Query 029891
Match_columns 186
No_of_seqs 143 out of 1104
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:17:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029891hhsearch_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 1.4E-25 3E-30 159.0 8.8 68 87-154 1-68 (68)
2 COG0694 Thioredoxin-like prote 99.9 3E-25 6.5E-30 166.6 9.2 77 84-160 11-90 (93)
3 TIGR03341 YhgI_GntY IscR-regul 99.9 7.6E-24 1.7E-28 176.3 9.6 78 84-161 107-186 (190)
4 PRK11190 Fe/S biogenesis prote 99.9 1.6E-23 3.4E-28 174.8 9.3 79 83-161 107-188 (192)
5 KOG2358 NifU-like domain-conta 99.9 1.4E-23 3.1E-28 176.2 4.7 149 8-158 38-202 (213)
6 TIGR02000 NifU_proper Fe-S clu 99.8 2.2E-20 4.7E-25 164.3 9.7 70 84-154 221-290 (290)
7 KOG2358 NifU-like domain-conta 99.5 1.9E-14 4.2E-19 121.3 2.3 121 66-186 61-181 (213)
8 PF08712 Nfu_N: Scaffold prote 98.5 6E-09 1.3E-13 77.1 -2.2 52 8-60 26-85 (87)
9 PF01883 DUF59: Domain of unkn 96.3 0.035 7.6E-07 38.5 7.8 68 84-153 1-72 (72)
10 TIGR02000 NifU_proper Fe-S clu 91.2 0.4 8.6E-06 42.7 5.1 65 120-185 166-241 (290)
11 TIGR02945 SUF_assoc FeS assemb 89.3 3.2 7E-05 30.4 7.8 67 84-152 3-74 (99)
12 COG1941 FrhG Coenzyme F420-red 87.9 1.5 3.2E-05 38.6 6.0 57 114-177 6-75 (247)
13 COG2151 PaaD Predicted metal-s 87.0 3.3 7.1E-05 32.2 6.9 68 83-152 13-86 (111)
14 TIGR03406 FeS_long_SufT probab 83.6 7.9 0.00017 32.1 8.1 78 81-160 72-160 (174)
15 TIGR02159 PA_CoA_Oxy4 phenylac 75.5 14 0.0003 29.8 6.8 65 103-170 15-82 (146)
16 COG0694 Thioredoxin-like prote 74.6 2.4 5.2E-05 32.1 2.1 36 29-65 33-70 (93)
17 PRK10862 SoxR reducing system 71.5 5.6 0.00012 32.2 3.7 26 105-130 6-33 (154)
18 PF07315 DUF1462: Protein of u 71.4 4.3 9.3E-05 30.8 2.8 32 122-154 11-43 (93)
19 PF04246 RseC_MucC: Positive r 70.0 4.5 9.7E-05 31.4 2.8 22 107-128 1-24 (135)
20 PF08821 CGGC: CGGC domain; I 69.9 32 0.00069 26.3 7.4 33 122-159 45-77 (107)
21 PRK11670 antiporter inner memb 67.0 30 0.00066 31.5 7.9 69 83-153 13-85 (369)
22 PF09580 Spore_YhcN_YlaJ: Spor 64.9 45 0.00097 26.6 7.7 45 111-157 98-142 (177)
23 PF01545 Cation_efflux: Cation 63.3 44 0.00096 28.1 7.8 50 101-152 217-275 (284)
24 PF09012 FeoC: FeoC like trans 61.6 15 0.00033 25.2 3.9 40 81-131 25-65 (69)
25 COG4837 Uncharacterized protei 54.0 30 0.00066 26.6 4.6 28 123-151 19-46 (106)
26 COG3086 RseC Positive regulato 52.0 26 0.00055 28.8 4.2 54 106-160 7-62 (150)
27 PF11718 CPSF73-100_C: Pre-mRN 48.2 1.6E+02 0.0034 25.1 8.6 103 40-144 90-209 (216)
28 PF02061 Lambda_CIII: Lambda P 47.3 25 0.00053 23.2 2.8 26 120-145 7-32 (45)
29 TIGR02174 CXXU_selWTH selT/sel 45.2 44 0.00095 23.4 4.1 24 123-148 6-29 (72)
30 PRK14464 ribosomal RNA large s 40.9 39 0.00084 31.0 4.1 71 101-176 84-165 (344)
31 KOG3348 BolA (bacterial stress 40.8 64 0.0014 24.2 4.5 59 82-152 3-70 (85)
32 PRK14459 ribosomal RNA large s 40.7 1.1E+02 0.0024 28.4 7.0 55 122-176 134-203 (373)
33 cd06406 PB1_P67 A PB1 domain i 39.7 1.5E+02 0.0032 21.9 6.2 49 128-178 21-71 (80)
34 PF15092 UPF0728: Uncharacteri 36.7 58 0.0013 24.5 3.7 30 92-121 28-58 (88)
35 cd04888 ACT_PheB-BS C-terminal 36.1 1.3E+02 0.0028 19.9 6.3 60 90-154 13-75 (76)
36 PF08777 RRM_3: RNA binding mo 35.5 49 0.0011 24.9 3.3 26 96-122 20-47 (105)
37 PRK11190 Fe/S biogenesis prote 35.2 23 0.00049 29.8 1.5 21 165-185 108-129 (192)
38 PF07045 DUF1330: Protein of u 33.4 44 0.00095 22.7 2.5 24 85-108 2-25 (65)
39 CHL00123 rps6 ribosomal protei 32.6 66 0.0014 23.9 3.5 29 81-109 17-45 (97)
40 PRK10597 DNA damage-inducible 32.4 1.4E+02 0.0031 21.9 5.2 46 128-175 16-70 (81)
41 TIGR01297 CDF cation diffusion 30.8 1.5E+02 0.0033 24.7 5.9 37 114-152 226-262 (268)
42 PF10262 Rdx: Rdx family; Int 28.4 93 0.002 21.7 3.6 37 114-155 2-39 (76)
43 PF00403 HMA: Heavy-metal-asso 28.1 1.2E+02 0.0027 19.5 4.0 25 121-153 7-31 (62)
44 PF14424 Toxin-deaminase: The 27.4 1.4E+02 0.0029 23.7 4.7 52 83-151 76-128 (133)
45 PF13192 Thioredoxin_3: Thiore 26.8 66 0.0014 22.1 2.5 25 115-144 3-27 (76)
46 TIGR03341 YhgI_GntY IscR-regul 26.7 40 0.00087 28.2 1.6 21 165-185 107-128 (190)
47 PF09883 DUF2110: Uncharacteri 26.1 1.3E+02 0.0028 26.4 4.6 51 88-148 12-66 (225)
48 PF02641 DUF190: Uncharacteriz 25.8 96 0.0021 23.0 3.4 27 83-111 73-99 (101)
49 TIGR00532 HMG_CoA_R_NAD hydrox 25.2 5.5E+02 0.012 24.1 8.9 65 84-148 143-215 (393)
50 cd06150 YjgF_YER057c_UK114_lik 24.5 1.5E+02 0.0033 21.6 4.3 52 83-147 27-78 (105)
51 KOG0079 GTP-binding protein H- 23.9 2.6E+02 0.0057 23.6 5.9 72 96-178 36-109 (198)
52 PF10437 Lip_prot_lig_C: Bacte 23.6 2.1E+02 0.0046 20.1 4.8 38 100-142 13-52 (86)
53 cd06154 YjgF_YER057c_UK114_lik 21.9 1.9E+02 0.0041 21.6 4.5 52 83-147 42-93 (119)
54 TIGR03421 FeS_CyaY iron donor 21.8 1.8E+02 0.0038 22.0 4.2 35 86-121 8-42 (102)
55 PF14789 THDPS_M: Tetrahydrodi 21.7 78 0.0017 20.5 1.9 22 91-112 17-38 (41)
56 PRK14461 ribosomal RNA large s 21.7 3.2E+02 0.0069 25.5 6.6 25 151-177 169-193 (371)
57 PRK00453 rpsF 30S ribosomal pr 21.5 1.2E+02 0.0027 22.5 3.3 29 81-109 13-41 (108)
58 cd03377 TPP_PFOR_PNO Thiamine 21.1 37 0.0008 31.5 0.4 14 117-130 3-16 (365)
59 PRK14466 ribosomal RNA large s 21.0 2.1E+02 0.0045 26.3 5.2 50 122-176 116-172 (345)
60 TIGR00595 priA primosomal prot 20.3 1.4E+02 0.0031 28.4 4.2 52 122-177 255-310 (505)
61 PF06183 DinI: DinI-like famil 20.3 2.9E+02 0.0063 19.2 4.7 20 129-148 5-24 (65)
62 PRK09509 fieF ferrous iron eff 20.2 4.3E+02 0.0094 22.9 6.9 21 131-151 261-281 (299)
63 PF10646 Germane: Sporulation 20.1 3.1E+02 0.0066 19.8 5.2 49 108-156 58-109 (117)
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=99.93 E-value=1.4e-25 Score=159.05 Aligned_cols=68 Identities=56% Similarity=0.949 Sum_probs=65.1
Q ss_pred HHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEc
Q 029891 87 IESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESV 154 (186)
Q Consensus 87 V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v 154 (186)
|+++|++|||+|++||||++|+++++++|+|||+|+|+|||++.+||+.+||++|++++|++.+|+++
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 68999999999999999999999999999999999999999999999999999999999999999875
No 2
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=3e-25 Score=166.58 Aligned_cols=77 Identities=55% Similarity=0.890 Sum_probs=73.7
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEe--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCcccc
Q 029891 84 AENIESVLD-EIRPYLISDGGNVALHEID--GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETG 160 (186)
Q Consensus 84 ~e~V~~~Ld-~IRP~L~~dGGdvelv~vd--~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~g 160 (186)
.++|+.+|+ +|||+|++||||++|++|+ +|+|+|||.|+|+|||||.+||+++||++|++.+|++.+|+++.+|..+
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 689999999 7999999999999999999 7899999999999999999999999999999999999999999998665
No 3
>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=99.90 E-value=7.6e-24 Score=176.31 Aligned_cols=78 Identities=40% Similarity=0.685 Sum_probs=75.0
Q ss_pred HHHHHHHHH-HhcchhhhCCCcEEEEEEe-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCccccc
Q 029891 84 AENIESVLD-EIRPYLISDGGNVALHEID-GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETGL 161 (186)
Q Consensus 84 ~e~V~~~Ld-~IRP~L~~dGGdvelv~vd-~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~g~ 161 (186)
.++|+.+|+ +|||+|++||||++|++|+ +++|+|||+|+|+|||++.+||+++||++|++.+|+|++|+.+++|.+|.
