RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780693|ref|YP_003065106.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
(235 letters)
>gnl|CDD|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon
(activates the bioluminescence operon.
Length = 58
Score = 73.3 bits (181), Expect = 4e-14
Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228
+LT RE L+L +G T++EIAE+LG+S TV +L + KL +R QA+ A
Sbjct: 1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
>gnl|CDD|163106 TIGR03020, EpsA, transcriptional regulator EpsA. Proteins in this
family include a C-terminal LuxR transcriptional
regulator domain (pfam00196). These proteins are
positioned proximal to either EpsH-containing
exopolysaccharide biosynthesis operons of the
Methylobacillus type, or the associated
PEP-CTERM-containing genes.
Length = 247
Score = 53.6 bits (129), Expect = 4e-08
Identities = 29/61 (47%), Positives = 35/61 (57%)
Query: 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAI 229
+A +T RE L DG T+EEIA LG+S TV +L KLD NR QA+AKAI
Sbjct: 187 SAGLITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAI 246
Query: 230 R 230
Sbjct: 247 A 247
>gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory,
chaperone HchA-associated. Members of this protein
family belong to the LuxR transcriptional regulator
family, and contain both autoinducer binding (pfam03472)
and transcriptional regulator (pfam00196) domains.
Members, however, occur only in a few members of the
Gammaproteobacteria that have the
chaperone/aminopeptidase HchA, and are always encoded by
the adjacent gene.
Length = 232
Score = 49.4 bits (118), Expect = 8e-07
Identities = 27/79 (34%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 160 FLELFKKRSSAARN----LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215
F + + L+ERE L G +IA LG+S TV +L SA K
Sbjct: 154 FFAARRLLEAPLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRK 213
Query: 216 LDAVNRIQAIAKAIRFGYI 234
L QAIA A+R G I
Sbjct: 214 LGVATTAQAIAIALRKGDI 232
>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB;
Provisional.
Length = 211
Score = 40.1 bits (94), Expect = 6e-04
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233
LT RE L+L +GYT+ +IAE+L +S+ TV + + KLD + + A R G
Sbjct: 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
Query: 234 I 234
I
Sbjct: 210 I 210
>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
family. Several PFAM models hit segments of these
sequences including Sigma-70 region 2 (pfam04542) and
Sigma-70, region 4 (pfam04545), but not always above
their respective trusted cutoffs.
Length = 158
Score = 38.1 bits (89), Expect = 0.002
Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 170 AARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
A L ERE L L +G + +EIAE LG+SV TV L A KL
Sbjct: 107 ALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA;
Provisional.
Length = 196
Score = 38.0 bits (88), Expect = 0.002
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 149 AHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAY 208
A G CY ++L R LT+RE + G +EIA +LGLS TV+ +
Sbjct: 116 ATGGCYLTPDIAIKLASGRQDP---LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVH 172
Query: 209 LGSATVKLDAVNRIQ 223
+ KL N ++
Sbjct: 173 RANLMEKLGVSNDVE 187
>gnl|CDD|182292 PRK10188, PRK10188, DNA-binding transcriptional activator SdiA;
Provisional.
Length = 240
Score = 35.9 bits (83), Expect = 0.009
Identities = 22/62 (35%), Positives = 32/62 (51%)
Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
N ++RE L+ +G TS EIA L +S +TVN + + K +A N+ Q A G
Sbjct: 179 NFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATG 238
Query: 233 YI 234
I
Sbjct: 239 LI 240
>gnl|CDD|182771 PRK10840, PRK10840, transcriptional regulator RcsB; Provisional.
Length = 216
Score = 36.0 bits (83), Expect = 0.009
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 159 DFLELFKKRSSAA---RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215
L +K S+ + L+ +E+ L+L +G+ EIA+KL S+ T+++ SA +K
Sbjct: 133 SVSRLLEKISAGGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMK 192
Query: 216 LDAVNRI 222
L N I
Sbjct: 193 LGVENDI 199
>gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional.
Length = 215
Score = 35.2 bits (81), Expect = 0.014
Identities = 19/63 (30%), Positives = 31/63 (49%)
Query: 162 ELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221
E+F LTERE L G ++++IA L +S TV ++ + KL+ +R
Sbjct: 142 EMFGAEEDPFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201
Query: 222 IQA 224
+ A
Sbjct: 202 VAA 204
>gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional.
