIlEtlad~a~~~kd~~~L~e~VR~~L~r~I~~~~~~~~~~L~VitL~~ 603 (696)
T COG1298 531 ISLSTLQKVLQNLLKERVS--IRDLPTILETLADYAPITKDPDELTEKVRQALGRQITQQLLDENGELEVITLDP 603 (696)
T ss_pred cCHHHHHHHHHHHHhcCCc--cccHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhCcCCeEEEEEeCh
Confidence 4667888888999999997 6666654221 13456778888888 588888888999999998864
No 52
>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=24.99 E-value=1e+02 Score=22.16 Aligned_cols=23 Identities=35% Similarity=0.647 Sum_probs=18.0
Q ss_pred cCCCCCchHHHHHHHHHHHHHHhCc
Q 027469 118 CGSCPSSTTTMSMGIERVLKEKFGD 142 (223)
Q Consensus 118 C~gCpss~~Tlk~~IE~~L~e~lp~ 142 (223)
|.+|...... ..+.+.|++.||+
T Consensus 6 C~~C~y~~Ra--~~l~q~L~~~Fp~ 28 (72)
T TIGR02174 6 CGSCGYKPRA--AWLKQELLEEFPD 28 (72)
T ss_pred CCCCCChHHH--HHHHHHHHHHCCC
Confidence 8999854444 4889999999985
No 53
>PRK15327 type III secretion system needle complex protein PrgH; Provisional
Probab=24.31 E-value=3e+02 Score=26.69 Aligned_cols=116 Identities=11% Similarity=0.157 Sum_probs=75.5
Q ss_pred HhhhhHHHhcCCceEEEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccchhhhhhHHHhhcc
Q 027469 87 EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEAVNGH 166 (223)
Q Consensus 87 ~~IrP~Lq~dGGdVelvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~e~l~e~I~~~ 166 (223)
..+.-.|+.+.+-+.++-=.||.+||-. +.+-.+.=..+..+++..++.++ |..+ ....++|+..
T Consensus 173 ~tL~~~L~g~~~p~~Il~grD~~iyVLa--------~~qrd~~W~~Q~L~k~~~~~~v~-v~~~------~~~~~~ie~~ 237 (393)
T PRK15327 173 AELDSLLGQEKERFQVLPGRDKMLYVAA--------QNERDTLWARQSLARGDYDKNAR-VINE------NEENKRVSTW 237 (393)
T ss_pred HHHHHHhcCCCCceEEEeCCCCcEEEEE--------ccccHhHHHHHHHhhCCCcCceE-Eech------HHHHHHHHHH
Confidence 3445567777788887777788999976 77777765666677766554333 2121 1456778887
Q ss_pred cccchhHHHhcCCcEEEEEEe---CCEEEEEEe-Ch--hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 167 LDILRPAIKNYGGSVEVLSVE---SGDCIVKYV-GP--DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 167 L~~IRP~L~~~GGdvelv~v~---~g~v~vrl~-G~--~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
|.+.-|.|+-| =|+++ .-++.|+=. |. .+-+..+.++|++.+|=.+.|.+.
T Consensus 238 L~~~~P~l~~l-----kv~l~~P~~Pvl~ls~~r~~l~~~~~~~l~~~l~~~~pya~~v~I~ 294 (393)
T PRK15327 238 LDTYYPQLAYY-----RLHFDEPRKPVLWLSRQRNVLSKKELEVLSQKLRALMPYADSVNIT 294 (393)
T ss_pred HHhcCCCceEE-----EEECCCCCCCEEEEEcccccCCHHHHHHHHHHHHHhCCccceeEEE
Confidence 77777765422 13332 346666533 55 455688999999999988887763
No 54
>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=24.11 E-value=3e+02 Score=23.87 Aligned_cols=52 Identities=27% Similarity=0.395 Sum_probs=32.0
Q ss_pred cchhHHHhcCCcEEEEEEe----CC-----EEEEEEeCh------hhHHHHHHHHHHhhCCCcceEE
Q 027469 169 ILRPAIKNYGGSVEVLSVE----SG-----DCIVKYVGP------DSIASGIRAAIKEKFPDIENVV 220 (223)
Q Consensus 169 ~IRP~L~~~GGdvelv~v~----~g-----~v~vrl~G~------~Tlk~gIE~~L~e~~Pei~~V~ 220 (223)
+++-.++...|..++-++. +. .+++++.+. ..+.+-|++.|++++|++..|.
