RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780694|ref|YP_003065107.1| probable transcriptional
regulator protein, LuxR family [Candidatus Liberibacter asiaticus str.
psy62]
(246 letters)
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein;
NMR {Erwinia amylovora} SCOP: a.4.6.2
Length = 99
Score = 77.2 bits (190), Expect = 4e-15
Identities = 17/64 (26%), Positives = 26/64 (40%)
Query: 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
D L+ +E E L +EG EIA L S T+++ S M K + Y
Sbjct: 32 DKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSS 91
Query: 243 NNIV 246
++
Sbjct: 92 VSMT 95
>2krf_A Transcriptional regulatory protein COMA; activator, competence,
DNA-binding, transcription regulation component
regulatory system; NMR {Bacillus subtilis}
Length = 73
Score = 76.9 bits (190), Expect = 4e-15
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
LT RE L + +G T+ EIA L +S+ ++ + SI K +R+ A+ A + +
Sbjct: 13 LTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGV 72
Query: 246 V 246
+
Sbjct: 73 L 73
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding
domain, activator, antibiotic resistance, cytoplasm,
DNA-binding; NMR {Staphylococcus aureus}
Length = 91
Score = 76.4 bits (188), Expect = 5e-15
Identities = 21/61 (34%), Positives = 39/61 (63%)
Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
LT RE+E L I++G ++ EIA I+ TV ++++I+ K + R+ A+ YA ++N+
Sbjct: 30 LTEREMEILLLIAKGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQAVIYAFQHNL 89
Query: 246 V 246
+
Sbjct: 90 I 90
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix,
two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}
Length = 236
Score = 75.3 bits (184), Expect = 1e-14
Identities = 23/122 (18%), Positives = 42/122 (34%)
Query: 125 GMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDF 184
G+ + +L + L+ + +
Sbjct: 115 GVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQ 174
Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244
L+ RE+ CL W S+GKT+ A + GI+ TV +Y+ K ++ +A A
Sbjct: 175 MLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRG 234
Query: 245 IV 246
+V
Sbjct: 235 LV 236
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory
proteins, LUXR family, structural genomics; 2.04A
{Bacteroides thetaiotaomicron vpi-5482}
Length = 258
Score = 75.5 bits (185), Expect = 1e-14
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
L+ RE E L I +G +S EIA L IS NTVN + +I+ K + A A +
Sbjct: 198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMKL 257
Query: 246 V 246
+
Sbjct: 258 L 258
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA
complex, two-component response regulator,
helix-turn-helix, DNA bending; 2.12A {Escherichia coli}
SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A
Length = 82
Score = 75.1 bits (185), Expect = 1e-14
Identities = 18/61 (29%), Positives = 33/61 (54%)
Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244
+LT RE + L I++G + IA L I+ +TV ++ +++K K+R A + +
Sbjct: 21 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER 80
Query: 245 I 245
I
Sbjct: 81 I 81
>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA
binding motif, alpha/beta/alpha sandwich; HET: LAE;
1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2
d.110.5.1 PDB: 1h0m_A*
Length = 234
Score = 73.4 bits (179), Expect = 4e-14
Identities = 23/128 (17%), Positives = 46/128 (35%), Gaps = 4/128 (3%)
Query: 123 PAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHW-- 180
G+ + + K I L + + A + +
Sbjct: 107 DFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTP 166
Query: 181 --GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIA 238
L +E L WI+ GKT +EIA + G+ N+V + M++ ++++ A
Sbjct: 167 TAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTA 226
Query: 239 YAVRNNIV 246
A+R ++
Sbjct: 227 LAIRRKLI 234
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR
{Sinorhizobium meliloti}
Length = 79
Score = 71.3 bits (175), Expect = 2e-13
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
L+ RE + L+ + G + IA L IS TV + A++M K K+ + A+
Sbjct: 17 LSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLVRMALAGGF 76
Query: 246 V 246
Sbjct: 77 G 77
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional
regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2
Length = 74
Score = 71.3 bits (175), Expect = 2e-13
