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= 0036.0418.p (533 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 160 2e-40 gi|300314016|ref|YP_003778108.1| two component transcription reg... 156 4e-39 gi|300313916|ref|YP_003778008.1| two component response regulato... 140 3e-34 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 139 8e-34 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 134 1e-32 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 160 bits (405), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 89/219 (40%), Positives = 125/219 (57%), Gaps = 8/219 (3%) Query: 207 SRAPMLLMGPTGAGKSFLARRIYELKKSRHQLEGRFVDINCATLQGDGAASTLFGHVRGS 266 SR+ MLL G +G GK +AR I+ L + +G F+ +NCA L S LFGH +G+ Sbjct: 223 SRSTMLLRGESGTGKEVIARAIHYLSPRK---DGPFIKVNCAALSETLLESELFGHEKGA 279 Query: 267 FTGAAHDRPGLLRSAHKGLLFLDEIGELGLDEQAMLLKAIEEKRFLPVGADVEAQSDFQL 326 FTGA +R G AH G LFLDEIGE+ QA LL+ ++E+ F VG + D +L Sbjct: 280 FTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRL 339 Query: 327 IAGTHRDLAREVAAGRFREDLFARINLWTYALPGLAQRREDIEPNLDYLLERFSAEHGQV 386 + T+RDL + VA G FR DL+ RIN+ + +P L +RREDI +++ LE+F E+ + Sbjct: 340 VTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRA 399 Query: 387 VRFNKEARMRYLAFAVSSAASWPGNFRDLSASIVRMATL 425 + M A V WPGN R+L + R AT+ Sbjct: 400 M-----VAMSPQAMKVMMNCYWPGNVRELENCVERTATM 433 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 156 bits (394), Expect = 4e-39, Method: Compositional matrix adjust. Identities = 112/327 (34%), Positives = 174/327 (53%), Gaps = 21/327 (6%) Query: 122 ICLFLMTEARY--LPGVLLQT--SPPRRQAAGSPGSYALIDLDLSRY---DLIAQRFSSE 174 + LF +RY LP +LL + P A + G++A + + D +AQ S Sbjct: 70 LALFAEIRSRYPALPVILLTAHGTIPDAVDATTQGAFAYLTKPFDGHVLLDKVAQALSLA 129 Query: 175 QREALALLKS---GIPTRNAHFNHMIEEIERVAIRSRAPMLLMGPTGAGKSFLARRIYEL 231 L+ +S I +R+ ++ E VA S A +L+ G +G GK LAR I+ Sbjct: 130 APAPLSPDQSWRADILSRSQRVAELLAEARLVAA-SDASILIRGDSGTGKELLARAIH-- 186 Query: 232 KKSRHQLEGRFVDINCATLQGDGAASTLFGHVRGSFTGAAHDRPGLLRSAHKGLLFLDEI 291 ++ + E F+ +NC + S LFGHV+G+FTGA R GL ++AH G LFLDEI Sbjct: 187 -RASARAEQPFIAVNCGAIPEQLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEI 245 Query: 292 GELGLDEQAMLLKAIEEKRFLPVGADVEAQSDFQLIAGTHRDLAREVAAGRFREDLFARI 351 G++ L Q LL+ ++EK VGA+ + D ++I+ THRDL + G+FREDL+ R+ Sbjct: 246 GDMPLPLQVKLLRVLQEKTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRL 305 Query: 352 NLWTYALPGLAQRREDIEPNLDYLLERFSAEHGQ-VVRFNKEARMRYLAFAVSSAASWPG 410 N+ T LP L +RREDI ++ L+ +A++ + + F + A + S A WPG Sbjct: 306 NVVTLHLPALEERREDIALLANHFLKTIAAKYPKRLTGFAPD------ALEILSLAHWPG 359 Query: 411 NFRDLSASIVRMATLADAGRIIDALVE 437 N R L + ++ L+ A I +LV+ Sbjct: 360 NVRQLYNVVEQVCALSTAPLIPASLVQ 386 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 140 bits (352), Expect = 3e-34, Method: Compositional matrix adjust. Identities = 83/234 (35%), Positives = 130/234 (55%), Gaps = 12/234 (5%) Query: 193 FNHMIEEIERVAIRSRAPMLLMGPTGAGKSFLARRIYELKKSRHQLEGRFVDINCATLQG 252 + ++I R A S A +L++G TG GK +AR ++ ++ + FV +NCA + Sbjct: 143 MRQVFKQIGRAAT-SDATVLVLGETGTGKELVARALH---RNGARAARPFVAVNCAAIPA 198 Query: 253 DGAASTLFGHVRGSFTGAAHDRPGLLRSAHKGLLFLDEIGELGLDEQAMLLKAIEEKRFL 312 + S