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 57999999999999999999999999999999999999999999999983
No 4
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.89 E-value=1.6e-23 Score=174.82 Aligned_cols=79 Identities=34% Similarity=0.646 Sum_probs=75.3
Q ss_pred cHHHHHHHHH-HhcchhhhCCCcEEEEEEe-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCC-CccEEEEccCccc
Q 029891 83 TAENIESVLD-EIRPYLISDGGNVALHEID-GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIP-EIVAVESVADEET 159 (186)
Q Consensus 83 ~~e~V~~~Ld-~IRP~L~~dGGdvelv~vd-~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iP-eI~~V~~v~~~~~ 159 (186)
..++|+.+|+ +|||+||+||||++|++|+ +++|+|||+|+|+|||+|.+||+++||++|++++| +|++|+.+++|.+
T Consensus 107 ~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~~~~ 186 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTEHQR 186 (192)
T ss_pred HHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEeccccc
Confidence 3789999998 7999999999999999998 57999999999999999999999999999999999 9999999999999
Q ss_pred cc
Q 029891 160 GL 161 (186)
Q Consensus 160 g~ 161 (186)
|.
T Consensus 187 ~~ 188 (192)
T PRK11190 187 GE 188 (192)
T ss_pred CC
Confidence 83
No 5
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.4e-23 Score=176.17 Aligned_cols=149 Identities=28% Similarity=0.430 Sum_probs=123.0
Q ss_pred CCCCCCCCCCCCCCccCCC---CCCceeeeeCCe-eEee------cCCccccchhHHHHHHhhccchhhhhhhhcCCCCc
Q 029891 8 PSYSRPHQTLDSPSCSRPA---SKSTKSFFGERV-SLTR------WRNPVCHSSCRLLLIRKRGAARRNVIKAVATPDSA 77 (186)
Q Consensus 8 ~s~~~~~~a~~spLa~~lf---~~v~~~~f~~~~-t~tr------w~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~p~~~ 77 (186)
-+|+++-++..+|||+++| .+|..+||+++| |+++ |.- |++.+++.++++...... .+.+.......+
T Consensus 38 ~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~-L~p~i~~~~sd~g~~g~p-li~g~~~~~~~~ 115 (213)
T KOG2358|consen 38 GDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSV-LDPEIPSLMSDGGNVGLP-LIDGNIVVLKLQ 115 (213)
T ss_pred cccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhh-hchhhHHHHhccccccch-hhccchhhhhhc
Confidence 4677788888999999999 599999999999 9999 998 999999999988433222 222222222221
Q ss_pred ---CCCCCcHHHHHHHHH-HhcchhhhCCCcEEEEEEeC--CEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEE
Q 029891 78 ---IELPLTAENIESVLD-EIRPYLISDGGNVALHEIDG--NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (186)
Q Consensus 78 ---~~~~l~~e~V~~~Ld-~IRP~L~~dGGdvelv~vd~--g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V 151 (186)
.+.+.+...++..|+ +|||.|+.||||++++++|+ |.|++||+|+|.+||++.+||++|||..|+.++|+++.|
T Consensus 116 ~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v 195 (213)
T KOG2358|consen 116 GACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGV 195 (213)
T ss_pred ccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEE
Confidence 112344678999998 69999999999999999997 599999999999999999999999999999999999999
Q ss_pred EEccCcc
Q 029891 152 ESVADEE 158 (186)
Q Consensus 152 ~~v~~~~ 158 (186)
+++.|.+
T Consensus 196 ~qv~d~e 202 (213)
T KOG2358|consen 196 IQVPDAE 202 (213)
T ss_pred EeccCcc
Confidence 9988754
No 6
>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=99.83 E-value=2.2e-20 Score=164.30 Aligned_cols=70 Identities=47% Similarity=0.816 Sum_probs=67.2
Q ss_pred HHHHHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEc
Q 029891 84 AENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESV 154 (186)
Q Consensus 84 ~e~V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v 154 (186)
.++|+++|++|||+|++|||||+|++|++++|+|||+|+|+|||++.+||+. ||++|++++|++..|+++
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 999999999999999875
No 7
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.46 E-value=1.9e-14 Score=121.29 Aligned_cols=121 Identities=45% Similarity=0.496 Sum_probs=113.2
Q ss_pred hhhhhhcCCCCcCCCCCcHHHHHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhC
Q 029891 66 NVIKAVATPDSAIELPLTAENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKI 145 (186)
Q Consensus 66 ~~~~~~~~p~~~~~~~l~~e~V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~i 145 (186)
.+.+....||.-...+++++.+..+|+..+|++.+|||.+-+--+++..+.++++|+|..|+.+.++++++||++||.++
T Consensus 61 gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i 140 (213)
T KOG2358|consen 61 GVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKI 140 (213)
T ss_pred CcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHHHhhhhhh
Confidence 45556666777777788899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccEEEEccCcccccccCHHHHHHHHHhhhhhhhcccCCC
Q 029891 146 PEIVAVESVADEETGLELNEENIEKVLEEIRPYLVGAAANS 186 (186)
Q Consensus 146 PeI~~V~~v~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (186)
||+-.++..-+-++|.+++.+|+|+++.+.+||+.++.+|.
T Consensus 141 ~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gi 181 (213)
T KOG2358|consen 141 QEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGI 181 (213)
T ss_pred hccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhH
Confidence 99999999999999999999999999999999999999884
No 8
>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=98.53 E-value=6e-09 Score=77.07 Aligned_cols=52 Identities=13% Similarity=0.286 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCCCCccCCC--CCCceeeeeCCe-eEee-----cCCccccchhHHHHHHhh
Q 029891 8 PSYSRPHQTLDSPSCSRPA--SKSTKSFFGERV-SLTR-----WRNPVCHSSCRLLLIRKR 60 (186)
Q Consensus 8 ~s~~~~~~a~~spLa~~lf--~~v~~~~f~~~~-t~tr-----w~~~l~~~~~~~~~~~~~ 60 (186)
-+|.+.++|.++|||++|| +||++|||++++ |+|| |+. +++.+...|++++.
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 99999999988753
No 9
>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=96.28 E-value=0.035 Score=38.53 Aligned_cols=68 Identities=24% Similarity=0.373 Sum_probs=51.5
Q ss_pred HHHHHHHHHH-hcchhhhC---CCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEE
Q 029891 84 AENIESVLDE-IRPYLISD---GGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVES 153 (186)
Q Consensus 84 ~e~V~~~Ld~-IRP~L~~d---GGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~ 153 (186)
+++|.++|.. .-|.+..+ =|-|+=+.++++.|+|.+.-...+|+ ....++..|+++|+ .+|++.+|..
