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= 0015.0373.p (620 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 1036 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 253 3e-68 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 253 4e-68 gi|300313916|ref|YP_003778008.1| two component response regulato... 234 1e-62 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 229 7e-61 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 1036 bits (2680), Expect = 0.0, Method: Compositional matrix adjust. Identities = 517/619 (83%), Positives = 548/619 (88%), Gaps = 13/619 (2%) Query: 1 MPPSQRISLAEMVRSQGSAAAPVQLSSASTDRWSVDAHPTLADLSECLFFSPGDGRIWLN 60 MP S RISLAEM R QG LSSA TDRWSVDAHPTLADLSECLFFSPGDGRIWLN Sbjct: 1 MPSSPRISLAEMARHQGGG-----LSSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLN 55 Query: 61 DQRMLLIHSRSMGTLRRELIDNLGIDKARGLLTRAGYISGARDAQLVRERWPEADPSTIL 120 DQRMLLIHSRSMGTLRRELID LGID+ARGLLTRAGYISGARDAQLVRERWP+ADPSTIL Sbjct: 56 DQRMLLIHSRSMGTLRRELIDQLGIDQARGLLTRAGYISGARDAQLVRERWPDADPSTIL 115 Query: 121 MAGTRLHTLEGVVKVIPVSFSYDPDSGRYEGEFLWHNSSEADEHLAAYGVATAPSCWQQI 180 MAGTRLHTLEG+VKV+PVSFSYDP++GRYEGEFLWHNS EADEHLAAYGVATAPSCWQQ+ Sbjct: 116 MAGTRLHTLEGLVKVVPVSFSYDPETGRYEGEFLWHNSCEADEHLAAYGVATAPSCWQQV 175 Query: 181 GYAIGYVSTLLGHLVIFREVECRAMGTPHCRVIGKSAELWSDAEDDLRYLNAQDFVGSGM 240 GYAIGYVSTLLGHLVIFREV+CRAMGT HCRVIG+SAELWSDAE+DLRYLNAQDFVGSGM Sbjct: 176 GYAIGYVSTLLGHLVIFREVQCRAMGTAHCRVIGRSAELWSDAEEDLRYLNAQDFVGSGM 235 Query: 241 LATDGQAAAISHSGLSAEAAEAMEADLTRALVGTSSAFNAACHLLNRVAPTDATVLFTGE 300 LA++ A+A G + + DL ALVGTSSAFNAACHLLNRVA TDATVLFTGE Sbjct: 236 LASEADASA--EDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDATVLFTGE 293 Query: 301 SGVGKERFARMLHQIGRRERQPFVAINCAAIPETLIETELFGVERGAYTGATQSRAGRFE 360 SGVGKERFARMLHQIG+R ++ +AINCAAIPETLIE ELFGVERGAYTGATQSRAGRFE Sbjct: 294 SGVGKERFARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFE 353 Query: 361 LADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSTRPLKVKVRVVAATNEDLAVAVR 420 LADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGS RP+KV VRVVAATNEDLA AVR Sbjct: 354 LADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVR 413 Query: 421 EGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKFYGQRHGIAVRGFTQRAVQALL 480 EGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLK YGQRHGIAVRGFTQRA+QALL Sbjct: 414 EGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALL 473 Query: 481 NYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGETLNDEVLSLALQGEGEGETGTLA 540 NYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGE LNDEVLSLALQ GETG LA Sbjct: 474 NYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQ----GETGMLA 529 Query: 541 GRQGER--RKETSHQPEGSLLETVQQWHGGRKEEGGALSLPALEQTLIAEAIERAGGNLS 598 G+ E+ K +H LL+ ++QW E AL+LP +E+ LIAEAIERA GNLS Sbjct: 530 GKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLS 589 Query: 599 AAARLLGITRAQLAYRQQK 617 AAARLLGI+RAQLAYRQQK Sbjct: 590 AAARLLGISRAQLAYRQQK 608 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 253 bits (646), Expect = 3e-68, Method: Compositional matrix adjust. Identities = 142/347 (40%), Positives = 209/347 (60%), Gaps = 15/347 (4%) Query: 271 LVGTSSAFNAACHLLNRVAPTDATVLFTGESGVGKERFARMLHQIGRRERQPFVAINCAA 330 ++G S A +++ AP+ +T+L GESG GKE AR +H + R+ PF+ +NCAA Sbjct: 203 VIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAA 262 Query: 331 IPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 390 + ETL+E+ELFG E+GA+TGA R GRFELA GGTLFLDE+G +S Q KLLRVLQE Sbjct: 263 LSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQER 322 Query: 391 EFERVGSTRPLKVKVRVVAATNEDLAVAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 450 EFERVG +R +KV VR+V ATN DL AV +G FR DL++R+NV I +PPLRERR+DIP Sbjct: 323 EFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIP 382 Query: 451 LLMNHFLKFYGQRHGIAVRGFTQRAVQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 510 L+ HFL+ + + A+ + +A++ ++N +PGN+REL+N +ER + +G + Sbjct: 383 YLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGDLITEV 442 Query: 511 HMFISGETLNDEVLSLALQGEGEGETGTLAGRQGERRKETSHQPEGSLLETVQQWHGGRK 570 H ++ L+ L G+ + + + + ++H S G K Sbjct: 443 HFSCQ----QNKCLTKVLHEPGQQQPVVVVPLE----RISAHTAPSS-------PSGMAK 487 Query: 571 EEGGALSLPALEQTLIAEAIERAGGNLSAAARLLGITRAQLAYRQQK 617 ++ A + P E+ + A+E+ G + AAR L I+ Q+ Y QK Sbjct: 488 DKPLAAAPPTSERERLIWAMEQCGWVQAKAARALNISPRQMGYALQK 