T Consensus 209 ~i~~~i~~~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~i~~v~ 275 (284)
T PF01545_consen 209 KIRRIIESVPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREKFPGIYDVT 275 (284)
T ss_dssp HHHHHHHHTSS-SEEEEEEEEEETT-EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHHSTTCEEEE
T ss_pred HHHHhhccCCceEeccceEEEEecCCcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCCcEEEE
Confidence 3444443455544554441 22 355555555 3467899999999999998754
No 55
>PF15092 UPF0728: Uncharacterised protein family UPF0728
Probab=23.47 E-value=1.1e+02 Score=23.75 Aligned_cols=32 Identities=19% Similarity=0.196 Sum_probs=25.6
Q ss_pred cccchhHHHhcCCcEEEEEEeC-CEEEEEEeCh
Q 027469 167 LDILRPAIKNYGGSVEVLSVES-GDCIVKYVGP 198 (223)
Q Consensus 167 L~~IRP~L~~~GGdvelv~v~~-g~v~vrl~G~ 198 (223)
|+-++-.|+++|=.|+|..+++ +.+-|-+.|-
T Consensus 27 L~GLqa~L~~dGh~v~L~~~~d~n~vel~vnge 59 (88)
T PF15092_consen 27 LEGLQAVLAKDGHEVILEKIEDWNVVELVVNGE 59 (88)
T ss_pred HHHHHHHHHhCCcEEEEEEeccccEEEEEECCe
Confidence 4677888999999999999965 6777766664
No 56
>TIGR00532 HMG_CoA_R_NAD hydroxymethylglutaryl-CoA reductase, degradative. Most known examples of hydroxymethylglutaryl-CoA reductase are NADP-dependent (EC 1.1.1.34) from eukaryotes and archaea, involved in the biosynthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA. This model, in contrast, is built from the two examples in completed genomes of sequences closely related to the degradative, NAD-dependent hydroxymethylglutaryl-CoA reductase of Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source.
Probab=23.21 E-value=3.8e+02 Score=26.01 Aligned_cols=65 Identities=14% Similarity=0.264 Sum_probs=45.9
Q ss_pred hHHHHHHHHHhhhhHHHhcCCceEEEee------eCCEEEEEEccccCCCCCchH--HHHHHHHHHHHHHhCc
Q 027469 78 TAKNVDLVLEDVRPYLIADGGNIDVVSV------EDGVVSVKLQGACGSCPSSTT--TMSMGIERVLKEKFGD 142 (223)
Q Consensus 78 ~~~~v~~~l~~IrP~Lq~dGGdVelvdv------~~g~V~Vrl~GaC~gCpss~~--Tlk~~IE~~L~e~lp~ 142 (223)
..+.+..+.+..-|.+...||.+.-+.. .++.++|||.-.|.--.++.+ |+.+.+-..|.+.+|.
T Consensus 142 ~~~~i~~~a~~~~~~~~~rggg~~~i~~r~~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~Eav~~~i~~~~~~ 214 (393)
T TIGR00532 142 LGDEIIERAEECDPMLNNLGGGCKDIEARVIDIIEGGILILHIIVDTCDAMGANALNSIAEKVAEFIELEFGG 214 (393)
T ss_pred HHHHHHHHHHHhCHHHHhhcCCeEEEEEEeeecccCCEEEEEEEEecccccccHHHHHHHHHHHHHHHHhCCC
Confidence 4455666667889999999999886663 356899999877766666554 3455666677777763
No 57
>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=22.90 E-value=1.7e+02 Score=25.23 Aligned_cols=32 Identities=28% Similarity=0.284 Sum_probs=23.5
Q ss_pred EEEEEEeChhhH------HHHHHHHHHhhCCCcceEEe
Q 027469 190 DCIVKYVGPDSI------ASGIRAAIKEKFPDIENVVF 221 (223)
Q Consensus 190 ~v~vrl~G~~Tl------k~gIE~~L~e~~Pei~~V~~ 221 (223)
.+.|.+.+.+|+ ...+|+.+++++|++..|.+
T Consensus 226 ~~~v~v~~~~~~~~ah~i~~~i~~~i~~~~~~v~~v~i 263 (268)
T TIGR01297 226 DVHVVVDPDLDLKQAHDIALEIEREILKRHPGIEHVTI 263 (268)
T ss_pred EEEEEECCCCChhHHHHHHHHHHHHHHHhcCCCCeEEE
Confidence 456666666555 45799999999999987753
No 58
>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=22.84 E-value=2.1e+02 Score=24.45 Aligned_cols=67 Identities=16% Similarity=0.169 Sum_probs=45.8
Q ss_pred hhHHHHHHHH-HhhhhHHHh---cCCceEEEeeeC---C--EEEEEEccccCCCCCchHHHHHHHHHHHHHHhCccccc
Q 027469 77 LTAKNVDLVL-EDVRPYLIA---DGGNIDVVSVED---G--VVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKD 146 (223)
Q Consensus 77 l~~~~v~~~l-~~IrP~Lq~---dGGdVelvdv~~---g--~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~ 146 (223)
...+.|..+| .-.-|.+.. +=|-|.=+++++ + .|+|.|.-...+|++. ..|+..|+.+|.. +| .+++
T Consensus 73 ~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~-~~L~~dV~~aL~~-l~-gV~~ 148 (174)
T TIGR03406 73 DNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMG-PVLVEDVEDKVLA-VP-NVDE 148 (174)
T ss_pred ccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHH-HHHHHHHHHHHHh-CC-Ccee
Confidence 3446688888 455666554 236666667766 5 8999999999999964 3466778888875 44 3443
No 59
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.70 E-value=64 Score=25.67 Aligned_cols=25 Identities=32% Similarity=0.545 Sum_probs=19.8
Q ss_pred ccCCCCCchHHHHHHHHHHHHHHhCc
Q 027469 117 ACGSCPSSTTTMSMGIERVLKEKFGD 142 (223)
Q Consensus 117 aC~gCpss~~Tlk~~IE~~L~e~lp~ 142 (223)
+|.+-|+|..|. .++|.+|+.++|.
