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= 0001.4500.p (447 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... 716 0.0 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 310 1e-85 gi|300314016|ref|YP_003778108.1| two component transcription reg... 306 2e-84 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 281 8e-77 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 273 2e-74 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 716 bits (1848), Expect = 0.0, Method: Compositional matrix adjust. Identities = 375/450 (83%), Positives = 395/450 (87%), Gaps = 7/450 (1%) Query: 1 MARILIVDDDLAFRGSLAETVGDLGHEVLEAGSTAAGLKLLAAHGVDAAIVDLRMADEDG 60 MARILIVDDD AFRGSLAETV DLGH+VLEAGSTAAGLKLLAAH VDAAIVDLRM DEDG Sbjct: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDG 60 Query: 61 LVFLQRAPAIAPIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQSA 120 L FLQRAPAIA IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQ A Sbjct: 61 LAFLQRAPAIAAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGA 120 Query: 121 ALSAPPASQETPPGSERNELVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVARA 180 + A + ERN+LVG+SEAMRQVFKQIGRAATSDATVL+LGETGTGKELVARA Sbjct: 121 STPAAASPAT----EERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARA 176 Query: 181 LHRNGSRAKRPFVAVNCAAIPAELIESELFGHVKGAFSGASANRIGRFQEADGGTLFLDE 240 LHRNG+RA RPFVAVNCAAIPAELIESELFGHVKGAFSGA++ R+GRFQEADGGTLFLDE Sbjct: 177 LHRNGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDE 236 Query: 241 IGDMAAPTQAKILRVLQERELTPVGGNQSVKVDVRVIAATHRDLPQEIREGRFREDLWYR 300 IGDM TQAKILRVLQERELTPVGGNQSV+VDVRVIAATHRDL EI +GRFREDLWYR Sbjct: 237 IGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYR 296 Query: 301 LQVLPIKVPPLRERPGDILAIAEHFLRQHGGDSPKRISPAAARRLLQHSWPGNVRELRNT 360 LQVL I VP LRERPGDIL IAEHFLRQ GGD+PKRISPAAAR LLQH+WPGNVRELRNT Sbjct: 297 LQVLTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHAWPGNVRELRNT 356 Query: 361 MERAAVMSHGACIEVEHIELP---ELAPASPESAVAIDWEGSLAQAVAQVERVMLQRALA 417 MERAAVMSHG CIE E I L AS SA AIDW+G LA A+A+VERVM++RAL Sbjct: 357 MERAAVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMIERALQ 416 Query: 418 AANGNRAEAARRLGISRQQLYRKLEEQGMS 447 A GNRAEAARRLGISRQQLYR+LEE G S Sbjct: 417 GAAGNRAEAARRLGISRQQLYRRLEEAGKS 446 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 310 bits (794), Expect = 1e-85, Method: Compositional matrix adjust. Identities = 203/503 (40%), Positives = 285/503 (56%), Gaps = 66/503 (13%) Query: 1 MARILIVDDDLAFRGSLAETVGDLGHEVLEAGSTAAGLKLLAA--HGVDAAIV-DLRMAD 57 M I IVDDD + R L + L E L S ++ +AA +G +V D+RM Sbjct: 1 MKPIWIVDDDESIRWVLEKA---LARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPG 57 Query: 58 EDGLVFLQRAPAIAP-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERAL 116 GL LQ A P IP I++TA++ D+ + A + GAF++L KP VE + RAL Sbjct: 58 ASGLELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRAL 117 Query: 117 RQSA-ALSAPPASQETPPGSERNELVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKE 175 +S + +TP E++G + AM+ VF+ IGR + S+ TVLI GE+G+GKE Sbjct: 118 DESLRETDIEQGAAQTP------EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKE 171 Query: 176 LVARALHRNGSRAKRPFVAVNCAAIPAELIESELFGHVKGAFSGASANRIGRFQEADGGT 235 LVARALH++ RA +PFVA+N AAIP +L+ESELFGH +GAF+GA A R GRF++A+GGT Sbjct: 172 LVARALHKHSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGT 231 Query: 236 LFLDEIGDMAAPTQAKILRVLQERELTPVGGNQSVKVDVRVIAATHRDLPQEIREGRFRE 295 LFLDEIGDM Q ++LRVL + VGG+QS+K +VRVIAATH++L Q +REG FRE Sbjct: 232 LFLDEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFRE 291 Query: 296 DLWYRLQVLPIKVPPLRERPGDILAIAEHFLRQHG---GDSPKRISPAAARRLLQHSWPG 352 DL++RL V+ +++P LRER DI +A +FL Q G KR+SP A + L Q +PG Sbjct: 292 DLYHRLNVIRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPG 351 Query: 353 NVRELRNTMERAAVMSHGACIEVEHI--ELPELAPASPESAVAI---------------- 394 NVR+L N VM+ G +E++ + +L E +P+ A + Sbjct: 352 NVRQLENLCNWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQTVAAPASAAALPTAYTEP 411 Query: 395 ---------------DW----EGSLAQAVA------------QVERVMLQRALAAANGNR 423 W E AQ +A Q E +++ AL +G + Sbjct: 412 APGVASASADGAAGASWITLLETEAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRK 471 Query: 424 AEAARRLGISRQQLYRKLEEQGM 446 +AA RLGI R + RK++E G+ Sbjct: 472 NDAAVRLGIGRNTITRKIQELGI 494 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 306 bits (784), Expect = 2e-84, Method: Compositional matrix adjust. Identities = 182/429 (42%), Positives = 258/429 (60%), Gaps = 24/429 (5%) Query: 25 GHEVLEAGSTAAGLKLLAAHGVDAAIVDLRMADEDGLVFL----QRAPAIAPIPCIMLTA 80 G+ +L S A L LA I D+R+ DGL R PA+ P I+LTA Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPAL---PVILLTA 90 Query: 81 YASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQSAALSAPPASQETPPGSERNEL 140 + + + ++A GAF +LTKP L++ + +AL +L+AP + +P S R ++ Sbjct: 91 HGTIPDAVDATTQGAFAYLTKPFDGHVLLDKVAQAL----SLAAP--APLSPDQSWRADI 144 Query: 141 VGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVARALHRNGSRAKRPFVAVNCAAI 200 + S+ + ++ + A SDA++LI G++GTGKEL+ARA+HR +RA++PF+AVNC AI Sbjct: 145 LSRSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAI 204 Query: 201 PAELIESELFGHVKGAFSGASANRIGRFQEADGGTLFLDEIGDMAAPTQAKILRVLQERE 260 P +L+ESELFGHVKGAF+GA +R G FQ A GGTLFLDEIGDM P Q K+LRVLQE+ Sbjct: 205 PEQLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKT 264 Query: 261 LTPVGGNQSVKVDVRVIAATHRDLPQEIREGRFREDLWYRLQVLPIKVPPLRERPGDILA 320 + VG NQ+ +VDVR+I+ATHRDL +REG+FREDL+YRL V+ + +P L ER DI Sbjct: 265 VRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIAL 324 Query: 321 IAEHFLRQHGGDSPKRIS---PAAARRLLQHSWPGNVRELRNTMERAAVMSHGACIEVEH 377 +A HFL+ PKR++ P A L WPGNVR+L N +E+ +S I Sbjct: 325 LANHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTAPLIPASL 384 Query: 378 IELPELAPASPESAVAIDWEGSLAQAVAQVERVMLQRALAAANGNRAEAARRLGISRQQL 437 ++ P +D A+A + ER L R L +GN ++AAR +R + Sbjct: 385 VQRALRTP-------TLDLL-RYAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEF 436 Query: 438 YRKLEEQGM 446 YR L++ G+ Sbjct: 437 YRLLQKNGL 445 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 281 bits (719), Expect = 8e-77, Method: Compositional matrix adjust. Identities = 157/327 (48%), Positives = 211/327 (64%), Gaps = 19/327 (5%) Query: 139 ELVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKELVARALHRNGSRAKRPFVAVNCA 198 EL+G S A RQ+ ++IG AA SD TVL+ GETGTGKELVA ALH RA +P +++NCA Sbjct: 199 ELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCA 258 Query: 