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= 0007.0132.p (518 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 704 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 250 2e-67 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 249 4e-67 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 248 7e-67 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 234 9e-63 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 704 bits (1816), Expect = 0.0, Method: Compositional matrix adjust. Identities = 368/525 (70%), Positives = 438/525 (83%), Gaps = 11/525 (2%) Query: 1 MLDALIPLMADLSRELHDSERYRRLLDTLRMLFPCDAAALLRLDGEILVPLAINGLSSDT 60 +LDAL+PL+ADLSRE+ D ERYRRLL TLR LFPCDAAALLRL+G++LVPLAI+GLSSDT Sbjct: 6 LLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDGLSSDT 65 Query: 61 LGRRFRVSEHPRFRVLLSNVPPTRFPANSSLPDPYDGLVEA----HSGELHVHDCMGCQI 116 LGRRFR++EHPRF +LL N PTRF A+S LPDPYDGLV+ HSGEL VHDCMGC + Sbjct: 66 LGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDCMGCAL 125 Query: 117 SMNGRPWGLLTLDALGPGRFDSVDTASLQAFASLAAATVNVAERIHNLAETSEQERQRAE 176 ++NGR WGL+TLDALG GRFD VD SLQAFA+LAAATVNVAERI +LA+ +Q +QRAE Sbjct: 126 TVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQAQQRAE 185 Query: 177 AYRLAANQSR--RELIGQSPAHKRMMKEVRLAGPSNMTVLITGETGTGKELVANAIHAAS 234 AYRL QS+ RELIGQSPAH+++M+E+ +A PS+MTVL+ GETGTGKELVA+A+HAAS Sbjct: 186 AYRLGLEQSQGQRELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAAS 245 Query: 235 PRARKPIISLNCAALPETLVESELFGHVRGAFSGAVSDRRGKFELADGGTLFLDEVGELS 294 PRA KP+ISLNCAALP+TLVESELFGHVRGAFSGAV+DRRGKFE+ADGGTLFLDEVGEL Sbjct: 246 PRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELP 305 Query: 295 LTVQAKLLRALQSGQIQRVGSDEEHKVDVRVIAATNRDLEEEVRLGRYRSDFYHRLSVYP 354 L VQAKLLR LQSGQ+QRVGSD EH+VDVR+IAATNRDL +EV+ G +R+DFYHRLSV+P Sbjct: 306 LAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFP 365 Query: 355 LAVPPLRERGHDILLISGFFLEENRFRLGLLSLRLATDAQEVLLNYRWPGNVRELEHVIA 414 + VPPLRERG D+LL++G+FLE+NR RLGL SLRL+ DAQ LL+Y WPGN+RELEH+I Sbjct: 366 IRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIG 425 Query: 415 RTALKALGKHPERPRILTLAAEDFDLSNEKANALSSHEGLHEQQVQTELDLQNASG-LRD 473 R+AL++L H RP ILTL A +L +++ E + E ASG LRD Sbjct: 426 RSALRSLATHRTRPTILTLDAAALELPAPSLATVAA----AEPSLPAESTPAQASGSLRD 481 Query: 474 AVSAYERRLVSACLARNGGNVASAARELGVDRANLNRMAKRLGLK 518 A+ YER+LVSA L R+GGN+A+ ARELGVDRANLNR+AKRLGL+ Sbjct: 482 ALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR 526 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 250 bits (638), Expect = 2e-67, Method: Compositional matrix adjust. Identities = 146/333 (43%), Positives = 201/333 (60%), Gaps = 19/333 (5%) Query: 184 QSRRELIGQSPAHKRMMKEVRLAGPSNMTVLITGETGTGKELVANAIHAASPRARKPIIS 243 + R +L+G+S A +++ K++ A S+ TVL+ GETGTGKELVA A+H RA +P ++ Sbjct: 131 EERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVA 190 Query: 244 LNCAALPETLVESELFGHVRGAFSGAVSDRRGKFELADGGTLFLDEVGELSLTVQAKLLR 303 +NCAA+P L+ESELFGHV+GAFSGA S R G+F+ ADGGTLFLDE+G++ L QAK+LR Sbjct: 191 VNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILR 250 Query: 304 ALQSGQIQRVGSDEEHKVDVRVIAATNRDLEEEVRLGRYRSDFYHRLSVYPLAVPPLRER 363 LQ ++ VG ++ +VDVRVIAAT+RDL+ E+ GR+R D ++RL V + VP LRER Sbjct: 251 VLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRER 310 Query: 364 GHDILLISGFFLEENRFRLGLLSLRLATDAQEVLLNYRWPGNVRELEHVIARTALKALGK 423 DIL I+ FL R G R++ A +LL + WPGNVREL + + R A+ + G Sbjct: 311 PGDILTIAEHFL---RQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG- 366 Query: 424 HPERPRILTLAAEDFDLSNEKANALSSHEGLHEQQVQTELDLQNASGLRDAVSAYERRLV 483 L + AED LS +S +D L A++ ER ++ Sbjct: 367 -------LCIEAEDIGLSARPPAGAAS------AASAPAIDWDGP--LAVALAEVERVMI 411 Query: 484 SACLARNGGNVASAARELGVDRANLNRMAKRLG 516 L GN A AAR LG+ R L R + G Sbjct: 412 ERALQGAAGNRAEAARRLGISRQQLYRRLEEAG 444 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 249 bits (636), Expect = 4e-67, Method: Compositional matrix adjust. Identities = 148/342 (43%), Positives = 202/342 (59%), Gaps = 25/342 (7%) Query: 189 LIGQSPAHKRMMKEVRLAGPSNMTVLITGETGTGKELVANAIHAASPRARKPIISLNCAA 248 L+G S A + ++ TVL TGE+G GKE A +H RA++ I++NCAA Sbjct: 