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= 0001.3125.p (312 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312460|ref|YP_003776552.1| LysR family transcription regul... 590 e-170 gi|300310906|ref|YP_003774998.1| LysR family transcription regul... 146 2e-36 gi|300313964|ref|YP_003778056.1| LysR family transcription regul... 132 3e-32 gi|300314051|ref|YP_003778143.1| transcription regulator protein... 129 2e-31 gi|300310443|ref|YP_003774535.1| LysR family transcription regul... 116 3e-27 >gi|300312460|ref|YP_003776552.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 590 bits (1520), Expect = e-170, Method: Compositional matrix adjust. Identities = 299/312 (95%), Positives = 304/312 (97%) Query: 1 MPSPLPPLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGV 60 MPS LPPLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGV Sbjct: 1 MPSSLPPLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGV 60 Query: 61 EPTEAALAFYAEVKASLDRIALAAEHLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDN 120 EPTEAAL+FYAEVKASLDRIALAAE LALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDN Sbjct: 61 EPTEAALSFYAEVKASLDRIALAAEQLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDN 120 Query: 121 PRIEVRVTTTMSEYFEDVKDPFDVIIWRSPLERSGYDCVRFLDDVSVPLASPHFLETHPI 180 PRIEVRVTTTMSEYFEDVKDPFDVIIWRSPLERSGY+C+RFLDDVSVPLASPHFLETHPI Sbjct: 121 PRIEVRVTTTMSEYFEDVKDPFDVIIWRSPLERSGYECMRFLDDVSVPLASPHFLETHPI 180 Query: 181 RVPRDFVEVPLIHLSSRSAAWSQWLGKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMG 240 RVPRDFVEVPLIHLSSRSAAWSQWL KAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMG Sbjct: 181 RVPRDFVEVPLIHLSSRSAAWSQWLSKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMG 240 Query: 241 TLALVDDDLAAGRLVRLFPEIVLHGEGYHMLYRSNADSNPALKTFITWLKQMGLASSFDA 300 TLALVDDDLAAGRLVRLFPEIVLHGEGYHML RS A++NPALKTFITWLKQMG ASSFD Sbjct: 241 TLALVDDDLAAGRLVRLFPEIVLHGEGYHMLCRSGAETNPALKTFITWLKQMGQASSFDP 300 Query: 301 QHTWPADFPGEY 312 Q TWPADFPGEY Sbjct: 301 QRTWPADFPGEY 312 >gi|300310906|ref|YP_003774998.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 146 bits (369), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 101/291 (34%), Positives = 145/291 (49%), Gaps = 4/291 (1%) Query: 7 PLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGVEPTEAA 66 PL A++ F AA R +S TLAAHEL +TH A+S+QIK+LE Y PLF R++R V TE Sbjct: 7 PLNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQVLLTERG 66 Query: 67 LAFYAEVKASLDRIALAAEHLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDNPRIEVR 126 F+ E +L+ +A AA + +R V + PS A+RWLIP LS F P I + Sbjct: 67 RQFFEEASPALEILANAARRVMRDAPTRTVVINVRPSFAVRWLIPHLSDFVERYPGIAPQ 126 Query: 127 VTTTMSEYFEDVKDPFDVIIWRSPLE-RSGYDCVRFLDDVSVPLASPHFLETHPIRVPRD 185 V T+ + + FD+ + R RF++D V +ASP L+ P+ Sbjct: 127 VVTSTATVGK-AGSSFDIAVRRGETNWPETLKVQRFMEDELVLVASPALLQAMPLEDVSG 185 Query: 186 FVEVPLIHLSSRSAAWSQWLGKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMGTLALV 245 ++ SR W W AG+ R ++H LQA GV + ++L Sbjct: 186 LARHTVLLSRSRRNDWEDWRKLAGLKRSRSQAMLHFDHVHFVLQAVVDGLGVALSPVSLA 245 Query: 246 DDDLAAGRLVRLFPEIVLHGEGYHMLYRSNADSNPALKTFITWLKQMGLAS 296 D+DL +GRLV FP++ L Y++ + A S L F WL + AS Sbjct: 246 DNDLRSGRLVCPFPDLRLTLAPYYLGINAQAGSEAQL--FARWLAEYRGAS 294 >gi|300313964|ref|YP_003778056.