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= 0001.2293.p (325 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300314016|ref|YP_003778108.1| two component transcription reg... 227 1e-60 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 217 1e-57 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 215 4e-57 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 208 5e-55 gi|300313916|ref|YP_003778008.1| two component response regulato... 207 1e-54 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 227 bits (578), Expect = 1e-60, Method: Compositional matrix adjust. Identities = 126/315 (40%), Positives = 190/315 (60%), Gaps = 4/315 (1%) Query: 2 DDFRRLHMIGSSPQMERVDAQLRKMASVEATVLIEGETGTGKELAARAIHYLGPRRDKPF 61 D R ++ S ++ + A+ R +A+ +A++LI G++GTGKEL ARAIH R ++PF Sbjct: 137 DQSWRADILSRSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPF 196 Query: 62 IPINCGALPEQLIESELFGHERGAFTDAKSAAPGLVADADGGTLFLDEVDALNYKAQTAI 121 I +NCGA+PEQL+ESELFGH +GAFT A GL A GGTLFLDE+ + Q + Sbjct: 197 IAVNCGAIPEQLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKL 256 Query: 122 LRFLQDHTYRRVGSGVTRKANVRIVAATNNRLNALVETGRFRRDLMYRLNVLSINLPPLR 181 LR LQ+ T R+VG+ + +VRI++AT+ L A + G+FR DL YRLNV++++LP L Sbjct: 257 LRVLQEKTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALE 316 Query: 182 ERGNDAVEMAQAFLSRFAHQYRMPDRRLHASALDFIAQYDWPGNIRELENMMHREFLMSD 241 ER D +A FL A +Y AL+ ++ WPGN+R+L N++ + +S Sbjct: 317 ERREDIALLANHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALST 376 Query: 242 TTDIYLGTQRPVQGSADEDVVQFKPMKEKMIHDFERRYVRDVLTRVDGNLTRAAKLAGQE 301 I + + D++++ K+K FER Y+ +L DGN++ AA+LA + Sbjct: 377 APLIPASLVQRALRTPTLDLLRYAEAKQK----FERDYLIRLLKLTDGNVSDAARLADRN 432 Query: 302 RSAFGKLARKHGLSP 316 R+ F +L +K+GL P Sbjct: 433 RTEFYRLLQKNGLDP 447 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 217 bits (552), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 124/301 (41%), Positives = 171/301 (56%), Gaps = 12/301 (3%) Query: 16 MERVDAQLRKMASVEATVLIEGETGTGKELAARAIHYLGPRRDKPFIPINCGALPEQLIE 75 M V + K+A A+V++ G +GTGKE+ ARA+H L PR + F+ INC A+PE L+E Sbjct: 155 MLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLE 214 Query: 76 SELFGHERGAFTDAKSAAPGLVADADGGTLFLDEVDALNYKAQTAILRFLQDHTYRRVGS 135 SELFG+E+GAFT A G V A GGT FLDEV L Q +LRFLQ+ RVG Sbjct: 215 SELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGG 274 Query: 136 GVTRKANVRIVAATNNRLNALVETGRFRRDLMYRLNVLSINLPPLRERGNDAVEMAQAFL 195 +VR++ AT+ L L +G FR DL YRL + I +P L+ER DAV +A+ F+ Sbjct: 275 HTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFV 334 Query: 196 SRFAHQYRMPDRRLHASALDFIAQYDWPGNIRELENMMHREFLMSDTTDIY---LGTQRP 252 +F + L A+ I +Y+WPGN+RE+EN + R +M+D I LG Sbjct: 335 QKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQITAEDLGLS-- 392 Query: 253 VQGSADEDVVQFKPMKEKMIHD-FERRYVRDVLTRVDGNLTRAAKLAGQERSAFGKLARK 311 V+G E P+ + + D ER+ V LTR+DGN+ +AA+L G R L + Sbjct: 393 VEGREAE------PLNLRQVRDEAERKAVVKALTRMDGNILKAAELLGVSRPTLYDLMSR 446 Query: 312 H 312 H Sbjct: 447 H 447 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 215 bits (547), Expect = 4e-57, Method: Compositional matrix adjust. Identities = 111/247 (44%), Positives = 152/247 (61%), Gaps = 3/247 (1%) Query: 8 HMIGSSPQMERVDAQLRKMASVEATVLIEGETGTGKELAARAIHYLGPRRDKPFIPINCG 67 ++IG S M+ V AQ+ + A +T+L+ GE+GTGKE+ ARAIHYL PR+D PFI +NC Sbjct: 202 NVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCA 261 Query: 68 