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= 0017.0053.p (445 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport resp... 889 0.0 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 280 2e-76 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 276 3e-75 gi|300314016|ref|YP_003778108.1| two component transcription reg... 275 5e-75 gi|300313916|ref|YP_003778008.1| two component response regulato... 244 1e-65 >gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 445 Score = 889 bits (2298), Expect = 0.0, Method: Compositional matrix adjust. Identities = 444/445 (99%), Positives = 444/445 (99%) Query: 1 MDKPGGAASALLIEDEQTVRRATAQALELGGFAVTACASAEEALPLITRDFAGVVVSDVR 60 MDKPGGAASALLIEDEQTVRRATAQALELGGFAVTAC SAEEALPLITRDFAGVVVSDVR Sbjct: 1 MDKPGGAASALLIEDEQTVRRATAQALELGGFAVTACGSAEEALPLITRDFAGVVVSDVR 60 Query: 61 LPGLSGLDVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIAL 120 LPGLSGLDVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIAL Sbjct: 61 LPGLSGLDVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIAL 120 Query: 121 RAQEKRNLVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGT 180 RAQEKRNLVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGT Sbjct: 121 RAQEKRNLVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGT 180 Query: 181 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANG 240 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANG Sbjct: 181 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANG 240 Query: 241 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQF 300 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQF Sbjct: 241 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQF 300 Query: 301 REDLYYRIGVVAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDW 360 REDLYYRIGVVAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDW Sbjct: 301 REDLYYRIGVVAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDW 360 Query: 361 PGNVRELRNFADRWVLGVEQMAASAVSSAVPVLSSLPEQVEQFEAGLIAAALKDSEGSVA 420 PGNVRELRNFADRWVLGVEQMAASAVSSAVPVLSSLPEQVEQFEAGLIAAALKDSEGSVA Sbjct: 361 PGNVRELRNFADRWVLGVEQMAASAVSSAVPVLSSLPEQVEQFEAGLIAAALKDSEGSVA 420 Query: 421 VAAERLGIPKKTLYDKIRKYQLAGS 445 VAAERLGIPKKTLYDKIRKYQLAGS Sbjct: 421 VAAERLGIPKKTLYDKIRKYQLAGS 445 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 280 bits (716), Expect = 2e-76, Method: Compositional matrix adjust. Identities = 170/444 (38%), Positives = 256/444 (57%), Gaps = 15/444 (3%) Query: 11 LLIEDEQTVRRATAQALELGGFAVTACASAEEALPLITRDFAGVVVSDVRLP----GLS- 65 L++ED+ +++ +L+ + V E AL ++ R VV D+ LP G S Sbjct: 9 LIVEDDPGLQKQLRWSLD--AYEVLVAGDRESALAMVRRHEPAVVTMDLGLPPDPDGASE 66 Query: 66 GLDVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIALRAQEK 125 G L +V+A+ D VI++TG+ D AV+A+ GAYDF +KP +TL + RA Sbjct: 67 GFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPCIDETLRLVVQRAFYL 126 Query: 126 RNLVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGTGKEVV 185 L EN+R+++A H L L+ + + V I + P+ V++ G +GTGKEV+ Sbjct: 127 HALQRENQRMQQAGGHTA-LGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVL 185 Query: 186 ARQLHAASGRKGP-FVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANGGTLF 244 AR LH S R G F+A+NC A+PE + ESE+FG+E GAFTGA K+ IGK+E A+GGT F Sbjct: 186 ARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFF 245 Query: 245 LDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQFREDL 304 LDE+ +P+ LQ KLLR LQER +ER+GG+ + +D RV+ A+ +L +L A G FREDL Sbjct: 246 LDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDL 305 Query: 305 YYRIGVVAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDWPGNV 364 YYR+ + I +PAL +R D LL HF Q + R + S + ++ +WPGNV Sbjct: 306 YYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNV 365 Query: 365 RELRNFADRWVLGV--EQMAASAVSSAVPVLSSLPEQVEQF----EAGLIAAALKDSEGS 418 RE+ N R V+ +Q+ A + +V + P + Q E + AL +G+ Sbjct: 366 REMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLNLRQVRDEAERKAVVKALTRMDGN 425 Query: 419 VAVAAERLGIPKKTLYDKIRKYQL 442 + AAE LG+ + TLYD + ++++ Sbjct: 426 ILKAAELLGVSRPTLYDLMSRHEI 449 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 276 bits (705), Expect = 3e-75, Method: Compositional matrix adjust. Identities = 152/365 (41%), Positives = 228/365 (62%), Gaps = 8/365 (2%) Query: 12 LIEDEQTVRRATAQALELGGFAVTACASAEEALPLITRDFAGVVVSDVRLPGLSGLDVLA 71 +++D++++R +AL A + +SA +A+ + V+VSD+R+PG SGL++L Sbjct: 6 IVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASGLELLQ 65 Query: 72 RVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIALRAQEKRNLVLE 131 V A +PVI++T D+ AV A + GA++++ KPF D +E+ RA ++ L Sbjct: 66 TVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES---LR 122 Query: 132 NRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGTGKEVVARQLHA 191 + + A