264 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 323 Query: 249 LPETLVESELFGHVRGAFSGAVSDRRGKFELADGGTLFLDEVGELSLTVQAKLLRALQSG 308 +PETL+E+ELFG RGA++GA R G+FELADGGTLFLDEVG LSL Q KLLR LQ G Sbjct: 324 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 383 Query: 309 QIQRVGSDEEHKVDVRVIAATNRDLEEEVRLGRYRSDFYHRLSVYPLAVPPLRERGHDIL 368 + +RVGS KVDVRV+AATN DL + VR GR+R D + RL+V+P+ +PPLRER DI Sbjct: 384 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 443 Query: 369 LISGFFLEENRFRLGLLSLRLATDAQEVLLNYRWPGNVRELEHVIARTALKALGKHPERP 428 L+ FL+ R G+ A + LLNY +PGN+REL+++I R + A G + P Sbjct: 444 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 503 Query: 429 RILT--------------------LAAEDFDLSNEKANALSSHEGLHEQQVQTELDLQNA 468 + LA + + S EK+ A + +GL + Q Q A Sbjct: 504 HMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWR---QEA 560 Query: 469 SGLRDAVS--AYERRLVSACLARNGGNVASAARELGVDRANL 508 +G A++ ERRL++ + R GN+++AAR LG+ RA L Sbjct: 561 AGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQL 602 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 248 bits (634), Expect = 7e-67, Method: Compositional matrix adjust. Identities = 160/397 (40%), Positives = 226/397 (56%), Gaps = 15/397 (3%) Query: 26 LDTLRMLFPCDAAALLRLDGEILVPLAINGLSSDTLGR-RFRVSEHPRFRVLLSNVP-PT 83 L+T R+L +L++ GE+ + AI GLS + R+RV E ++ + P Sbjct: 45 LETKRVLL-----SLMQDSGELQLVSAI-GLSYEEFQSGRYRVGEGITGKIFQTETPIVV 98 Query: 84 RFPANSSLPDPYDGLVEAHSGELHVHDCMGCQISMNGRPWGLLTL--DALGPGRFDSVDT 141 R A L ++ GE V +G I G+L + D P R + Sbjct: 99 RDLAQEPLFLARTSPRQSQDGE--VISFVGVPIKAAREMLGVLCVFRDGQSPSRSVDHEV 156 Query: 142 ASLQAFASLAAATVNVAERIHNLAETSE-QERQRAEAYRLAANQSRRELIGQSPAHKRMM 200 L A+L TV + + AE + QE +R + +L +IG S A + + Sbjct: 157 RLLTMVANLIGQTVRLYRSVA--AERQQLQEEKRQLSRQLQGKYKLDNVIGISKAMQEVF 214 Query: 201 KEVRLAGPSNMTVLITGETGTGKELVANAIHAASPRARKPIISLNCAALPETLVESELFG 260 +V + PS T+L+ GE+GTGKE++A AIH SPR P I +NCAAL ETL+ESELFG Sbjct: 215 AQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFG 274 Query: 261 HVRGAFSGAVSDRRGKFELADGGTLFLDEVGELSLTVQAKLLRALQSGQIQRVGSDEEHK 320 H +GAF+GA +R+G+FELA GGTLFLDE+GE+S QAKLLR LQ + +RVG K Sbjct: 275 HEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIK 334 Query: 321 VDVRVIAATNRDLEEEVRLGRYRSDFYHRLSVYPLAVPPLRERGHDILLISGFFLEENRF 380 VDVR++ ATNRDLE+ V G +R+D Y+R++V + +PPLRER DI + FLE+ R Sbjct: 335 VDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRV 394 Query: 381 RLGLLSLRLATDAQEVLLNYRWPGNVRELEHVIARTA 417 + ++ A +V++N WPGNVRELE+ + RTA Sbjct: 395 ENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTA 431 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 234 bits (598), Expect = 9e-63, Method: Compositional matrix adjust. Identities = 118/239 (49%), Positives = 170/239 (71%) Query: 188 ELIGQSPAHKRMMKEVRLAGPSNMTVLITGETGTGKELVANAIHAASPRARKPIISLNCA 247 E++GQ+PA + + + + SN+TVLITGE+G+GKELVA A+H SPRA +P ++LN A Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTA 194 Query: 248 ALPETLVESELFGHVRGAFSGAVSDRRGKFELADGGTLFLDEVGELSLTVQAKLLRALQS 307 A+P+ L+ESELFGH RGAF+GA + RRG+FE A+GGTLFLDE+G++ L +Q +LLR L Sbjct: 195 AIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSD 254 Query: 308 GQIQRVGSDEEHKVDVRVIAATNRDLEEEVRLGRYRSDFYHRLSVYPLAVPPLRERGHDI 367 G RVG + K +VRVIAAT+++LE+ VR G +R D YHRL+V L +P LRER DI Sbjct: 255 GHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDI 314 Query: 368 LLISGFFLEENRFRLGLLSLRLATDAQEVLLNYRWPGNVRELEHVIARTALKALGKHPE 426 +++ +FL ++ +LG+ + RL+ A + L +PGNVR+LE++ + A G+ E Sbjct: 315 PILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTVE 373 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 0.319 0.135 0.384 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: 1,563,729 Number of extensions: 66539 Number of successful extensions: 309 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 289 Number of HSP's successfully gapped: 12 Length of query: 518 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 429 Effective length of database: 1,198,455 Effective search space: 514137195 Effective search space used: 514137195 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 (21.8 bits) S2: 133 (55.8 bits)