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= 0013.0029.p (380 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcriptio... 767 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 241 7e-65 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 236 3e-63 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 228 5e-61 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 228 8e-61 >gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 767 bits (1980), Expect = 0.0, Method: Compositional matrix adjust. Identities = 380/380 (100%), Positives = 380/380 (100%) Query: 1 MHASHRSAHLYALPSSPEGHGDLAARASPPLLTLPHARKLGTSIRATAQVFHDPVSLALL 60 MHASHRSAHLYALPSSPEGHGDLAARASPPLLTLPHARKLGTSIRATAQVFHDPVSLALL Sbjct: 1 MHASHRSAHLYALPSSPEGHGDLAARASPPLLTLPHARKLGTSIRATAQVFHDPVSLALL 60 Query: 61 ERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFG 120 ERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFG Sbjct: 61 ERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFG 120 Query: 121 HEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 180 HEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP Sbjct: 121 HEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 180 Query: 181 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQ 240 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQ Sbjct: 181 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQ 240 Query: 241 RLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERRLD 300 RLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERRLD Sbjct: 241 RLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERRLD 300 Query: 301 YAVAAADERGNDPLHALEQALQGLFNQSQEGLFEKIEDTVFRTAFEFCERNQVQAARLLD 360 YAVAAADERGNDPLHALEQALQGLFNQSQEGLFEKIEDTVFRTAFEFCERNQVQAARLLD Sbjct: 301 YAVAAADERGNDPLHALEQALQGLFNQSQEGLFEKIEDTVFRTAFEFCERNQVQAARLLD 360 Query: 361 ISRNVLRARLIRNGQISALK 380 ISRNVLRARLIRNGQISALK Sbjct: 361 ISRNVLRARLIRNGQISALK 380 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 241 bits (615), Expect = 7e-65, Method: Compositional matrix adjust. Identities = 142/317 (44%), Positives = 187/317 (58%), Gaps = 17/317 (5%) Query: 59 LLERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESEL 118 + +++ R A SDA V+++G TGTGKEL+AR +H R PFVAVNC A L ESEL Sbjct: 146 VFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAAIPAELIESEL 205 Query: 119 FGHEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRS 178 FGH KGAF+GA + + G F+ A+GGTLFLDEIGD+ LA Q K+LRVLQERE+ +G +S Sbjct: 206 FGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELTPVGGNQS 265 Query: 179 IPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEY 238 + +DVR+IAAT+ LQ + G FR+DL+YRLQV+ + +P LRERP DIL +A HFL Sbjct: 266 VRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIAEHFL--- 322 Query: 239 RQRLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERR 298 RQ G RI R L QH WPGN+REL N + A ++ C+ AE LS Sbjct: 323 RQLGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAEDIGLSARPPA 382 Query: 299 LDYAVAAADERGNDPLHALEQALQGLFNQSQEGLFEKIEDTVFRTAFEFCERNQVQAARL 358 + A+A D A+ A ++E + A + N+ +AAR Sbjct: 383 GAASAASAPAIDWDGPLAVALA--------------EVERVMIERALQGAAGNRAEAARR 428 Query: 359 LDISRNVLRARLIRNGQ 375 L ISR L RL G+ Sbjct: 429 LGISRQQLYRRLEEAGK 445 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 236 bits (601), Expect = 3e-63, Method: Compositional matrix adjust. Identities = 118/229 (51%), Positives = 152/229 (66%) Query: 62 RVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFGH 121 +V + APS + +++ G +GTGKE+IAR +H LS R+D PF+ VNC A SE+L ESELFGH Sbjct: 216 QVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGH 275 Query: 122 EKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIPI 181 EKGAFTGA + G FE A+GGTLFLDEIG++ A Q KLLRVLQERE R+G RSI + Sbjct: 276 EKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKV 335 Query: 182 DVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQR 241 DVR++ ATN L+ AVA G FR DLYYR+ VV + IP LRER DI L HFL ++R Sbjct: 336 DVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVE 395 Query: 242 LGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHF 290 + + + + WPGN+RELEN + + + D + HF Sbjct: 396 NQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGDLITEVHF 444 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 228 bits (582), Expect = 5e-61, Method: Compositional matrix adjust. Identities = 114/229 (49%), Positives = 153/229 (66%) Query: 50 VFHDPVSLALLERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAF 109 + P L++ + APSD V++ G TGTGKEL+A +H S R P +++NC A Sbjct: 201 IGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAAL 260 Query: 110 SESLAESELFGHEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 169 ++L ESELFGH +GAF+GA+ + G FE A+GGTLFLDE+G+LPLA+Q KLLRVLQ + Sbjct: 261 PDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSGQ 320 Query: 170 VVRLGSRRSIPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILP 229 + R+GS R +DVR+IAATN L D V GHFR D Y+RL V + +P LRER D+L Sbjct: 321 LQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVLL 380 Query: 230 LAYHFLHEYRQRLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALL 278 LA +FL + R RLG + R+ + +R L + WPGNIRELE+ I + L Sbjct: 381 LAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSAL 429 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 228 bits (580), Expect = 8e-61, Method: Compositional matrix adjust. Identities = 110/244 (45%), Positives = 163/244 (66%) Query: 50 VFHDPVSLALLERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAF 109 + D LA+ +++VAPS A+V+++G++GTGKE++AR +H+LS R F+A+NC A Sbjct: 149 ITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAI 208 Query: 110 SESLAESELFGHEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 169 E+L ESELFG+EKGAFTGA G E A+GGT FLDE+GDLP+ +Q KLLR LQER Sbjct: 209 PENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERV 268 Query: 170 VVRLGSRRSIPIDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILP 229 + R+G IP+DVR+I AT+ L++ A+G FR+DLYYRL + + IP L+ER D + Sbjct: 269 IERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVL 328 Query: 230 LAYHFLHEYRQRLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEH 289 LA HF+ ++ + G + + + +++WPGN+RE+EN + A+++ + AE Sbjct: 329 LARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQITAED 388 Query: 290 FHLS 293 LS Sbjct: 389 LGLS 392 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 0.323 0.138 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: 1,209,844 Number of extensions: 52150 Number of successful extensions: 225 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 210 Number of HSP's successfully gapped: 12 Length of query: 380 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 293 Effective length of database: 1,207,925 Effective search space: 353922025 Effective search space used: 353922025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 131 (55.1 bits)