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= 0301.0006.p (179 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_347066.1| Transcriptional regulator (HTH_ARAC-domain) [Cl... 156 3e-37 ref|NP_469828.1| lin0485 [Listeria innocua] >gi|25515685|pir||AE... 132 3e-30 ref|NP_464011.1| lmo0483 [Listeria monocytogenes EGD-e] >gi|2551... 132 4e-30 ref|ZP_00098933.1| COG3708: Uncharacterized protein conserved in... 111 7e-24 ref|NP_977538.1| transcriptional regulator, AraC family [Bacillu... 111 9e-24 >ref|NP_347066.1| Transcriptional regulator (HTH_ARAC-domain) [Clostridium acetobutylicum] pir||C96952 transcription regulator (HTH_ARAC-domain) [imported] - Clostridium acetobutylicum gb|AAK78406.1| Transcriptional regulator (HTH_ARAC-domain) [Clostridium acetobutylicum] Length = 288 Score = 156 bits (394), Expect = 3e-37, Method: Compositional matrix adjust. Identities = 79/179 (44%), Positives = 106/179 (59%), Gaps = 2/179 (1%) Query: 2 QLKAFPRLTFHLSLKGDQEMEYKIVEKPAFTVIGKSMEVTTRDGENLRRIPEFWNECNAD 61 LKA P L+F + +KG++ M YKI K +F + G S ++T++G N + IPEFW+E Sbjct: 109 NLKAIPPLSFQVIVKGEENMNYKIETKKSFKIAGVSKRISTKEGNNFKIIPEFWDEVKKS 168 Query: 62 GTSDELIEIGKGK-DWLGICMSMDMEKELLSYWIGVEGTPETDPQGYETAVVPAASWAVF 120 G E+IE GK +G+C + D E + Y I VEG Y VP S+AVF Sbjct: 169 GQC-EIIEKNAGKLGVMGVCTNFDCEYQEFDYLIAVEGDKIEGLDNYVVIEVPELSFAVF 227 Query: 121 TSAGPMPHAIQKVWQRIFQEWFPGTGYEHTGGPEFELYPPGDTGAEDYVCEVWIPVQKK 179 S GPMP A+Q V +RIF EWFP T YE GPE E+Y PG+ +DY E+W+PV +K Sbjct: 228 ESIGPMPDALQDVTRRIFSEWFPATKYEEAEGPEIEVYLPGNPQDKDYRAEIWVPVVEK 286 >ref|NP_469828.1| lin0485 [Listeria innocua] pir||AE1493 hypothetical protein lin0485 [imported] - Listeria innocua (strain Clip11262) emb|CAC95717.1| lin0485 [Listeria innocua] Length = 159 Score = 132 bits (333), Expect = 3e-30, Method: Compositional matrix adjust. Identities = 64/159 (40%), Positives = 93/159 (58%), Gaps = 1/159 (0%) Query: 21 MEYKIVEKPAFTVIGKSMEVTTRDGENLRRIPEFWNECNADGTSDELIEIGKGKDWLGIC 80 ME +IVE+ AFT +GK + + +I +FW E NA+G ++ + E+ + GI Sbjct: 1 MEVEIVERNAFTAVGKKRTFSVENDAQKEKISQFWQEANANGDAERINELAEFATIDGIL 60 Query: 81 MSMDMEKELLSYWIGVEGTPETDPQGYETAVVPAASWAVFTSAGPMPHAIQKVWQRIFQE 140 M + + Y+I +E + T P+ E +PA+ WA+F S GP+P +IQKVW+ I+ E Sbjct: 61 GVCQMNGDKMDYYIAIE-SELTPPEDMEKLTIPASKWAIFKSVGPLPSSIQKVWEYIYGE 119 Query: 141 WFPGTGYEHTGGPEFELYPPGDTGAEDYVCEVWIPVQKK 179 WF + Y H PE E+Y GDT A DY EVWIPV +K Sbjct: 120 WFHTSNYNHGNAPELEVYTEGDTTAVDYYSEVWIPVVEK 158 >ref|NP_464011.1| lmo0483 [Listeria monocytogenes EGD-e] pir||AD1135 hypothetical protein lmo0483 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAC98562.1| lmo0483 [Listeria monocytogenes] Length = 159 Score = 132 bits (332), Expect = 4e-30, Method: Compositional matrix adjust. Identities = 65/159 (40%), Positives = 92/159 (57%), Gaps = 1/159 (0%) Query: 21 MEYKIVEKPAFTVIGKSMEVTTRDGENLRRIPEFWNECNADGTSDELIEIGKGKDWLGIC 80 ME +IVE+ AFT +GK + + +I +FW E NA+G ++ + E+ + GI Sbjct: 1 MEVEIVERNAFTAVGKKRTFSVENDAQKEKISQFWQEVNANGDAERINELAEFATIDGIL 60 Query: 81 MSMDMEKELLSYWIGVEGTPETDPQGYETAVVPAASWAVFTSAGPMPHAIQKVWQRIFQE 140 M + + Y+I +E + T P E +PA+ WA+F S GP+P+AIQKVW+ I+ E Sbjct: 61 GVCQMNGDQMDYYIAIE-SELTPPADMEKLTIPASKWAIFKSVGPLPNAIQKVWEYIYGE 119 Query: 141 WFPGTGYEHTGGPEFELYPPGDTGAEDYVCEVWIPVQKK 179 WF Y H PE E+Y GDT A DY EVWIPV +K Sbjct: 120 WFQTCNYTHGNAPELEVYTEGDTTAVDYYSEVWIPVVEK 158 >ref|ZP_00098933.1| COG3708: Uncharacterized protein conserved in bacteria [Desulfitobacterium hafniense] Length = 291 Score = 111 bits (278), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 66/189 (34%), Positives = 94/189 (49%), Gaps = 19/189 (10%) Query: 1 VQLKAFPRLTFHLSLKGDQEMEYKIVEKPAFTVIGKSMEVTTR--------DGENLRRIP 52 +LK P +TF L++KG EM Y++VEK F ++G +T + D + P Sbjct: 108 AELKVMPPMTFQLTIKGGTEMNYRLVEKDEFYIVGFKKRITMQFKGINPEMDSLVQKLTP 167 Query: 53 EFWNECNADGTSDELIEIGKGKDWLGICMSMD---MEKELLSYWIGVEGTPETDPQGYET 109 + E + ++ K L + + D E L +IGV T + Y+ Sbjct: 168 QIIAELKSLCDTEP-------KGMLSVSANFDERTAEGSQLDQYIGV-ATSQAMSNHYDL 219 Query: 110 AVVPAASWAVFTSAGPMPHAIQKVWQRIFQEWFPGTGYEHTGGPEFELYPPGDTGAEDYV 169 VPAA+WAVF + G P A+Q W +I+ EWFP +GYE TGGPE DT DY Sbjct: 220 LHVPAATWAVFKAVGTFPEALQDTWAKIYAEWFPASGYEMTGGPELLWNETPDTSKPDYK 279 Query: 170 CEVWIPVQK 178 E+WIPV+K Sbjct: 280 SEIWIPVRK 288 >ref|NP_977538.1| transcriptional regulator, AraC family [Bacillus cereus ATCC 10987] gb|AAS40146.1| transcriptional regulator, AraC family [Bacillus cereus ATCC 10987] Length = 300 Score = 111 bits (277), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 65/173 (37%), Positives = 93/173 (53%), Gaps = 11/173 (6%) Query: 17 GDQEMEYKIVEKPAFTVIGKSMEVTTRDGENLRRIPEFWNECNADGTSDELIEIGKGKDW 76 G +MEY+IV KP F V G ++ T+++G+N + IP FW E + W Sbjct: 129 GGIQMEYRIVNKPEFLVAGYELKTTSKEGKNHQDIPAFWQEYLQKDLGTTIPNRKDTSQW 188 Query: 77 --LGICMSMDMEKELLSYWIGVEGTP-ETDPQGYETAVVPAASWAVFTSAGPMPH----- 128 LG+C ++E +Y IG+E T E P G P+A++AVFT+ +PH Sbjct: 189 VELGLCTDFNLETGDFTYIIGMEVTDFENVPDGIAKRTFPSATYAVFTTP-KVPHEEMVS 247 Query: 129 AIQKVWQRIFQEWFPGTGYEHTGGPEFELYPP--GDTGAEDYVCEVWIPVQKK 179 +I + W +F EWFP +GYEH G EFELY + +E E+WIPV+KK Sbjct: 248 SIHQTWNAVFSEWFPHSGYEHCGVTEFELYDERCHEDKSEFAQVELWIPVKKK 300 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 0.317 0.137 0.442 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: 331,453,157 Number of extensions: 14855679 Number of successful extensions: 25512 Number of sequences better than 1.0e-05: 38 Number of HSP's gapped: 25472 Number of HSP's successfully gapped: 38 Length of query: 179 Length of database: 757,237,578 Length adjustment: 118 Effective length of query: 61 Effective length of database: 436,855,896 Effective search space: 26648209656 Effective search space used: 26648209656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 122 (51.6 bits)