T Consensus 1 k~~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 1 KQAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEEE
T ss_pred CHHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEeC
Confidence 3567777764 45655432 37788899999999999999999999 66679999999999 8999988863
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=91.22 E-value=0.4 Score=42.69 Aligned_cols=65 Identities=29% Similarity=0.370 Sum_probs=40.4
Q ss_pred cccCCCCcchHHHHHHHHHHHHHhhCCCc---cEEEEccCcc--cc--cccCH----HHHHHHHHhhhhhhhcccCC
Q 029891 120 QGACGSCPSSVMTMKMGIERRLMEKIPEI---VAVESVADEE--TG--LELNE----ENIEKVLEEIRPYLVGAAAN 185 (186)
Q Consensus 120 ~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI---~~V~~v~~~~--~g--~~~~~----~~~~~~~~~~~~~~~~~~~~ 185 (186)
+++.++|.+..-.++..|+..+.+. +.. .......+|. ++ +.|+. +.|+++|+.|||||..-||.
T Consensus 166 t~agt~CG~C~~~~~~il~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~irP~l~~dGGd 241 (290)
T TIGR02000 166 TKAGGGCGSCHEKIEDVLKEVLANK-GATNPANAGGSKPTNKPNSGQKRPLTNVQRIQLIQKVLEEVRPVLQADGGD 241 (290)
T ss_pred ccCCCCCcchHHHHHHHHHHHHHhc-cccccccccccCcccccccCcchhcChHHHHHHHHHHHHHhCchHhhcCCc
Confidence 4555566666667777777777654 211 1123333332 11 24553 68899999999999988775
No 11
>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=89.25 E-value=3.2 Score=30.36 Aligned_cols=67 Identities=16% Similarity=0.280 Sum_probs=47.5
Q ss_pred HHHHHHHHHH-hcchhhhC---CCcEEEEEEeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE
Q 029891 84 AENIESVLDE-IRPYLISD---GGNVALHEIDG-NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (186)
Q Consensus 84 ~e~V~~~Ld~-IRP~L~~d---GGdvelv~vd~-g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~ 152 (186)
.++|.++|.. .-|.+..+ =|-|.=+.+++ +.|+|.+.-+..+|+.... ++..|+.+|.. +|++..|.
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 KDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGS-MPGEVENAVRA-VPGVGSVT 74 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHH-HHHHHHHHHHh-CCCCceEE
Confidence 4667777775 45655542 24455567775 8899999887778886655 78899998964 78887775
No 12
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=87.85 E-value=1.5 Score=38.58 Aligned_cols=57 Identities=30% Similarity=0.485 Sum_probs=40.5
Q ss_pred EEEEEEcccCCCCcchHHHHHHHHHHHHHhh-------------CCCccEEEEccCcccccccCHHHHHHHHHhhhh
Q 029891 114 VVRLKLQGACGSCPSSVMTMKMGIERRLMEK-------------IPEIVAVESVADEETGLELNEENIEKVLEEIRP 177 (186)
Q Consensus 114 ~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~-------------iPeI~~V~~v~~~~~g~~~~~~~~~~~~~~~~~ 177 (186)
+.++.|. +|+||..|-..|.+.+-..|... +|| ..|..+.+.-. |++++|. +.|+|-
T Consensus 6 va~~~L~-gC~GC~~slldl~E~L~dll~~~div~~~~l~D~keiPE-vDValVEGsV~----~ee~lE~-v~ElRe 75 (247)
T COG1941 6 VATVWLT-GCSGCHMSLLDLYEKLLDLLEDADIVYCPTLVDEKEIPE-VDVALVEGSVC----DEEELEL-VKELRE 75 (247)
T ss_pred EEEEEec-cccchHHHHHhHHHHHHHhhhhhcEEEeecccccccCCc-ccEEEEecccC----cHHHHHH-HHHHHH
Confidence 4556666 49999999999998888877732 777 66767766544 7778874 455553
No 13
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=87.04 E-value=3.3 Score=32.19 Aligned_cols=68 Identities=32% Similarity=0.427 Sum_probs=48.2
Q ss_pred cHHHHHHHHHH-hcchhhhC---CCcEEEEEEeC--CEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE
Q 029891 83 TAENIESVLDE-IRPYLISD---GGNVALHEIDG--NVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (186)
Q Consensus 83 ~~e~V~~~Ld~-IRP~L~~d---GGdvelv~vd~--g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~ 152 (186)
+.++|..+|.. +-|.|--| =|=|.=+++++ +.++|+++..-.|||++.. +...++.+|++ +|.+..|+
T Consensus 13 ~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~-i~~~v~~al~~-~~~v~~v~ 86 (111)
T COG2151 13 TLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEV-IADQVEAALEE-IPGVEDVE 86 (111)
T ss_pred hHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHH-HHHHHHHHHHh-cCCcceEE
Confidence 35677777764 66766433 12233355654 4899999999999999987 66899999886 77676665
No 14
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=83.64 E-value=7.9 Score=32.11 Aligned_cols=78 Identities=15% Similarity=0.213 Sum_probs=56.0
Q ss_pred CCcHHHHHHHHHH-hcchhhhC---CCcEEEEEEeC---C--EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEE
Q 029891 81 PLTAENIESVLDE-IRPYLISD---GGNVALHEIDG---N--VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (186)
Q Consensus 81 ~l~~e~V~~~Ld~-IRP~L~~d---GGdvelv~vd~---g--~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V 151 (186)
+.++++|.++|.. .-|.+..+ =|-|.=+.+++ + .|+|+|.-...+|++... ++..|+.+|.. +|.+.+|
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 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPV-LVEDVEDKVLA-VPNVDEV 149 (174)
T ss_pred cccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHHH-HHHHHHHHHHh-CCCceeE
Confidence 4557889999986 56666542 35565567776 5 899999999999987765 77889998874 7888776
Q ss_pred E--EccCcccc
Q 029891 152 E--SVADEETG 160 (186)
Q Consensus 152 ~--~v~~~~~g 160 (186)
. ...+..|.
T Consensus 150 ~V~l~~dp~W~ 160 (174)
T TIGR03406 150 EVELVFDPPWS 160 (174)
T ss_pred EEEEEecCCCC
Confidence 4 44554444
No 15
>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=75.46 E-value=14 Score=29.83 Aligned_cols=65 Identities=23% Similarity=0.297 Sum_probs=45.0
Q ss_pred CcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE--EccCcccc-cccCHHHHHH
Q 029891 103 GNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE--SVADEETG-LELNEENIEK 170 (186)
Q Consensus 103 Gdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~--~v~~~~~g-~~~~~~~~~~ 170 (186)
|-|.=+.++++.|.|.+.-.-.+||... .|++.|+++|+.. .+..|. ..-.-.+. +.++++--+|
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~~ 82 (146)
T TIGR02159 15 GMVREVDVDGGGVVVKFTPTYSGCPALE-VIRQDIRDAVRAL--GVEVVEVSTSLDPPWTTDWITEDAREK 82 (146)
T ss_pred CCeeEEEEECCEEEEEEEeCCCCCchHH-HHHHHHHHHHHhc--CCCeEEEeEeeCCCCChHHCCHHHHHH
Confidence 6677678888899999998889999776 5889999999874 555443 22222332 4566654443
No 16
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=74.63 E-value=2.4 Score=32.06 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=29.0
Q ss_pred Cceeeee--CCeeEeecCCccccchhHHHHHHhhccchh
Q 029891 29 STKSFFG--ERVSLTRWRNPVCHSSCRLLLIRKRGAARR 65 (186)
Q Consensus 29 v~~~~f~--~~~t~trw~~~l~~~~~~~~~~~~~~~~r~ 65 (186)
|.-+-|- ++.+++|..+ +|..|+++.+|-|.|+++.
T Consensus 33 ve~~~i~~~~g~V~l~l~G-aC~gC~sS~~TLk~gIE~~ 70 (93)
T COG0694 33 VELVGIDEEDGVVYLRLGG-ACSGCPSSTVTLKNGIERQ 70 (93)
T ss_pred EEEEEEecCCCeEEEEeCC-cCCCCcccHHHHHHHHHHH
Confidence 4445555 4468999999 9999999999999998874
No 17
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=71.47 E-value=5.6 Score=32.15 Aligned_cols=26 Identities=19% Similarity=0.482 Sum_probs=20.7
Q ss_pred EEEEEEeCCEEEEEEc--ccCCCCcchH
Q 029891 105 VALHEIDGNVVRLKLQ--GACGSCPSSV 130 (186)
Q Consensus 105 velv~vd~g~V~Vrl~--GaC~gCpss~ 130 (186)
-.+++++++.++|+.. .+|++|.+..