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
LT RE E + + KT+ EIA L IS TV N+I++ M+K K RS A+ +R
Sbjct: 12 LTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGE 71
Query: 246 V 246
+
Sbjct: 72 L 72
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein
structure initiative; NMR {Salmonella typhimurium}
Length = 61
Score = 69.7 bits (171), Expect = 5e-13
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246
RE + L I EG T+ I+ L IS TV + ++MRK + + A R ++
Sbjct: 2 RERQVLKLIDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTELLNCARRMRLI 59
>3c57_A Two component transcriptional regulatory protein DEVR; response
regulator, two-component regulatory system, DNA- binding
protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A
1zlj_A
Length = 95
Score = 67.6 bits (165), Expect = 2e-12
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244
LT +E L +SEG T+ +IA + ++ TV NY++ ++ K + R+ A +A
Sbjct: 27 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELK 86
Query: 245 IV 246
Sbjct: 87 RS 88
>3klo_A Transcriptional regulator VPST; REC domain, HTH domain,
DNA-binding, transcription regulation; HET: C2E TAR;
2.80A {Vibrio cholerae} PDB: 3kln_A*
Length = 225
Score = 60.5 bits (146), Expect = 3e-10
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243
+LT RE + + + G ++ EIA L +S NTV ++ ++ +K K R A+ +A N
Sbjct: 159 KLTKREQQIIKLLGSGASNIEIADKLFVSENTVKTHLHNVFKKINAKNRLQALIWAKNN 217
>3c3w_A Two component transcriptional regulatory protein DEVR; response
regulator, two-component regulatory system, DNA- binding
protein; 2.20A {Mycobacterium tuberculosis}
Length = 225
Score = 59.6 bits (143), Expect = 6e-10
Identities = 20/81 (24%), Positives = 35/81 (43%)
Query: 166 AAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225
AA + LT +E L +SEG T+ +IA + ++ TV NY++ ++
Sbjct: 130 AAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLL 189
Query: 226 RKTATKTRSGAIAYAVRNNIV 246
K + R+ A +A
Sbjct: 190 AKLGMERRTQAAVFATELKRS 210
>1a04_A Nitrate/nitrite response regulator protein NARL; signal
transduction protein, response regulators, two-
component systems; 2.20A {Escherichia coli} SCOP:
a.4.6.2 c.23.1.1 PDB: 1rnl_A
Length = 215
Score = 52.2 bits (124), Expect = 1e-07
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
+LT RE + L I++G + IA L I+ +TV ++ +++K K+R A +
Sbjct: 150 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWV 209
Query: 241 VRNNI 245
+ I
Sbjct: 210 HQERI 214
>1yio_A Response regulatory protein; transcription regulation, DNA binding
protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2
c.23.1.1 PDB: 1zn2_A
Length = 208
Score = 44.2 bits (103), Expect = 3e-05
Identities = 14/54 (25%), Positives = 26/54 (48%)
Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
RE + L G + +IA LGI+ TV + +IM+K ++ + + +
Sbjct: 146 REQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLANLVHLVEK 199
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 39.9 bits (93), Expect = 6e-04
Identities = 49/281 (17%), Positives = 84/281 (29%), Gaps = 139/281 (49%)
Query: 48 RMYAL------TEYVGASHFLLVRWDLFQEQKLDSIVSSDWPF--DLVRCMA-----LS- 93
++ A+ T+ D F+E L + + DL++ A L
Sbjct: 155 QLVAIFGGQGNTD------------DYFEE--LRDLYQTYHVLVGDLIKFSAETLSELIR 200
Query: 94 ---EKDKYY----NV---LQRPTELFCPVFHTLPENITPPAGMDNRY-------CSLTFD 136
+ +K + N+ L+ P+ TP D Y C L
Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSN-------------TP----DKDYLLSIPISCPL--- 240
Query: 137 VARIRIGLMLL--F----------PKGRIILRDRLWEI-----GLLAAYQANMFKSYDVH 179
IG++ L + P G LR L GL+ A S
Sbjct: 241 -----IGVIQLAHYVVTAKLLGFTP-GE--LRSYLKGATGHSQGLVTAVAIAETDS---- 288
Query: 180 WGKDFELTGRE-VECLTWISEG--------KTS-------DEIA----------VILGIS 213
W + F ++ R+ + L +I G TS D + I ++
Sbjct: 289 W-ESFFVSVRKAITVLFFI--GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT 345
Query: 214 RNTVNNYIASIMRKTATKT-----RSGAIAYAVRN---NIV 246
+ V +Y+ KT + ++ N N+V
Sbjct: 346 QEQVQDYV--------NKTNSHLPAGKQVEISLVNGAKNLV 378
Score = 39.5 bits (92), Expect = 6e-04
Identities = 40/212 (18%), Positives = 57/212 (26%), Gaps = 96/212 (45%)
Query: 5 IQQVNIVLNREDEQ--------RTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEY- 55
+ + N L +Q + V P +S +Y L
Sbjct: 353 VNKTNSHLP-AGKQVEISLVNGAKNLVVSGPPQS------------------LYGLNLTL 393
Query: 56 --VGASHFLLVRWD----LFQEQKLDSI------VSSDWPFD---LVRCMALSEKD-KYY 99
