Query 023823
Match_columns 276
No_of_seqs 206 out of 1252
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 06:54:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023823.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023823hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2358 NifU-like domain-conta 100.0 1.2E-46 2.5E-51 331.7 7.6 203 71-275 7-212 (213)
2 PF08712 Nfu_N: Scaffold prote 100.0 5.1E-31 1.1E-35 206.2 8.2 87 77-163 1-87 (87)
3 COG0694 Thioredoxin-like prote 99.9 2.4E-27 5.2E-32 187.5 9.9 86 183-268 6-91 (93)
4 TIGR03341 YhgI_GntY IscR-regul 99.9 1E-23 2.2E-28 186.3 10.1 82 183-265 102-183 (190)
5 PF01106 NifU: NifU-like domai 99.9 1.4E-23 3E-28 157.2 8.1 68 191-261 1-68 (68)
6 PRK11190 Fe/S biogenesis prote 99.9 1.7E-23 3.7E-28 185.2 9.8 83 183-266 103-186 (192)
7 TIGR02000 NifU_proper Fe-S clu 99.8 7.1E-19 1.5E-23 164.5 12.4 73 185-261 218-290 (290)
8 KOG2358 NifU-like domain-conta 97.9 5E-06 1.1E-10 74.5 1.4 76 189-267 80-155 (213)
9 PF01883 DUF59: Domain of unkn 96.5 0.02 4.3E-07 42.4 8.1 67 189-259 2-71 (72)
10 COG2151 PaaD Predicted metal-s 94.3 0.36 7.7E-06 39.8 8.6 76 185-262 11-89 (111)
11 TIGR02945 SUF_assoc FeS assemb 93.6 0.4 8.8E-06 37.5 7.5 73 187-261 2-76 (99)
12 TIGR03406 FeS_long_SufT probab 89.3 2.3 5.1E-05 37.4 8.3 75 185-261 72-152 (174)
13 PRK11670 antiporter inner memb 67.8 28 0.00061 33.8 8.4 72 187-262 13-87 (369)
14 PF10646 Germane: Sporulation 67.6 29 0.00063 27.2 7.1 80 183-265 22-111 (117)
15 PF02061 Lambda_CIII: Lambda P 66.1 7.2 0.00016 26.9 2.7 25 227-251 7-31 (45)
16 TIGR02159 PA_CoA_Oxy4 phenylac 63.9 28 0.0006 29.8 6.7 48 208-260 15-62 (146)
17 PF01545 Cation_efflux: Cation 53.2 74 0.0016 28.7 8.0 77 184-265 203-281 (284)
18 PRK10862 SoxR reducing system 49.0 22 0.00048 30.5 3.6 24 211-236 7-32 (154)
19 PF11718 CPSF73-100_C: Pre-mRN 47.1 2.2E+02 0.0048 25.7 12.4 114 135-252 89-210 (216)
20 PF08821 CGGC: CGGC domain; I 47.0 49 0.0011 26.9 5.2 23 229-253 45-67 (107)
21 PF09012 FeoC: FeoC like trans 44.5 27 0.00058 25.5 3.0 38 185-239 29-66 (69)
22 PF04246 RseC_MucC: Positive r 43.2 22 0.00049 29.3 2.7 20 213-234 2-23 (135)
23 PF01264 Chorismate_synt: Chor 42.8 17 0.00036 35.6 2.1 33 100-136 214-246 (346)
24 COG1941 FrhG Coenzyme F420-red 42.1 42 0.00092 31.4 4.5 29 222-251 7-35 (247)
25 PF07315 DUF1462: Protein of u 41.0 38 0.00083 27.1 3.5 27 229-256 11-37 (93)
26 cd07304 Chorismate_synthase Ch 38.9 23 0.00049 34.7 2.4 36 100-139 216-251 (344)
27 PF13192 Thioredoxin_3: Thiore 37.9 52 0.0011 24.2 3.8 25 222-251 3-27 (76)
28 PRK05382 chorismate synthase; 37.2 25 0.00054 34.6 2.4 37 100-140 214-250 (359)
29 PF01883 DUF59: Domain of unkn 35.4 1.5E+02 0.0033 21.3 5.9 46 116-161 17-62 (72)
30 PRK12463 chorismate synthase; 35.2 33 0.00072 34.1 2.9 37 102-141 235-271 (390)
31 PHA02782 hypothetical protein; 34.2 83 0.0018 31.9 5.4 57 185-250 369-428 (503)
32 PLN02754 chorismate synthase 34.0 29 0.00063 34.7 2.3 30 111-140 256-285 (413)
33 TIGR00033 aroC chorismate synt 29.9 33 0.00072 33.6 1.9 29 111-139 222-250 (351)
34 PF00403 HMA: Heavy-metal-asso 28.8 1.8E+02 0.0039 20.0 5.1 40 114-153 15-57 (62)
35 COG3086 RseC Positive regulato 26.1 74 0.0016 27.7 3.1 30 218-248 12-43 (150)
36 COG2946 Putative phage replica 26.0 1.4E+02 0.0031 29.4 5.5 52 209-265 117-172 (377)
37 PRK11702 hypothetical protein; 25.2 2.6E+02 0.0056 23.0 6.0 65 184-261 35-100 (108)
38 PRK09509 fieF ferrous iron eff 23.8 4.3E+02 0.0092 24.5 8.1 76 184-264 211-286 (299)
39 COG4837 Uncharacterized protei 23.1 1.3E+02 0.0028 24.5 3.8 27 229-256 18-44 (106)
40 TIGR01297 CDF cation diffusion 23.0 4.6E+02 0.01 23.4 8.0 75 185-264 191-267 (268)
41 PF08141 SspH: Small acid-solu 23.0 1.6E+02 0.0035 21.5 4.0 41 188-228 3-43 (58)
42 TIGR03820 lys_2_3_AblA lysine- 22.0 2.7E+02 0.0059 27.9 6.7 54 116-170 178-252 (417)
43 PRK11023 outer membrane lipopr 21.5 5.6E+02 0.012 22.5 8.9 118 126-262 70-187 (191)
44 TIGR02174 CXXU_selWTH selT/sel 21.5 1.5E+02 0.0033 21.9 3.8 24 230-255 6-29 (72)
45 PF08777 RRM_3: RNA binding mo 21.3 75 0.0016 25.4 2.2 33 188-229 15-47 (105)
46 PRK05473 hypothetical protein; 20.5 1.7E+02 0.0036 23.3 3.9 55 142-206 17-84 (86)
47 cd03009 TryX_like_TryX_NRX Try 20.3 1.3E+02 0.0029 23.7 3.5 50 204-256 5-55 (131)
48 PF09961 DUF2195: Uncharacteri 20.2 2.1E+02 0.0046 24.0 4.7 56 189-252 24-86 (121)
49 cd04888 ACT_PheB-BS C-terminal 20.1 3.2E+02 0.0069 19.1 5.3 53 202-260 20-74 (76)
50 COG0082 AroC Chorismate syntha 20.0 57 0.0012 32.2 1.5 37 111-147 227-268 (369)
No 1
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-46 Score=331.73 Aligned_cols=203 Identities=51% Similarity=0.767 Sum_probs=187.3
Q ss_pred cceeEEEEeeCCCCCCceeEeCCcccC-CCcceecCChhhhcCcHHHhcccCCC-CeeEEEEeCCeEEEEecCC-CChhh
Q 023823 71 QRRTMFIQTQPTPNPSSLMFYPGKPVM-EVGSADFPNARAAMNSPLAKSLYGVD-GITRVFFGSDFITVTKSED-TSWDL 147 (276)
Q Consensus 71 ~~R~m~I~~E~TPNPn~LKF~p~~~l~-~~gs~~F~~~~~A~~sPLA~~LF~i~-gV~sVfi~~dFITVtK~~~-~dW~~ 147 (276)
++| |+||++.||||+++||+|+.+++ ..+..+|.+...+..+|||+++|.++ ||++||+++|||||+|..+ ..|..
