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= 0564.0026.p (524 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_563003.1| two-component response regulator [Clostridium p... 138 3e-31 ref|NP_815879.1| DNA-binding response regulator, AraC family [En... 122 2e-26 ref|NP_244313.1| BH3446~unknown conserved protein [Bacillus halo... 101 6e-20 ref|NP_242776.1| two-component response regulator [Bacillus halo... 94 8e-18 ref|NP_242975.1| BH2109~unknown conserved protein [Bacillus halo... 87 1e-15 >ref|NP_563003.1| two-component response regulator [Clostridium perfringens] dbj|BAB81793.1| two-component response regulator [Clostridium perfringens str. 13] Length = 507 Score = 138 bits (348), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 128/535 (23%), Positives = 247/535 (46%), Gaps = 53/535 (9%) Query: 2 KVMIVEDEILVRLGLRKSIPWSSLGLELVCEAKDGAEACDMFTRHLPDIVLVDIELPKMD 61 KVM+ +DE L+ GL I W LGLE+V +A +G EA D F + DIV+ DI +P++ Sbjct: 3 KVMLADDENLILQGLENIIEWEELGLEIVNKASNGQEAIDKFKENPVDIVVTDINMPQVT 62 Query: 62 GLKFIRFAKTHGSGTHFIVLTCHQDMKYMREAIKLQVTDFILKSTLDMKELCDILQNITL 121 GL+ ++ K S FI+L+ + D Y ++AI+L V ++ILK +D +EL L+N T+ Sbjct: 63 GLELLKELKKINSDVKFIILSGYDDFSYAKKAIELGVENYILKP-IDEEELEKTLKN-TI 120 Query: 122 ERLRDTSVDKAGLQDAAAAMPAEDFYRSWLNGSLRDSGQIRQQLAQMNVNRPVGRFIACV 181 +++ ++ +++ + + G L G+I + +N R+ C+ Sbjct: 121 NKIKQEK------EENKSSLGKHNILIKLIKGKLA-QGEIEENKEGFYMNLNSERYSLCI 173 Query: 182 MQLDVRPPADHKLSDADIRSXXXXXXXXXXXXHGEHVLGSVEE--MHMQRWHFIVSDRLA 239 + R ++ L + + ++ +++E + + W + L+ Sbjct: 174 INTRSRYDSEEMLHNI-------VNVIKENTQNNFEIIYTLDEELILINSW----DEALS 222 Query: 240 VSEMIQWMDTVKE------NAGIAFSVG--------WSASFVHPHEWRAYDRKAVELLQH 285 E+ ++ D +KE + SVG S+S+ + + Y + L + Sbjct: 223 KKEIKKYYDKLKEQIINEYGIDVFLSVGEPVCDLYKISSSYKEANNLKKY---VLTLGYN 279 Query: 286 QYYDAEGRLYTGEGQLGETLSELVHKAKKQIYDMIGSLRFAETRLMLADLLKELQRSPRL 345 + E E + SE++ K K+I + + AE +++E +L Sbjct: 280 KCITTEDVKDINEKNIN--FSEVLDKLNKRI--IAKDIEGAEK------IIEETVEDKKL 329 Query: 346 HPHIVKNMFTEFLFRIWSACEELAAGNPIANHQLVDQIYA--TQKLDQTVSLLLADMQRA 403 +P + ++ + LF + EE + L ++I A ++ + + LL R Sbjct: 330 NPRNIYDLSVKILFLLDGIVEEFKVEKQYTGNSLGEEIVALCSEDTREDIKTLLCSEIRE 389 Query: 404 ERQLEMTNSVNDKTKIVVLVKQYIKNHLQQEISLQEIADTFHINRSYLSRLFREVSQMSF 463 +L M + + ++ + Y+ + +E+SL+ +A +HIN SYL ++F + SF Sbjct: 390 VIEL-MHPTTIKYSPVIQQIISYVNENYYEEVSLKTLAQKYHINTSYLGQVFTKEVGCSF 448 Query: 464 TEFVLYEKTELAI-VMMQSGKSLTEISEKLGYLNLSSFTRMFKKVRGASPSLFVN 517 +E++ K A +++ + + +I++K+GYL+ S F R FKK G PS N Sbjct: 449 SEYLNKTKNMKAKELILNTNMKINDIAKKVGYLDTSYFYRKFKKYYGVCPSTLRN 503 >ref|NP_815879.1| DNA-binding response regulator, AraC family [Enterococcus faecalis V583] gb|AAO81949.1| DNA-binding response regulator, AraC family [Enterococcus faecalis V583] Length = 493 Score = 122 bits (306), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 122/536 (22%), Positives = 246/536 (45%), Gaps = 80/536 (14%) Query: 2 KVMIVEDEILVRLGLRKSIPWSSLGLELVCEAKDGAEACDMFTRHLPDIVLVDIELPKMD 61 +VM V+DE ++ GL+ IPW LG E+V A+ EA D++L