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C~a~~ 33 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSCASRA 33 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCcCCCC
Confidence 4688999998888874 7999998643
No 18
>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=71.45 E-value=4.3 Score=30.81 Aligned_cols=32 Identities=28% Similarity=0.373 Sum_probs=21.3
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCCCc-cEEEEc
Q 029891 122 ACGSCPSSVMTMKMGIERRLMEKIPEI-VAVESV 154 (186)
Q Consensus 122 aC~gCpss~~Tl~~~Ie~~L~~~iPeI-~~V~~v 154 (186)
+|.+=|+|.-|. ++++++|++++|+. -+++=+
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~~f~~~Yi 43 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQPFEFTYI 43 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS-EEEEEE
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCCceEEEEE
Confidence 355557888877 89999999999997 344433
No 19
>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=70.01 E-value=4.5 Score=31.37 Aligned_cols=22 Identities=27% Similarity=0.838 Sum_probs=17.8
Q ss_pred EEEEeCCEEEEEE--cccCCCCcc
Q 029891 107 LHEIDGNVVRLKL--QGACGSCPS 128 (186)
Q Consensus 107 lv~vd~g~V~Vrl--~GaC~gCps 128 (186)
+++++++.++|+. +.+|++|.+
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~ 24 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSA 24 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCC
Confidence 4788999888888 478999973
No 20
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=69.90 E-value=32 Score=26.34 Aligned_cols=33 Identities=15% Similarity=0.306 Sum_probs=19.7
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCccc
Q 029891 122 ACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEET 159 (186)
Q Consensus 122 aC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~ 159 (186)
.|.|||.. .+...++..++. ++..|..-+-...
T Consensus 45 ~CgGCpg~--~~~~~~~~l~~~---~~d~IHlssC~~~ 77 (107)
T PF08821_consen 45 TCGGCPGR--KLVRRIKKLKKN---GADVIHLSSCMVK 77 (107)
T ss_pred eCCCCChh--HHHHHHHHHHHC---CCCEEEEcCCEec
Confidence 49999944 444567776655 3446655444333
No 21
>PRK11670 antiporter inner membrane protein; Provisional
Probab=67.01 E-value=30 Score=31.51 Aligned_cols=69 Identities=12% Similarity=0.055 Sum_probs=51.5
Q ss_pred cHHHHHHHHHH-hcchhhhC---CCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEE
Q 029891 83 TAENIESVLDE-IRPYLISD---GGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVES 153 (186)
Q Consensus 83 ~~e~V~~~Ld~-IRP~L~~d---GGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~ 153 (186)
++++|..+|.. .-|.+..+ =|-|.=+.++++.+++.+.-.-..||.... ++..++++|+. +|++.+|..
T Consensus 13 ~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~ 85 (369)
T PRK11670 13 LRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAFEE-LKEQCSAELLR-ITGAKAIDW 85 (369)
T ss_pred hHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHHHH-HHHHHHHHHHh-cCCCceEEE
Confidence 46888888886 56666553 355655678889999888877678886654 88899999985 788887754
No 22
>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=64.87 E-value=45 Score=26.61 Aligned_cols=45 Identities=13% Similarity=0.090 Sum_probs=33.3
Q ss_pred eCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCc
Q 029891 111 DGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADE 157 (186)
Q Consensus 111 d~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~ 157 (186)
.+..++|-+.=. .. ......++.-|++++++..|.+..|...++.
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 344555555433 22 4666789999999999999999999888774
No 23
>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=63.32 E-value=44 Score=28.13 Aligned_cols=50 Identities=24% Similarity=0.436 Sum_probs=30.8
Q ss_pred CCCcEEEEEEe----CC-----EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE
Q 029891 101 DGGNVALHEID----GN-----VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (186)
Q Consensus 101 dGGdvelv~vd----~g-----~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~ 152 (186)
..|..++.++. +. .++|++.+.+ .......+++.|++.|++++|+|.+|.
T Consensus 217 ~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~~i~~v~ 275 (284)
T PF01545_consen 217 VPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDM--SVEEAHEIRERIEKRLREKFPGIYDVT 275 (284)
T ss_dssp TSS-SEEEEEEEEEETT-EEEEEEEEEETTTS--BHHHHHHHHHHHHHHHHHHSTTCEEEE
T ss_pred CCceEeccceEEEEecCCcEEEEEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCCCcEEEE
Confidence 44544555553 33 3445545554 222344578999999999999998743
No 24
>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=61.61 E-value=15 Score=25.19 Aligned_cols=40 Identities=25% Similarity=0.579 Sum_probs=24.1
Q ss_pred CCcHHHHHHHHHH-hcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHH
Q 029891 81 PLTAENIESVLDE-IRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVM 131 (186)
Q Consensus 81 ~l~~e~V~~~Ld~-IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~ 131 (186)
.++.+.|+..|+. +| -|.|+=++....- .|.|.+|+....
T Consensus 25 ~~s~~~ve~mL~~l~~------kG~I~~~~~~~~~-----~~~C~~C~~~~~ 65 (69)
T PF09012_consen 25 GISPEAVEAMLEQLIR------KGYIRKVDMSSCC-----GGSCSSCGPASK 65 (69)
T ss_dssp T--HHHHHHHHHHHHC------CTSCEEEEEE--S-----SSSSSS-SS---
T ss_pred CcCHHHHHHHHHHHHH------CCcEEEecCCCCC-----CCCCCCCCCccc
Confidence 4457778888875 43 5888877766533 899999998765
No 25
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.04 E-value=30 Score=26.64 Aligned_cols=28 Identities=29% Similarity=0.287 Sum_probs=22.0
Q ss_pred CCCCcchHHHHHHHHHHHHHhhCCCccEE
Q 029891 123 CGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (186)
Q Consensus 123 C~gCpss~~Tl~~~Ie~~L~~~iPeI~~V 151 (186)
|.+-|+|.-|. +|+|.+|++++|+.--+
T Consensus 19 CV~aPtsKdt~-eWLeaalkRKyp~~~F~ 46 (106)
T COG4837 19 CVNAPTSKDTY-EWLEAALKRKYPNQPFK 46 (106)
T ss_pred hcCCCcchhHH-HHHHHHHhccCCCCCcE
Confidence 44447777777 89999999999987544
No 26
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=52.02 E-value=26 Score=28.82 Aligned_cols=54 Identities=24% Similarity=0.358 Sum_probs=35.5
Q ss_pred EEEEEeCCEEEEEE--cccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCcccc
Q 029891 106 ALHEIDGNVVRLKL--QGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETG 160 (186)
Q Consensus 106 elv~vd~g~V~Vrl--~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~g 160 (186)
-+++.++|.+.|+= +-+|++|++...-- ..+..+|-.+-..+-.|+...+-..|
T Consensus 7 ~vv~~q~G~a~V~c~~~S~CgsC~a~~~CG-s~~l~kLg~~~~h~~~~~t~~pL~~G 62 (150)
T COG3086 7 TVVSWQNGQAKVSCQRQSACGSCAARAGCG-SGLLSKLGPQTEHIFRVETDEPLEPG 62 (150)
T ss_pred EEEEccCCeEEEEeeccCccccchhhcccc-hHHHHHhccccceEEEEecCCcCCCC
Confidence 35888899777776 57999999987655 46666663333345666555554444
No 27
>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=48.24 E-value=1.6e+02 Score=25.05 Aligned_cols=103 Identities=13% Similarity=0.124 Sum_probs=60.3
Q ss_pred EeecCCc-cccchhHHHHHHhhccch-hhhhhhhcCCC-------CcCCCCCc----HHHHHHHHHH-hcchhh--hCCC
Q 029891 40 LTRWRNP-VCHSSCRLLLIRKRGAAR-RNVIKAVATPD-------SAIELPLT----AENIESVLDE-IRPYLI--SDGG 103 (186)
Q Consensus 40 ~trw~~~-l~~~~~~~~~~~~~~~~r-~~~~~~~~~p~-------~~~~~~l~----~e~V~~~Ld~-IRP~L~--~dGG 103 (186)
++.|..- +--.++.++.++.+.++. |+..+...... .......+ .+++...|+. --+-.. ..++
T Consensus 90 ~lEW~s~~~nDmiADsv~a~il~~~ssp~svk~~~~~~~h~h~~~~~~~~~~~~~~~~~~l~~~L~~qFG~~~~~~~~~~ 169 (216)
T PF11718_consen 90 VLEWESSPVNDMIADSVVAVILQIDSSPASVKLSSKSCSHSHSHDPNPHEKSDEEERLERLIELLEAQFGDVEVPDIEKP 169 (216)
T ss_pred EEEEcCCcchhHHHHHHHHHHHHHhhCCccccccccccccccccccccccccCHHHHHHHHHHHHHHHcCCCcccccccc
Confidence 3347652 566678888888877664 44443333321 00000111 2345555542 333322 2344
Q ss_pred cE-EEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhh
Q 029891 104 NV-ALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEK 144 (186)
Q Consensus 104 dv-elv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~ 144 (186)
.. -.+.+++..+.|.|.--..-|. +..|++.||.+|++-
T Consensus 170 ~~~~~v~vd~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~ 209 (216)
T PF11718_consen 170 KEPLSVTVDGKVAHIDLSTLEVECE--DEPLKQRVETALKRL 209 (216)
T ss_pred ceeEEEEeCCcEEEEecCCCceecC--CHHHHHHHHHHHHHH
Confidence 44 4567778899999988888888 678999999998863
No 28
>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=47.31 E-value=25 Score=23.17 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=21.9
Q ss_pred cccCCCCcchHHHHHHHHHHHHHhhC
Q 029891 120 QGACGSCPSSVMTMKMGIERRLMEKI 145 (186)
Q Consensus 120 ~GaC~gCpss~~Tl~~~Ie~~L~~~i 145 (186)
.++|.|||--+-+|.+.|-..||+-+
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~gw 32 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDGW 32 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHHH
Confidence 47999999877888899999998754
No 29
>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=45.22 E-value=44 Score=23.39 Aligned_cols=24 Identities=29% Similarity=0.728 Sum_probs=19.3
Q ss_pred CCCCcchHHHHHHHHHHHHHhhCCCc
Q 029891 123 CGSCPSSVMTMKMGIERRLMEKIPEI 148 (186)
Q Consensus 123 C~gCpss~~Tl~~~Ie~~L~~~iPeI 148 (186)
|.+|...... ..+.++|+..||+.