ALPEQLIESELFGHERGAFTDAKSAAPGLVADADGGTLFLDEVDALNYKAQTAILRFLQD 127 AL E L+ESELFGHE+GAFT A+ G A GGTLFLDE+ ++ Q +LR LQ+ Sbjct: 262 ALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQE 321 Query: 128 HTYRRVGSGVTRKANVRIVAATNNRLNALVETGRFRRDLMYRLNVLSINLPPLRERGNDA 187 + RVG + K +VR+V ATN L V G FR DL YR+NV+SI +PPLRER D Sbjct: 322 REFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDI 381 Query: 188 VEMAQAFLSRFAHQYRMPDRRLHASALDFIAQYDWPGNIRELENMMHREFLMSD---TTD 244 + + FL +F + + + A+ + WPGN+RELEN + R M T+ Sbjct: 382 PYLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGDLITE 441 Query: 245 IYLGTQR 251 ++ Q+ Sbjct: 442 VHFSCQQ 448 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 208 bits (529), Expect = 5e-55, Method: Compositional matrix adjust. Identities = 130/326 (39%), Positives = 173/326 (53%), Gaps = 20/326 (6%) Query: 9 MIGSSPQMERVDAQLRKMASVEATVLIEGETGTGKELAARAIHYLGPRRDKPFIPINCGA 68 +IG SP ++ ++ A + TVL+ GETGTGKEL A A+H PR KP I +NC A Sbjct: 200 LIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAA 259 Query: 69 LPEQLIESELFGHERGAFTDAKSAAPGLVADADGGTLFLDEVDALNYKAQTAILRFLQDH 128 LP+ L+ESELFGH RGAF+ A + G ADGGTLFLDEV L Q +LR LQ Sbjct: 260 LPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSG 319 Query: 129 TYRRVGSGVTRKANVRIVAATNNRLNALVETGRFRRDLMYRLNVLSINLPPLRERGNDAV 188 +RVGS + +VR++AATN L V+ G FR D +RL+V I +PPLRERG D + Sbjct: 320 QLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 Query: 189 EMAQAFLSRFAHQYRMPDRRLHASALDFIAQYDWPGNIRELENMMHREFLMSDTTD---- 244 +A FL + + + RL A A + Y WPGNIRELE+++ R L S T Sbjct: 380 LLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRSLATHRTRP 439 Query: 245 --------------IYLGTQRPVQGS--ADEDVVQFKPMKEKMIHDFERRYVRDVLTRVD 288 L T + S A+ Q + +ER+ V L R Sbjct: 440 TILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERYERQLVSAALQRHG 499 Query: 289 GNLTRAAKLAGQERSAFGKLARKHGL 314 GNL A+ G +R+ +LA++ GL Sbjct: 500 GNLAATARELGVDRANLNRLAKRLGL 525 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 207 bits (526), Expect = 1e-54, Method: Compositional matrix adjust. Identities = 107/235 (45%), Positives = 147/235 (62%), Gaps = 3/235 (1%) Query: 6 RLHMIGSSPQMERVDAQLRKMASVEATVLIEGETGTGKELAARAIHYLGPRRDKPFIPIN 65 R ++G S M +V Q+ + A+ +ATVL+ GETGTGKEL ARA+H G R +PF+ +N Sbjct: 133 RNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVN 192 Query: 66 CGALPEQLIESELFGHERGAFTDAKSAAPGLVADADGGTLFLDEVDALNYKAQTAILRFL 125 C A+P +LIESELFGH +GAF+ A S G +ADGGTLFLDE+ + Q ILR L Sbjct: 193 CAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 126 QDHTYRRVGSGVTRKANVRIVAATNNRLNALVETGRFRRDLMYRLNVLSINLPPLRERGN 185 Q+ VG + + +VR++AAT+ L + GRFR DL YRL VL+I +P LRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 186 DAVEMAQAFLSRFAHQYRMPDRRLHASALDFIAQYDWPGNIRELENMMHREFLMS 240 D + +A+ FL + +R+ +A + Q+ WPGN+REL N M R +MS Sbjct: 313 DILTIAEHFLRQLGGD---APKRISPAAARLLLQHAWPGNVRELRNTMERAAVMS 364 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 0.136 0.391 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: 995,214 Number of extensions: 41269 Number of successful extensions: 158 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 144 Number of HSP's successfully gapped: 12 Length of query: 325 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 240 Effective length of database: 1,217,395 Effective search space: 292174800 Effective search space used: 292174800 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: 131 (55.1 bits)