BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0502.0025.p (186 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_463642.1| similar to transcriptional regulatory proteins,... 82 7e-15 ref|NP_469502.1| similar to transcriptional regulatory proteins,... 81 1e-14 ref|NP_388045.1| alternate gene name: yzbC~similar to transcript... 80 3e-14 ref|NP_349215.1| Trancriptional regulator of AraC family [Clostr... 79 5e-14 ref|ZP_00060402.1| COG2207: AraC-type DNA-binding domain-contain... 78 1e-13 >ref|NP_463642.1| similar to transcriptional regulatory proteins, AraC family [Listeria monocytogenes EGD-e] pir||AF1088 transcription regulatory proteins, AraC family homolog lmo0109 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAC98324.1| lmo0109 [Listeria monocytogenes] Length = 277 Score = 82.0 bits (201), Expect = 7e-15, Method: Compositional matrix adjust. Identities = 37/96 (38%), Positives = 65/96 (67%), Gaps = 1/96 (1%) Query: 88 VEKVINYIAANYTRKLTLDELADSIHISRSHLGHIFKETTGETPFEFIIKYRIARAKEFL 147 V ++I+Y+ ++T ++L L+ +++IS +++ +FKE TGE+P ++IK R+ RA+E L Sbjct: 176 VNEIIHYMEKHHTEDVSLSTLSQTMYISPAYISKVFKEETGESPINYLIKIRLTRAEELL 235 Query: 148 EN-GCSVTDTARLVGFGDMFYFSRYFKKIEGISPNK 182 +N SV A +VG+ D +YFS+ FKK G P++ Sbjct: 236 KNKDVSVKQAANMVGYNDAYYFSKLFKKYYGFPPSE 271 >ref|NP_469502.1| similar to transcriptional regulatory proteins, AraC family [Listeria innocua] pir||AF1452 transcription regulatory protein, AraC family homolog lin0157 [imported] - Listeria innocua (strain Clip11262) emb|CAC95390.1| lin0157 [Listeria innocua] Length = 277 Score = 80.9 bits (198), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 36/96 (37%), Positives = 65/96 (67%), Gaps = 1/96 (1%) Query: 88 VEKVINYIAANYTRKLTLDELADSIHISRSHLGHIFKETTGETPFEFIIKYRIARAKEFL 147 V ++I+Y+ ++T ++L L+ +++IS +++ +FKE TGE+P ++IK R+ RA+E L Sbjct: 176 VNEIIHYMEKHHTEDVSLSTLSQTMYISPAYISKVFKEETGESPINYLIKIRLTRAEELL 235 Query: 148 EN-GCSVTDTARLVGFGDMFYFSRYFKKIEGISPNK 182 +N +V A +VG+ D +YFS+ FKK G P++ Sbjct: 236 KNKDVTVKQAANMVGYNDAYYFSKLFKKYYGFPPSE 271 >ref|NP_388045.1| alternate gene name: yzbC~similar to transcriptional regulator (AraC/XylS family) [Bacillus subtilis] sp|P40408|YBBB_BACSU Putative HTH-type transcriptional regulator ybbB pir||I39841 transcription regulator AraC/XylS family homolog ybbB - Bacillus subtilis gb|AAA64353.1| putative initiation codon GUG. Homology with transcriptional regulators (Salmonella typhimurium AraC, Bacillus subtilis AdaA).; putative dbj|BAA19497.1| YbbB [Bacillus subtilis] emb|CAB11940.1| ybbB [Bacillus subtilis subsp. subtilis str. 168] Length = 529 Score = 79.7 bits (195), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 47/145 (32%), Positives = 73/145 (50%), Gaps = 5/145 (3%) Query: 42 FEEFMRHWSSGHENRTFRCRADFMEILL-LISKYMEHNTINYSAIHKVEKVINYIAANYT 100 +E W+ + +C + ++ L + + T +SAI EK +YI + Sbjct: 121 LQELAALWNESSQLSQLKCVIEVQSLIYDLFTASLSDQTDTHSAI---EKTKHYIETHAD 177 Query: 101 RKLTLDELADSIHISRSHLGHIFKETTGETPFEFIIKYRIARAKEFL-ENGCSVTDTARL 159 K+TL +L+ IS H FK+ TG++ EFI K RI +AK + ++ C + + A Sbjct: 178 TKITLAQLSQMAGISAKHYSESFKKWTGQSVTEFITKTRITKAKRLMAKSNCKLKEIAHQ 237 Query: 160 VGFGDMFYFSRYFKKIEGISPNKYI 184 G+ D FYFSR FKK G SP Y+ Sbjct: 238 TGYQDEFYFSRIFKKYTGCSPTSYM 262 >ref|NP_349215.1| Trancriptional regulator of AraC family [Clostridium acetobutylicum] pir||H97220 trancriptional regulator of AraC family [imported] - Clostridium acetobutylicum gb|AAK80555.1| Trancriptional regulator of AraC family [Clostridium acetobutylicum] Length = 284 Score = 79.0 bits (193), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 46/126 (36%), Positives = 71/126 (56%), Gaps = 4/126 (3%) Query: 62 ADFMEILLLISKYMEHNTINYSAIHK----VEKVINYIAANYTRKLTLDELADSIHISRS 117 A F+E+++ ++ +N + + I+K +E++I YI N T +T+ LA+ +S S Sbjct: 153 ASFIELMIFLTSLFINNGESLTPIYKYSNQIEEIIRYINDNVTNDITVKHLAEHFFLSES 212 Query: 118 HLGHIFKETTGETPFEFIIKYRIARAKEFLENGCSVTDTARLVGFGDMFYFSRYFKKIEG 177 ++ IFK +TG T ++I RI+ AK L NG S+ D GF D F + FKK G Sbjct: 213 YICRIFKLSTGTTINKYITARRISMAKALLSNGSSINDVYVKCGFNDYSNFLKSFKKAVG 272 Query: 178 ISPNKY 183 ISP KY Sbjct: 273 ISPKKY 278 >ref|ZP_00060402.1| COG2207: AraC-type DNA-binding domain-containing proteins [Clostridium thermocellum ATCC 27405] Length = 204 Score = 77.8 bits (190), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 37/101 (36%), Positives = 67/101 (66%), Gaps = 1/101 (0%) Query: 87 KVEKVINYIAANYTRKLTLDELADSIHISRSHLGHIFKETTGETPFEFIIKYRIARAKEF 146 ++E +I Y+ ++ +K+T++ELA ++S+SH +FK+ TG +P +++I RI +AK+ Sbjct: 100 EIENIIEYMHQHFGQKITVEELAKKTNMSKSHFIRVFKKITGLSPMDYLINIRIEKAKKL 159 Query: 147 LENGC-SVTDTARLVGFGDMFYFSRYFKKIEGISPNKYIGL 186 L G ++++ + L GF + +FS F KI G+SP+KY L Sbjct: 160 LGAGTKNISEISFLCGFNSLSHFSSTFSKIVGVSPSKYNSL 200 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.327 0.140 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 272,640,914 Number of extensions: 10035720 Number of successful extensions: 33102 Number of sequences better than 1.0e-05: 489 Number of HSP's gapped: 33363 Number of HSP's successfully gapped: 489 Length of query: 186 Length of database: 757,237,578 Length adjustment: 118 Effective length of query: 68 Effective length of database: 436,855,896 Effective search space: 29706200928 Effective search space used: 29706200928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 122 (51.6 bits)