199 AIPAELIESELFGHVKGAFSGASANRIGRFQEADGGTLFLDEIGDMAAPTQAKILRVLQE 258 A+P L+ESELFGHV+GAFSGA A+R G+F+ ADGGTLFLDE+G++ QAK+LRVLQ Sbjct: 259 ALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQS 318 Query: 259 RELTPVGGNQSVKVDVRVIAATHRDLPQEIREGRFREDLWYRLQVLPIKVPPLRERPGDI 318 +L VG ++ +VDVR+IAAT+RDL E++ G FR D ++RL V PI+VPPLRER D+ Sbjct: 319 GQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDV 378 Query: 319 LAIAEHFLRQHG---GDSPKRISPAAARRLLQHSWPGNVRELRNTMERAAVMSHGA---- 371 L +A +FL Q+ G S R+S A R LL ++WPGN+REL + + R+A+ S Sbjct: 379 LLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRTR 438 Query: 372 ----CIEVEHIEL--PELA------PASPESAVAIDWEGSLAQAVAQVERVMLQRALAAA 419 ++ +EL P LA P+ P + GSL A+ + ER ++ AL Sbjct: 439 PTILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERYERQLVSAALQRH 498 Query: 420 NGNRAEAARRLGISRQQLYRKLEEQGM 446 GN A AR LG+ R L R + G+ Sbjct: 499 GGNLAATARELGVDRANLNRLAKRLGL 525 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 273 bits (699), Expect = 2e-74, Method: Compositional matrix adjust. Identities = 172/446 (38%), Positives = 251/446 (56%), Gaps = 21/446 (4%) Query: 3 RILIVDDDLAFRGSLAETVGDLGHEVLEAGSTAAGLKLLAAHGVDAAIVDLRMADE---- 58 ++LIV+DD + L ++ +EVL AG + L ++ H +DL + + Sbjct: 7 KLLIVEDDPGLQKQLRWSLD--AYEVLVAGDRESALAMVRRHEPAVVTMDLGLPPDPDGA 64 Query: 59 -DGLVFLQRAPAIAP-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERAL 116 +G LQ+ A+AP IMLT + ++AI +GA+D KP L ++RA Sbjct: 65 SEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPCIDETLRLVVQRAF 124 Query: 117 RQSAALSAPPASQETPPGSERNELVGDSEAMRQVFKQIGRAATSDATVLILGETGTGKEL 176 A Q+ + L+ M V + I + A S A+V++LG +GTGKE+ Sbjct: 125 YLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEV 184 Query: 177 VARALHRNGSRAKRPFVAVNCAAIPAELIESELFGHVKGAFSGASANRIGRFQEADGGTL 236 +ARALH+ R+ R F+A+NCAAIP L+ESELFG+ KGAF+GA+ IG+ + A GGT Sbjct: 185 LARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTF 244 Query: 237 FLDEIGDMAAPTQAKILRVLQERELTPVGGNQSVKVDVRVIAATHRDLPQEIREGRFRED 296 FLDE+GD+ P QAK+LR LQER + VGG+ + VDVRVI ATH++L + G FRED Sbjct: 245 FLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFRED 304 Query: 297 LWYRLQVLPIKVPPLRERPGDILAIAEHFLRQHG---GDSPKRISPAAARRLLQHSWPGN 353 L+YRL + IK+P L+ER GD + +A HF+++ G + +S A + ++ WPGN Sbjct: 305 LYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGN 364 Query: 354 VRELRNTMERAAVMSHGACIEVEHIELP-ELAPASPESAVAIDWEGSLAQAVAQVERVML 412 VRE+ N + RA +M+ G I E + L E A P +L Q + ER + Sbjct: 365 VREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPL---------NLRQVRDEAERKAV 415 Query: 413 QRALAAANGNRAEAARRLGISRQQLY 438 +AL +GN +AA LG+SR LY Sbjct: 416 VKALTRMDGNILKAAELLGVSRPTLY 441 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 0.318 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: 1,343,312 Number of extensions: 57851 Number of successful extensions: 373 Number of sequences better than 1.0e-08: 19 Number of HSP's gapped: 366 Number of HSP's successfully gapped: 19 Length of query: 447 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 359 Effective length of database: 1,203,190 Effective search space: 431945210 Effective search space used: 431945210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 132 (55.5 bits)