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= 0022.0342.p (448 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... 874 0.0 gi|300314016|ref|YP_003778108.1| two component transcription reg... 314 1e-86 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 301 6e-83 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 276 3e-75 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 272 3e-74 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 874 bits (2259), Expect = 0.0, Method: Compositional matrix adjust. Identities = 441/448 (98%), Positives = 442/448 (98%) Query: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIIDLRMPDEDG 60 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAI+DLRMPDEDG Sbjct: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDG 60 Query: 61 LAFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGA 120 LAFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGA Sbjct: 61 LAFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGA 120 Query: 121 SAPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRK 180 S PAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHR Sbjct: 121 STPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRN 180 Query: 181 GARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDM 240 GARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDM Sbjct: 181 GARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDM 240 Query: 241 ELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVL 300 ELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVL Sbjct: 241 ELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVL 300 Query: 301 TIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERA 360 TIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERA Sbjct: 301 TIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERA 360 Query: 361 AVMSHGLCIEAEDIGLSARHPVGAAGAASAPAIDWDGPLAAALAEVERVMIERALQGAAG 420 AVMSHGLCIEAEDIGLSAR P GAA AASAPAIDWDGPLA ALAEVERVMIERALQGAAG Sbjct: 361 AVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMIERALQGAAG 420 Query: 421 NRAEAARRLGISRQQLYRRLEEAGKSHD 448 NRAEAARRLGISRQQLYRRLEEAGKSHD Sbjct: 421 NRAEAARRLGISRQQLYRRLEEAGKSHD 448 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 314 bits (804), Expect = 1e-86, Method: Compositional matrix adjust. Identities = 185/427 (43%), Positives = 257/427 (60%), Gaps = 23/427 (5%) Query: 25 GHDVLEAGSTAAGLKLLAAHAVDAAIIDLRMPDEDGLAFL----QRAPAIAAIPCIMLTA 80 G+ +L S A L LA I D+R+P DGLA R PA+ P I+LTA Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPAL---PVILLTA 90 Query: 81 YASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGASAPAAASPATEERNQLVGES 140 + + + ++A GAF +LTKP L++ + +AL +APA SP R ++ S Sbjct: 91 HGTIPDAVDATTQGAFAYLTKPFDGHVLLDKVAQAL--SLAAPAPLSPDQSWRADILSRS 148 Query: 141 EAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRKGARAARPFVAVNCAAIPAEL 200 + + ++ + A SDA++L+ G++GTGKEL+ARA+HR ARA +PF+AVNC AIP +L Sbjct: 149 QRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPEQL 208 Query: 201 IESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELTPV 260 +ESELFGHVKGAF+GA R G FQ A GGTLFLDEIGDM L Q K+LRVLQE+ + V Sbjct: 209 LESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVRQV 268 Query: 261 GGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIAEH 320 G NQ+ VDVR+I+ATHRDL+ + +G+FREDL+YRL V+T+ +PAL ER DI +A H Sbjct: 269 GANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLANH 328 Query: 321 FLRQLGGDAPKRIS---PAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAEDIGLS 377 FL+ + PKR++ P A +L WPGNVR+L N +E+ +S I A + + Sbjct: 329 FLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTAPLIPASLVQRA 388 Query: 378 ARHPVGAAGAASAPAIDWDGPLAAALAEVERVMIERALQGAAGNRAEAARRLGISRQQLY 437 R P +D A A + ER + R L+ GN ++AAR +R + Y Sbjct: 389 LR----------TPTLDLLR-YAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEFY 437 Query: 438 RRLEEAG 444 R L++ G Sbjct: 438 RLLQKNG 444 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 301 bits (771), Expect = 6e-83, Method: Compositional matrix adjust. Identities = 170/384 (44%), Positives = 242/384 (63%), Gaps = 17/384 (4%) Query: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIIDLRMPDEDG 60 M I IVDDD + R L + ++ S + L + D+RMP G Sbjct: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASG 60 Query: 61 LAFLQRAPAI-AAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQG 119 L LQ A IP I++TA++ D+ + A + GAF++L KP VE + RAL + Sbjct: 61 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES 120 Query: 120 ASAP-----AAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVA 174 AA +P +++G++ AM+ VF+ IGR + S+ TVL+ GE+G+GKELVA Sbjct: 121 LRETDIEQGAAQTP------EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVA 174 Query: 175 RALHRKGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFL 234 RALH+ RA++PFVA+N AAIP +L+ESELFGH +GAF+GA + R GRF++A+GGTLFL Sbjct: 175 RALHKHSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFL 234 Query: 235 DEIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLW 294 DEIGDM L Q ++LRVL + VGG+QS++ +VRVIAATH++L+ + +G FREDL+ Sbjct: 235 DEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLY 294 Query: 295 YRLQVLTIMVPALRERPGDILTIAEHFL----RQLGGDAPKRISPAAARLLLQHAWPGNV 350 +RL V+ + +P+LRER DI +A +FL RQLG +A KR+SP A + L Q +PGNV Sbjct: 295 HRLNVIRLRLPSLRERSEDIPILARYFLAQSARQLGVEA-KRLSPQAMQFLSQLEFPGNV 353 Query: 351 RELRNTMERAAVMSHGLCIEAEDI 374 R+L N VM+ G +E +D+ Sbjct: 354 RQLENLCNWITVMAPGQTVEIKDL 377 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 276 bits (705), Expect = 3e-75, Method: Compositional matrix adjust. Identities = 173/448 (38%), Positives = 251/448 (56%), Gaps = 26/448 (5%) Query: 3 RILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIIDLRMPDE---- 58 ++LIV+DD + L ++ ++VL AG + L ++ H +DL +P + Sbjct: 7 KLLIVEDDPGLQKQLRWSLD--AYEVLVAGDRESALAMVRRHEPAVVTMDLGLPPDPDGA 64 Query: 59 -DGLAFLQRAPAIAA-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERAL 116 +G A LQ+ A+A IMLT + ++AI +GA+D KP L ++RA Sbjct: 65 SEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPCIDETLRLVVQRAF 124 Query: 117 R----QGASAPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKEL 172 Q + + L+ M V + I + A S A+V++LG +GTGKE+ Sbjct: 125 YLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEV 184 Query: 173 VARALHRKGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTL 232 +ARALH+ R+ R F+A+NCAAIP L+ESELFG+ KGAF+GA +G+ + A GGT Sbjct: 185 LARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTF 244 Query: 233 FLDEIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFRED 292 FLDE+GD+ + QAK+LR LQER + VGG+ + VDVRVI ATH++L+ G FRED Sbjct: 245 FLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFRED 304 Query: 293 LWYRLQVLTIMVPALRERPGDILTIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGN 349 L+YRL + I +PAL+ER GD + +A HF+++ G A +S A + ++ WPGN Sbjct: 305 LYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGN 364 Query: 350 VRELRNTMERAAVMSHGLCIEAEDIGLSARHPVGAAGAASAPAIDWDGPLAAALAEVERV 409 VRE+ N + RA +M+ G I AED+GLS G + P L E ER Sbjct: 365 VREMENCVMRAVIMADGQQITAEDLGLSVE------GREAEPL-----NLRQVRDEAERK 413 Query: 410 MIERALQGAAGNRAEAARRLGISRQQLY 437 + +AL GN +AA LG+SR LY Sbjct: 414 AVVKALTRMDGNILKAAELLGVSRPTLY 441 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 272 bits (696), Expect = 3e-74, Method: Compositional matrix adjust. Identities = 159/327 (48%), Positives = 212/327 (64%), Gaps = 20/327 (6%) Query: 130 TEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRKGARAARPFV 189 ++ + +L+G+S A RQ+ ++IG AA SD TVLV GETGTGKELVA ALH RA +P + Sbjct: 194 SQGQRELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMI 253 Query: 190 AVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKIL 249 ++NCAA+P L+ESELFGHV+GAFSGA + R G+F+ ADGGTLFLDE+G++ LA QAK+L Sbjct: 254 SLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLL 313 Query: 250 RVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRE 309 RVLQ +L VG ++ RVDVR+IAAT+RDL E+ +G FR D ++RL V I VP LRE Sbjct: 314 RVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRE 373 Query: 310 RPGDILTIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG 366 R D+L +A +FL Q G + R+S A R LL +AWPGN+REL + + R+A+ S Sbjct: 374 RGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLA 433 Query: 367 --------LCIEAEDIGLSARHPVGAAGAASAPAIDWD-------GPLAAALAEVERVMI 411 L ++A + L A P A AA+ P++ + G L AL ER ++ Sbjct: 434 THRTRPTILTLDAAALELPA--PSLATVAAAEPSLPAESTPAQASGSLRDALERYERQLV 491 Query: 412 ERALQGAAGNRAEAARRLGISRQQLYR 438 ALQ GN A AR LG+ R L R Sbjct: 492 SAALQRHGGNLAATARELGVDRANLNR 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 0.320 0.134 0.379 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: 1,281,274 Number of extensions: 53568 Number of successful extensions: 415 Number of sequences better than 1.0e-08: 32 Number of HSP's gapped: 407 Number of HSP's successfully gapped: 32 Length of query: 448 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 360 Effective length of database: 1,203,190 Effective search space: 433148400 Effective search space used: 433148400 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)