LFGHV+G+F+GA R G + A G LFLDEIG++ L QA +L+ ++E+ Sbjct: 199 ELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELT 258 Query: 313 PVGADVEAQSDFQLIAGTHRDLAREVAAGRFREDLFARINLWTYALPGLAQRREDIEPNL 372 PVG + + D ++IA THRDL E+ GRFREDL+ R+ + T +P L +R DI Sbjct: 259 PVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIA 318 Query: 373 DYLLERFSAEHGQVVRFNKEARMRYLAFAVSSAASWPGNFRDLSASIVRMATLA 426 ++ L + + + R + A L A WPGN R+L ++ R A ++ Sbjct: 319 EHFLRQLGGDAPK--RISPAAARLLLQHA------WPGNVRELRNTMERAAVMS 364 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 139 bits (349), Expect = 8e-34, Method: Compositional matrix adjust. Identities = 84/247 (34%), Positives = 132/247 (53%), Gaps = 9/247 (3%) Query: 185 GIPTRNAHFNHMIEEIERVAIRSRAPMLLMGPTGAGKSFLARRIYELKKSRHQLEGRFVD 244 G+ TR+A + IE+VA S A ++L+G +G GK LAR +++L + RF+ Sbjct: 147 GLITRDAGMLAVCRSIEKVA-PSSASVMLLGSSGTGKEVLARALHQLSPRSGR---RFMA 202 Query: 245 INCATLQGDGAASTLFGHVRGSFTGAAHDRPGLLRSAHKGLLFLDEIGELGLDEQAMLLK 304 INCA + + S LFG+ +G+FTGAA G + AH G FLDE+G+L + QA LL+ Sbjct: 203 INCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLR 262 Query: 305 AIEEKRFLPVGADVEAQSDFQLIAGTHRDLAREVAAGRFREDLFARINLWTYALPGLAQR 364 ++E+ VG E D ++I TH++L A+G FREDL+ R+ +P L +R Sbjct: 263 FLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKER 322 Query: 365 REDIEPNLDYLLERFSAEHGQVVRFNKEARMRYLAFAVSSAASWPGNFRDLSASIVRMAT 424 D + +++F A+ G+ + A A WPGN R++ ++R Sbjct: 323 HGDAVLLARHFVQKFCAKEGRAT-----LHLSQDAVAAIERYEWPGNVREMENCVMRAVI 377 Query: 425 LADAGRI 431 +AD +I Sbjct: 378 MADGQQI 384 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 134 bits (338), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 91/256 (35%), Positives = 137/256 (53%), Gaps = 12/256 (4%) Query: 172 SSEQREALALLKSGIPTRNAHFNHMIEEIERVAIRSRAPMLLMGPTGAGKSFLARRIYEL 231 + EQ + L+ + + T +A FN + RVA + A +L G +G GK AR ++++ Sbjct: 251 AGEQDDDTDLVTALVGTSSA-FNAACHLLNRVAA-TDATVLFTGESGVGKERFARMLHQI 308 Query: 232 KKSRHQLEGRFVDINCATLQGDGAASTLFGHVRGSFTGAAHDRPGLLRSAHKGLLFLDEI 291 K + + INCA + + LFG RG++TGA R G A G LFLDE+ Sbjct: 309 GKRAKRA---CIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEV 365 Query: 292 GELGLDEQAMLLKAIEEKRFLPVGADVEAQSDFQLIAGTHRDLAREVAAGRFREDLFARI 351 G L L Q LL+ ++E F VG+ + D +++A T+ DLA+ V GRFR+DLF R+ Sbjct: 366 GTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRL 425 Query: 352 NLWTYALPGLAQRREDIEPNLDYLLERFSAEHGQVVR-FNKEARMRYLAFAVSSAASWPG 410 N++ LP L +RR+DI +++ L+ + HG VR F + A L + S+PG Sbjct: 426 NVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNY------SFPG 479 Query: 411 NFRDLSASIVRMATLA 426 N R+L I R LA Sbjct: 480 NIRELQNLIERGVILA 495 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 0.322 0.137 0.405 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: 1,709,912 Number of extensions: 74495 Number of successful extensions: 346 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 323 Number of HSP's successfully gapped: 12 Length of query: 533 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 443 Effective length of database: 1,193,720 Effective search space: 528817960 Effective search space used: 528817960 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)