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= 0001.4457.p (607 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... 1059 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 249 5e-67 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 248 1e-66 gi|300313916|ref|YP_003778008.1| two component response regulato... 242 6e-65 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 233 3e-62 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 1059 bits (2738), Expect = 0.0, Method: Compositional matrix adjust. Identities = 526/615 (85%), Positives = 556/615 (90%), Gaps = 16/615 (2%) Query: 1 MPPSPRISLAEMARSQGAPLTQLSSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQ 60 MP SPRISLAEMAR QG L SSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQ Sbjct: 1 MPSSPRISLAEMARHQGGGL---SSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQ 57 Query: 61 RMLLIHSRSMGTLRRELIDNLGIDKARGLLTRAGYISGARDAQLVRERWPEADPSTILMA 120 RMLLIHSRSMGTLRRELID LGID+ARGLLTRAGYISGARDAQLVRERWP+ADPSTILMA Sbjct: 58 RMLLIHSRSMGTLRRELIDQLGIDQARGLLTRAGYISGARDAQLVRERWPDADPSTILMA 117 Query: 121 GTRLHTLEGVVKVVPVSFSYDPDSGRYEGEFLWHNSSEADEHLAAYGIAAAPSCWQQIGY 180 GTRLHTLEG+VKVVPVSFSYDP++GRYEGEFLWHNS EADEHLAAYG+A APSCWQQ+GY Sbjct: 118 GTRLHTLEGLVKVVPVSFSYDPETGRYEGEFLWHNSCEADEHLAAYGVATAPSCWQQVGY 177 Query: 181 AIGYVSTLLGHLVIFREVECRAMGTPHCRVIGKSAELWSDAEDDLRYLNAQDFVGSGMLA 240 AIGYVSTLLGHLVIFREV+CRAMGT HCRVIG+SAELWSDAE+DLRYLNAQDFVGSGMLA Sbjct: 178 AIGYVSTLLGHLVIFREVQCRAMGTAHCRVIGRSAELWSDAEEDLRYLNAQDFVGSGMLA 237 Query: 241 SDGEIAGDSATPAEQAEAGEAELTRALVGTSSAFNAACHLLNRVAATDATVLFTGESGVG 300 S+ + + + + + +L ALVGTSSAFNAACHLLNRVAATDATVLFTGESGVG Sbjct: 238 SEADASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDATVLFTGESGVG 297 Query: 301 KERFARMLHQIGKRERQPFIAINCAAIPETLIETELFGVERGAYTGATQSRAGRFELADG 360 KERFARMLHQIGKR ++ IAINCAAIPETLIE ELFGVERGAYTGATQSRAGRFELADG Sbjct: 298 KERFARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFELADG 357 Query: 361 GTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSTRPVKVNVRVVAATNEDLAQAVRQGRF 420 GTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGS RPVKV+VRVVAATNEDLAQAVR+GRF Sbjct: 358 GTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRF 417 Query: 421 RQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKFYGQRHGVAVRGFTQRAIQALLNYSF 480 RQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLK YGQRHG+AVRGFTQRAIQALLNYSF Sbjct: 418 RQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSF 477 Query: 481 PGNIRELQNLVERGVILAQGHPLDLPHMFISGETLNDEVLSLALQGETGTLAGRQEDK-- 538 PGNIRELQNL+ERGVILAQGHPLDLPHMFISGE LNDEVLSLALQGETG LAG+ +K Sbjct: 478 PGNIRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETGMLAGKSVEKSV 537 Query: 539 ------PDAGGQQSLLDLLTQWR--STQQDAALSLPDMESTLIAEAIARAEGNLSAAARL 590 P A Q LLD+L QWR + + AAL+LP+ME LIAEAI RAEGNLSAAARL Sbjct: 538 EKSVAHPTA---QGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARL 594 Query: 591 LGISRAQLAYRQQKG 605 LGISRAQLAYRQQKG Sbjct: 595 LGISRAQLAYRQQKG 609 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 249 bits (635), Expect = 5e-67, Method: Compositional matrix adjust. Identities = 120/234 (51%), Positives = 166/234 (70%) Query: 267 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRERQPFIAINCAA 326 ++G S A +++ A + +T+L GESG GKE AR +H + R+ PFI +NCAA Sbjct: 203 VIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAA 262 Query: 327 IPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 386 + ETL+E+ELFG E+GA+TGA R GRFELA GGTLFLDE+G +S Q KLLRVLQE Sbjct: 263 LSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQER 322 Query: 387 EFERVGSTRPVKVNVRVVAATNEDLAQAVRQGRFRQDLFFRLNVFPIHLPPLRERRDDIP 446 EFERVG +R +KV+VR+V ATN DL +AV +G FR DL++R+NV I +PPLRERR+DIP Sbjct: 323 EFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIP 382 Query: 447 LLMNHFLKFYGQRHGVAVRGFTQRAIQALLNYSFPGNIRELQNLVERGVILAQG 500 L+ HFL+ + + A+ + +A++ ++N +PGN+REL+N VER + +G Sbjct: 383 YLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRG 436 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 248 bits (632), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 147/338 (43%), Positives = 199/338 (58%), Gaps = 23/338 (6%) Query: 265 RALVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRERQPFIAINC 324 R L+G S A + A +D TVL GE+G GKE A LH R +P I++NC Sbjct: 198 RELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNC 257 Query: 325 AAIPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQ 384 AA+P+TL+E+ELFG RGA++GA R G+FE+ADGGTLFLDEVG L L Q KLLRVLQ Sbjct: 258 AALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQ 317 Query: 385 EGEFERVGSTRPVKVNVRVVAATNEDLAQAVRQGRFRQDLFFRLNVFPIHLPPLRERRDD 444 G+ +RVGS R +V+VR++AATN DLA V++G FR D + RL+VFPI +PPLRER D Sbjct: 318 SGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRD 377 Query: 445 IPLLMNHFLKFYGQRHGVAVRGFTQRAIQALLNYSFPGNIRELQNLVERGVILAQGHPLD 504 + LL +FL+ R G++ + A +ALL+Y++PGNIREL++L+ R + + Sbjct: 378 VLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRT 437 Query: 505 LPHMFISGETLNDEVLSLALQGETGTLAGRQEDKP----DAGGQQSLLDLLTQWRSTQQD 560 P + TL+ L L T+A + P A SL D L ++ Sbjct: 438 RPTIL----TLDAAALELP-APSLATVAAAEPSLPAESTPAQASGSLRDALERY------ 486 Query: 561 AALSLPDMESTLIAEAIARAEGNLSAAARLLGISRAQL 598 E L++ A+ R GNL+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 = 242 bits (618), Expect = 6e-65, Method: Compositional matrix adjust. Identities = 144/338 (42%), Positives = 197/338 (58%), Gaps = 31/338 (9%) Query: 267 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRERQPFIAINCAA 326 LVG S A + R A +DATVL GE+G GKE AR LH+ G R +PF+A+NCAA Sbjct: 136 LVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAA 195 Query: 327 IPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 386 IP LIE+ELFG +GA++GAT R GRF+ ADGGTLFLDE+G + L Q K+LRVLQE Sbjct: 196 IPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQER 255 Query: 387 EFERVGSTRPVKVNVRVVAATNEDLAQAVRQGRFRQDLFFRLNVFPIHLPPLRERRDDIP 446 E VG + V+V+VRV+AAT+ DL + QGRFR+DL++RL V I +P LRER DI Sbjct: 256 ELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDIL 315 Query: 447 LLMNHFLKFYGQRHGVAVRGFTQRAIQALLNYSFPGNIRELQNLVERGVILAQGHPLDLP 506 + HFL+ G G A + + A + LL +++PGN+REL+N +ER +++ G Sbjct: 316 TIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG------ 366 Query: 507 HMFISGETLNDEVLSLALQGETGTLAGRQEDKPDAGGQQSLLDLLTQWRSTQQDAALSLP 566 L ++ E L+ R + +D W A++L Sbjct: 367 ---------------LCIEAEDIGLSARPPAGAASAASAPAID----WDGP---LAVALA 404 Query: 567 DMESTLIAEAIARAEGNLSAAARLLGISRAQLAYRQQK 604 ++E +I A+ A GN + AAR LGISR QL R ++ Sbjct: 405 EVERVMIERALQGAAGNRAEAARRLGISRQQLYRRLEE 442 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 233 bits (594), Expect = 3e-62, Method: Compositional matrix adjust. Identities = 123/257 (47%), Positives = 170/257 (66%), Gaps = 4/257 (1%) Query: 257 EAGEAELTRALVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRER 316 E G A+ T ++G + A + R++ ++ TVL TGESG GKE AR LH+ R Sbjct: 127 EQGAAQ-TPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRAS 185 Query: 317 QPFIAINCAAIPETLIETELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQ 376 QPF+A+N AAIP+ L+E+ELFG ERGA+TGA R GRFE A+GGTLFLDE+G + L Q Sbjct: 186 QPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQ 245 Query: 377 GKLLRVLQEGEFERVGSTRPVKVNVRVVAATNEDLAQAVRQGRFRQDLFFRLNVFPIHLP 436 +LLRVL +G F RVG + +K NVRV+AAT+++L Q VR+G FR+DL+ RLNV + LP Sbjct: 246 TRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLP 305 Query: 437 PLRERRDDIPLLMNHFLKFYGQRHGVAVRGFTQRAIQALLNYSFPGNIRELQNLVERGVI 496 LRER +DIP+L +FL ++ GV + + +A+Q L FPGN+R+L+NL + Sbjct: 306 SLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLCNWITV 365 Query: 497 LAQGHPL---DLPHMFI 510 +A G + DLP + Sbjct: 366 MAPGQTVEIKDLPQDLV 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 0.396 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: 1,983,917 Number of extensions: 89214 Number of successful extensions: 340 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 320 Number of HSP's successfully gapped: 12 Length of query: 607 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 516 Effective length of database: 1,188,985 Effective search space: 613516260 Effective search space used: 613516260 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)