A L D F E+KL V+S PF LV L KD
Sbjct: 394 RKAKAPSGL----DQSRIPFSERKL-KFSNRFLPVAS--PFHSHLLVPASDLINKDLVKN 446
Query: 100 NVLQRPTELFCPVFHT--------LPENITP-------------------PA-------- 124
NV ++ PV+ T L +I+ A
Sbjct: 447 NVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGP 506
Query: 125 GMDNRYCSLTFDVARIRIGLMLLFPKG-RIIL 155
G + LT R + G G R+I+
Sbjct: 507 GGASGLGVLT---HRNKDG------TGVRVIV 529
>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding,
transcription, transcription regulator, transcription
regulation; 3.20A {Klebsiella pneumoniae}
Length = 315
Score = 34.6 bits (79), Expect = 0.023
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222
+ T +IA LGI R T++ +
Sbjct: 20 QDMTQAQIARELGIYRTTISRLLK 43
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics,
midwest center for structura genomics, protein structure
initiative; 2.50A {Fusobacterium nucleatum subsp}
Length = 164
Score = 33.7 bits (76), Expect = 0.041
Identities = 14/57 (24%), Positives = 26/57 (45%)
Query: 171 NMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
+ + + + E E LT++ G + EIA IL + +++N I I +K
Sbjct: 95 LKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRKK 151
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding
anti-sigma factor, oxidative stress, transcription
regulation; 2.35A {Mycobacterium tuberculosis}
Length = 92
Score = 32.3 bits (74), Expect = 0.100
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227
G ++ +IA LGI+ TV + + +R
Sbjct: 52 RGWSTAQIATDLGIAEGTVKSRLHYAVRA 80
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition,
protein-DNA complex, A10G mutant, DNA binding
protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2
PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C
Length = 52
Score = 31.2 bits (71), Expect = 0.19
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 192 ECLTWISEGKTSDEIAVILGISRNTVNNYI 221
+ + +G ++A+I GI +T+ Y
Sbjct: 13 QISRLLEKGHPRQQLAIIFGIGVSTLYRYF 42
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A
{Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1
PDB: 1sc5_A
Length = 239
Score = 30.7 bits (68), Expect = 0.29
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 186 LTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRK 227
L RE + I E + E+A IL S + V+ A + +
Sbjct: 188 LPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALER 230
>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex,
double helix, overhanging base, DNA binding protein/DNA
complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1
PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A
Length = 183
Score = 30.5 bits (68), Expect = 0.39
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 178 VHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221
V +G+ ++ V L +G + I+ + I+R+TV I
Sbjct: 138 VVFGRKRKIDRDAV--LNMWQQGLGASHISKTMNIARSTVYKVI 179
>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific
recombinase, resolvase, DNA-binding protein, protein-DNA
complex, DNA integration, DNA invertase, DNA
recombination; 3.20A {Staphylococcus aureus}
Length = 209
Score = 30.4 bits (67), Expect = 0.43
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 2/80 (2%)
Query: 144 LMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREV--ECLTWISEGK 201
L ++ + R + R + +A + ++ + R + + + EG+
Sbjct: 117 LAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQ 176
Query: 202 TSDEIAVILGISRNTVNNYI 221
+IA + I+R TV
Sbjct: 177 AISKIAKEVNITRQTVYRIK 196
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc binding
transcription factor; 2.40A {Rhodobacter sphaeroides 2}
PDB: 2z2s_A
Length = 184
Score = 30.0 bits (66), Expect = 0.48
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227
T E+A G+ T+ + I + +
Sbjct: 150 GDLTHRELAAETGLPLGTIKSRIRLALDR 178
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding,
transmembrane, transcription; 2.00A {Escherichia coli}
SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A
Length = 194
Score = 29.8 bits (66), Expect = 0.57
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
R L + +G + +EIA I+ TV + I
Sbjct: 146 RMAITLREL-DGLSYEEIAAIMDCPVGTVRSRIFRAREA 183
>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding
protein, DNA-binding, transcription regulation; 1.90A
{Sulfolobus solfataricus}
Length = 144