T Consensus 7 a~r-~~i~t~~tPn~~Sl~f~p~~~i~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~ 85 (213)
T KOG2358|consen 7 AAR-MFIQTQITPNPSSLLFLPGKQILSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSV 85 (213)
T ss_pred hhh-hcccccCCCCcccccccCCCcccccccccccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhh
Confidence 677 99999999999999999999998 67888999988889999999999887 8999999999999999888 89999
Q ss_pred hHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCCchHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEec
Q 023823 148 LKPEIFAAIMDFYSSGQPLFLDSETAAAKDTAINEDDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQ 227 (276)
Q Consensus 148 Lkp~I~~~I~DflsSG~PVv~e~~~~~~~~~~~~~~~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~ 227 (276)
|+|+|...++|+++.|+|++.+.......+. +.+++.++...|+++|+++|||.|+.||||++|+++|.+.|+|+++|+
T Consensus 86 L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~-~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklq 164 (213)
T KOG2358|consen 86 LDPEIPSLMSDGGNVGLPLIDGNIVVLKLQG-ACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQ 164 (213)
T ss_pred hchhhHHHHhccccccchhhccchhhhhhcc-cccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHh
Confidence 9999999999999999999988755333332 456788999999999999999999999999999999976789999999
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecCCcchHHHhhccCC
Q 023823 228 GACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDEVATLAGQM 275 (276)
Q Consensus 228 GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~~~~~~~~~~~~~~ 275 (276)
|+|.+||++.+||++|||+||++|+|+||.|+++.|+|+++.+++..+
T Consensus 165 gact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv~d~e~~~v~~e~~~ 212 (213)
T KOG2358|consen 165 GACTECPSSLVTLKNGIENMLEIYVPEVKGVIQVPDAEVMTVTVELTK 212 (213)
T ss_pred hhhccCCcccchhhhhHHHHHHhhcceeeEEEeccCccceEEeeeccc
Confidence 999999999999999999999999999999999999999988877654
No 2
>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=99.97 E-value=5.1e-31 Score=206.19 Aligned_cols=87 Identities=49% Similarity=0.877 Sum_probs=71.2
Q ss_pred EEeeCCCCCCceeEeCCcccCCCcceecCChhhhcCcHHHhcccCCCCeeEEEEeCCeEEEEecCCCChhhhHHHHHHHH
Q 023823 77 IQTQPTPNPSSLMFYPGKPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAAI 156 (276)
Q Consensus 77 I~~E~TPNPn~LKF~p~~~l~~~gs~~F~~~~~A~~sPLA~~LF~i~gV~sVfi~~dFITVtK~~~~dW~~Lkp~I~~~I 156 (276)
||+|+|||||+|||+++++++++|+++|++.++|..+|||++||+|+||++||+++|||||+|.++++|++|+++|+++|
T Consensus 1 I~~e~TPNPn~lKF~~~~~~~~~~s~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~~~~W~~l~~~I~~~I 80 (87)
T PF08712_consen 1 IQIEPTPNPNALKFVLDEPLLPGGSFEFKSAEEASDSPLAQALFAIPGVKSVFIGDDFITVTKNPDADWEDLKPEIREVI 80 (87)
T ss_dssp EEEEE-SSSSEEEEEESS-SSTS---EEESSS-TTS-HHHHHHHTSTTEEEEEEETTEEEEEE-TTS-HHHHHHHHHHHT
T ss_pred CEeecCCCcccEEEECCceeecCccEEeCChHHcccCHHHHHhcCCCCEeEEEEECCEEEEeeCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcC
Q 023823 157 MDFYSSG 163 (276)
Q Consensus 157 ~DflsSG 163 (276)
++||++|
T Consensus 81 ~~~l~sG 87 (87)
T PF08712_consen 81 MEFLESG 87 (87)
T ss_dssp H------
T ss_pred hhhccCC
Confidence 9999887
No 3
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=2.4e-27 Score=187.52 Aligned_cols=86 Identities=50% Similarity=0.820 Sum_probs=81.2
Q ss_pred CchHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecC
Q 023823 183 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 262 (276)
Q Consensus 183 ~~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~ 262 (276)
.++++.++|+++|+++|||+|++|||||+|++|++.+|+|+|||+|||+|||||++|||++||++|++++|+|++|++++
T Consensus 6 ~~~~~~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~ 85 (93)
T COG0694 6 TDAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVT 85 (93)
T ss_pred ccHHHHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEcc
Confidence 46789999999999999999999999999999998789999999999999999999999999999999999999999999
Q ss_pred CcchHH
Q 023823 263 DAEDEV 268 (276)
Q Consensus 263 ~~~~~~ 268 (276)
++.+++
T Consensus 86 ~~~~~~ 91 (93)
T COG0694 86 EHARGE 91 (93)
T ss_pred Cccccc
Confidence 876543
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=99.90 E-value=1e-23 Score=186.29 Aligned_cols=82 Identities=32% Similarity=0.605 Sum_probs=77.4
Q ss_pred CchHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecC
Q 023823 183 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 262 (276)
Q Consensus 183 ~~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~ 262 (276)
+++++.++|+++|+++|||+|++|||||+|+++++ +++|+|||+|+|+|||+|.+||+++||++|++++|||++|+.++
T Consensus 102 ~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~-~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~~ 180 (190)
T TIGR03341 102 DDAPLEERINYVLQSEINPQLASHGGKVTLVEITD-DGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDAT 180 (190)
T ss_pred cchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcC-CCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEec
Confidence 46679999999999999999999999999999984 57999999999999999999999999999999999999999998
Q ss_pred Ccc
Q 023823 263 DAE 265 (276)
Q Consensus 263 ~~~ 265 (276)
|+.
T Consensus 181 ~~~ 183 (190)
T TIGR03341 181 DHT 183 (190)
T ss_pred Ccc
Confidence 875
No 5
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=99.89 E-value=1.4e-23 Score=157.23 Aligned_cols=68 Identities=56% Similarity=0.909 Sum_probs=63.7
Q ss_pred HHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 191 IKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 191 I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
|+++|++ |||+|++|||||+|++++ +++|+|+|+|+|+|||++.+||+++||++|++++|+++.|+.+
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 VEEVLEE-IRPYLQSDGGDVELVDVD--DGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHH-CHHHHHHTTEEEEEEEEE--TTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHH-hChHHHhcCCcEEEEEec--CCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 6889997 999999999999999999 5699999999999999999999999999999999999999864
No 6
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.89 E-value=1.7e-23 Score=185.18 Aligned_cols=83 Identities=30% Similarity=0.590 Sum_probs=77.9
Q ss_pred CchHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCC-CcceEeec
Q 023823 183 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVP-EVKSVEQE 261 (276)
Q Consensus 183 ~~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vP-eV~~V~~~ 261 (276)
+++++.++|+++|+++|||+|++|||||+|+++++ +|+|+|||+|||+|||+|.+||+++||++|++++| +|++|+++
T Consensus 103 ~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~-~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v 181 (192)
T PRK11190 103 DDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITE-DGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDL 181 (192)
T ss_pred ccHHHHHHHHHHHHhccChhHHhcCCcEEEEEEcC-CCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEe
Confidence 46679999999999999999999999999999984 58999999999999999999999999999999999 99999999
Q ss_pred CCcch
Q 023823 262 LDAED 266 (276)
Q Consensus 262 ~~~~~ 266 (276)
+++..