Length = 217
Score = 34.7 bits (80), Expect = 0.019
Identities = 21/59 (35%), Positives = 30/59 (50%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
L+ERE + + G EI+E+L LS TVN+Y KL+ ++ AIR G
Sbjct: 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207
>gnl|CDD|116865 pfam08281, Sigma70_r4_2, Sigma-70, region 4. Region 4 of sigma-70
like sigma-factors are involved in binding to the -35
promoter element via a helix-turn-helix motif.
Length = 54
Score = 34.4 bits (80), Expect = 0.030
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYL 209
L R+ L +G + EIAE LG+S TV + L
Sbjct: 11 LPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRL 47
>gnl|CDD|132030 TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor,
Bacteroides expansion family 1. This group of sigma
factors are members of the sigma-70 family (TIGR02937)
and are found primarily in the genus Bacteroides. This
family appears to have resulted from a lineage-specific
expansion as B. thetaiotaomicron VPI-5482, Bacteroides
forsythus ATCC 43037, Bacteroides fragilis YCH46 and
Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23
members, respectively. There are currentlyonly two known
members of this family outside of the Bacteroides, in
Rhodopseudomonas and Bradyrhizobium.
Length = 161
Score = 33.3 bits (77), Expect = 0.048
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
G + +EIAE+LG+SV TV ++ A +L
Sbjct: 129 GKSYKEIAEELGISVKTVEYHISKALKEL 157
>gnl|CDD|184142 PRK13558, PRK13558, bacterio-opsin activator; Provisional.
Length = 665
Score = 33.3 bits (76), Expect = 0.053
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 167 RSSAARNLTERETSCLQLAG-DGY-------TSEEIAEKLGLSVHTVNAYLGSATVKL 216
R+S +LT+R+ + LQ A GY EE+AE +G+S T + +L +A KL
Sbjct: 601 RASLENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKL 658
>gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional.
Length = 210
Score = 32.9 bits (75), Expect = 0.066
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 166 KRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI 225
SS L+ RE + L+ G +++EIA++L LS TV+A+ + KL + ++ I
Sbjct: 142 TNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELI 201
Query: 226 AKA 228
A
Sbjct: 202 DYA 204
>gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional.
Length = 216
Score = 33.1 bits (76), Expect = 0.073
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 163 LFKKRSSAAR---NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219
L R++ R LT RE L+L G ++ IA +L ++ TV ++ K+
Sbjct: 142 LRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201
Query: 220 NRIQA 224
+R++A
Sbjct: 202 SRVEA 206
>gnl|CDD|179885 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
Length = 903
Score = 33.0 bits (76), Expect = 0.076
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228
LT+RE L L GY++E+IA +L ++ T+ ++ + KL +R +A+ A
Sbjct: 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893
>gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD;
Provisional.
Length = 216
Score = 32.5 bits (74), Expect = 0.094
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228
LT RE L G ++ EIA L +S +TV +L + K+ NR QA++ A
Sbjct: 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210
>gnl|CDD|182015 PRK09646, PRK09646, RNA polymerase sigma factor SigK; Reviewed.
Length = 194
Score = 32.3 bits (74), Expect = 0.11
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 172 RNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTV 205
LT+ + + LA G T E+AE+L + + TV
Sbjct: 141 DALTDTQRESVTLAYYGGLTYREVAERLAVPLGTV 175
>gnl|CDD|132028 TIGR02983, SigE-fam_strep, RNA polymerase sigma-70 factor, sigma-E
family. This group of similar sigma-70 factors includes
the sigE factor from Streptomyces coelicolor. The family
appears to include a paralagous expansion in the
Streptomycetes lineage, while related Actinomycetales
have at most two representatives.
Length = 162
Score = 31.6 bits (72), Expect = 0.18
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 170 AARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
A R L R+ + + L + + ++AE LG+SV TV + L A +L
Sbjct: 107 ALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154
>gnl|CDD|179690 PRK03975, tfx, putative transcriptional regulator; Provisional.
Length = 141
Score = 31.0 bits (71), Expect = 0.24
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLS 201
LTER+ L+L G T +EIA+ LG S
Sbjct: 6 FLTERQIEVLRLRERGLTQQEIADILGTS 34
>gnl|CDD|182011 PRK09639, PRK09639, RNA polymerase sigma factor SigX; Provisional.