T Consensus 18 SCV~aPtsKdt~-eWLeaalkRKyp~ 42 (106)
T COG4837 18 SCVNAPTSKDTY-EWLEAALKRKYPN 42 (106)
T ss_pred HhcCCCcchhHH-HHHHHHHhccCCC
Confidence 355557788887 5999999999994
No 60
>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=22.37 E-value=93 Score=22.07 Aligned_cols=24 Identities=21% Similarity=0.545 Sum_probs=16.0
Q ss_pred EEEEEccccCCCCCchHHHHHHHHHHHHH
Q 027469 110 VSVKLQGACGSCPSSTTTMSMGIERVLKE 138 (223)
Q Consensus 110 V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e 138 (223)
+.+ ++-.|..|+ .+.+.+++++.+
T Consensus 3 I~v-~~~~C~~C~----~~~~~~~~~~~~ 26 (76)
T PF13192_consen 3 IKV-FSPGCPYCP----ELVQLLKEAAEE 26 (76)
T ss_dssp EEE-ECSSCTTHH----HHHHHHHHHHHH
T ss_pred EEE-eCCCCCCcH----HHHHHHHHHHHh
Confidence 566 776799998 344456666665
No 61
>PRK11670 antiporter inner membrane protein; Provisional
Probab=21.84 E-value=2.2e+02 Score=26.76 Aligned_cols=64 Identities=13% Similarity=0.234 Sum_probs=0.0
Q ss_pred hhHHHhhccc-ccchhHHHhc---CCcEEEEEEeCCEEEEEEeCh-------hhHHHHHHHHHHhhCCCcceEEeC
Q 027469 158 TTVEAVNGHL-DILRPAIKNY---GGSVEVLSVESGDCIVKYVGP-------DSIASGIRAAIKEKFPDIENVVFT 222 (223)
Q Consensus 158 ~l~e~I~~~L-~~IRP~L~~~---GGdvelv~v~~g~v~vrl~G~-------~Tlk~gIE~~L~e~~Pei~~V~~v 222 (223)
...+.|.++| .-.-|.+..+ =|-|.=+.++++.+.+.+.-+ ..++..+++.|.+ +|+++.|...