T Consensus 182 ~~~~~ 186 (192)
T PRK11190 182 TEHQR 186 (192)
T ss_pred ccccc
Confidence 88764
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=99.79 E-value=7.1e-19 Score=164.46 Aligned_cols=73 Identities=37% Similarity=0.636 Sum_probs=68.2
Q ss_pred hHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 185 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
.+..++|+++| ++|||+|++|||||+|++|+ +|+|+|||+|+|+|||++.+||++ ||++|++++|++..|+.+
T Consensus 218 ~~~~~~v~~~l-~~irP~l~~dGGdv~lv~v~--~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 218 VQRIQLIQKVL-EEVRPVLQADGGDVELYDVD--GKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred HHHHHHHHHHH-HHhCchHhhcCCcEEEEEEe--CCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 45678999999 58999999999999999998 689999999999999999999998 999999999999999864
No 8
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=97.86 E-value=5e-06 Score=74.52 Aligned_cols=76 Identities=28% Similarity=0.393 Sum_probs=68.7
Q ss_pred HHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecCCcchH
Q 023823 189 AMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDE 267 (276)
Q Consensus 189 ~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~~~~~~ 267 (276)
+....+|+ .++|++-+|||+.-+--++ +..+.+.++|+|..||.+++++|.+||..||..+||.-.+++..+.|+.
T Consensus 80 e~~w~~L~-p~i~~~~sd~g~~g~pli~--g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g 155 (213)
T KOG2358|consen 80 ENVWSVLD-PEIPSLMSDGGNVGLPLID--GNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETG 155 (213)
T ss_pred hhhHhhhc-hhhHHHHhccccccchhhc--cchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCc
Confidence 46677887 6999999999999998887 5688999999999999999999999999999999999999998877774
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=96.52 E-value=0.02 Score=42.35 Aligned_cols=67 Identities=24% Similarity=0.431 Sum_probs=52.6
Q ss_pred HHHHHHHHhcCCcchhcC---CCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEe
Q 023823 189 AMIKELLETRIRPAVQDD---GGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVE 259 (276)
Q Consensus 189 ~~I~~vL~~~IrP~l~~d---GGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~ 259 (276)
+.|.++|.+-.-|.+..+ =|-|.=+.++ +|.|+|.|.-.+.+|| ....|++.|++.|+ .+|+|++|.
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~--~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~gv~~V~ 71 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIE--GGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVK 71 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEEC--TCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEE--CCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEe
Confidence 578888888888888665 3667777776 7999999999999999 55579999999999 899999886
No 10
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=94.30 E-value=0.36 Score=39.77 Aligned_cols=76 Identities=34% Similarity=0.460 Sum_probs=55.7
Q ss_pred hHHHHHHHHHHHhcCCcchhcCC---CcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 185 SETVAMIKELLETRIRPAVQDDG---GDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~dG---GdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
.++.++|.+.|..-+-|.|--|= |=|.=+.++.++|.++|.|...-.|||++.. +.+-++++|++ +|.|+.|+..
T Consensus 11 ~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~-i~~~v~~al~~-~~~v~~v~V~ 88 (111)
T COG2151 11 KVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEV-IADQVEAALEE-IPGVEDVEVE 88 (111)
T ss_pred hhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHH-HHHHHHHHHHh-cCCcceEEEE
Confidence 45678888889888999995542 2223333443256899999999999999996 66789999887 6668877765
Q ss_pred C
Q 023823 262 L 262 (276)
Q Consensus 262 ~ 262 (276)
+
T Consensus 89 l 89 (111)
T COG2151 89 L 89 (111)
T ss_pred E
Confidence 3
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=93.58 E-value=0.4 Score=37.52 Aligned_cols=73 Identities=25% Similarity=0.368 Sum_probs=52.1
Q ss_pred HHHHHHHHHHhcCCcchhcCCCcEEEE-EEecCC-CEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 187 TVAMIKELLETRIRPAVQDDGGDIEYR-GFDPET-GTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 187 l~~~I~~vL~~~IrP~l~~dGGdIelv-~~d~~~-g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
+.+.|.++|..-.-|.+..+-.+..++ ++..++ |.|+|.+.-...+||.... |++.|+..|.. +|++..|...
T Consensus 2 ~~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~~-l~~~i~~al~~-l~gv~~v~v~ 76 (99)
T TIGR02945 2 LKDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGS-MPGEVENAVRA-VPGVGSVTVE 76 (99)
T ss_pred HHHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHH-HHHHHHHHHHh-CCCCceEEEE
Confidence 357788999888888887653333333 233334 7899999888888887664 88889999965 7888877654
No 12
>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=89.27 E-value=2.3 Score=37.45 Aligned_cols=75 Identities=23% Similarity=0.296 Sum_probs=56.9
Q ss_pred hHHHHHHHHHHHhcCCcchhcC---CCcEEEEEEec---CCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceE
Q 023823 185 SETVAMIKELLETRIRPAVQDD---GGDIEYRGFDP---ETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSV 258 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~d---GGdIelv~~d~---~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V 258 (276)
+...++|.++|.+-.-|.+..+ =|-|.=+.++. +++.|+|.|.-...+|++.. .|++.|+.+|.. +|.|++|
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 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGP-VLVEDVEDKVLA-VPNVDEV 149 (174)
T ss_pred cccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHH-HHHHHHHHHHHh-CCCceeE
Confidence 3446889999998889988765 35565556664 12389999999999999877 478889999974 7888877
Q ss_pred eec
Q 023823 259 EQE 261 (276)
Q Consensus 259 ~~~ 261 (276)
...
T Consensus 150 ~V~ 152 (174)
T TIGR03406 150 EVE 152 (174)
T ss_pred EEE
Confidence 654
No 13
>PRK11670 antiporter inner membrane protein; Provisional
Probab=67.80 E-value=28 Score=33.84 Aligned_cols=72 Identities=14% Similarity=0.155 Sum_probs=53.8
Q ss_pred HHHHHHHHHHhcCCcchhcC---CCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecC
Q 023823 187 TVAMIKELLETRIRPAVQDD---GGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 262 (276)
Q Consensus 187 l~~~I~~vL~~~IrP~l~~d---GGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~ 262 (276)
..+.|.+.|..-+-|.+..+ -|-|.=+.++ ++.|++.+.-.-.+||... .++..+++.|+. +|++++|....
T Consensus 13 ~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~ 87 (369)
T PRK11670 13 LRAMVAGTLANFQHPTLKHNLTTLKALHHVALL--DDTLHIELVMPFVWNSAFE-ELKEQCSAELLR-ITGAKAIDWKL 87 (369)
T ss_pred hHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEe--CCEEEEEEEECCCCchHHH-HHHHHHHHHHHh-cCCCceEEEEE
Confidence 45788889988888888775 3445444555 6788888876666888766 488899999986 78888777544
No 14
>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=67.60 E-value=29 Score=27.19 Aligned_cols=80 Identities=20% Similarity=0.264 Sum_probs=49.1
Q ss_pred CchHHHHHHHHHHHhc-------CCcchhcCCCcEEEEEEecC-CCEEEEEeccCCC--CCcchHHHHHHHHHHHHHHhC
Q 023823 183 DDSETVAMIKELLETR-------IRPAVQDDGGDIEYRGFDPE-TGTVKLRMQGACS--GCPSSSVTLKSGIENMLMHYV 252 (276)
Q Consensus 183 ~~~el~~~I~~vL~~~-------IrP~l~~dGGdIelv~~d~~-~g~V~Vrl~GaC~--gCpss~~TLk~~Ie~~L~~~v 252 (276)
.++...+.++.++... .++.+ -.++++.++..+ +++++|.|..+=. .=.+...-+.+.|-..|.+.+
T Consensus 22 ~~~~~~~~v~~L~~gp~~~~~~~~~~~~---p~~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~ 98 (117)
T PF10646_consen 22 EEDDAEAAVNALLKGPSDSEGPGLRSAL---PPGTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQF 98 (117)
T ss_pred CchHHHHHHHHHHhCCCccccceeeecC---CCccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhc
Confidence 3455667777777653 22222 344555454433 4599999976332 122224456677888888899
Q ss_pred CCcceEeecCCcc
Q 023823 253 PEVKSVEQELDAE 265 (276)
Q Consensus 253 PeV~~V~~~~~~~ 265 (276)
++|+.|....|..