Score = 29.7 bits (66), Expect = 0.69
Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 162 IGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEG-KTSDEIAVILGISRNTVNNY 220
+ +A K ++ GK L+ + L SE ++ +A ++++ +
Sbjct: 11 MNTIAKIYRGSIKEFNNRLGKLMNLSYLDFSILKATSEEPRSMVYLANRYFVTQSAITAA 70
Query: 221 IASIMRK 227
+ + K
Sbjct: 71 VDKLEAK 77
>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET:
CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A
Length = 192
Score = 29.6 bits (66), Expect = 0.75
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 197 ISEGKTSDEIAVILGISRNTVNNYIA 222
++G + +IA G+S+ V +
Sbjct: 21 KNDGMSQKDIAAKEGLSQAKVTRALQ 46
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon
DNA, bipartite DNA-binding, HTH- motif, DNA binding
protein/DNA complex; 2.69A {Caenorhabditis elegans}
SCOP: a.4.1.2 a.4.1.2
Length = 141
Score = 29.0 bits (64), Expect = 1.00
Identities = 6/46 (13%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 181 GKDFELTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225
+ L+ E + + E++ + SR+ + Y+ +
Sbjct: 2 PRGSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPV 47
>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning,
protein-DNA complex, heilx-turn- helix motif,
transcription factor; HET: BRU; 2.20A {Escherichia coli}
SCOP: a.4.14.1
Length = 178
Score = 28.9 bits (64), Expect = 1.0
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 193 CLTWISEGKTSDEIAVILGISRNTVNNYIA 222
+++GK +IA +G S + ++
Sbjct: 45 IGRELAKGKKKGDIAKEIGKSPAFITQHVT 74
>1upi_A DTDP-4-dehydrorhamnose 3,5-epimerase; rhamnose pathway, PSI,
protein structure initiative, TB structural genomics
consortium, TB; HET: CME; 1.7A {Mycobacterium
tuberculosis} SCOP: b.82.1.1 PDB: 2ixc_A* 1pm7_A*
Length = 225
Score = 28.9 bits (64), Expect = 1.1
Identities = 9/58 (15%), Positives = 17/58 (29%), Gaps = 7/58 (12%)
Query: 40 DCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDK 97
+ MY + + D ++ DWP +LS++D
Sbjct: 142 LALQDNSTVMYLCSAEYNPQREHTICAT-------DPTLAVDWPLVDGAAPSLSDRDA 192
>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding
protein- complex; HET: DNA; 2.86A {Escherichia coli}
PDB: 3mkw_B* 3mkz_A*
Length = 189
Score = 28.9 bits (64), Expect = 1.1
Identities = 5/23 (21%), Positives = 7/23 (30%)
Query: 200 GKTSDEIAVILGISRNTVNNYIA 222
+A ISR + I
Sbjct: 42 AGNISALADAENISRKIITRCIN 64
>1ep0_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; racemase,
DTDP-4-dehydrorhamnose epimerase, structural genomics,
PSI; 1.50A {Methanothermobacterthermautotrophicus} SCOP:
b.82.1.1 PDB: 1epz_A*
Length = 185
Score = 29.0 bits (65), Expect = 1.2
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 49 MYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDK 97
Y TE + + WD D + DWP ++V + +SEKD+
Sbjct: 132 NYKCTELYHPEYDSGIPWD-------DPDIGIDWPLEMVDDLIISEKDR 173
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding;
HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP:
a.4.13.2
Length = 243
Score = 28.6 bits (63), Expect = 1.2
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
EL RE + + +T E+A LGIS+ ++ I++
Sbjct: 198 ELDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKILQH 241
>1nt2_B Conserved hypothetical protein; adeMet, binding motif, coiled coil,
RNA binding protein; HET: SAM; 2.90A {Archaeoglobus
fulgidus} SCOP: a.183.1.1
Length = 258
Score = 28.6 bits (64), Expect = 1.2
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 69 FQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQR 104
F+E L + S PF++ A + YY +L++
Sbjct: 21 FEESFLKAENPSPLPFNVSEVGAKALGKDYYRILRK 56
>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm,
transcription regulation, binding, transcription
regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB:
3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A
Length = 151
Score = 28.2 bits (63), Expect = 1.7
Identities = 7/47 (14%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 182 KDFELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRK 227
++ ++ + L +S E T +I G+++ V+ + ++
Sbjct: 32 TEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNA 78
>2v79_A DNA replication protein DNAD; primosome, DNA remodelling,
oligomerization domain, DNA-binding protein; HET: DNA;
2.00A {Bacillus subtilis}
Length = 135
Score = 28.0 bits (62), Expect = 1.8