T Consensus 6 C~~C~y~~Ra--~~l~q~L~~~Fp~~ 29 (72)
T TIGR02174 6 CGSCGYKPRA--AWLKQELLEEFPDL 29 (72)
T ss_pred CCCCCChHHH--HHHHHHHHHHCCCC
Confidence 7777766555 58999999999985
No 30
>PRK14464 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=40.91 E-value=39 Score=30.95 Aligned_cols=71 Identities=18% Similarity=0.185 Sum_probs=40.6
Q ss_pred CCCcEEEEEEeCCEEEEEEccc----CCCCcchHH------HHHHHHHHHHH-hhCCCccEEEEccCcccccccCHHHHH
Q 029891 101 DGGNVALHEIDGNVVRLKLQGA----CGSCPSSVM------TMKMGIERRLM-EKIPEIVAVESVADEETGLELNEENIE 169 (186)
Q Consensus 101 dGGdvelv~vd~g~V~Vrl~Ga----C~gCpss~~------Tl~~~Ie~~L~-~~iPeI~~V~~v~~~~~g~~~~~~~~~ 169 (186)
||-.||-|-+...++.|--+.. |..|....+ +..+.+++.+. ...|.|..|+. ++.|++| .|.+
T Consensus 84 Dg~~iEtV~i~~~t~CvSsQvGC~~~C~FC~tg~~g~~RnLs~~EI~~Qv~~~~~~~~i~nIVf---mGmGEPl--~N~d 158 (344)
T PRK14464 84 DGQMVESVLLPRDGLCVSTQVGCAVGCVFCMTGRSGLLRQLGSAEIVAQVVLARRRRAVKKVVF---MGMGEPA--HNLD 158 (344)
T ss_pred CCCEEEEEEecCCcEEEEccCCcCCCCCcCcCCCCCCCCCCCHHHHHHHHHHHHhcCCCCEEEE---eccCccc--CCHH
Confidence 5556666666656677766654 567766543 34444554432 12466666655 4556666 3566
Q ss_pred HHHHhhh
Q 029891 170 KVLEEIR 176 (186)
Q Consensus 170 ~~~~~~~ 176 (186)
+++..++
T Consensus 159 ~vl~ai~ 165 (344)
T PRK14464 159 NVLEAID 165 (344)
T ss_pred HHHHHHH
Confidence 6666644
No 31
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=40.76 E-value=64 Score=24.16 Aligned_cols=59 Identities=25% Similarity=0.463 Sum_probs=42.0
Q ss_pred CcHHHHHHHHH-HhcchhhhCCCcEEEEEEeCC--------EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE
Q 029891 82 LTAENIESVLD-EIRPYLISDGGNVALHEIDGN--------VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (186)
Q Consensus 82 l~~e~V~~~Ld-~IRP~L~~dGGdvelv~vd~g--------~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~ 152 (186)
.++++++..|. .|.|.. +++.|+.+| +|.=.|.|.| ...=...|..+|++.+++|..-.
T Consensus 3 ~~e~~l~~~L~~~l~p~~------v~V~D~SgGCG~~F~v~IvS~~FeGKs------~L~rHRlVN~~L~Eeik~iHalt 70 (85)
T KOG3348|consen 3 VTEERLEELLTEALEPEH------VEVQDVSGGCGSMFDVVIVSAAFEGKS------LLARHRLVNSILAEEIKEIHALT 70 (85)
T ss_pred chHHHHHHHHHhhcCceE------EEEEEcCCCccceEEEEEEccccCChH------HHHHHHHHHHHHHHHHHHHhhhe
Confidence 46788999997 588875 788888764 3444677876 12223578899999888886655
No 32
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=40.70 E-value=1.1e+02 Score=28.35 Aligned_cols=55 Identities=16% Similarity=0.211 Sum_probs=32.7
Q ss_pred cCCCCcch------HHHHHHHHHHHHHhh--CCC------ccEEEEccCccccccc-CHHHHHHHHHhhh
Q 029891 122 ACGSCPSS------VMTMKMGIERRLMEK--IPE------IVAVESVADEETGLEL-NEENIEKVLEEIR 176 (186)
Q Consensus 122 aC~gCpss------~~Tl~~~Ie~~L~~~--iPe------I~~V~~v~~~~~g~~~-~~~~~~~~~~~~~ 176 (186)
.|..|... ..|..+.+++.+... +.. -..|.-+.=++.|++| |-+|+-+.++.++
T Consensus 134 ~C~FCatg~~g~~RnLt~~EIv~Qv~~~~~~~~~~~~~~~~~~i~nVvfmGmGEPLlN~d~V~~~i~~l~ 203 (373)
T PRK14459 134 ACPFCATGQGGLTRNLSTAEIVEQVRAAARALRDGEVPGGPGRLSNVVFMGMGEPLANYKRVVAAVRRIT 203 (373)
T ss_pred cCCCCCCCCCCCCCccCHHHHHHHHHHHHHHhhhcccccCCCceeEEEEecCCcchhhHHHHHHHHHHHh
Confidence 47777644 256667777766432 111 0224333335568888 6888888887775
No 33
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=39.69 E-value=1.5e+02 Score=21.87 Aligned_cols=49 Identities=24% Similarity=0.298 Sum_probs=30.7
Q ss_pred chHHHHHHHHHHHHHhhCCCccEEEEccCcccc--cccCHHHHHHHHHhhhhh
Q 029891 128 SSVMTMKMGIERRLMEKIPEIVAVESVADEETG--LELNEENIEKVLEEIRPY 178 (186)
Q Consensus 128 ss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~g--~~~~~~~~~~~~~~~~~~ 178 (186)
.+-.+|...|..+|+-. |+-..+ ...+.++| .++++++.|.+++..+.+
T Consensus 21 ~~y~~L~~ki~~kLkl~-~e~i~L-sYkde~s~~~v~l~d~dle~aws~~~~~ 71 (80)
T cd06406 21 LSYATLLQKISSKLELP-AEHITL-SYKSEASGEDVILSDTNMEDVWSQAKDG 71 (80)
T ss_pred CCHHHHHHHHHHHhCCC-chhcEE-EeccCCCCCccCcChHHHHHHHHhhcCC
Confidence 45567777777777632 333222 33333443 467999999999887754
No 34
>PF15092 UPF0728: Uncharacterised protein family UPF0728
Probab=36.70 E-value=58 Score=24.52 Aligned_cols=30 Identities=37% Similarity=0.633 Sum_probs=25.7
Q ss_pred HHhcchhhhCCCcEEEEEEeC-CEEEEEEcc
Q 029891 92 DEIRPYLISDGGNVALHEIDG-NVVRLKLQG 121 (186)
Q Consensus 92 d~IRP~L~~dGGdvelv~vd~-g~V~Vrl~G 121 (186)
+-++-.|+.+|-.|+|..+++ +.|.+-+.|
T Consensus 28 ~GLqa~L~~dGh~v~L~~~~d~n~vel~vng 58 (88)
T PF15092_consen 28 EGLQAVLAKDGHEVILEKIEDWNVVELVVNG 58 (88)
T ss_pred HHHHHHHHhCCcEEEEEEeccccEEEEEECC
Confidence 446888999999999999986 788888877
No 35
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.09 E-value=1.3e+02 Score=19.88 Aligned_cols=60 Identities=18% Similarity=0.139 Sum_probs=36.6
Q ss_pred HHHHhcchhhhCCCcEEEEEEe---CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEc
Q 029891 90 VLDEIRPYLISDGGNVALHEID---GNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESV 154 (186)
Q Consensus 90 ~Ld~IRP~L~~dGGdvelv~vd---~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v 154 (186)
.|.+|--.|..+|.++..+... ++...++|.=.- ......+ ..|-.+|+. +|+|.+|+.+
T Consensus 13 ~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v---~~~~~~l-~~l~~~L~~-i~~V~~v~~~ 75 (76)
T cd04888 13 VLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDT---STMNGDI-DELLEELRE-IDGVEKVELV 75 (76)
T ss_pred hHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEc---CchHHHH-HHHHHHHhc-CCCeEEEEEe
Confidence 3455566678899999988763 355555554221 1111134 566666774 8888888764
No 36
>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=35.53 E-value=49 Score=24.93 Aligned_cols=26 Identities=12% Similarity=0.110 Sum_probs=15.5
Q ss_pred chhhhCCCcEEEEEEeC--CEEEEEEccc
Q 029891 96 PYLISDGGNVALHEIDG--NVVRLKLQGA 122 (186)
Q Consensus 96 P~L~~dGGdvelv~vd~--g~V~Vrl~Ga 122 (186)
-.++.+| +|.+|++.. ...+|||..+
T Consensus 20 ~~f~~~g-~V~yVD~~~G~~~g~VRf~~~ 47 (105)
T PF08777_consen 20 EAFSQFG-EVAYVDFSRGDTEGYVRFKTP 47 (105)
T ss_dssp HHT-SS---EEEEE--TT-SEEEEEESS-
T ss_pred HHHHhcC-CcceEEecCCCCEEEEEECCc
Confidence 3444444 999999974 4999999976
No 37
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=35.16 E-value=23 Score=29.81 Aligned_cols=21 Identities=38% Similarity=0.615 Sum_probs=17.9
Q ss_pred HHHHHHHHH-hhhhhhhcccCC
Q 029891 165 EENIEKVLE-EIRPYLVGAAAN 185 (186)
Q Consensus 165 ~~~~~~~~~-~~~~~~~~~~~~ 185 (186)
.+.|+.+|+ +|||||..-||.