T Consensus 99 ~~v~~V~i~vdG~ 111 (117)
T PF10646_consen 99 PGVKKVQILVDGK 111 (117)
T ss_pred CCccEEEEEECCE
Confidence 9999999866554
No 15
>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=66.06 E-value=7.2 Score=26.92 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.1
Q ss_pred ccCCCCCcchHHHHHHHHHHHHHHh
Q 023823 227 QGACSGCPSSSVTLKSGIENMLMHY 251 (276)
Q Consensus 227 ~GaC~gCpss~~TLk~~Ie~~L~~~ 251 (276)
+++|.|||.-+..|.+.|-..|+.-
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~g 31 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDG 31 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHH
Confidence 5899999988888999999999874
No 16
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=63.92 E-value=28 Score=29.83 Aligned_cols=48 Identities=25% Similarity=0.448 Sum_probs=36.6
Q ss_pred CcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEee
Q 023823 208 GDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQ 260 (276)
Q Consensus 208 GdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~ 260 (276)
|-|.=+.++ ++.|.|.|.-.-.|||... .|++.|++.|+.. .+..|+.
T Consensus 15 G~Vr~V~v~--gd~V~VtIt~Ty~gcpa~e-~L~~~I~~aL~~~--Gv~~V~V 62 (146)
T TIGR02159 15 GMVREVDVD--GGGVVVKFTPTYSGCPALE-VIRQDIRDAVRAL--GVEVVEV 62 (146)
T ss_pred CCeeEEEEE--CCEEEEEEEeCCCCCchHH-HHHHHHHHHHHhc--CCCeEEE
Confidence 556555666 5688899988889999877 6889999999884 5665544
No 17
>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=53.16 E-value=74 Score=28.71 Aligned_cols=77 Identities=17% Similarity=0.299 Sum_probs=43.9
Q ss_pred chHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCC--EEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 184 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETG--TVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 184 ~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g--~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
+++..+++++.+++ .|.+..- .++.+..+..+.- .++|++.+.+ .....-.+.+.|++.|++++|+|.+|...
T Consensus 203 ~~~~~~~i~~~i~~--~~~v~~v-~~~~~~~~g~~~~~v~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~~i~~v~I~ 277 (284)
T PF01545_consen 203 DPELVEKIRRIIES--VPGVIEV-HDLRVWQVGRNKYVVEIHVQVDPDM--SVEEAHEIRERIEKRLREKFPGIYDVTIH 277 (284)
T ss_dssp HHHHHHHHHHHHHH--TSS-SEE-EEEEEEEETT-EEEEEEEEEETTTS--BHHHHHHHHHHHHHHHHHHSTTCEEEEEE
T ss_pred cccchhHHHHhhcc--CCceEec-cceEEEEecCCcEEEEEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCCCcEEEEEE
Confidence 45667888888864 2322110 1233333321011 2455555655 22334557899999999999999986655
Q ss_pred CCcc
Q 023823 262 LDAE 265 (276)
Q Consensus 262 ~~~~ 265 (276)
.+++
T Consensus 278 ~~p~ 281 (284)
T PF01545_consen 278 IEPD 281 (284)
T ss_dssp EEEC
T ss_pred EEec
Confidence 4443
No 18
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=48.99 E-value=22 Score=30.53 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=17.5
Q ss_pred EEEEEecCCCEEEEEe--ccCCCCCcch
Q 023823 211 EYRGFDPETGTVKLRM--QGACSGCPSS 236 (276)
Q Consensus 211 elv~~d~~~g~V~Vrl--~GaC~gCpss 236 (276)
.++.+| ++.++|+. +.+|++|.+.
T Consensus 7 ~Vv~v~--~~~a~Ve~~r~saCg~C~a~ 32 (154)
T PRK10862 7 TVVSWQ--NGIALLRCEVKAGCSSCASR 32 (154)
T ss_pred EEEEEE--CCEEEEEEecCCCCcCcCCC
Confidence 456666 67888776 5899999864
No 19
>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=47.06 E-value=2.2e+02 Score=25.73 Aligned_cols=114 Identities=18% Similarity=0.212 Sum_probs=69.4
Q ss_pred EEEEecCCCChhhhHHHHHHHHHHHHhcCCCCcccchhhh-----hccccCCCCchHHHHHHHHHHHhcCCcchhcC--C
Q 023823 135 ITVTKSEDTSWDLLKPEIFAAIMDFYSSGQPLFLDSETAA-----AKDTAINEDDSETVAMIKELLETRIRPAVQDD--G 207 (276)
Q Consensus 135 ITVtK~~~~dW~~Lkp~I~~~I~DflsSG~PVv~e~~~~~-----~~~~~~~~~~~el~~~I~~vL~~~IrP~l~~d--G 207 (276)
|+++=..+.-=+.+...|.+.|.+.-.+...+-....... ........+.....+++..+|+..-.+....+ +
T Consensus 89 v~lEW~s~~~nDmiADsv~a~il~~~ssp~svk~~~~~~~h~h~~~~~~~~~~~~~~~~~~l~~~L~~qFG~~~~~~~~~ 168 (216)
T PF11718_consen 89 VVLEWESSPVNDMIADSVVAVILQIDSSPASVKLSSKSCSHSHSHDPNPHEKSDEEERLERLIELLEAQFGDVEVPDIEK 168 (216)
T ss_pred EEEEEcCCcchhHHHHHHHHHHHHHhhCCccccccccccccccccccccccccCHHHHHHHHHHHHHHHcCCCccccccc
Confidence 4444333333345677777777776655443332221100 00111123456678889999998888874443 4
Q ss_pred CcE-EEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhC
Q 023823 208 GDI-EYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYV 252 (276)
Q Consensus 208 GdI-elv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~v 252 (276)
|.. -.+.+| +..+.|.+..-..-|. +..|++.||..|++-.
T Consensus 169 ~~~~~~v~vd--~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~~ 210 (216)
T PF11718_consen 169 PKEPLSVTVD--GKVAHIDLSTLEVECE--DEPLKQRVETALKRLH 210 (216)
T ss_pred cceeEEEEeC--CcEEEEecCCCceecC--CHHHHHHHHHHHHHHH
Confidence 553 334455 6788999988778888 6679999999998743
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=46.97 E-value=49 Score=26.86 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=15.7
Q ss_pred CCCCCcchHHHHHHHHHHHHHHhCC
Q 023823 229 ACSGCPSSSVTLKSGIENMLMHYVP 253 (276)
Q Consensus 229 aC~gCpss~~TLk~~Ie~~L~~~vP 253 (276)
.|.|||.. .+...++.+++..+.
T Consensus 45 ~CgGCpg~--~~~~~~~~l~~~~~d 67 (107)
T PF08821_consen 45 TCGGCPGR--KLVRRIKKLKKNGAD 67 (107)
T ss_pred eCCCCChh--HHHHHHHHHHHCCCC
Confidence 69999944 455677777765543
No 21
>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=44.53 E-value=27 Score=25.48 Aligned_cols=38 Identities=26% Similarity=0.471 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHH
Q 023823 185 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVT 239 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~T 239 (276)
+.+...++.++. -|.|+-+.... .. .|.|.+|+.....
T Consensus 29 ~~ve~mL~~l~~----------kG~I~~~~~~~-~~------~~~C~~C~~~~~~ 66 (69)
T PF09012_consen 29 EAVEAMLEQLIR----------KGYIRKVDMSS-CC------GGSCSSCGPASKE 66 (69)
T ss_dssp HHHHHHHHHHHC----------CTSCEEEEEE---S------SSSSSS-SS----
T ss_pred HHHHHHHHHHHH----------CCcEEEecCCC-CC------CCCCCCCCCcccc
Confidence 445555555544 58888765542 22 8999999987653
No 22
>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=43.16 E-value=22 Score=29.26 Aligned_cols=20 Identities=20% Similarity=0.564 Sum_probs=14.5
Q ss_pred EEEecCCCEEEEEe--ccCCCCCc
Q 023823 213 RGFDPETGTVKLRM--QGACSGCP 234 (276)
Q Consensus 213 v~~d~~~g~V~Vrl--~GaC~gCp 234 (276)
+.++ ++.++|+. +.+|++|.