Length = 166
Score = 30.7 bits (70), Expect = 0.32
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTV 205
+TER+ + L L GY+ +EIAE LG+ +V
Sbjct: 112 KMTERDRTVLLLRFSGYSYKEIAEALGIKESSV 144
>gnl|CDD|163591 TIGR03879, near_KaiC_dom, probable regulatory domain. This model
describes a common domain shared by two different
families of proteins, each of which occurs regularly
next to its corresponding partner family, a probable
regulatory with homology to KaiC. By implication, this
protein family likely is also involved in sensory
transduction and/or regulation.
Length = 73
Score = 30.1 bits (68), Expect = 0.46
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 172 RNLTERET-------SCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSAT 213
+ L ER T + LA + G T+ EIAE+LG + TV +L T
Sbjct: 7 KKLAERLTWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGET 57
>gnl|CDD|183569 PRK12517, PRK12517, RNA polymerase sigma factor; Provisional.
Length = 188
Score = 30.0 bits (68), Expect = 0.50
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
RE LQ+ G G++ EEIAE L L+ +TV L
Sbjct: 134 REPLLLQVIG-GFSGEEIAEILDLNKNTVMTRL 165
>gnl|CDD|183572 PRK12523, PRK12523, RNA polymerase sigma factor; Reviewed.
Length = 172
Score = 30.2 bits (68), Expect = 0.50
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSA 212
DG EIAE+LG+SV V YL
Sbjct: 134 DGMGHAEIAERLGVSVSRVRQYLAQG 159
>gnl|CDD|182018 PRK09651, PRK09651, RNA polymerase sigma factor FecI; Provisional.
Length = 172
Score = 30.2 bits (68), Expect = 0.53
Identities = 15/27 (55%), Positives = 18/27 (66%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSAT 213
DG T EIA KLG+SV +V Y+ AT
Sbjct: 134 DGLTYSEIAHKLGVSVSSVKKYVAKAT 160
>gnl|CDD|116253 pfam07638, Sigma70_ECF, ECF sigma factor. These proteins are
probably RNA polymerase sigma factors belonging to the
extra-cytoplasmic function (ECF) subfamily and show
sequence similarity to pfam04542 and pfam04545.
Length = 185
Score = 30.1 bits (68), Expect = 0.58
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 187 DGYTSEEIAEKLGLSVHTV 205
G +++EIAE+LG+S TV
Sbjct: 150 AGLSNDEIAERLGVSERTV 168
>gnl|CDD|171561 PRK12528, PRK12528, RNA polymerase sigma factor; Provisional.
Length = 161
Score = 29.4 bits (66), Expect = 0.81
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215
DG EIA +LG+S+ TV YL A ++
Sbjct: 128 DGLGYGEIATELGISLATVKRYLNKAAMR 156
>gnl|CDD|164986 PHA02591, PHA02591, hypothetical protein; Provisional.
Length = 83
Score = 29.3 bits (65), Expect = 0.88
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 183 QLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211
+LA G+T E+IA LG+SV V YL S
Sbjct: 54 ELARKGFTVEKIASLLGVSVRKVRRYLES 82
>gnl|CDD|165035 PHA02656, PHA02656, viral TNFR II-like protein; Provisional.
Length = 199
Score = 29.2 bits (65), Expect = 0.89
Identities = 14/54 (25%), Positives = 28/54 (51%)
Query: 149 AHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSV 202
+ G+ Y+ I + +F + +NL R+ SC++ D + S I +K +S+
Sbjct: 20 SKGSNYEEIQNKFTMFVDLTVYDKNLINRDVSCIRYDHDDFYSMYIIDKFNVSI 73
>gnl|CDD|179909 PRK04984, PRK04984, fatty acid metabolism regulator; Provisional.
Length = 239
Score = 28.7 bits (65), Expect = 1.3
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 14/55 (25%)
Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95
AL F + +CE N+D +P + YG SG IW +Q+
Sbjct: 189 ALGFYHKLSALCEEGNHD----QVPE-CVRQYG------IESGE---IWHRMQKN 229
>gnl|CDD|132044 TIGR02999, Sig-70_X6, RNA polymerase sigma factor, TIGR02999
family. This group of sigma factors are members of the
sigma-70 family (TIGR02937) and are found in a variety
of species including Rhodopirellula baltica which
encodes a paralogous group of five.
Length = 183
Score = 28.8 bits (65), Expect = 1.4
Identities = 13/18 (72%), Positives = 14/18 (77%)
Query: 188 GYTSEEIAEKLGLSVHTV 205
G T EEIAE LG+SV TV
Sbjct: 150 GLTVEEIAELLGVSVRTV 167
>gnl|CDD|171568 PRK12537, PRK12537, RNA polymerase sigma factor; Provisional.