T Consensus 108 ~~~i~~~l~~~irP~l~~dGGd 129 (192)
T PRK11190 108 MERVEYVLQSQINPQLAGHGGR 129 (192)
T ss_pred HHHHHHHHHhccChhHHhcCCc
Confidence 568999997 999999987774
No 38
>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=33.36 E-value=44 Score=22.68 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=19.0
Q ss_pred HHHHHHHHHhcchhhhCCCcEEEE
Q 029891 85 ENIESVLDEIRPYLISDGGNVALH 108 (186)
Q Consensus 85 e~V~~~Ld~IRP~L~~dGGdvelv 108 (186)
+..++..+.+.|.|+.+||.+-+.
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 566788889999999999987655
No 39
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=32.58 E-value=66 Score=23.87 Aligned_cols=29 Identities=14% Similarity=0.203 Sum_probs=24.7
Q ss_pred CCcHHHHHHHHHHhcchhhhCCCcEEEEE
Q 029891 81 PLTAENIESVLDEIRPYLISDGGNVALHE 109 (186)
Q Consensus 81 ~l~~e~V~~~Ld~IRP~L~~dGGdvelv~ 109 (186)
.+++++++.+++++.-.|...||.+.-++
T Consensus 17 ~l~e~~~~~~~~~~~~~i~~~gg~i~~~~ 45 (97)
T CHL00123 17 DLNEEELLKWIENYKKLLRKRGAKNISVQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 45789999999999999999999875444
No 40
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=32.36 E-value=1.4e+02 Score=21.94 Aligned_cols=46 Identities=17% Similarity=0.375 Sum_probs=29.0
Q ss_pred chHHHHHHHHHHHHHhhCCCcc---EEEEccCccccccc------CHHHHHHHHHhh
Q 029891 128 SSVMTMKMGIERRLMEKIPEIV---AVESVADEETGLEL------NEENIEKVLEEI 175 (186)
Q Consensus 128 ss~~Tl~~~Ie~~L~~~iPeI~---~V~~v~~~~~g~~~------~~~~~~~~~~~~ 175 (186)
.+...|..-+.++|...||+.. +|..- ..+|+.+ .-+.|+..|.++
T Consensus 16 ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~--s~n~lsv~g~~k~dK~~i~eiLqE~ 70 (81)
T PRK10597 16 GAIDALAGELSRRIQYAFPDNEGHVSVRYA--AANNLSVIGATKEDKDRISEILQET 70 (81)
T ss_pred hHHHHHHHHHHHHHHhhCCCCCccEEEeec--CCCceEecCCCcchHHHHHHHHHHH
Confidence 4556688899999999999984 44432 2233221 234566666665
No 41
>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=30.77 E-value=1.5e+02 Score=24.71 Aligned_cols=37 Identities=19% Similarity=0.270 Sum_probs=24.5
Q ss_pred EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEE
Q 029891 114 VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVE 152 (186)
Q Consensus 114 ~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~ 152 (186)
.+.|.+.+.++-.- .-.+...||+.+++++|++..|.
T Consensus 226 ~~~v~v~~~~~~~~--ah~i~~~i~~~i~~~~~~v~~v~ 262 (268)
T TIGR01297 226 DVHVVVDPDLDLKQ--AHDIALEIEREILKRHPGIEHVT 262 (268)
T ss_pred EEEEEECCCCChhH--HHHHHHHHHHHHHHhcCCCCeEE
Confidence 45566666653222 23455789999999999997775
No 42
>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=28.45 E-value=93 Score=21.71 Aligned_cols=37 Identities=24% Similarity=0.522 Sum_probs=25.9
Q ss_pred EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCC-ccEEEEcc
Q 029891 114 VVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPE-IVAVESVA 155 (186)
Q Consensus 114 ~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPe-I~~V~~v~ 155 (186)
.|.|.| |.+|.....- ..+++.|...+|+ +.+|....
T Consensus 2 ~V~IeY---C~~C~~~~~a--~~l~~~l~~~fp~~~~~v~~~~ 39 (76)
T PF10262_consen 2 KVTIEY---CTSCGYRPRA--LELAQELLQTFPDRIAEVELSP 39 (76)
T ss_dssp EEEEEE---ETTTTCHHHH--HHHHHHHHHHSTTTCSEEEEEE
T ss_pred EEEEEE---CCCCCCHHHH--HHHHHHHHHHCCCcceEEEEEe
Confidence 456666 6677766654 5899999999998 45665443
No 43
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=28.15 E-value=1.2e+02 Score=19.50 Aligned_cols=25 Identities=24% Similarity=0.611 Sum_probs=17.3
Q ss_pred ccCCCCcchHHHHHHHHHHHHHhhCCCccEEEE
Q 029891 121 GACGSCPSSVMTMKMGIERRLMEKIPEIVAVES 153 (186)
Q Consensus 121 GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~ 153 (186)
-.|.+|. ..|+++|+. +|+|..|..
T Consensus 7 m~C~~C~-------~~v~~~l~~-~~GV~~v~v 31 (62)
T PF00403_consen 7 MTCEGCA-------KKVEKALSK-LPGVKSVKV 31 (62)
T ss_dssp TTSHHHH-------HHHHHHHHT-STTEEEEEE
T ss_pred cccHHHH-------HHHHHHHhc-CCCCcEEEE
Confidence 3566662 467787875 799988864
No 44
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=27.37 E-value=1.4e+02 Score=23.65 Aligned_cols=52 Identities=17% Similarity=0.330 Sum_probs=29.6
Q ss_pred cHHHHHHHH-HHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEE
Q 029891 83 TAENIESVL-DEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAV 151 (186)
Q Consensus 83 ~~e~V~~~L-d~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V 151 (186)
++.+|-+.| +++..-....+|.|.+.. -.-.|.+|. .|=...+..+|.|+.-
T Consensus 76 sE~KiL~~ia~~l~~~~~~~~G~i~l~t---------e~~pC~SC~--------~vi~qF~~~~pni~~~ 128 (133)
T PF14424_consen 76 SEYKILEDIAKKLGDNPDPSGGTIDLFT---------ELPPCESCS--------NVIEQFKKDFPNIKVN 128 (133)
T ss_pred HHHHHHHHHHHHhccccccCCceEEEEe---------cCCcChhHH--------HHHHHHHHHCCCcEEE
Confidence 344544444 456554444456655433 235898883 3344477889998643
No 45
>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=26.79 E-value=66 Score=22.10 Aligned_cols=25 Identities=16% Similarity=0.448 Sum_probs=16.1
Q ss_pred EEEEEcccCCCCcchHHHHHHHHHHHHHhh
Q 029891 115 VRLKLQGACGSCPSSVMTMKMGIERRLMEK 144 (186)
Q Consensus 115 V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~ 144 (186)
++| |+-.|..|+ .+...++..+.+.
T Consensus 3 I~v-~~~~C~~C~----~~~~~~~~~~~~~ 27 (76)
T PF13192_consen 3 IKV-FSPGCPYCP----ELVQLLKEAAEEL 27 (76)
T ss_dssp EEE-ECSSCTTHH----HHHHHHHHHHHHT
T ss_pred EEE-eCCCCCCcH----HHHHHHHHHHHhc
Confidence 566 665688887 3446667766654
No 46
>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=26.69 E-value=40 Score=28.19 Aligned_cols=21 Identities=43% Similarity=0.615 Sum_probs=17.4
Q ss_pred HHHHHHHHH-hhhhhhhcccCC
Q 029891 165 EENIEKVLE-EIRPYLVGAAAN 185 (186)
Q Consensus 165 ~~~~~~~~~-~~~~~~~~~~~~ 185 (186)
.+.|+.+|+ +|||||.--||.