T Consensus 2 v~v~--~~~~~V~~~r~saC~~C~ 23 (135)
T PF04246_consen 2 VAVE--GGIAWVEVQRSSACGSCS 23 (135)
T ss_pred EEEe--CCEEEEEEccCCcCcccC
Confidence 4455 67888877 58888887
No 23
>PF01264 Chorismate_synt: Chorismate synthase; InterPro: IPR000453 Chorismate synthase (4.2.3.5 from EC) catalyzes the last of the seven steps in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows a high degree of sequence conservation [, ]. It is a protein of about 360 to 400 amino-acid residues.; GO: 0004107 chorismate synthase activity, 0009073 aromatic amino acid family biosynthetic process; PDB: 4ECD_B 1Q1L_D 1QXO_A 1UMF_B 1UM0_D 1SQ1_A 2O12_A 2O11_A 1ZTB_A 2QHF_A ....
Probab=42.78 E-value=17 Score=35.62 Aligned_cols=33 Identities=30% Similarity=0.520 Sum_probs=26.0
Q ss_pred cceecCChhhhcCcHHHhcccCCCCeeEEEEeCCeEE
Q 023823 100 GSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFIT 136 (276)
Q Consensus 100 gs~~F~~~~~A~~sPLA~~LF~i~gV~sVfi~~dFIT 136 (276)
|+.-|++. .+-||++||.|+.||.|.||..|=.
T Consensus 214 G~p~fdkL----da~la~al~sIpAvKgvEfG~Gf~~ 246 (346)
T PF01264_consen 214 GSPVFDKL----DARLAQALMSIPAVKGVEFGDGFEA 246 (346)
T ss_dssp SBSSCCSH----HHHHHHHHHTSTTEEEEEETTGGGG
T ss_pred CCCCcCcH----HHHHHHHhhCCCCeeeEEecCcHHH
Confidence 34336643 4789999999999999999988753
No 24
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=42.06 E-value=42 Score=31.37 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=23.3
Q ss_pred EEEEeccCCCCCcchHHHHHHHHHHHHHHh
Q 023823 222 VKLRMQGACSGCPSSSVTLKSGIENMLMHY 251 (276)
Q Consensus 222 V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~ 251 (276)
.++.| ++|+||-.|-.-|..++-..|..+
T Consensus 7 a~~~L-~gC~GC~~slldl~E~L~dll~~~ 35 (247)
T COG1941 7 ATVWL-TGCSGCHMSLLDLYEKLLDLLEDA 35 (247)
T ss_pred EEEEe-ccccchHHHHHhHHHHHHHhhhhh
Confidence 44555 569999999999999998888844
No 25
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=40.96 E-value=38 Score=27.15 Aligned_cols=27 Identities=30% Similarity=0.433 Sum_probs=19.3
Q ss_pred CCCCCcchHHHHHHHHHHHHHHhCCCcc
Q 023823 229 ACSGCPSSSVTLKSGIENMLMHYVPEVK 256 (276)
Q Consensus 229 aC~gCpss~~TLk~~Ie~~L~~~vPeV~ 256 (276)
+|.+=|+|..|. .++|.+|.+.+|+..
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~~ 37 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQP 37 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS-
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCCc
Confidence 566668888877 899999999999863
No 26
>cd07304 Chorismate_synthase Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway. Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the biosynthesis of aromatic compounds. This process has an absolute requirement for reduced FMN as a co-factor which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate, having no overall change its redox state. Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two classes: Enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctiona,l while those that can generate reduced FMN at the expense of NADPH, such as found in fun
Probab=38.93 E-value=23 Score=34.65 Aligned_cols=36 Identities=28% Similarity=0.460 Sum_probs=28.2
Q ss_pred cceecCChhhhcCcHHHhcccCCCCeeEEEEeCCeEEEEe
Q 023823 100 GSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTK 139 (276)
Q Consensus 100 gs~~F~~~~~A~~sPLA~~LF~i~gV~sVfi~~dFITVtK 139 (276)
|+.-|.+ ..+-||+++|.||.||.|-||..|=.-..
T Consensus 216 G~p~f~k----lda~la~a~~sIpAvKgve~G~Gf~~a~~ 251 (344)
T cd07304 216 GSPVFDK----LDARLAQALMSIPAVKGVEIGSGFEAARM 251 (344)
T ss_pred Ccccccc----chHHHHHHhcCcCceeEEEECcchhhhhc
Confidence 4555633 46889999999999999999998875443
No 27
>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=37.88 E-value=52 Score=24.15 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=17.0
Q ss_pred EEEEeccCCCCCcchHHHHHHHHHHHHHHh
Q 023823 222 VKLRMQGACSGCPSSSVTLKSGIENMLMHY 251 (276)
Q Consensus 222 V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~ 251 (276)
|.| ++-.|..|+ .+.+.++..+...
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 666688888 3445677777766
No 28
>PRK05382 chorismate synthase; Validated
Probab=37.21 E-value=25 Score=34.58 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=29.0
Q ss_pred cceecCChhhhcCcHHHhcccCCCCeeEEEEeCCeEEEEec
Q 023823 100 GSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTKS 140 (276)
Q Consensus 100 gs~~F~~~~~A~~sPLA~~LF~i~gV~sVfi~~dFITVtK~ 140 (276)
|+.-|.+ ..+-||++||.||.||.|-||..|=.....
T Consensus 214 G~p~f~k----Lda~la~a~msIpAvKgvE~G~Gf~~a~~~ 250 (359)
T PRK05382 214 GEPVFDK----LDADLAHALMSINAVKGVEIGDGFAAARLR 250 (359)
T ss_pred Ccccccc----chHHHHHHhcCcCceeEEEECcchhhcccc
Confidence 4555633 468899999999999999999998755543
No 29
>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=35.43 E-value=1.5e+02 Score=21.34 Aligned_cols=46 Identities=9% Similarity=0.013 Sum_probs=36.0
Q ss_pred HhcccCCCCeeEEEEeCCeEEEEecCCCChhhhHHHHHHHHHHHHh
Q 023823 116 AKSLYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAAIMDFYS 161 (276)
Q Consensus 116 A~~LF~i~gV~sVfi~~dFITVtK~~~~dW~~Lkp~I~~~I~Dfls 161 (276)
-..|.....|++|.+.++-|+|+-.....|......+.+.|.+.+.
T Consensus 17 ~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~ 62 (72)
T PF01883_consen 17 GKDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK 62 (72)
T ss_dssp SSBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH
T ss_pred CCCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH
Confidence 3567777889999999999999998888777777777777777765
No 30
>PRK12463 chorismate synthase; Reviewed
Probab=35.16 E-value=33 Score=34.10 Aligned_cols=37 Identities=11% Similarity=0.311 Sum_probs=28.6
Q ss_pred eecCChhhhcCcHHHhcccCCCCeeEEEEeCCeEEEEecC
Q 023823 102 ADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTKSE 141 (276)
Q Consensus 102 ~~F~~~~~A~~sPLA~~LF~i~gV~sVfi~~dFITVtK~~ 141 (276)
++|... ..+-||+++|.|+.||.|-||..|=.-.+..