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 7/53 (13%)
Query: 182 KDFELTGREVECL----TWISEGK---TSDEIAVILGISRNTVNNYIASIMRK 227
K L E+ L + +G T +++ + IS N + ++K
Sbjct: 26 KQLGLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQK 78
>2i3f_A Glycolipid transfer-like protein; GLTP superfamily, GLTP-like,
protein structure initiative, PSI; 1.38A {Galdieria
sulphuraria} PDB: 2q52_A
Length = 224
Score = 27.9 bits (62), Expect = 2.2
Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 6/57 (10%)
Query: 26 LPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRW-DLFQEQKLDSIVSSD 81
P+R ++ P + E++ H L F +++L+ D
Sbjct: 152 APSRERFYRKLHPDLNIAKAKIE-----EFLIELHDPLCCIVQFFFQRELEDQCWGD 203
>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural
genomics, PSI, protein structure initiative; 1.60A
{Enterococcus faecalis} SCOP: a.4.5.28
Length = 144
Score = 27.9 bits (62), Expect = 2.3
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227
K+ LT + L + E G ++IA ++ + R T I + +
Sbjct: 23 KELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ 70
>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor,
winged helix motif, DNA-binding; 1.40A {Methanobacterium
thermoautotrophicum} PDB: 3bpx_A*
Length = 138
Score = 27.6 bits (61), Expect = 2.9
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227
LT +V CL I G DE+A + + T+ + +
Sbjct: 23 GHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEES 70
>1xd7_A YWNA; structural genomics, protein structure initiative, winged
helix DNA binding, hypothetical protein, PSI; 2.30A
{Bacillus subtilis subsp} SCOP: a.4.5.55
Length = 145
Score = 27.3 bits (60), Expect = 3.5
Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 191 VECLTWISEGK--TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244
+ L+ IS + +S+ IA + + V I+ + + +R+G +++ +
Sbjct: 12 IHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASLKKD 67
>1jid_A Signal recognition particle 19 kDa protein; signal recognition
particle (SRP), protein-RNA complex, GGAG tetraloop,
signaling protein/RNA complex; HET: 5BU A23; 1.80A {Homo
sapiens} SCOP: d.201.1.1 PDB: 1mfq_B* 1ry1_B* 2go5_B
2j37_B
Length = 128
Score = 27.1 bits (60), Expect = 3.6
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 155 LRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGI-S 213
++D +GL + N K Y W +D + GR L K D ++ S
Sbjct: 49 IQDVCSAVGLNVFLEKN--KMYSREWNRDVQYRGRVRVQL------KQEDGSLCLVQFPS 100
Query: 214 RNTVNNYIASIMRKTATKTR 233
R +V Y A ++ K T+T+
Sbjct: 101 RKSVMLYAAEMIPKLKTRTQ 120
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP:
a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A*
3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 26.9 bits (58), Expect = 4.5
Identities = 13/70 (18%), Positives = 24/70 (34%)
Query: 168 YQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
N + + G+ V I+ + I I G+ TV+ +AS+ R+
Sbjct: 145 NTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRE 204
Query: 228 TATKTRSGAI 237
+ I
Sbjct: 205 NILDKKKNKI 214
>2vn2_A DNAD, chromosome replication initiation protein; DNA replication,
primosome; 2.3A {Geobacillus kaustophilus HTA426}
Length = 128
Score = 26.8 bits (59), Expect = 4.5
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 182 KDFELTGREVECL----TWISEGK---TSDEIAVILGISRNTVNNYIASIMRK 227
K L E+ L ++ EG T E+A + +S + +++K
Sbjct: 26 KQLGLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQK 78
>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription
regulator, activator, DNA-binding, repressor; HET: SAL;
2.30A {Salmonella typhimurium} SCOP: a.4.5.28
Length = 166
Score = 26.8 bits (59), Expect = 4.9
Identities = 10/49 (20%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 182 KDFELTGREVECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMRK 227
K ELT L I + ++ ++A +GI + ++ + + K
Sbjct: 47 KPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDK 95
>3onq_A Regulator of polyketide synthase expression; structural genomics,
PSI-2, protein structure initiative; HET: MSE; 2.10A
{Bifidobacterium adolescentis}
Length = 262
Score = 26.5 bits (58), Expect = 5.1
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 195 TWISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228
T++ G + + A L + NTV + T
Sbjct: 204 TFLKYGSSLENTAKELNVHPNTVRYRLKRAAETT 237
>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