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 132 bits (333), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 92/302 (30%), Positives = 139/302 (46%), Gaps = 15/302 (4%) Query: 3 SPLPPLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGVEP 62 + LPPL AL+ FEA R S T AA EL +T SAVS+Q++ LE + EQ LF+R +R +E Sbjct: 2 NKLPPLTALRAFEATARLLSFTAAADELHVTQSAVSRQVRILEAHLEQKLFVRLTRRIEL 61 Query: 63 TEAALAFYAEVKASLDRIALAAEHLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDNPR 122 T A A++ +++ + +RI A E L + + + P +A WL+PRL F +N Sbjct: 62 TRAGAAYFQQIRQAFERICAAGEQLHARRQRHTLTIGVLPGLASLWLVPRLELFWRENKE 121 Query: 123 IEVRVT----------TTMSEYFEDVKDPFDVIIWRSPLERSGYDCVRFLDDVSVP---- 168 I+VR+ TTM + P +R D D+ P Sbjct: 122 IDVRIVVATGAADFGRTTMDMSIQVGNLPGTTSQGLPLKKRMAVDWHDLRADLLFPDALV 181 Query: 169 -LASPHFLETHPIRVPRDFVEVPLIHLSSRSAAWSQWLGKAGVAVRRKMPGTVYEHSFLS 227 L P HP+R D + LIH + R AW+ WL + G + + G ++ Sbjct: 182 ALCHPRLWRQHPVRSVADLSQHRLIHTAIRPDAWAHWLQQHGSRLGARQAGMECSQYPVA 241 Query: 228 LQAAATDQGVGMGTLALVDDDLAAGRLVRLFPEIVLHGEGYHMLYRSNADSNPALKTFIT 287 LQAA +G+ + L + RL RLF Y++L + + A++ F Sbjct: 242 LQAAMNGEGIALVPSVLAESFDPQHRLRRLFGGPTPSAGQYYLLTPGDRYDDSAVRRFRQ 301 Query: 288 WL 289 WL Sbjct: 302 WL 303 >gi|300314051|ref|YP_003778143.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 129 bits (325), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 88/285 (30%), Positives = 143/285 (50%), Gaps = 10/285 (3%) Query: 26 AAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGVEPTEAALAFYAEVKASLDRIALAAE 85 AA E+ +T A+S Q+++LEE LFLR + + TE F A ++ SL IALAAE Sbjct: 28 AAEEVHVTPGAISHQVRALEEDLGLQLFLRHGKRISITETGQRFAATIRKSLSEIALAAE 87 Query: 86 HLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDNPRIEVRVTTTMSEYFEDVK-DPFDV 144 HL + + + + PS A RWL PRL +F +P +EV + + + + D++ D DV Sbjct: 88 HLRSQNRQQRLVISTTPSFASRWLAPRLWRFIDAHPELEVVLQS--AAHLNDLRLDGIDV 145 Query: 145 IIWRSPLERSGYDCVRFLDDVSVPLASPHFLETHPIRV--PRDFVEVPLIHLSSRSAAWS 202 + SG + DD P+A+P + ++ P D L+ + SR +W Sbjct: 146 GLRFGRGNYSGLVSEKLSDDYYYPVAAPGYRGKRSKKLARPADLAHCSLLRVDSRE-SWQ 204 Query: 203 QWLGKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGMGTLALVDDDLAAGRLVRLFPEIV 262 WL +AG+ + G + E S L+L+ AA +GV + + +++ G LVRLF +V Sbjct: 205 PWLAEAGLELPEPTGGLLVEDSSLTLRQAAEGKGVALARHVIASQEISTGELVRLFDVVV 264 Query: 263 LHGEGYHMLYRSNADSNPALKTFITWL-KQMGLASSFDAQHTWPA 306 + ++ ++ A P + F W+ ++M L F A WP Sbjct: 265 PSEDAHYFVHLPEALEKPGVAAFKEWIFEEMRL---FHASAAWPG 306 >gi|300310443|ref|YP_003774535.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 295 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 87/293 (29%), Positives = 138/293 (47%), Gaps = 13/293 (4%) Query: 5 LPPLKALKVFEAAVRTRSLTLAAHELFITHSAVSQQIKSLEEYFEQPLFLRQSRGVEPTE 64 LPPL L+ FEA R +S LAA EL +T SAVS Q+ LE Y LF R + GV T Sbjct: 4 LPPLPNLQAFEAVARRKSFALAAAELHLTASAVSHQVARLESYLGIRLFERSAHGVRITT 63 Query: 65 AALAFYAEVKASLDRIALAAEHLALAGKSRVVRLIAAPSVAMRWLIPRLSQFQIDNPRIE 124 A A+ A ++ ++ I AA G S + + +APS+A WL+ RL+ F P I Sbjct: 64 AGEAYLARIQGAISAIT-AASMDVRQGVSNTLYIHSAPSIASLWLMARLNDFARSYPEIT 122 Query: 125 VRVTTTMSE-YFE----DVKDPFDVIIWRSPLERSGYDCVRFLDDVSVPLASPHFLETHP 179 ++ S+ FE D+ + + W G ++ VPLASP F+ + Sbjct: 123 FNLSAAHSQSNFELGEVDIDIRYGIPNW------PGLVVEPLFEERIVPLASPAFIREYR 176 Query: 180 IRVPRDFVEVPLIHLSSRSAAWSQWLGKAGVAVRRKMPGTVYEHSFLSLQAAATDQGVGM 239 +R P D + V LI + W+ W G+ + ++ + +SL AA GV + Sbjct: 177 LRKPADLLGVKLIRSNVSVVQWADWFGEFADVRAPEQFAVRFDRAQMSLDAATQGLGVAL 236 Query: 240 GTLALVDDDLAAGRLVRLFP-EIVLHGEGYHMLYRSNADSNPALKTFITWLKQ 291 + + L +L +F E + + + +Y ++ PA+ F+ WL++ Sbjct: 237 ESATVAARHLEEKKLKPIFGLERAIKVKAHFAVYPAHHARRPAVAAFLEWLRE 289 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.322 0.135 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,016,084 Number of extensions: 41896 Number of successful extensions: 227 Number of sequences better than 1.0e-08: 31 Number of HSP's gapped: 220 Number of HSP's successfully gapped: 31 Length of query: 312 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 227 Effective length of database: 1,217,395 Effective search space: 276348665 Effective search space used: 276348665 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: 130 (54.7 bits)