T Consensus 235 v~fd~k---Lda~LA~A~msIpAVKgVE~G~Gf~~a~~~G 271 (390)
T PRK12463 235 VHYDRK---LDAKLAGAIMSINAFKGAEIGVGFEAARQPG 271 (390)
T ss_pred cccccc---chHHHHHHhcCcCceeEEEEccchhhhhCCC
Confidence 446632 3578999999999999999999987555433
No 31
>PHA02782 hypothetical protein; Provisional
Probab=34.21 E-value=83 Score=31.94 Aligned_cols=57 Identities=23% Similarity=0.352 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHH---HHHHHHHHH
Q 023823 185 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLK---SGIENMLMH 250 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk---~~Ie~~L~~ 250 (276)
..+.++|+++|-++|-.+.-.+||-+ |+|+|++++.|. ||..-...|+ ..|+..+++
T Consensus 369 kkl~~rIKEiLP~yVSAFANT~GGyL-fIGVdDdt~~Ii--------G~~~e~e~L~~Le~aIe~cI~K 428 (503)
T PHA02782 369 KQLRTRIRQQLPSILSSFANTEGGYL-FIGVDNNTHKVI--------GFTVGQDYLKLVENDIEKYIKR 428 (503)
T ss_pred HHHHHHHHHHhhHHhHhheeCCCCEE-EEEEcCCCCeEe--------eeecCHHHHHHHHHHHHHHHHh
Confidence 45889999999988887777776655 789986434332 6775444443 555555543
No 32
>PLN02754 chorismate synthase
Probab=34.01 E-value=29 Score=34.74 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=25.5
Q ss_pred cCcHHHhcccCCCCeeEEEEeCCeEEEEec
Q 023823 111 MNSPLAKSLYGVDGITRVFFGSDFITVTKS 140 (276)
Q Consensus 111 ~~sPLA~~LF~i~gV~sVfi~~dFITVtK~ 140 (276)
..+-||++||.|+.||.|-||..|=.....
T Consensus 256 Lda~LA~Al~SIpAVKGVEfG~GF~~a~~~ 285 (413)
T PLN02754 256 LEAELAKAMMSLPATKGFEIGSGFAGTLLT 285 (413)
T ss_pred chHHHHHHhcCcCceeEEEEccchhhhhcc
Confidence 468899999999999999999998755443
No 33
>TIGR00033 aroC chorismate synthase. Homotetramer (noted in E.coli) suggests reason for good conservation.
Probab=29.92 E-value=33 Score=33.64 Aligned_cols=29 Identities=17% Similarity=0.373 Sum_probs=24.7
Q ss_pred cCcHHHhcccCCCCeeEEEEeCCeEEEEe
Q 023823 111 MNSPLAKSLYGVDGITRVFFGSDFITVTK 139 (276)
Q Consensus 111 ~~sPLA~~LF~i~gV~sVfi~~dFITVtK 139 (276)
..+-||++||.||.||.|-||..|=.-..
T Consensus 222 Lda~La~a~msIpAvKgvE~G~Gf~~a~~ 250 (351)
T TIGR00033 222 LDARLAHAMMSIPAVKGVEIGDGFELASM 250 (351)
T ss_pred chHHHHHHhcCcCceeEEEECcchhhccc
Confidence 46889999999999999999998864443
No 34
>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=28.80 E-value=1.8e+02 Score=20.01 Aligned_cols=40 Identities=25% Similarity=0.275 Sum_probs=29.1
Q ss_pred HHHhcccCCCCeeEEEEe--CCeEEEEecCCC-ChhhhHHHHH
Q 023823 114 PLAKSLYGVDGITRVFFG--SDFITVTKSEDT-SWDLLKPEIF 153 (276)
Q Consensus 114 PLA~~LF~i~gV~sVfi~--~dFITVtK~~~~-dW~~Lkp~I~ 153 (276)
-+-++|.+++||.+|-+. .+-++|+-.++. +.+.|...|.
T Consensus 15 ~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~ 57 (62)
T PF00403_consen 15 KVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE 57 (62)
T ss_dssp HHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH
T ss_pred HHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH
Confidence 345678899999988876 478999887763 6666555554
No 35
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=26.07 E-value=74 Score=27.66 Aligned_cols=30 Identities=30% Similarity=0.540 Sum_probs=23.6
Q ss_pred CCCEEEEEe--ccCCCCCcchHHHHHHHHHHHH
Q 023823 218 ETGTVKLRM--QGACSGCPSSSVTLKSGIENML 248 (276)
Q Consensus 218 ~~g~V~Vrl--~GaC~gCpss~~TLk~~Ie~~L 248 (276)
++|.+.|+- +-+|+.|++...-- .++.+.|
T Consensus 12 q~G~a~V~c~~~S~CgsC~a~~~CG-s~~l~kL 43 (150)
T COG3086 12 QNGQAKVSCQRQSACGSCAARAGCG-SGLLSKL 43 (150)
T ss_pred cCCeEEEEeeccCccccchhhcccc-hHHHHHh
Confidence 478888885 69999999988766 4566666
No 36
>COG2946 Putative phage replication protein RstA [DNA replication, recombination, and repair]
Probab=26.03 E-value=1.4e+02 Score=29.44 Aligned_cols=52 Identities=21% Similarity=0.354 Sum_probs=36.0
Q ss_pred cEEEEEEecCCCEEEEEeccCCCCCc----chHHHHHHHHHHHHHHhCCCcceEeecCCcc
Q 023823 209 DIEYRGFDPETGTVKLRMQGACSGCP----SSSVTLKSGIENMLMHYVPEVKSVEQELDAE 265 (276)
Q Consensus 209 dIelv~~d~~~g~V~Vrl~GaC~gCp----ss~~TLk~~Ie~~L~~~vPeV~~V~~~~~~~ 265 (276)
++-.|.+...+++|.|.|.| .||- ....+|.++++..++ |-|+.|....|+=
T Consensus 117 ~yGkV~~gG~rntvlielsG--~GC~~~~~~we~rl~~fLq~~~r---~riTRvDlA~Ddf 172 (377)
T COG2946 117 DYGKVHYGGQRNTVLIELSG--TGCTVAKEGWELRLYQFLQDCGR---PRITRVDLALDDF 172 (377)
T ss_pred eEEEEEecCCCceEEEEEec--CccceecccHHHHHHHHHHHhCC---CceeEEEEeeecc
Confidence 34445566667899999998 4773 344566666666665 8999998776654
No 37
>PRK11702 hypothetical protein; Provisional
Probab=25.21 E-value=2.6e+02 Score=23.04 Aligned_cols=65 Identities=20% Similarity=0.409 Sum_probs=43.8
Q ss_pred chHHHHHHHHHHHhcCCcc-hhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeec
Q 023823 184 DSETVAMIKELLETRIRPA-VQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 261 (276)
Q Consensus 184 ~~el~~~I~~vL~~~IrP~-l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~ 261 (276)
++++..-+...|++.|.|. |.-+||. +..++ |.|...-.|.| +..-+..|+.=|+.+ +|++|+.-
T Consensus 35 ~e~~D~~vD~fIde~Ie~ngL~f~G~G--~~~~e---G~vc~~~~gs~------tEe~R~~V~~WL~~r--~v~~v~vs 100 (108)
T PRK11702 35 EEQIDATVDAFIDEVIEPNGLAFDGSG--YLAWE---GLICLQKIGKC------TEEHRALVKKWLEGR--KLTDVEVS 100 (108)
T ss_pred HHHHHHHHHHHHHHHHhcCCceecCCc--ceeEE---EEEeecccCCC------CHHHHHHHHHHHHhC--CCceEEee
Confidence 3456667777777667775 4455544 22343 67777666777 456778899999998 88888753
No 38
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=23.80 E-value=4.3e+02 Score=24.54 Aligned_cols=76 Identities=18% Similarity=0.225 Sum_probs=40.1
Q ss_pred chHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecCC
Q 023823 184 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELD 263 (276)
Q Consensus 184 ~~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~~ 263 (276)
+++..++|++.+.+ + |.+..-. ++....... .-.|.+.+.=...-+-...-.+.+.||+.|++.+|++. |....+
T Consensus 211 ~~~~~~~I~~~i~~-~-~~v~~v~-~l~~~~~G~-~~~v~v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~~~~-v~ihve 285 (299)
T PRK09509 211 PDEERQEIIDIVTS-W-PGVSGAH-DLRTRQSGP-TRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFPGSD-VIIHQD 285 (299)
T ss_pred CHHHHHHHHHHHHh-C-CCCcCce-eeeeEeeCC-eEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCCCCE-EEEEeC
Confidence 45678888888864 3 4332211 444443211 11223332222112222233466889999999999865 665544
Q ss_pred c
Q 023823 264 A 264 (276)
Q Consensus 264 ~ 264 (276)
+
T Consensus 286 P 286 (299)
T PRK09509 286 P 286 (299)
T ss_pred C
Confidence 4
No 39
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.07 E-value=1.3e+02 Score=24.47 Aligned_cols=27 Identities=26% Similarity=0.390 Sum_probs=21.9
Q ss_pred CCCCCcchHHHHHHHHHHHHHHhCCCcc
Q 023823 229 ACSGCPSSSVTLKSGIENMLMHYVPEVK 256 (276)
Q Consensus 229 aC~gCpss~~TLk~~Ie~~L~~~vPeV~ 256 (276)
+|.+-|+|..|. .|+|.+|++.+|+..