prnai nucleotide-binding domain; HET: MSE; 1.80A
{Sulfolobus solfataricus}
Length = 244
Score = 26.6 bits (58), Expect = 5.3
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 185 ELTGREVECLTWISEGK--TSDEIAVILGISRNTVNNYIASIMRK 227
+ + E++ L + E K E+A +L S T+ N IA + +
Sbjct: 149 DYSREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF 193
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition,
transcription regulation, helix-turn- helix motif; 3.00A
{Mycobacterium tuberculosis H37RV}
Length = 70
Score = 26.7 bits (59), Expect = 5.3
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
RE LT + G + + A + G T+ + +A
Sbjct: 21 REALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDA 58
>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural
genomics, PSI, protein structure initiative; 1.85A
{Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1
Length = 170
Score = 26.4 bits (58), Expect = 5.4
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 200 GKTSDEIAVILGISRNTVNNY 220
+ A LGISR V+ Y
Sbjct: 103 NLSLTTAAEALGISRRMVSYY 123
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
1ku2_A
Length = 423
Score = 26.8 bits (58), Expect = 5.4
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 185 ELTGREVECLTW-----ISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
+L+ RE L T +E+ G++R + +RK
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK 407
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA
complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Length = 438
Score = 26.4 bits (57), Expect = 6.5
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227
T +E+ G++R + +RK
Sbjct: 394 REHTLEEVGAYFGVTRERIRQIENKALRK 422
>2o0m_A Transcriptional regulator, SORC family; structural genomics, PSI-2,
protein structure initiative; 1.60A {Enterococcus
faecalis V583} SCOP: c.124.1.8
Length = 345
Score = 26.4 bits (58), Expect = 6.6
Identities = 2/24 (8%), Positives = 8/24 (33%)
Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222
+ ++ +GI+ +
Sbjct: 33 QPIGRRSLSETMGITERVLRTETD 56
>1jgs_A Multiple antibiotic resistance protein MARR; transcription
regulation, DNA-binding, repressor; HET: SAL; 2.30A
{Escherichia coli} SCOP: a.4.5.28
Length = 138
Score = 26.4 bits (58), Expect = 6.9
Identities = 9/73 (12%), Positives = 24/73 (32%), Gaps = 2/73 (2%)
Query: 157 DRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISE--GKTSDEIAVILGISR 214
+ + +G L + ++T + + L I T E+ +L +
Sbjct: 3 NEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDL 62
Query: 215 NTVNNYIASIMRK 227
+ + ++ K
Sbjct: 63 GALTRMLDRLVCK 75
>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix;
1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A
3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A
Length = 146
Score = 26.2 bits (57), Expect = 8.2
Identities = 7/47 (14%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 182 KDFELTGREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRK 227
+ L+ + L S+G KT +A ++++ + + +
Sbjct: 31 GELNLSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEM 77
>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural
genomics, MI center for structural genomics, MCSG,
unknown function; 1.78A {Listeria innocua}
Length = 143
Score = 25.8 bits (57), Expect = 8.6
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227
+++T + L I + EIA+ TVN + ++RK
Sbjct: 31 ASYDVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRK 78
>2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding,
phosphorylation, DNA-binding protein; NMR {Mycobacterium
tuberculosis}
Length = 148
Score = 25.7 bits (56), Expect = 9.5
Identities = 4/20 (20%), Positives = 9/20 (45%)
Query: 202 TSDEIAVILGISRNTVNNYI 221
+A +LG+ + V +
Sbjct: 33 DLPRVAELLGVPVSKVAQQL 52
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.324 0.137 0.423
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,142,765
Number of extensions: 96685
Number of successful extensions: 548
Number of sequences better than 10.0: 1
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 85
Length of query: 246
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 156
Effective length of database: 3,511,270
Effective search space: 547758120
Effective search space used: 547758120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.0 bits)