534 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 253 bits (645), Expect = 4e-68, Method: Compositional matrix adjust. Identities = 149/344 (43%), Positives = 204/344 (59%), Gaps = 26/344 (7%) Query: 269 RALVGTSSAFNAACHLLNRVAPTDATVLFTGESGVGKERFARMLHQIGRRERQPFVAINC 328 R L+G S A + AP+D TVL GE+G GKE A LH R +P +++NC Sbjct: 198 RELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNC 257 Query: 329 AAIPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQ 388 AA+P+TL+E+ELFG RGA++GA R G+FE+ADGGTLFLDEVG L L Q KLLRVLQ Sbjct: 258 AALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQ 317 Query: 389 EGEFERVGSTRPLKVKVRVVAATNEDLAVAVREGRFRQDLFFRLNVFPIHLPPLRERRDD 448 G+ +RVGS R +V VR++AATN DLA V+ G FR D + RL+VFPI +PPLRER D Sbjct: 318 SGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRD 377 Query: 449 IPLLMNHFLKFYGQRHGIAVRGFTQRAVQALLNYSFPGNIRELQNLIERGVILAQGHPLD 508 + LL +FL+ R G++ + A +ALL+Y++PGNIREL++LI R + + Sbjct: 378 VLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRT 437 Query: 509 LPHMFISGETLNDEVLSLALQGEGEGETGTLAGRQGERRKE-TSHQPEGSLLETVQQWHG 567 P + TL+ L L T+A + E T Q GSL + ++++ Sbjct: 438 RPTIL----TLDAAALELP-----APSLATVAAAEPSLPAESTPAQASGSLRDALERY-- 486 Query: 568 GRKEEGGALSLPALEQTLIAEAIERAGGNLSAAARLLGITRAQL 611 E+ L++ A++R GGNL+A AR LG+ RA L Sbjct: 487 --------------ERQLVSAALQRHGGNLAATARELGVDRANL 516 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 234 bits (598), Expect = 1e-62, Method: Compositional matrix adjust. Identities = 142/345 (41%), Positives = 196/345 (56%), Gaps = 41/345 (11%) Query: 271 LVGTSSAFNAACHLLNRVAPTDATVLFTGESGVGKERFARMLHQIGRRERQPFVAINCAA 330 LVG S A + R A +DATVL GE+G GKE AR LH+ G R +PFVA+NCAA Sbjct: 136 LVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAA 195 Query: 331 IPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 390 IP LIE+ELFG +GA++GAT R GRF+ ADGGTLFLDE+G + L Q K+LRVLQE Sbjct: 196 IPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQER 255 Query: 391 EFERVGSTRPLKVKVRVVAATNEDLAVAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 450 E VG + ++V VRV+AAT+ DL + +GRFR+DL++RL V I +P LRER DI Sbjct: 256 ELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDIL 315 Query: 451 LLMNHFLKFYGQRHGIAVRGFTQRAVQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 510 + HFL+ G G A + + A + LL +++PGN+REL+N +ER +++ G Sbjct: 316 TIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG------ 366 Query: 511 HMFISGETLNDEVLSLALQGEGEGETGTLAGRQGERRKETSHQPEGSLLETVQQWHGGRK 570 L ++ E G + + +G L Sbjct: 367 ---------------LCIEAEDIGLSARPPAGAASAASAPAIDWDGPL------------ 399 Query: 571 EEGGALSLPALEQTLIAEAIERAGGNLSAAARLLGITRAQLAYRQ 615 A++L +E+ +I A++ A GN + AAR LGI+R QL YR+ Sbjct: 400 ----AVALAEVERVMIERALQGAAGNRAEAARRLGISRQQL-YRR 439 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 229 bits (583), Expect = 7e-61, Method: Compositional matrix adjust. Identities = 120/250 (48%), Positives = 164/250 (65%), Gaps = 3/250 (1%) Query: 268 TRALVGTSSAFNAACHLLNRVAPTDATVLFTGESGVGKERFARMLHQIGRRERQPFVAIN 327 T ++G + A + R++ ++ TVL TGESG GKE AR LH+ R QPFVA+N Sbjct: 133 TPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALN 192 Query: 328 CAAIPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVL 387 AAIP+ L+E+ELFG ERGA+TGA R GRFE A+GGTLFLDE+G + L Q +LLRVL Sbjct: 193 TAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVL 252 Query: 388 QEGEFERVGSTRPLKVKVRVVAATNEDLAVAVREGRFRQDLFFRLNVFPIHLPPLRERRD 447 +G F RVG + LK VRV+AAT+++L VREG FR+DL+ RLNV + LP LRER + Sbjct: 253 SDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSE 312 Query: 448 DIPLLMNHFLKFYGQRHGIAVRGFTQRAVQALLNYSFPGNIRELQNLIERGVILAQGHPL 507 DIP+L +FL ++ G+ + + +A+Q L FPGN+R+L+NL ++A G + Sbjct: 313 DIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTV 372 Query: 508 ---DLPHMFI 514 DLP + Sbjct: 373 EIKDLPQDLV 382 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 0.394 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: 1,948,982 Number of extensions: 85091 Number of successful extensions: 340 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 326 Number of HSP's successfully gapped: 12 Length of query: 620 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 529 Effective length of database: 1,188,985 Effective search space: 628973065 Effective search space used: 628973065 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)