T Consensus 18 SCV~aPtsKdt~-eWLeaalkRKyp~~~ 44 (106)
T COG4837 18 SCVNAPTSKDTY-EWLEAALKRKYPNQP 44 (106)
T ss_pred HhcCCCcchhHH-HHHHHHHhccCCCCC
Confidence 455558888776 899999999999865
No 40
>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=23.03 E-value=4.6e+02 Score=23.35 Aligned_cols=75 Identities=17% Similarity=0.239 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHhcCCcchhcCCCcEEEEEEecCC--CEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecC
Q 023823 185 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPET--GTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 262 (276)
Q Consensus 185 ~el~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~--g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~ 262 (276)
++..++|++.+. .+ |.+..- -++.......+. ..+.|.+.+.+.-.-+ -.+...||+.+++.+|++..|....
T Consensus 191 ~~~~~~i~~~i~-~~-~~v~~v-~~~~~~~~G~~~~~v~~~v~v~~~~~~~~a--h~i~~~i~~~i~~~~~~v~~v~ih~ 265 (268)
T TIGR01297 191 EEDLEEIKKAIL-SI-PGVKGV-HDLHIWRIGPGKLFLDVHVVVDPDLDLKQA--HDIALEIEREILKRHPGIEHVTIQV 265 (268)
T ss_pred cccHHHHHHHHh-cC-CCcccc-eEeEEEEcCCCCEEEEEEEEECCCCChhHH--HHHHHHHHHHHHHhcCCCCeEEEEe
Confidence 345677777765 22 333111 023333332101 1355666676643222 3455689999999999998887765
Q ss_pred Cc
Q 023823 263 DA 264 (276)
Q Consensus 263 ~~ 264 (276)
++
T Consensus 266 ep 267 (268)
T TIGR01297 266 EP 267 (268)
T ss_pred CC
Confidence 43
No 41
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=23.03 E-value=1.6e+02 Score=21.53 Aligned_cols=41 Identities=24% Similarity=0.217 Sum_probs=33.0
Q ss_pred HHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEecc
Q 023823 188 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQG 228 (276)
Q Consensus 188 ~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~G 228 (276)
.++++++++....--+.=.|=-|=+.++|+++++.+|...+
T Consensus 3 ~~RAkeI~~S~~~i~V~y~G~pV~Ie~vde~~~tA~V~~l~ 43 (58)
T PF08141_consen 3 VQRAKEIAESPDMIEVTYNGVPVWIEHVDEENGTARVHPLD 43 (58)
T ss_pred HHHHHHHHcCCceEEEEECCEEEEEEEEcCCCCeEEEEECC
Confidence 46788888876666677778888888899889999999864
No 42
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=22.01 E-value=2.7e+02 Score=27.92 Aligned_cols=54 Identities=13% Similarity=0.122 Sum_probs=34.3
Q ss_pred HhcccCCCCeeEEEEeCCeE---------------------EEEecCCCChhhhHHHHHHHHHHHHhcCCCCcccc
Q 023823 116 AKSLYGVDGITRVFFGSDFI---------------------TVTKSEDTSWDLLKPEIFAAIMDFYSSGQPLFLDS 170 (276)
Q Consensus 116 A~~LF~i~gV~sVfi~~dFI---------------------TVtK~~~~dW~~Lkp~I~~~I~DflsSG~PVv~e~ 170 (276)
+..|-+||+|+.|-++.+.- .|.-+-+.. .++-+++.++|.....+|-++.+..
T Consensus 178 L~~L~~IphV~~IRI~TR~pvv~P~RIT~ell~~Lk~~~~~~v~~h~nhp-~Eit~~a~~Al~~L~~aGI~l~nQs 252 (417)
T TIGR03820 178 LTELRAIPHVEVIRIGTRVPVVLPQRITDELVAILKKHHPVWLNTHFNHP-REITASSKKALAKLADAGIPLGNQS 252 (417)
T ss_pred HHHHhhcCCCceEEEeeccccccccccCHHHHHHHHhcCCeEEEEeCCCh-HhChHHHHHHHHHHHHcCCEEEeec
Confidence 45666788888777776522 222222222 5678888888888887887665543
No 43
>PRK11023 outer membrane lipoprotein; Provisional
Probab=21.53 E-value=5.6e+02 Score=22.47 Aligned_cols=118 Identities=14% Similarity=0.104 Sum_probs=63.9
Q ss_pred eEEEEeCCeEEEEecCCCChhhhHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCCchHHHHHHHHHHHhcCCcchhc
Q 023823 126 TRVFFGSDFITVTKSEDTSWDLLKPEIFAAIMDFYSSGQPLFLDSETAAAKDTAINEDDSETVAMIKELLETRIRPAVQD 205 (276)
Q Consensus 126 ~sVfi~~dFITVtK~~~~dW~~Lkp~I~~~I~DflsSG~PVv~e~~~~~~~~~~~~~~~~el~~~I~~vL~~~IrP~l~~ 205 (276)
-+|....+.|+++ ..++|...+..+....... ..-..+.++-............+|..+..+|+..|.. .+.+.
T Consensus 70 I~V~v~~G~V~L~--G~V~~~~~k~~A~~ia~~v-~GV~~V~N~l~V~~~~~~~~~~~D~~It~kik~~L~~--~~~v~- 143 (191)
T PRK11023 70 INVTAYQGKVLLT--GQSPNAELSERAKQIAMGV-EGVNEVYNEIRQGQPIGLGTASKDTWITTKVRSQLLT--SDSVK- 143 (191)
T ss_pred EEEEEECCEEEEE--EEeCCHHHHHHHHHHHhcC-CCceeecceeeeccccccccccCcHHHHHHHHHHHhc--CCCCC-
Confidence 3455556655444 5677888777775554432 1111222222111111111123466788999888852 55554
Q ss_pred CCCcEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHHhCCCcceEeecC
Q 023823 206 DGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 262 (276)
Q Consensus 206 dGGdIelv~~d~~~g~V~Vrl~GaC~gCpss~~TLk~~Ie~~L~~~vPeV~~V~~~~ 262 (276)
+.+|++.-+ +|+|||. |.-.. ...+ ... .+-..++.|++|.-..
T Consensus 144 -~~~I~V~t~---~G~V~L~------G~v~~-~e~~-~a~-~iA~~v~GVk~Vv~~~ 187 (191)
T PRK11023 144 -SSNVKVTTE---NGEVFLL------GLVTQ-REAK-AAA-DIASRVSGVKRVTTAF 187 (191)
T ss_pred -cceEEEEEE---CcEEEEE------EEeCH-HHHH-HHH-HHHhcCCCeeEEeeee
Confidence 678887654 5899985 44332 2333 333 3456689999887543
No 44
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=21.48 E-value=1.5e+02 Score=21.93 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=19.4
Q ss_pred CCCCcchHHHHHHHHHHHHHHhCCCc
Q 023823 230 CSGCPSSSVTLKSGIENMLMHYVPEV 255 (276)
Q Consensus 230 C~gCpss~~TLk~~Ie~~L~~~vPeV 255 (276)
|.+|...... ..+.+.|.+.+|+.
