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= 0002.0069.p (545 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312421|ref|YP_003776513.1| propionate catabolism operon re... 1068 0.0 gi|300314016|ref|YP_003778108.1| two component transcription reg... 224 1e-59 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 221 1e-58 gi|300313916|ref|YP_003778008.1| two component response regulato... 217 1e-57 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 211 2e-55 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 1068 bits (2762), Expect = 0.0, Method: Compositional matrix adjust. Identities = 536/544 (98%), Positives = 538/544 (98%) Query: 1 MKRPAPVDRHADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERLA 60 MKRPAPVDRHADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERLA Sbjct: 1 MKRPAPVDRHADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERLA 60 Query: 61 TERCDVVISAGSNGAYLKSRLPVPVIVARPSGFDVMQALARARQLTRRIALVTYQEAMPA 120 TERCDVVISAGSNGAYLKSRLPVPVIVAR SGFDVMQALARARQLTRRIALVTYQEAMPA Sbjct: 61 TERCDVVISAGSNGAYLKSRLPVPVIVARASGFDVMQALARARQLTRRIALVTYQEAMPA 120 Query: 121 LAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLYS 180 LAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLYS Sbjct: 121 LAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLYS 180 Query: 181 AATVRQAFEDALELARLTQLESTRGPILPVADSLRARHHLKDLRGDSAVMETVRQSITLF 240 AATVRQAFEDALELARLTQLESTR PILPVADSLRARHHLKDLRGDSA METVRQSITLF Sbjct: 181 AATVRQAFEDALELARLTQLESTRSPILPVADSLRARHHLKDLRGDSAEMETVRQSITLF 240 Query: 241 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESELFG 300 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESELFG Sbjct: 241 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESELFG 300 Query: 301 YEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI 360 YEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI Sbjct: 301 YEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI 360 Query: 361 PVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPLRERRDDIAALAEWHLKHAL 420 PVQVRIISATHCDL+ARVREGRFRADLYYRLSVL LQLPPLRERRDDIAALAEWHLKHAL Sbjct: 361 PVQVRIISATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALAEWHLKHAL 420 Query: 421 AALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQR 480 AALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQR Sbjct: 421 AALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQR 480 Query: 481 VAPELGQTPPSPAAPDAAQESITPDNASIAAALRRFRGNRAAAARYLGMSRTTLWRKLKE 540 VAPELGQ PPSPAAPD AQE+ITPDNASIAAALRRFRGNRAAAARYLGMSRTTLWRKLKE Sbjct: 481 VAPELGQAPPSPAAPDEAQENITPDNASIAAALRRFRGNRAAAARYLGMSRTTLWRKLKE 540 Query: 541 SGTT 544 SGTT Sbjct: 541 SGTT 544 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 224 bits (572), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 142/308 (46%), Positives = 190/308 (61%), Gaps = 27/308 (8%) Query: 239 LFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESEL 298 L A S A++LI+G++GTGKEL A+AIHRA +A PF+A+NCGA+ E LLESEL Sbjct: 160 LVAASDASILIRGDSGTGKELLARAIHRA------SARAEQPFIAVNCGAIPEQLLESEL 213 Query: 299 FGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTR 358 FG+ +GAFTG+ R G+F+AAH GTL LDEIG+MPLPLQ +LLRVL+E+ V +VG + Sbjct: 214 FGHVKGAFTGAVEH-REGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVRQVGANQ 272 Query: 359 PIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPLRERRDDIAALAEWHLKH 418 V VRIISATH DLEA +REG+FR DLYYRL+V+ L LP L ERR+DIA LA LK Sbjct: 273 AGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLANHFLKT 332 Query: 419 ALAALDVRPHANLGAEIVRCAP----LLCRYDWPGNVRELRNLMERLALFLAAEPLQALT 474 A R + AP +L WPGNVR+L N++E++ L+ PL + Sbjct: 333 IAAKYPKR--------LTGFAPDALEILSLAHWPGNVRQLYNVVEQVCA-LSTAPL--IP 381 Query: 475 PALIQRVAPELGQTPPSPAAPDAAQESITPDNASIAAALRRFRGNRAAAARYLGMSRTTL 534 +L+QR P+ A+ + + L+ GN + AAR +RT Sbjct: 382 ASLVQR-----ALRTPTLDLLRYAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEF 436 Query: 535 WRKLKESG 542 +R L+++G Sbjct: 437 YRLLQKNG 444 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 221 bits (563), Expect = 1e-58, Method: Compositional matrix adjust. Identities = 127/287 (44%), Positives = 175/287 (60%), Gaps = 16/287 (5%) Query: 214 LRARHHLKDLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQG 273 L+ ++ L ++ G S M+ V + A S + +L++GE+GTGKE+ A+AIH P G Sbjct: 194 LQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDG 253 Query: 274 KTQAAHPFVAINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGE 333 PF+ +NC AL+E+LLESELFG+E+GAFTG++ G R G FE AH GTL LDEIGE Sbjct: 254 ------PFIKVNCAALSETLLESELFGHEKGAFTGAQ-GERKGRFELAHGGTLFLDEIGE 306 Query: 334 MPLPLQTRLLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSV 393 + Q +LLRVL+ERE RVGG+R I V VR+++AT+ DLE V +G FRADLYYR++V Sbjct: 307 ISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINV 366 Query: 394 LRLQLPPLRERRDDIAALAEWHLKHALAALDVRPHANLGAEIVRCAPLLCRYDWPGNVRE 453 + + +PPLRERR+DI L E H L V + A + ++ WPGNVRE Sbjct: 367 VSIFIPPLRERREDIPYLVE----HFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNVRE 422 Query: 454 LRNLMERLALFLAAEPLQALTPALIQ-----RVAPELGQTPPSPAAP 495 L N +ER A + + + + + Q +V E GQ P P Sbjct: 423 LENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPVVVVP 469 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 217 bits (553), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 144/333 (43%), Positives = 190/333 (57%), Gaps = 29/333 (8%) Query: 221 KDLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHP 280 L G+S M V + I A S A VL+ GETGTGKEL A+A+HR +AA P Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHR------NGARAARP 187 Query: 281 FVAINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQT 340 FVA+NC A+ L+ESELFG+ +GAF+G+ R G F+ A GTL LDEIG+M L Q Sbjct: 188 FVAVNCAAIPAELIESELFGHVKGAFSGAT-SPRLGRFQEADGGTLFLDEIGDMELATQA 246 Query: 341 RLLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPP 400 ++LRVL+ERE+ VGG + + V VR+I+ATH DL+ + +GRFR DL+YRL VL + +P Sbjct: 247 KILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPA 306 Query: 401 LRERRDDIAALAEWHLKH--ALAALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLM 458 LRER DI +AE L+ A + P A A LL ++ WPGNVRELRN M Sbjct: 307 LRERPGDILTIAEHFLRQLGGDAPKRISPAA---------ARLLLQHAWPGNVRELRNTM 357 Query: 459 ERLALFLAAEPLQALTPALIQRVAPELGQTP-------PSPAAPDAAQESITPDNASIAA 511 ER A+ ++A L R P A A+ + I Sbjct: 358 ERAAVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAE----VERVMIER 413 Query: 512 ALRRFRGNRAAAARYLGMSRTTLWRKLKESGTT 544 AL+ GNRA AAR LG+SR L+R+L+E+G + Sbjct: 414 ALQGAAGNRAEAARRLGISRQQLYRRLEEAGKS 446 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 211 bits (536), Expect = 2e-55, Method: Compositional matrix adjust. Identities = 147/374 (39%), Positives = 204/374 (54%), Gaps = 68/374 (18%) Query: 222 DLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPF 281 ++ G + M+ V ++I ++S VLI GE+G+GKEL A+A+H+ P +A+ PF Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSP------RASQPF 188 Query: 282 VAINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTR 341 VA+N A+ + LLESELFG+E GAFTG++ R G FE A GTL LDEIG+MPL LQTR Sbjct: 189 VALNTAAIPKDLLESELFGHERGAFTGAQ-AMRRGRFEQAEGGTLFLDEIGDMPLDLQTR 247 Query: 342 LLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPL 401 LLRVL + RVGG + + VR+I+ATH +LE RVREG FR DLY+RL+V+RL+LP L Sbjct: 248 LLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSL 307 Query: 402 RERRDDIAALAEWHLKHALAALDVRPHANLGAEIVRCAP----LLCRYDWPGNVRELRNL 457 RER +DI LA + L + LG E R +P L + ++PGNVR+L NL Sbjct: 308 RERSEDIPILARYFLAQSA--------RQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 Query: 458 MERLALFLAAEP--LQALTPALI-QRV-APELGQ---------------TPPSPAA---- 494 + + + ++ L L+ +RV AP+ Q T P+P Sbjct: 360 CNWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQTVAAPASAAALPTAYTEPAPGVASAS 419 Query: 495 --------------PDAAQ--ESITP----------DNASIAAALRRFRGNRAAAARYLG 528 +AAQ S P + A I AL+ G + AA LG Sbjct: 420 ADGAAGASWITLLETEAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRKNDAAVRLG 479 Query: 529 MSRTTLWRKLKESG 542 + R T+ RK++E G Sbjct: 480 IGRNTITRKIQELG 493 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 0.321 0.135 0.390 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: 1,551,343 Number of extensions: 61433 Number of successful extensions: 386 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 349 Number of HSP's successfully gapped: 12 Length of query: 545 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 455 Effective length of database: 1,193,720 Effective search space: 543142600 Effective search space used: 543142600 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 (21.9 bits) S2: 133 (55.8 bits)