T Consensus 107 ~~~i~~~l~~~irP~l~~dGGd 128 (190)
T TIGR03341 107 EERINYVLQSEINPQLASHGGK 128 (190)
T ss_pred HHHHHHHHHhccCHHHHhcCCc
Confidence 458999997 899999987764
No 47
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.06 E-value=1.3e+02 Score=26.35 Aligned_cols=51 Identities=27% Similarity=0.369 Sum_probs=39.7
Q ss_pred HHHHHHhcchhhhCCCcEEE---EEE-eCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCc
Q 029891 88 ESVLDEIRPYLISDGGNVAL---HEI-DGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEI 148 (186)
Q Consensus 88 ~~~Ld~IRP~L~~dGGdvel---v~v-d~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI 148 (186)
++.|++++-.++++=||+++ +++ +++.+.|++.|.-. ..=...|++.|.+|
T Consensus 12 ~r~ld~L~~~v~n~lgdLdV~~~i~~~~~~wv~vtl~GeD~----------eva~Nll~eefGei 66 (225)
T PF09883_consen 12 ERALDSLRSLVENDLGDLDVEWDIGITKDDWVKVTLEGEDE----------EVAANLLREEFGEI 66 (225)
T ss_pred HHHHHHHHHHHHHhhcCeeEEEEeccccCCceEEEEecCcH----------HHHHHHHHHHhCCC
Confidence 78899999999999898886 333 36899999999851 24456788888877
No 48
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=25.85 E-value=96 Score=23.00 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=20.6
Q ss_pred cHHHHHHHHHHhcchhhhCCCcEEEEEEe
Q 029891 83 TAENIESVLDEIRPYLISDGGNVALHEID 111 (186)
Q Consensus 83 ~~e~V~~~Ld~IRP~L~~dGGdvelv~vd 111 (186)
++++++++|+++++.++. |-|.+-+++
T Consensus 73 ~~eki~~~l~~l~~~~~~--glit~~~v~ 99 (101)
T PF02641_consen 73 TEEKIEAFLPELKELVKD--GLITLEDVE 99 (101)
T ss_dssp EHHHHHHHHHHHCTT-SS--SEEEEEEEE
T ss_pred CHHHHHHHHHHHHHHcCC--CEEEEEEEE
Confidence 489999999999999976 766665543
No 49
>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=25.24 E-value=5.5e+02 Score=24.12 Aligned_cols=65 Identities=14% Similarity=0.134 Sum_probs=42.5
Q ss_pred HHHHHHHHHHhcchhhhCCCcEEEEEE------eCCEEEEEEcccCCCCcchH--HHHHHHHHHHHHhhCCCc
Q 029891 84 AENIESVLDEIRPYLISDGGNVALHEI------DGNVVRLKLQGACGSCPSSV--MTMKMGIERRLMEKIPEI 148 (186)
Q Consensus 84 ~e~V~~~Ld~IRP~L~~dGGdvelv~v------d~g~V~Vrl~GaC~gCpss~--~Tl~~~Ie~~L~~~iPeI 148 (186)
.+++.++.++.-|.+...||.+.-+.. .++.++|||.--|.-=..+. .+..+.+-..|.+.+|.-
T Consensus 143 ~~~i~~~a~~~~~~~~~rggg~~~i~~r~~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~Eav~~~i~~~~~~~ 215 (393)
T TIGR00532 143 GDEIIERAEECDPMLNNLGGGCKDIEARVIDIIEGGILILHIIVDTCDAMGANALNSIAEKVAEFIELEFGGE 215 (393)
T ss_pred HHHHHHHHHHhCHHHHhhcCCeEEEEEEeeecccCCEEEEEEEEecccccccHHHHHHHHHHHHHHHHhCCCc
Confidence 456777777889999999998775553 35689999975442111122 234456666777788763
No 50
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=24.48 E-value=1.5e+02 Score=21.57 Aligned_cols=52 Identities=15% Similarity=0.164 Sum_probs=35.7
Q ss_pred cHHHHHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCC
Q 029891 83 TAENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPE 147 (186)
Q Consensus 83 ~~e~V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPe 147 (186)
.+++.+.+++.|+-.|+..|++.+ ++++++..=. ++.-...+.+...+.|++
T Consensus 27 ~~~Q~~~~~~nl~~~L~~~G~~~~------dvvk~~vyl~-------d~~~~~~~~~~~~~~f~~ 78 (105)
T cd06150 27 ITGQTRQVLAKIDALLAEAGSDKS------RILSATIWLA-------DMADFAAMNAVWDAWVPP 78 (105)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHH------HEEEEEEEEc-------cHHHHHHHHHHHHHHcCC
Confidence 378999999999999999999875 4555544311 123335666667777764
No 51
>KOG0079 consensus GTP-binding protein H-ray, small G protein superfamily [General function prediction only]
Probab=23.92 E-value=2.6e+02 Score=23.56 Aligned_cols=72 Identities=24% Similarity=0.311 Sum_probs=48.7
Q ss_pred chhhhCCCcEEE--EEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccEEEEccCcccccccCHHHHHHHHH
Q 029891 96 PYLISDGGNVAL--HEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPEIVAVESVADEETGLELNEENIEKVLE 173 (186)
Q Consensus 96 P~L~~dGGdvel--v~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~~~~g~~~~~~~~~~~~~ 173 (186)
.|+---|=|..+ ++|.|..|.+.+--.- =++...+++...+-.-..|..+.|-.+|+-|| |+.+-|+
T Consensus 36 sYitTiGvDfkirTv~i~G~~VkLqIwDtA---------GqErFrtitstyyrgthgv~vVYDVTn~ESF~--Nv~rWLe 104 (198)
T KOG0079|consen 36 SYITTIGVDFKIRTVDINGDRVKLQIWDTA---------GQERFRTITSTYYRGTHGVIVVYDVTNGESFN--NVKRWLE 104 (198)
T ss_pred ceEEEeeeeEEEEEeecCCcEEEEEEeecc---------cHHHHHHHHHHHccCCceEEEEEECcchhhhH--hHHHHHH
Confidence 344444555544 5556778888775431 23566666777777788888888877777765 7888899
Q ss_pred hhhhh
Q 029891 174 EIRPY 178 (186)
Q Consensus 174 ~~~~~ 178 (186)
+||.-
T Consensus 105 ei~~n 109 (198)
T KOG0079|consen 105 EIRNN 109 (198)
T ss_pred HHHhc
Confidence 99864
No 52
>PF10437 Lip_prot_lig_C: Bacterial lipoate protein ligase C-terminus; InterPro: IPR019491 This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with IPR004143 from INTERPRO, further upstream. This C-terminal domain is more stable than IPR004143 from INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues. ; PDB: 1X2G_A 3A7R_A 3A7A_A 1X2H_C 1VQZ_A 3R07_C.
Probab=23.61 E-value=2.1e+02 Score=20.10 Aligned_cols=38 Identities=16% Similarity=0.233 Sum_probs=25.6
Q ss_pred hCCCcEEE-EEEeCC-EEEEEEcccCCCCcchHHHHHHHHHHHHH
Q 029891 100 SDGGNVAL-HEIDGN-VVRLKLQGACGSCPSSVMTMKMGIERRLM 142 (186)
Q Consensus 100 ~dGGdvel-v~vd~g-~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~ 142 (186)
-.||.|++ +.|++| +-.+++.|-|-+... + ..++.+|+
T Consensus 13 f~~G~v~v~~~V~~G~I~~i~i~gDf~~~~~----i-~~le~~L~ 52 (86)
T PF10437_consen 13 FPWGTVEVHLNVKNGIIKDIKIYGDFFGPED----I-EELEEALI 52 (86)
T ss_dssp ETTEEEEEEEEEETTEEEEEEEEECBS-CCC----H-HHHHHHHT
T ss_pred cCCceEEEEEEEECCEEEEEEEECCCCCchH----H-HHHHHHHH
Confidence 46888887 677777 567999998865522 2 45666664
No 53
>cd06154 YjgF_YER057c_UK114_like_6 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=21.89 E-value=1.9e+02 Score=21.59 Aligned_cols=52 Identities=19% Similarity=0.233 Sum_probs=35.9
Q ss_pred cHHHHHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCC
Q 029891 83 TAENIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQGACGSCPSSVMTMKMGIERRLMEKIPE 147 (186)
Q Consensus 83 ~~e~V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~GaC~gCpss~~Tl~~~Ie~~L~~~iPe 147 (186)
..++.+.+++.|+-.|+..|++. +++++++..=.+ .. .+ ..+.+.+++.|++
T Consensus 42 ~~~Q~~~~~~ni~~~L~~aG~~~------~dVvk~~vyl~d----~~--~~-~~~~~~~~~~f~~ 93 (119)
T cd06154 42 AYEQTRQCLEIIEAALAEAGASL------EDVVRTRMYVTD----IA--DF-EAVGRAHGEVFGD 93 (119)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCH------HHEEEEEEEECC----HH--HH-HHHHHHHHHHcCC
Confidence 37899999999999999999885 446666554332 11 22 3566677777765
No 54
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=21.85 E-value=1.8e+02 Score=22.02 Aligned_cols=35 Identities=23% Similarity=0.360 Sum_probs=21.6
Q ss_pred HHHHHHHHhcchhhhCCCcEEEEEEeCCEEEEEEcc
Q 029891 86 NIESVLDEIRPYLISDGGNVALHEIDGNVVRLKLQG 121 (186)
Q Consensus 86 ~V~~~Ld~IRP~L~~dGGdvelv~vd~g~V~Vrl~G 121 (186)
.++..|+.|.-.|...+.|++ ++..+|+++|.+..