T Consensus 12 ~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 86 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQCSAELLR-ITGAKAIDWK 86 (369)
T ss_pred chHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHHHHHHHHHHHHHHh-cCCCceEEEE
No 62
>cd02008 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
Probab=21.49 E-value=81 Score=26.00 Aligned_cols=22 Identities=27% Similarity=0.570 Sum_probs=16.3
Q ss_pred ccccCCCCCchHHHHHHHHHHHHHHhCc
Q 027469 115 QGACGSCPSSTTTMSMGIERVLKEKFGD 142 (223)
Q Consensus 115 ~GaC~gCpss~~Tlk~~IE~~L~e~lp~ 142 (223)
.+.|.|||. ..+-..|++.+|+
T Consensus 4 ~~~c~gc~~------~~~~~~l~~~l~~ 25 (178)
T cd02008 4 PGLCPGCPH------RPSFYALRKAFKK 25 (178)
T ss_pred CCcCCCCCC------hHHHHHHHHHhcC
Confidence 468999999 4555667777774
No 63
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=21.45 E-value=1.6e+02 Score=22.10 Aligned_cols=35 Identities=11% Similarity=0.336 Sum_probs=29.2
Q ss_pred EEEEEEeCCEEEEEEeCh-hhHHHHHHHHHHhhCCCc
Q 027469 181 VEVLSVESGDCIVKYVGP-DSIASGIRAAIKEKFPDI 216 (223)
Q Consensus 181 velv~v~~g~v~vrl~G~-~Tlk~gIE~~L~e~~Pei 216 (223)
+++++-+++.+.+.|.|- .||-+.+...|.+. |.|
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V 36 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD-PGV 36 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC-CCe
Confidence 467777889999999999 89999999999873 443
No 64
>PRK00321 rdgC recombination associated protein; Reviewed
Probab=21.33 E-value=4.8e+02 Score=24.19 Aligned_cols=83 Identities=12% Similarity=0.167 Sum_probs=54.8
Q ss_pred EEeeeCCEEEEEEccccCCCCCchHHHHHHHHHHHHHHhCcccccccccccchhhhhhHHHhh-cccccchhHHHhcCCc
Q 027469 102 VVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEAVN-GHLDILRPAIKNYGGS 180 (223)
Q Consensus 102 lvdv~~g~V~Vrl~GaC~gCpss~~Tlk~~IE~~L~e~lp~~vk~V~~V~~~~~~e~l~e~I~-~~L~~IRP~L~~~GGd 180 (223)
++|.++|.++|-- ++......+...|++.++. +. +..+.... ....... ++.+.=-|.-=.-|-+
T Consensus 128 ~id~~~g~l~Vda---------sS~k~aE~~l~lLrkslgs-Lp-v~p~~~~~---~p~~~mt~WL~~~~~P~~f~l~~~ 193 (303)
T PRK00321 128 WIDPVNGLIVVDA---------ASAKKAEDVLALLRKSLGS-LP-VVPLSTEQ---SPEATMTEWLASGEAPAGFTLDDE 193 (303)
T ss_pred EEECCCCEEEEeC---------CCHHHHHHHHHHHHHhcCC-Cc-eeccccCC---CHHHHHHHHHccCCCCCCcEecce
Confidence 6777899998854 4445556888999999973 55 33332221 1122332 3334445666667999
Q ss_pred EEEEEEeCCEEEEEEeCh
Q 027469 181 VEVLSVESGDCIVKYVGP 198 (223)
Q Consensus 181 velv~v~~g~v~vrl~G~ 198 (223)
+||.+..++...||+++.
T Consensus 194 ~eL~~~~e~~~~vr~k~~ 211 (303)
T PRK00321 194 CELKSALEDGAVVRCKRQ 211 (303)
T ss_pred eEEecCCCCccEEEEeCC
Confidence 999999777779999987
No 65
>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=20.47 E-value=3e+02 Score=23.49 Aligned_cols=64 Identities=19% Similarity=0.251 Sum_probs=42.5
Q ss_pred hhhHHHhhccc-ccchhHHHhc---CCcEEEEEEeC---C--EEEEEEeCh-------hhHHHHHHHHHHhhCCCcceEE
Q 027469 157 ETTVEAVNGHL-DILRPAIKNY---GGSVEVLSVES---G--DCIVKYVGP-------DSIASGIRAAIKEKFPDIENVV 220 (223)
Q Consensus 157 e~l~e~I~~~L-~~IRP~L~~~---GGdvelv~v~~---g--~v~vrl~G~-------~Tlk~gIE~~L~e~~Pei~~V~ 220 (223)
+...++|.++| .-.-|.+..+ =|-|.=+++++ + .|.|.|.=+ ..|+.-|+.+|.. +|.++.|.
T Consensus 72 ~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL~~-l~gV~~V~ 150 (174)
T TIGR03406 72 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVLA-VPNVDEVE 150 (174)
T ss_pred cccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHHHh-CCCceeEE
Confidence 35557788888 4666766553 35555567755 5 777777755 4677778888864 78888765
Q ss_pred e
Q 027469 221 F 221 (223)
Q Consensus 221 ~ 221 (223)
+
T Consensus 151 V 151 (174)
T TIGR03406 151 V 151 (174)
T ss_pred E
Confidence 3
No 66
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=20.17 E-value=2e+02 Score=25.85 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=18.7
Q ss_pred EEEEEeChhh------HHHHHHHHHHhhCCCcc
Q 027469 191 CIVKYVGPDS------IASGIRAAIKEKFPDIE 217 (223)
Q Consensus 191 v~vrl~G~~T------lk~gIE~~L~e~~Pei~ 217 (223)
+.+.+-+.+| +.+.||++|++++|++.
T Consensus 247 v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~~~~ 279 (299)
T PRK09509 247 LHLEMEDNLPLVQAHMIADQVEQALLRRFPGSD 279 (299)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHhCCCCE
Confidence 4444554444 45779999999999765
Done!