Length = 182
Score = 28.6 bits (64), Expect = 1.7
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
R L DG + EIA++LG + TV A++
Sbjct: 138 RRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170
>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Length = 56
Score = 28.3 bits (64), Expect = 2.0
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 188 GYTSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIR 230
G T EE+AEKLG+S T++ G L+ ++ +AKA+
Sbjct: 10 GLTQEELAEKLGVSRSTLSRIENGKRKPSLE---TLKKLAKALG 50
>gnl|CDD|132005 TIGR02960, SigX5, RNA polymerase sigma-70 factor, TIGR02960 family.
This group of sigma factors are members of the sigma-70
family (TIGR02937). They and appear by homology, tree
building, bidirectional best hits and one-to-a-genome
distribution, to represent a conserved family.
Length = 324
Score = 27.9 bits (62), Expect = 2.6
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219
G+ + E AE LG S +VN+ L A LD V
Sbjct: 158 GWRAAETAELLGTSTASVNSALQRARATLDEV 189
>gnl|CDD|181072 PRK07661, PRK07661, acetyl-CoA acetyltransferase; Provisional.
Length = 391
Score = 27.8 bits (62), Expect = 2.8
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
G G+T+E++A K G+S +A+ AV Q AKA+ G
Sbjct: 146 GMGHTAEQVAVKYGISREDQDAF---------AVRSHQRAAKALAEG 183
>gnl|CDD|132034 TIGR02989, Sig-70_gvs1, RNA polymerase sigma-70 factor,
Rhodopirellula/Verrucomicrobium family. This group of
sigma factors are members of the sigma-70 family
(TIGR02937) and are abundantly found in the species
Rhodopirellula baltica (11), and Verrucomicrobium
spinosum (16) and to a lesser extent in Gemmata
obscuriglobus (2).
Length = 159
Score = 27.2 bits (61), Expect = 3.4
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
L ER+ LQL G + +AE+LG +V+ V L V+L
Sbjct: 112 LPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155
>gnl|CDD|116452 pfam07840, FadR_C, FadR C-terminal domain. This family contains
sequences that are similar to the fatty acid metabolism
regulator protein (FadR). This functions as a dimer,
with each monomer being composed of an N-terminal
DNA-binding domain and a regulatory C-terminal domain. A
linker comprising two short alpha helices joins the two
domains. In the C-terminal domain, an antiparallel array
of six alpha helices forms a barrel-like structure,
while a seventh alpha helix forms a 'lid' at the end
closest to the N-terminal domain. This structure was
found to be similar to that of the C-terminal domain of
the Tet repressor. Long-chain acyl-CoA thioesters
interact directly and reversibly with the C-terminal
domain, and this interaction affects the structure and
therefore the DNA binding properties of the N-terminal
domain.
Length = 164
Score = 27.2 bits (61), Expect = 3.5
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 14/55 (25%)
Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95
AL F R +CE NYD +P++ + YG SG IWQS+++E
Sbjct: 118 ALKFYRDLLELCEEGNYD----KVPDV-VRQYG------IESGK---IWQSMRDE 158
>gnl|CDD|129804 TIGR00721, tfx, DNA-binding protein, Tfx family. Tfx from
Methanobacterium thermoautotrophicum is associated with
the operon for molybdenum formyl-methanofuran
dehydrogenase and binds a DNA sequence near its
promoter.
Length = 137
Score = 27.1 bits (60), Expect = 3.7
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNA 207
LTER+ L+L G + +EIA++L + V+A
Sbjct: 7 LTERQIKVLELREKGLSQKEIAKELKTTRANVSA 40
>gnl|CDD|181003 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
Length = 289
Score = 27.3 bits (61), Expect = 3.7
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 169 SAARNLTERETSCL---QLAGDGYTSEEIAEKLGLS 201
A + L ERE + +L DG T E + E+LG+S
Sbjct: 223 QALQTLNERELRIIRERRLREDGATLEALGEELGIS 258
>gnl|CDD|128648 smart00354, HTH_LACI, helix_turn _helix lactose operon repressor.
Length = 70
Score = 27.2 bits (61), Expect = 3.8
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 190 TSEEIAEKLGLSVHTVNAYL-GSATVKLDAVNRIQAIAKAIRFGYI 234
T +++A G+S TV+ L G+ V + ++ A + GYI
Sbjct: 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAME--ELGYI 45
>gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional.