T Consensus 8 ~ad~~l~~ie~~ld~~~~d~D-~e~~~gVLti~f~~ 42 (102)
T TIGR03421 8 LAEALLDAIEEAIDDADADID-CERAGGVLTLTFEN 42 (102)
T ss_pred HHHHHHHHHHHHHhccCCCee-eecCCCEEEEEECC
Confidence 455555666666655566654 23348899998853
No 55
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=21.67 E-value=78 Score=20.50 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=14.2
Q ss_pred HHHhcchhhhCCCcEEEEEEeC
Q 029891 91 LDEIRPYLISDGGNVALHEIDG 112 (186)
Q Consensus 91 Ld~IRP~L~~dGGdvelv~vd~ 112 (186)
+++.|..++..|+.+++.+||.
T Consensus 17 ~~~~r~~lr~~g~~~~V~~VDK 38 (41)
T PF14789_consen 17 FEENRLRLRARGRPLTVYSVDK 38 (41)
T ss_dssp HHHHHHHHHHTT----EEEEES
T ss_pred HHHHHHHHHhCCCCcEEEEEcC
Confidence 3456888999998999999874
No 56
>PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.67 E-value=3.2e+02 Score=25.49 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=16.4
Q ss_pred EEEccCcccccccCHHHHHHHHHhhhh
Q 029891 151 VESVADEETGLELNEENIEKVLEEIRP 177 (186)
Q Consensus 151 V~~v~~~~~g~~~~~~~~~~~~~~~~~ 177 (186)
|.-+.=++.|++|. |.++++..|+=
T Consensus 169 i~NIVfMGMGEPL~--NydnV~~ai~i 193 (371)
T PRK14461 169 VTNLVFMGMGEPFA--NYDRWWQAVER 193 (371)
T ss_pred eeeEEEEccCCchh--hHHHHHHHHHH
Confidence 44444467888864 77777777763
No 57
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=21.49 E-value=1.2e+02 Score=22.49 Aligned_cols=29 Identities=17% Similarity=0.487 Sum_probs=24.8
Q ss_pred CCcHHHHHHHHHHhcchhhhCCCcEEEEE
Q 029891 81 PLTAENIESVLDEIRPYLISDGGNVALHE 109 (186)
Q Consensus 81 ~l~~e~V~~~Ld~IRP~L~~dGGdvelv~ 109 (186)
.+++++++.+++.+...|...||.+.-++
T Consensus 13 ~~~~~~~~~~~~~~~~~i~~~gg~i~~~~ 41 (108)
T PRK00453 13 DLSEEQVKALVERFKGVITENGGTIHKVE 41 (108)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCEEEEEe
Confidence 35789999999999999999999876554
No 58
>cd03377 TPP_PFOR_PNO Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The PFOR from cyanobacterium Anabaena (NifJ) is required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gra
Probab=21.11 E-value=37 Score=31.51 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=11.3
Q ss_pred EEEcccCCCCcchH
Q 029891 117 LKLQGACGSCPSSV 130 (186)
Q Consensus 117 Vrl~GaC~gCpss~ 130 (186)
+.|.|+|.||+-..
T Consensus 3 ~ef~gACaGCget~ 16 (365)
T cd03377 3 FEFSGACAGCGETP 16 (365)
T ss_pred ccccccCCCCchHH
Confidence 56899999998654
No 59
>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.02 E-value=2.1e+02 Score=26.27 Aligned_cols=50 Identities=16% Similarity=0.258 Sum_probs=28.3
Q ss_pred cCCCCcchH------HHHHHHHHHHHHh-hCCCccEEEEccCcccccccCHHHHHHHHHhhh
Q 029891 122 ACGSCPSSV------MTMKMGIERRLME-KIPEIVAVESVADEETGLELNEENIEKVLEEIR 176 (186)
Q Consensus 122 aC~gCpss~------~Tl~~~Ie~~L~~-~iPeI~~V~~v~~~~~g~~~~~~~~~~~~~~~~ 176 (186)
.|..|.... .|..+.+++.+.- ....+..|+. ++.|++| .|.+.+++.++
T Consensus 116 ~C~FC~Tg~~g~~rnLt~~EIl~Qv~~~~~~~~i~nIvf---mGmGEPL--~N~d~vi~al~ 172 (345)
T PRK14466 116 NCLFCMTGKQGFTGNLTAAQILNQIYSLPERDKLTNLVF---MGMGEPL--DNLDEVLKALE 172 (345)
T ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCeEEE---eeeCcCc--ccHHHHHHHHH
Confidence 677777554 4555556654432 1123444443 4558787 47777777665
No 60
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.34 E-value=1.4e+02 Score=28.38 Aligned_cols=52 Identities=17% Similarity=0.268 Sum_probs=31.2
Q ss_pred cCCCCcchHHHH----HHHHHHHHHhhCCCccEEEEccCcccccccCHHHHHHHHHhhhh
Q 029891 122 ACGSCPSSVMTM----KMGIERRLMEKIPEIVAVESVADEETGLELNEENIEKVLEEIRP 177 (186)
Q Consensus 122 aC~gCpss~~Tl----~~~Ie~~L~~~iPeI~~V~~v~~~~~g~~~~~~~~~~~~~~~~~ 177 (186)
.|..|.+..... .+.++..|++.||+..-...-.+...... ..++.++.++.
T Consensus 255 ~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~----~~~~~l~~f~~ 310 (505)
T TIGR00595 255 TCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKG----AHEALLNQFAN 310 (505)
T ss_pred CCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCcc----HHHHHHHHHhc
Confidence 577776643221 26889999999999765555555433332 34445555543
No 61
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=20.28 E-value=2.9e+02 Score=19.24 Aligned_cols=20 Identities=15% Similarity=0.448 Sum_probs=14.7
Q ss_pred hHHHHHHHHHHHHHhhCCCc
Q 029891 129 SVMTMKMGIERRLMEKIPEI 148 (186)
Q Consensus 129 s~~Tl~~~Ie~~L~~~iPeI 148 (186)
+...|..-+.++|...||+.
T Consensus 5 a~~AL~~EL~kRl~~~yPd~ 24 (65)
T PF06183_consen 5 ALEALESELTKRLHRQYPDA 24 (65)
T ss_dssp HHHHHHHHHHHHHHHH-SS-
T ss_pred HHHHHHHHHHHHHHHHCCCc
Confidence 34567788899999999994
No 62
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=20.21 E-value=4.3e+02 Score=22.90 Aligned_cols=21 Identities=14% Similarity=0.319 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHhhCCCccEE
Q 029891 131 MTMKMGIERRLMEKIPEIVAV 151 (186)
Q Consensus 131 ~Tl~~~Ie~~L~~~iPeI~~V 151 (186)
-.+.+.||++|++++|++...
T Consensus 261 h~i~~~ie~~l~~~~~~~~v~ 281 (299)
T PRK09509 261 HMIADQVEQALLRRFPGSDVI 281 (299)
T ss_pred HHHHHHHHHHHHHhCCCCEEE
Confidence 346688999999999986533
No 63
>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=20.14 E-value=3.1e+02 Score=19.82 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=32.2
Q ss_pred EEEe-CCEEEEEEcccCC--CCcchHHHHHHHHHHHHHhhCCCccEEEEccC
Q 029891 108 HEID-GNVVRLKLQGACG--SCPSSVMTMKMGIERRLMEKIPEIVAVESVAD 156 (186)
Q Consensus 108 v~vd-~g~V~Vrl~GaC~--gCpss~~Tl~~~Ie~~L~~~iPeI~~V~~v~~ 156 (186)
+.++ +++++|.|...=. .=.+...-+...|-..|.+.+++|.+|...-+
T Consensus 58 v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i~vd 109 (117)
T PF10646_consen 58 VTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVKKVQILVD 109 (117)
T ss_pred EEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCccEEEEEEC
Confidence 4445 4599999976332 12223344557777888888999999986543
Done!