DI +P+M Sbjct: 3 RVMFVDDEYMILEGLKWIIPWQELGFEIVKTARSAQEALAFLETESIDVLLTDITMPEMS 62 Query: 62 GLKFIRFAKTHGSGTHFIVLTCHQDMKYMREAIKLQVTDFILKSTLDMKELCDILQNITL 121 G++ I AK G ++L+ +Q+ Y+++ + LQV D++LK ++ +EL +Q I + Sbjct: 63 GIELIEQAKKKGHQFISLILSGYQEFDYVKKGMALQVQDYLLKP-VNKQELLANIQRIKI 121 Query: 122 ERLRDTSVDKAGLQDAAAAMPAEDFYRSWLNGSLRDSGQIRQQLAQMNVNRPVGRFIACV 181 E +D+ A + E+ WLN + + G + + Sbjct: 122 E------LDQQKKSHARVRLYLENGLMRWLNDEISE-----------------GEYEELM 158 Query: 182 MQLDVRPPADHK--LSDADIRSXXXXXXXXXXXXHGEHVLGSVEEMHMQRWH--FIVSDR 237 Q P D L +A++ L +++E+ M++ FI S Sbjct: 159 QQFATIKPGDFTVLLVEAEM-----------------SFLETIKELFMKKGQLLFIESWM 201 Query: 238 LAVSEMIQWMDTVKENAGI------AFSVGWSASFVHP--HEWR----AYDR----KAVE 281 +++ ++ A + A G FV +EW +Y++ +A+E Sbjct: 202 STYHQLLLIYKGARQEAFLFIREIEAILAGQGQIFVGESVNEWETVYESYEKVKQLQAIE 261 Query: 282 LLQHQYYDAEGRLYTGEGQLGETLSELVHKAKKQIYDMIGSLRFAETRL-MLADLLKELQ 340 ++ + Q+ + + A Q MIG ++ + L + + L + Sbjct: 262 TFYQEFLPNNQK-----EQMNRSAEDFTFLAFNQAL-MIGDMQTIQRELDAIFNQLSQQH 315 Query: 341 RSPRLHPHIVKNMFTEFLFRIWSACEELAAGNPIANHQLVDQIYATQKLDQTVSLLLADM 400 +P ++V +F++ + + EE ++V++I A+ L+ L A M Sbjct: 316 ATPEYVRYVVFLLFSDISRQYPTVLEE-------NYEKIVEEIRASNNLN----TLYALM 364 Query: 401 QRAERQLEMTNSVNDKTKIVVLVKQYIKNHLQQEISLQEIADTFHINRSYLSRLFREVSQ 460 Q+ +++ + ++ V + I+ +E++L+ +AD H+N SYL ++F++ ++ Sbjct: 365 QQVLAEVKNKPKIKKYSESVSQAVERIEQGYLEELNLKTVADELHLNPSYLGQIFKKETK 424 Query: 461 MSFTEFVLYEKTELA-IVMMQSGKSLTEISEKLGYLNLSSFTRMFKKVRGASPSLF 515 SF++++ +T+ A +++ + ++ EISEK+G+ N + F++MFKK+ G +P F Sbjct: 425 RSFSQYLNQVRTKHAQKLLLYTDDTINEISEKVGFNNTNYFSKMFKKLNGITPKEF 480 >ref|NP_244313.1| BH3446~unknown conserved protein [Bacillus halodurans] pir||F84080 hypothetical protein BH3446 [imported] - Bacillus halodurans (strain C-125) dbj|BAB07165.1| BH3446~unknown conserved protein [Bacillus halodurans] Length = 200 Score = 101 bits (251), Expect = 6e-20, Method: Compositional matrix adjust. Identities = 60/190 (31%), Positives = 107/190 (56%), Gaps = 9/190 (4%) Query: 2 KVMIVEDEILVRLGLRKSIPWSSLGLELVCEAKDGAEACDMFTRHLPDIVLVDIELPKMD 61 V+I +DEI++R G+R +I WS L L +V EA+DG EA ++ H DI+L D+ +P M+ Sbjct: 5 NVLIADDEIIIREGIRDAINWSELQLTVVAEAEDGEEALELALEHQVDILLADLNMPIMN 64 Query: 62 GLKFIRFAKTHGSGTHFIVLTCHQDMKYMREAIKLQVTDFILKSTLDMKELCDILQNITL 121 GL I+ +T I++T H + Y +EAI+L V D+I+K +D +L ++L+ + + Sbjct: 65 GLTLIKQLRTALPHCKVIIITGHDEFVYAQEAIRLSVVDYIIKP-VDADQLYEVLKKVCI 123 Query: 122 E------RLRDTSVDKAGLQDAAAAMPAEDFYRSWLNGSLRDSGQIRQQLAQMNVNRPVG 175 E R R+ + L+ + E F +W+ G+L + ++ +QL+ + + + Sbjct: 124 ELTEGQNRKREETFTAKQLEKNITLL-REQFCSNWVMGALTNE-EVAEQLSFLQLPDTLP 181 Query: 176 RFIACVMQLD 185 FI + L+ Sbjct: 182 SFIGVIRCLN 191 >ref|NP_242776.1| two-component response regulator [Bacillus halodurans] pir||F83888 two-component response regulator BH1910 [imported] - Bacillus halodurans (strain C-125) dbj|BAB05629.1| two-component response regulator [Bacillus halodurans] Length = 506 Score = 94.0 bits (232), Expect = 8e-18, Method: Compositional matrix