Length = 234
Score = 27.3 bits (60), Expect = 3.9
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230
L +E + L+ G T EEIA+ G+ ++V L A + D ++ A AIR
Sbjct: 174 LDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIR 230
>gnl|CDD|128696 smart00419, HTH_CRP, helix_turn_helix, cAMP Regulatory protein.
Length = 48
Score = 27.0 bits (61), Expect = 4.2
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 190 TSEEIAEKLGLSVHTVN 206
T +EIAE LGL+ TV+
Sbjct: 10 TRQEIAELLGLTRETVS 26
>gnl|CDD|182019 PRK09652, PRK09652, RNA polymerase sigma factor RpoE; Provisional.
Length = 182
Score = 27.1 bits (61), Expect = 4.5
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 187 DGYTSEEIAEKLGLSVHTV 205
+G + EEIAE +G + TV
Sbjct: 143 EGLSYEEIAEIMGCPIGTV 161
>gnl|CDD|181314 PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated.
Length = 339
Score = 26.8 bits (60), Expect = 4.8
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224
G+++ E+AE L SV VN+ L A L A
Sbjct: 169 GWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAA 205
>gnl|CDD|179404 PRK02277, PRK02277, orotate phosphoribosyltransferase-like protein;
Provisional.
Length = 200
Score = 26.8 bits (60), Expect = 5.2
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 182 LQLAGDGYTSEEIAEKLGLSVHTV 205
+L G ++ EIA++L +S T
Sbjct: 12 AELKNKGLSTGEIADELNVSRETA 35
>gnl|CDD|148279 pfam06577, DUF1134, Protein of unknown function (DUF1134). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 161
Score = 26.4 bits (59), Expect = 5.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 71 TYGDDFLFHFNSGLLPIIWQ 90
YG+ L+ N+G + WQ
Sbjct: 56 RYGEGTLYTKNAGEHKVYWQ 75
>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
Length = 208
Score = 26.4 bits (59), Expect = 6.5
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTV-NA 207
L+E E L+L DG + +EIAE+L V ++ NA
Sbjct: 155 LLSELEKEVLELYLDGKSYQEIAEELNRHVKSIDNA 190
>gnl|CDD|132004 TIGR02959, SigZ, RNA polymerase sigma factor, SigZ family. This
family of RNA polymerase sigma factors is a member of
the Sigma-70 subfamily (TIGR02937). One of these is
designated as SigZ in B. subtilis (Swiss_Prot:
SIGZ_BACSU). Interestingly, this group has a very
sporatic distribution, B. subtilis, for instance, being
the only sequenced strain of Bacilli with a member.
Dechloromonas aromatica RCB appears to have two of these
sigma factors. A member appears on a plasmid found in
Photobacterium profundum SS9 and Vibrio fischeri ES114
(where a second one is chromosomally encoded).
Length = 170
Score = 26.6 bits (59), Expect = 6.7
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
+G + +EIAEKLGLS+ + + KL
Sbjct: 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRKKL 144
>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 26.5 bits (59), Expect = 6.8
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
+G + EIAE LG+ V TV + L A L
Sbjct: 140 EGLSYREIAEILGVPVGTVKSRLRRARQLL 169
>gnl|CDD|114760 pfam06056, Terminase_5, Putative ATPase subunit of terminase
(gpP-like). This family of proteins are annotated as
ATPase subunits of phage terminase after. Terminases are
viral proteins that are involved in packaging viral DNA
into the capsid.
Length = 58
Score = 26.1 bits (58), Expect = 7.2
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 188 GYTSEEIAEKLGLSVHTVNAY 208
GY EIA++LGL TV ++
Sbjct: 13 GYRPAEIAQELGLKARTVYSW 33
>gnl|CDD|185431 PTZ00077, PTZ00077, asparagine synthetase-like protein;
Provisional.
Length = 586
Score = 26.2 bits (58), Expect = 7.6
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 121 PVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQV 156
P+ +G+ K+G + F+SE L H C +V
Sbjct: 152 PLYIGYAKDGSIWFSSELKAL--------HDQCVEV 179
>gnl|CDD|179124 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 26.0 bits (58), Expect = 7.8
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 50 LICELHNYDLDSGDIPNILIETYGDDFLFHFNS-GLLPIIWQSIQEETVIESSGQLSVRL 108
L C L + I + + F+F S G LP+ EE ++E+ L +
Sbjct: 199 LNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPV------EEILLEALKILKRKA 252
Query: 109 E 109
+
Sbjct: 253 D 253
>gnl|CDD|183153 PRK11475, PRK11475, DNA-binding transcriptional activator BglJ;
Provisional.