PE+ +GQ+PA++ V I L ++V VLI G++G+GKE+VAR LH Sbjct: 123 ETDIEQGAAQTPEI---LGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHK 179 Query: 192 ASGRKG-PFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANGGTLFLDEIES 250 S R PFVALN A+P+ + ESE+FGHE GAFTGAQ R G+ E A GGTLFLDEI Sbjct: 180 HSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGD 239 Query: 251 MPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQFREDLYYRIGV 310 MPL LQ +LLRVL + R+GG++S+ + RV+AA+ +L + EG FREDLY+R+ V Sbjct: 240 MPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNV 299 Query: 311 VAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDWPGNVRELRNF 370 + + LP+L +R EDI +L +F +A + E+ S MQ Q ++PGNVR+L N Sbjct: 300 IRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 Query: 371 ADRWV 375 + W+ Sbjct: 360 CN-WI 363 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 275 bits (704), Expect = 5e-75, Method: Compositional matrix adjust. Identities = 164/421 (38%), Positives = 242/421 (57%), Gaps = 29/421 (6%) Query: 31 GFAVTACASAEEALPLITRDFAGVVVSDVRLPGLSGLDVLARVVAIDHDLPVIVVTGHGD 90 G+ + A SAE AL + +V++DVRLPG+ GL + A + + LPVI++T HG Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGT 93 Query: 91 VGMAVEAMRAGAYDFVEKPFSSDTLLEIALRAQEKRNLVLENRRLREAWAHDPELPPLVG 150 + AV+A GA+ ++ KPF LL+ AQ ++W D ++ Sbjct: 94 IPDAVDATTQGAFAYLTKPFDGHVLLDKV--AQALSLAAPAPLSPDQSWRAD-----ILS 146 Query: 151 QSPAIERVRTLIRSLGPADVDVLINGQTGTGKEVVARQLHAASGR-KGPFVALNCGALPE 209 +S + + R + +D +LI G +GTGKE++AR +H AS R + PF+A+NCGA+PE Sbjct: 147 RSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPE 206 Query: 210 TVFESEIFGHEPGAFTGAQKRRIGKLEYANGGTLFLDEIESMPLALQVKLLRVLQERRLE 269 + ESE+FGH GAFTGA + R G + A+GGTLFLDEI MPL LQVKLLRVLQE+ + Sbjct: 207 QLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVR 266 Query: 270 RLGGNESVAIDCRVVAASKADLLKLAAEGQFREDLYYRIGVVAIDLPALNQRREDIALLL 329 ++G N++ +D R+++A+ DL EGQFREDLYYR+ VV + LPAL +RREDIALL Sbjct: 267 QVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLA 326 Query: 330 AHFCQAAAVRYRRESPAWSAAQMQQWQQRDWPGNVRELRNFADRWVLGVEQMAASAVSSA 389 HF + A +Y + ++ ++ WPGNVR+L N VEQ+ A + + Sbjct: 327 NHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNV-------VEQVCALSTAPL 379 Query: 390 VPV-------------LSSLPEQVEQFEAGLIAAALKDSEGSVAVAAERLGIPKKTLYDK 436 +P L E ++FE + LK ++G+V+ AA RL +T + + Sbjct: 380 IPASLVQRALRTPTLDLLRYAEAKQKFERDYLIRLLKLTDGNVSDAA-RLADRNRTEFYR 438 Query: 437 I 437 + Sbjct: 439 L 439 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 244 bits (622), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 168/451 (37%), Positives = 239/451 (52%), Gaps = 29/451 (6%) Query: 8 ASALLIEDEQTVRRATAQALELGGFAVTACASAEEALPLITRDFAGVVVSDVRLPGLSGL 67 A L+++D+ R + A+ + G V S L L+ + D+R+P GL Sbjct: 2 ARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDGL 61 Query: 68 DVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIALRAQEKRN 127 L R AI +P I++T + +EA+R GA+D + KP L+E RA + Sbjct: 62 AFLQRAPAIAA-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQGA 120 Query: 128 LVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGTGKEVVAR 187 A E LVG+S A+ +V I +D VL+ G+TGTGKE+VAR Sbjct: 121 STPAA-----ASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVAR 175 Query: 188 QLHAASGRKG-PFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANGGTLFLD 246 LH R PFVA+NC A+P + ESE+FGH GAF+GA R+G+ + A+GGTLFLD Sbjct: 176 ALHRNGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLD 235 Query: 247 EIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQFREDLYY 306 EI M LA Q K+LRVLQER L +GGN+SV +D RV+AA+ DL +G+FREDL+Y Sbjct: 236 EIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWY 295 Query: 307 RIGVVAIDLPALNQRREDIALLLAHFC-QAAAVRYRRESPAWSAAQMQQWQQRDWPGNVR 365 R+ V+ I +PAL +R DI + HF Q +R SPA + +Q WPGNVR Sbjct: 296 RLQVLTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAARLLLQHA----WPGNVR 351 Query: 366 ELRNFADR-------WVLGVEQMAASAVSSAVPVLSSLPEQVE----------QFEAGLI 408 ELRN +R + E + SA A ++ ++ + E +I Sbjct: 352 ELRNTMERAAVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMI 411 Query: 409 AAALKDSEGSVAVAAERLGIPKKTLYDKIRK 439 AL+ + G+ A AA RLGI ++ LY ++ + Sbjct: 412 ERALQGAAGNRAEAARRLGISRQQLYRRLEE 442 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 0.385 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: 1,222,172 Number of extensions: 47490 Number of successful extensions: 338 Number of sequences better than 1.0e-08: 25 Number of HSP's gapped: 341 Number of HSP's successfully gapped: 25 Length of query: 445 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 357 Effective length of database: 1,203,190 Effective search space: 429538830 Effective search space used: 429538830 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)