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= 0033.0051.p (450 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313916|ref|YP_003778008.1| two component response regulato... 721 0.0 gi|300314016|ref|YP_003778108.1| two component transcription reg... 300 1e-82 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 298 8e-82 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 277 1e-75 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 264 1e-71 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 721 bits (1861), Expect = 0.0, Method: Compositional matrix adjust. Identities = 377/449 (83%), Positives = 395/449 (87%), Gaps = 8/449 (1%) Query: 1 MARILIVDDDAAFRGSLAETVGDLGHEVLEAGSTAAGLTLLAAHAVDAAIVDLRMPEEDG 60 MARILIVDDDAAFRGSLAETV DLGH+VLEAGSTAAGL LLAAHAVDAAIVDLRMP+EDG Sbjct: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDG 60 Query: 61 LVFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAPHXVETLERALRQS 120 L FLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRA VETLERALRQ Sbjct: 61 LAFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAA-LVETLERALRQG 119 Query: 121 PAATEAASATQSATGDERNALVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVAR 180 + AAS +ERN LVG+SEAMRQVFKQIGRAATSDATVL+LGETGTGKELVAR Sbjct: 120 ASTPAAASPAT----EERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVAR 175 Query: 181 ALHRNGLRAARPFVAINCAAIPAELIESELFGHVKGAFSGATAARLGRFQEAHGGTLFLD 240 ALHRNG RAARPFVA+NCAAIPAELIESELFGHVKGAFSGAT+ RLGRFQEA GGTLFLD Sbjct: 176 ALHRNGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLD 235 Query: 241 EIGDMALPTQAKILRVLQERELTPVGGQQAVKVDVRVIAATHRDLPQEISEGRFREDLWY 300 EIGDM L TQAKILRVLQERELTPVGG Q+V+VDVRVIAATHRDL EI++GRFREDLWY Sbjct: 236 EIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWY 295 Query: 301 RLQVLPIKVPPLRERPGDILAIAEHFLRQQGGDAPKRISPAAARRLLQHAWPGNVRELRN 360 RLQVL I VP LRERPGDIL IAEHFLRQ GGDAPKRISPAAAR LLQHAWPGNVRELRN Sbjct: 296 RLQVLTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRN 355 Query: 361 TMERAAVMSHGACIEPEDIALA---DRSVTENTSDVAIDWDGELAVAIAQVERVMLQRAL 417 TMERAAVMSHG CIE EDI L+ S AIDWDG LAVA+A+VERVM++RAL Sbjct: 356 TMERAAVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMIERAL 415 Query: 418 AAANGNRAEAARRLGISRQQLYRKLEEQG 446 A GNRAEAARRLGISRQQLYR+LEE G Sbjct: 416 QGAAGNRAEAARRLGISRQQLYRRLEEAG 444 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 300 bits (769), Expect = 1e-82, Method: Compositional matrix adjust. Identities = 184/426 (43%), Positives = 253/426 (59%), Gaps = 19/426 (4%) Query: 25 GHEVLEAGSTAAGLTLLAAHAVDAAIVDLRMPEEDGL-VFLQRAPAIAAIPCIMLTAYAS 83 G+ +L S A L LA I D+R+P DGL +F + A+P I+LTA+ + Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGT 93 Query: 84 GDNTIEAIRLGAFDHLTKPVPRAPHXVETLERALRQSPAATEAASATQSATGDERNALVG 143 + ++A GAF +LTKP ++ + +AL S AA S QS D ++ Sbjct: 94 IPDAVDATTQGAFAYLTKPFD-GHVLLDKVAQAL--SLAAPAPLSPDQSWRAD----ILS 146 Query: 144 DSEAMRQVFKQIGRAATSDATVLILGETGTGKELVARALHRNGLRAARPFVAINCAAIPA 203 S+ + ++ + A SDA++LI G++GTGKEL+ARA+HR RA +PF+A+NC AIP Sbjct: 147 RSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPE 206 Query: 204 ELIESELFGHVKGAFSGATAARLGRFQEAHGGTLFLDEIGDMALPTQAKILRVLQERELT 263 +L+ESELFGHVKGAF+GA R G FQ AHGGTLFLDEIGDM LP Q K+LRVLQE+ + Sbjct: 207 QLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVR 266 Query: 264 PVGGQQAVKVDVRVIAATHRDLPQEISEGRFREDLWYRLQVLPIKVPPLRERPGDILAIA 323 VG QA +VDVR+I+ATHRDL + EG+FREDL+YRL V+ + +P L ER DI +A Sbjct: 267 QVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLA 326 Query: 324 EHFLRQQGGDAPKRIS---PAAARRLLQHAWPGNVRELRNTMERAAVMSHGACIEPEDIA 380 HFL+ PKR++ P A L WPGNVR+L N +E+ +S I + Sbjct: 327 NHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTAPLIPA---S 383 Query: 381 LADRSVTENTSDVAIDWDGELAVAIAQVERVMLQRALAAANGNRAEAARRLGISRQQLYR 440 L R++ T D+ A A + ER L R L +GN ++AAR +R + YR Sbjct: 384 LVQRALRTPTLDLL-----RYAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEFYR 438 Query: 441 KLEEQG 446 L++ G Sbjct: 439 LLQKNG 444 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 298 bits (762), Expect = 8e-82, Method: Compositional matrix adjust. Identities = 171/383 (44%), Positives = 234/383 (61%), Gaps = 10/383 (2%) Query: 1 MARILIVDDDAAFRGSLAETVGDLGHEVLEAGSTAAGLTLLAAHAVDAAIVDLRMPEEDG 60 M I IVDDD + R L + + S + L + D+RMP G Sbjct: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASG 60 Query: 61 LVFLQRAPAI-AAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAPHXVETLERALRQ 119 L LQ A IP I++TA++ D+ + A + GAF++L KP VE + RAL + Sbjct: 61 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFD-VDKAVELIRRALDE 119 Query: 120 SPAATEAASATQSATGDERNALVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVA 179 S T+ ++G + AM+ VF+ IGR + S+ TVLI GE+G+GKELVA Sbjct: 120 SLRETDIEQGAAQTP-----EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVA 174 Query: 180 RALHRNGLRAARPFVAINCAAIPAELIESELFGHVKGAFSGATAARLGRFQEAHGGTLFL 239 RALH++ RA++PFVA+N AAIP +L+ESELFGH +GAF+GA A R GRF++A GGTLFL Sbjct: 175 RALHKHSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFL 234 Query: 240 DEIGDMALPTQAKILRVLQERELTPVGGQQAVKVDVRVIAATHRDLPQEISEGRFREDLW 299 DEIGDM L Q ++LRVL + VGG Q++K +VRVIAATH++L Q + EG FREDL+ Sbjct: 235 DEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLY 294 Query: 300 YRLQVLPIKVPPLRERPGDILAIAEHFLRQ---QGGDAPKRISPAAARRLLQHAWPGNVR 356 +RL V+ +++P LRER DI +A +FL Q Q G KR+SP A + L Q +PGNVR Sbjct: 295 HRLNVIRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVR 354 Query: 357 ELRNTMERAAVMSHGACIEPEDI 379 +L N VM+ G +E +D+ Sbjct: 355 QLENLCNWITVMAPGQTVEIKDL 377 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 277 bits (709), Expect = 1e-75, Method: Compositional matrix adjust. Identities = 173/450 (38%), Positives = 252/450 (56%), Gaps = 28/450 (6%) Query: 3 RILIVDDDAAFRGSLAETVGDLGHEVLEAGSTAAGLTLLAAHAVDAAIVDLRMPEE---- 58 ++LIV+DD + L ++ +EVL AG + L ++ H +DL +P + Sbjct: 7 KLLIVEDDPGLQKQLRWSLD--AYEVLVAGDRESALAMVRRHEPAVVTMDLGLPPDPDGA 64 Query: 59 -DGLVFLQRAPAIAA-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAPHXVETL--- 113 +G LQ+ A+A IMLT + ++AI +GA+D KP ETL Sbjct: 65 SEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPC-----IDETLRLV 