Length = 207
Score = 26.2 bits (58), Expect = 7.9
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216
TERE L+ GY+ +IAE+L ++ T+ A+ + KL
Sbjct: 138 TEREI--LRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177
>gnl|CDD|180498 PRK06266, PRK06266, transcription initiation factor E subunit
alpha; Validated.
Length = 178
Score = 26.1 bits (58), Expect = 8.4
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 190 TSEEIAEKLGLSVHTV 205
T EEIAE+ G+ ++TV
Sbjct: 38 TDEEIAEQTGIKLNTV 53
>gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional.
Length = 200
Score = 26.2 bits (58), Expect = 8.5
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209
K + LT +E +L G + EIA KLG+S T+ +L
Sbjct: 149 KGSTPKKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
>gnl|CDD|184503 PRK14096, pgi, glucose-6-phosphate isomerase; Provisional.
Length = 528
Score = 26.0 bits (58), Expect = 8.5
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLG 199
KK ++A +L ++ L+ G + EEIA LG
Sbjct: 455 KKAAAAILDLQKKVEELLKEDGGELSIEEIAAALG 489
>gnl|CDD|163028 TIGR02812, fadR_gamma, fatty acid metabolism transcriptional
regulator FadR. Members of this family are FadR, a
transcriptional regulator of fatty acid metabolism,
including both biosynthesis and beta-oxidation. It is
found exclusively in a subset of Gammaproteobacteria,
with strictly one copy per genome. It has an N-terminal
DNA-binding domain and a less well conserved C-terminal
long chain acyl-CoA-binding domain. FadR from this
family heterologously expressed in Escherichia coli show
differences in regulatory response and fatty acid
binding profiles. The family is nevertheless designated
equivalog, as all member proteins have at least
nominally the same function.
Length = 235
Score = 25.8 bits (57), Expect = 8.9
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 14/55 (25%)
Query: 41 ALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEE 95
AL F + Q +C+ N+D ++P+ I YG SG IW +Q+E
Sbjct: 188 ALQFYKELQALCKAGNHD----EVPD-CIRQYG------IESGE---IWHQMQDE 228
>gnl|CDD|182010 PRK09638, PRK09638, RNA polymerase sigma factor SigY; Reviewed.
Length = 176
Score = 25.8 bits (57), Expect = 9.1
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 188 GYTSEEIAEKLGLSVHTV 205
GYT EEIA+ L + TV
Sbjct: 142 GYTYEEIAKMLNIPEGTV 159
>gnl|CDD|137446 PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional.
Length = 181
Score = 26.1 bits (58), Expect = 9.3
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 187 DGYTSEEIAEKLGLSVHTV 205
+G + +EIAEKLGLS+
Sbjct: 121 EGLSQKEIAEKLGLSLSGA 139
>gnl|CDD|179487 PRK02866, PRK02866, cyanate hydratase; Validated.
Length = 147
Score = 25.9 bits (58), Expect = 9.3
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 188 GYTSEEIAEKLGLS-VHTVNAYLGSAT 213
G T +IAE +GLS V A LG T
Sbjct: 18 GLTWADIAEAIGLSEVWVTAALLGQMT 44
>gnl|CDD|139037 PRK12525, PRK12525, RNA polymerase sigma factor; Provisional.
Length = 168
Score = 26.1 bits (57), Expect = 9.4
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 187 DGYTSEEIAEKLGLSVHTVNAYLGSA 212
+G T EI E+LG+S+ ++ Y+ A
Sbjct: 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158
>gnl|CDD|128638 smart00344, HTH_ASNC, helix_turn_helix ASNC type. AsnC: an
autogenously regulated activator of asparagine
synthetase A transcription in Escherichia coli.
Length = 108
Score = 25.9 bits (58), Expect = 9.5
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 184 LAGDGYTS-EEIAEKLGLSVHTV 205
L D S E+A+K+GLS TV
Sbjct: 12 LQKDARISLAELAKKVGLSPSTV 34
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.321 0.138 0.395
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,756,961
Number of extensions: 237941
Number of successful extensions: 682
Number of sequences better than 10.0: 1
Number of HSP's gapped: 682
Number of HSP's successfully gapped: 77
Length of query: 235
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 145
Effective length of database: 4,049,753
Effective search space: 587214185
Effective search space used: 587214185
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.5 bits)