adjust. Identities = 45/117 (38%), Positives = 70/117 (59%), Gaps = 1/117 (0%) Query: 3 VMIVEDEILVRLGLRKSIPWSSLGLELVCEAKDGAEACDMFTRHLPDIVLVDIELPKMDG 62 VMIV+DE +VR GL+ I W G ++ A++G E + + PD+++VDI +P++DG Sbjct: 4 VMIVDDEAMVREGLKALISWEEYGFRVIDTARNGKEGFTKYRQLSPDLMIVDIRMPEVDG 63 Query: 63 LKFIRFAKTHGSGTHFIVLTCHQDMKYMREAIKLQVTDFILKSTLDMKELCDILQNI 119 L I + S HFI+L+ H D Y ++A+ Q D++LK LD EL D L+ + Sbjct: 64 LSLIESIRAEDSAIHFIILSGHSDFNYAKKALGCQCDDYLLKP-LDEDELIDSLKKV 119 Score = 66.2 bits (160), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 34/97 (35%), Positives = 54/97 (55%), Gaps = 5/97 (5%) Query: 419 IVVLVKQYIKNHLQQEISLQEIADTFHINRSYLSRLFREVSQMSFTEFVLYEKTELAIVM 478 I ++ K Y KN + L+ +A F+ NR+YL +LF+ + F ++ + E + Sbjct: 403 IALIHKDYAKN-----LRLETLASVFNYNRAYLGKLFKNYTGEYFNTYLDKVRIENGKRL 457 Query: 479 MQSGKSLTEISEKLGYLNLSSFTRMFKKVRGASPSLF 515 +Q G + E++EK+GY N+ F R FKK G SPS F Sbjct: 458 LQKGYKVYEVAEKIGYANVDYFHRKFKKYVGVSPSTF 494 >ref|NP_242975.1| BH2109~unknown conserved protein [Bacillus halodurans] pir||E83913 hypothetical protein BH2109 [imported] - Bacillus halodurans (strain C-125) dbj|BAB05828.1| BH2109~unknown conserved protein [Bacillus halodurans] Length = 525 Score = 86.7 bits (213), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 54/171 (31%), Positives = 88/171 (51%), Gaps = 8/171 (4%) Query: 2 KVMIVEDEILVRLGLRKSIPWSSLGLELVCEAKDGAEACDMFTRHLPDIVLVDIELPKMD 61 KV++ +DE VR GL+ I W G E+ EA +G +A + PD+V+ DI +P D Sbjct: 3 KVLLADDEFFVRHGLKSLIEWEKCGYEVAAEADNGEDAFKLVQEIKPDLVITDIRMPVFD 62 Query: 62 GLKFI-RFAKTHGSGTHFIVLTCHQDMKYMREAIKLQVTDFILKSTLDMKELCDILQNIT 120 GL+ I + +T T FI+++ + D Y ++A++ DF+LK +D EL L I Sbjct: 63 GLQLIQKVNETLSFNTKFIIISGYNDFSYAQKAVRFGAVDFVLKP-IDQDELEAAL--IK 119 Query: 121 LERLRDTSVDKAGLQDAAAAMPAEDFYRSWLNGSLRDSGQIRQQLAQMNVN 171 L D +KA D + + F S G + ++R+ A++N+N Sbjct: 120 LAATLDQ--EKATNSDQEKVLLDQIFIHSL--GENKKENEVRRWAAKLNIN 166 Score = 58.2 bits (139), Expect = 5e-07, Method: Compositional matrix adjust. Identities = 29/96 (30%), Positives = 57/96 (59%), Gaps = 1/96 (1%) Query: 423 VKQYIKNHLQQEISLQEIADTFHINRSYLSRLFREVSQMSFTEFVLYEK-TELAIVMMQS 481 VK YI+NH + ISL+ IA F++N Y+ +LF++ + F E++L + E ++ Q+ Sbjct: 426 VKTYIENHYHENISLKSIASLFYMNPVYMGQLFKKTFGVYFKEYLLKLRMNEAKKLLRQT 485 Query: 482 GKSLTEISEKLGYLNLSSFTRMFKKVRGASPSLFVN 517 + E++E++G+ + F F+K+ +P+ + N Sbjct: 486 DMRVYEVAERVGFGSTDYFVTQFEKINKMTPTEYRN 521 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 0.322 0.135 0.392 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: 687,784,854 Number of extensions: 26055137 Number of successful extensions: 81502 Number of sequences better than 1.0e-05: 463 Number of HSP's gapped: 82827 Number of HSP's successfully gapped: 488 Length of query: 524 Length of database: 757,237,578 Length adjustment: 130 Effective length of query: 394 Effective length of database: 404,274,708 Effective search space: 159284234952 Effective search space used: 159284234952 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: 128 (53.9 bits)