119 Query: 114 -ERALRQSPAATEAASATQSATGDERNALVGDSEAMRQVFKQIGRAATSDATVLILGETG 172 +RA E Q+ L+ M V + I + A S A+V++LG +G Sbjct: 120 VQRAFYLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSG 179 Query: 173 TGKELVARALHRNGLRAARPFVAINCAAIPAELIESELFGHVKGAFSGATAARLGRFQEA 232 TGKE++ARALH+ R+ R F+AINCAAIP L+ESELFG+ KGAF+GA +G+ + A Sbjct: 180 TGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELA 239 Query: 233 HGGTLFLDEIGDMALPTQAKILRVLQERELTPVGGQQAVKVDVRVIAATHRDLPQEISEG 292 HGGT FLDE+GD+ +P QAK+LR LQER + VGG + VDVRVI ATH++L + + G Sbjct: 240 HGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASG 299 Query: 293 RFREDLWYRLQVLPIKVPPLRERPGDILAIAEHFLRQ---QGGDAPKRISPAAARRLLQH 349 FREDL+YRL + IK+P L+ER GD + +A HF+++ + G A +S A + ++ Sbjct: 300 GFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERY 359 Query: 350 AWPGNVRELRNTMERAAVMSHGACIEPEDIALADRSVTENTSDVAIDWDGELAVAIAQVE 409 WPGNVRE+ N + RA +M+ G I ED+ L+ ++ D + E Sbjct: 360 EWPGNVREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLNLRQVRD--------EAE 411 Query: 410 RVMLQRALAAANGNRAEAARRLGISRQQLY 439 R + +AL +GN +AA LG+SR LY Sbjct: 412 RKAVVKALTRMDGNILKAAELLGVSRPTLY 441 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 264 bits (674), Expect = 1e-71, Method: Compositional matrix adjust. Identities = 152/319 (47%), Positives = 199/319 (62%), Gaps = 19/319 (5%) Query: 141 LVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVARALHRNGLRAARPFVAINCAA 200 L+G S A RQ+ ++IG AA SD TVL+ GETGTGKELVA ALH RA +P +++NCAA Sbjct: 200 LIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAA 259 Query: 201 IPAELIESELFGHVKGAFSGATAARLGRFQEAHGGTLFLDEIGDMALPTQAKILRVLQER 260 +P L+ESELFGHV+GAFSGA A R G+F+ A GGTLFLDE+G++ L QAK+LRVLQ Sbjct: 260 LPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSG 319 Query: 261 ELTPVGGQQAVKVDVRVIAATHRDLPQEISEGRFREDLWYRLQVLPIKVPPLRERPGDIL 320 +L VG + +VDVR+IAAT+RDL E+ G FR D ++RL V PI+VPPLRER D+L Sbjct: 320 QLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 Query: 321 AIAEHFLRQQG---GDAPKRISPAAARRLLQHAWPGNVRELRNTMERAAVMS-------- 369 +A +FL Q G + R+S A R LL +AWPGN+REL + + R+A+ S Sbjct: 380 LLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRTRP 439 Query: 370 -----HGACIEPEDIALADRSVTENT---SDVAIDWDGELAVAIAQVERVMLQRALAAAN 421 A +E +LA + E + G L A+ + ER ++ AL Sbjct: 440 TILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERYERQLVSAALQRHG 499 Query: 422 GNRAEAARRLGISRQQLYR 440 GN A AR LG+ R L R Sbjct: 500 GNLAATARELGVDRANLNR 518 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 0.133 0.377 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: 1,281,168 Number of extensions: 52240 Number of successful extensions: 365 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 358 Number of HSP's successfully gapped: 17 Length of query: 450 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 362 Effective length of database: 1,203,190 Effective search space: 435554780 Effective search space used: 435554780 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: 132 (55.5 bits)