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 7888866655 47999999999985
No 45
>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=21.29 E-value=75 Score=25.44 Aligned_cols=33 Identities=21% Similarity=0.290 Sum_probs=19.8
Q ss_pred HHHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEeccC
Q 023823 188 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGA 229 (276)
Q Consensus 188 ~~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl~Ga 229 (276)
.+.|++++.. + |+|.||+|..++..-+|||..+
T Consensus 15 re~iK~~f~~--------~-g~V~yVD~~~G~~~g~VRf~~~ 47 (105)
T PF08777_consen 15 REDIKEAFSQ--------F-GEVAYVDFSRGDTEGYVRFKTP 47 (105)
T ss_dssp HHHHHHHT-S--------S---EEEEE--TT-SEEEEEESS-
T ss_pred HHHHHHHHHh--------c-CCcceEEecCCCCEEEEEECCc
Confidence 5666666542 3 4999999987778899999763
No 46
>PRK05473 hypothetical protein; Provisional
Probab=20.54 E-value=1.7e+02 Score=23.26 Aligned_cols=55 Identities=15% Similarity=0.410 Sum_probs=28.2
Q ss_pred CCChhhhHHHHHHHHHH-----------HHhcCCCCcccchhhhhccccCCCCchHHHHHHH--HHHHhcCCcchhcC
Q 023823 142 DTSWDLLKPEIFAAIMD-----------FYSSGQPLFLDSETAAAKDTAINEDDSETVAMIK--ELLETRIRPAVQDD 206 (276)
Q Consensus 142 ~~dW~~Lkp~I~~~I~D-----------flsSG~PVv~e~~~~~~~~~~~~~~~~el~~~I~--~vL~~~IrP~l~~d 206 (276)
..+=.++...|..+|.+ |+-||.|...... .+.-.++.+|+ ++|++-++-+|..+
T Consensus 17 ~~~v~eiL~~Vy~AL~EKGYNPinQiVGYllSGDPaYItsh----------~nAR~lIrkiERDEilEeLv~~Yl~~~ 84 (86)
T PRK05473 17 KKDVREILTTVYDALEEKGYNPINQIVGYLLSGDPAYIPRH----------NDARNLIRKLERDEILEELVKSYLKGN 84 (86)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHHHhhhccCCCCccCCc----------ccHHHHHHHHhHHHHHHHHHHHHHHhc
Confidence 33455666667666654 5666666544321 11223444443 45555555555443
No 47
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the
Probab=20.30 E-value=1.3e+02 Score=23.66 Aligned_cols=50 Identities=20% Similarity=0.339 Sum_probs=30.3
Q ss_pred hcCCCcEEEEEEecCCCEEEEEec-cCCCCCcchHHHHHHHHHHHHHHhCCCcc
Q 023823 204 QDDGGDIEYRGFDPETGTVKLRMQ-GACSGCPSSSVTLKSGIENMLMHYVPEVK 256 (276)
Q Consensus 204 ~~dGGdIelv~~d~~~g~V~Vrl~-GaC~gCpss~~TLk~~Ie~~L~~~vPeV~ 256 (276)
..+|..+.+-.+. +..|.|-+- .-|..|-...-.|.+ +.+.+++.-+.++
T Consensus 5 ~~~G~~v~l~~~~--gk~vll~Fwa~wC~~C~~~~p~l~~-~~~~~~~~~~~~~ 55 (131)
T cd03009 5 RNDGGKVPVSSLE--GKTVGLYFSASWCPPCRAFTPKLVE-FYEKLKESGKNFE 55 (131)
T ss_pred ccCCCCccHHHhC--CcEEEEEEECCCChHHHHHhHHHHH-HHHHHHhcCCCEE
Confidence 4577788887665 567777774 568877776555544 3334444333444
No 48
>PF09961 DUF2195: Uncharacterized protein conserved in bacteria (DUF2195); InterPro: IPR018696 This family of various bacterial proteins has no known function.
Probab=20.16 E-value=2.1e+02 Score=24.03 Aligned_cols=56 Identities=18% Similarity=0.388 Sum_probs=36.9
Q ss_pred HHHHHHHHhcCCcchhcCCCcEEEEEEecCCCEEEEEe-ccCCCCCcchHHHH------HHHHHHHHHHhC
Q 023823 189 AMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRM-QGACSGCPSSSVTL------KSGIENMLMHYV 252 (276)
Q Consensus 189 ~~I~~vL~~~IrP~l~~dGGdIelv~~d~~~g~V~Vrl-~GaC~gCpss~~TL------k~~Ie~~L~~~v 252 (276)
.++.+-++ ++|.-..-.+++..+..+ +.++= .|.| ||-|+-.+- ..+++..|++-+
T Consensus 24 N~LaaCv~--~~~~~~~~~~n~v~l~~~-----~~l~~siG~C-GC~SAL~~Y~s~v~~~~g~~~~LQ~G~ 86 (121)
T PF09961_consen 24 NALAACVD--VKPGQPQTADNQVSLKAT-----FSLRRSIGEC-GCMSALANYTSSVEQDNGVRQVLQEGL 86 (121)
T ss_pred CcHHHHhc--CcccCccccCCeEEEEEE-----EEEecccCcc-chHHHHHHHHHHHHhhhhHHHHHHHhh
Confidence 44455554 888888777777776553 55554 4999 999965433 356666777754
No 49
>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=20.13 E-value=3.2e+02 Score=19.14 Aligned_cols=53 Identities=13% Similarity=0.146 Sum_probs=30.7
Q ss_pred chhcCCCcEEEEEEecC-CCEEEEEeccCCCCCcchHHH-HHHHHHHHHHHhCCCcceEee
Q 023823 202 AVQDDGGDIEYRGFDPE-TGTVKLRMQGACSGCPSSSVT-LKSGIENMLMHYVPEVKSVEQ 260 (276)
Q Consensus 202 ~l~~dGGdIelv~~d~~-~g~V~Vrl~GaC~gCpss~~T-Lk~~Ie~~L~~~vPeV~~V~~ 260 (276)
.|+.+|.+|..+..... ++...+.+.=. .+... -.+.|-+.|+. +|.|.+|+.
T Consensus 20 ~la~~~inI~~i~~~~~~~~~~~i~~~v~-----v~~~~~~l~~l~~~L~~-i~~V~~v~~ 74 (76)
T cd04888 20 TIAQVRGNVLTINQNIPIHGRANVTISID-----TSTMNGDIDELLEELRE-IDGVEKVEL 74 (76)
T ss_pred HHHHcCCCEEEEEeCCCCCCeEEEEEEEE-----cCchHHHHHHHHHHHhc-CCCeEEEEE
Confidence 45678999988876422 35555554221 12222 22456666665 788888875
No 50
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=20.00 E-value=57 Score=32.19 Aligned_cols=37 Identities=19% Similarity=0.328 Sum_probs=29.6
Q ss_pred cCcHHHhcccCCCCeeEEEEeCCeEEEEecC-----CCChhh
Q 023823 111 MNSPLAKSLYGVDGITRVFFGSDFITVTKSE-----DTSWDL 147 (276)
Q Consensus 111 ~~sPLA~~LF~i~gV~sVfi~~dFITVtK~~-----~~dW~~ 147 (276)
..+.||.+||.|+-||.|-||..|-...+.. +..|..
T Consensus 227 Lda~lA~AlmsI~AvKGVEiG~GF~~a~~~GSe~~De~~~~~ 268 (369)
T COG0082 227 LDAKLAHALMSIPAVKGVEIGDGFEAARMRGSEANDEITLDG 268 (369)
T ss_pred chHHHHHHhhCCccceeEEeccchhhhhcccccccCceeeCC
Confidence 3578999999999999999999998666643 335655
Done!