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= 0030.0111.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... 697 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 237 1e-63 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 235 3e-63 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 234 1e-62 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 227 1e-60 >gi|300310282|ref|YP_003774374.1| sigma-54 dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 697 bits (1798), Expect = 0.0, Method: Compositional matrix adjust. Identities = 348/380 (91%), Positives = 355/380 (93%) Query: 1 MHASPRSAHLYALPSSPEGDGDVAARTASPLLTLPHARKLGTSIRATAQVFHDPVSVALL 60 MHAS RSAHLYALPSSPEG GD+AAR + PLLTLPHARKLGTSIRATAQVFHDPVS+ALL Sbjct: 1 MHASHRSAHLYALPSSPEGHGDLAARASPPLLTLPHARKLGTSIRATAQVFHDPVSLALL 60 Query: 61 ERVQRVAPSDANVVIIGATGTGKELIARHVHALSHRRDAPFVAVNCGAFSESLAESELFG 120 ERVQRVAPSDANVVIIGATGTGKELIARHVH LS RRDAPFVAVNCGAFSESLAESELFG Sbjct: 61 ERVQRVAPSDANVVIIGATGTGKELIARHVHELSQRRDAPFVAVNCGAFSESLAESELFG 120 Query: 121 HEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 180 HEKGAFTGAI HK GWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP Sbjct: 121 HEKGAFTGAITHKPGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIP 180 Query: 181 IDVRVIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPADILPLAYHFLHEYRQ 240 IDVR+IAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERP DILPLAYHFLHEYRQ Sbjct: 181 IDVRIIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPLDILPLAYHFLHEYRQ 240 Query: 241 RLGYGAPRIDAEGERKLREHDWPGNIRELENAIHHALLICQEDSLRPEHFHLSHVERRPA 300 RLGYGA RID EGERKLR+HDWPGNIRELENAIHHALLICQ+D LR EHFHLSHVERR Sbjct: 241 RLGYGAARIDGEGERKLRQHDWPGNIRELENAIHHALLICQDDCLRAEHFHLSHVERRLD 300 Query: 301 YAAHGGMDCSNDPLQALEQALQNLFNQSQAGLFEKIEDTVFRTAFEFCERNQVQAARLLD 360 YA + NDPL ALEQALQ LFNQSQ GLFEKIEDTVFRTAFEFCERNQVQAARLLD 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 = 237 bits (604), Expect = 1e-63, Method: Compositional matrix adjust. Identities = 142/319 (44%), Positives = 186/319 (58%), Gaps = 21/319 (6%) Query: 59 LLERVQRVAPSDANVVIIGATGTGKELIARHVHALSHRRDAPFVAVNCGAFSESLAESEL 118 + +++ R A SDA V+++G TGTGKEL+AR +H R PFVAVNC A L ESEL Sbjct: 146 VFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAAIPAELIESEL 205 Query: 119 FGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRS 178 FGH KGAF+GA + + G F+ A+GGTLFLDEIGD+ LA Q K+LRVLQERE+ +G +S Sbjct: 206 FGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELTPVGGNQS 265 Query: 179 IPIDVRVIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPADILPLAYHFLHEY 238 + +DVRVIAAT+ LQ + G FR+DL+YRLQV+ + +P LRERP DIL +A HFL + Sbjct: 266 VRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIAEHFLRQ- 324 Query: 239 RQRLGYGAP-RIDAEGERKLREHDWPGNIRELENAIHHALLICQEDSLRPEHFHLSHVER 297 LG AP RI R L +H WPGN+REL N + A ++ + E LS Sbjct: 325 ---LGGDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAEDIGLSARPP 381 Query: 298 RPAYAAHGGMDCSND-PLQALEQALQNLFNQSQAGLFEKIEDTVFRTAFEFCERNQVQAA 356 A +A D PL A ++E + A + N+ +AA Sbjct: 382 AGAASAASAPAIDWDGPL---------------AVALAEVERVMIERALQGAAGNRAEAA 426 Query: 357 RLLDISRNVLRARLIRNGQ 375 R L ISR L RL G+ Sbjct: 427 RRLGISRQQLYRRLEEAGK 445 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 235 bits (600), Expect = 3e-63, Method: Compositional matrix adjust. Identities = 118/229 (51%), Positives = 152/229 (66%) Query: 62 RVQRVAPSDANVVIIGATGTGKELIARHVHALSHRRDAPFVAVNCGAFSESLAESELFGH 121 +V + APS + +++ G +GTGKE+IAR +H LS R+D PF+ VNC A SE+L ESELFGH Sbjct: 216 QVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGH 275 Query: 122 EKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQEREVVRLGSRRSIPI 181 EKGAFTGA + G FE A+GGTLFLDEIG++ A Q KLLRVLQERE R+G RSI + Sbjct: 276 EKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKV 335 Query: 182 DVRVIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPADILPLAYHFLHEYRQR 241 DVR++ ATN L+ AVA G FR DLYYR+ VV + IP LRER DI L HFL ++R Sbjct: 336 DVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVE 395 Query: 242 LGYGAPRIDAEGERKLREHDWPGNIRELENAIHHALLICQEDSLRPEHF 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 = 234 bits (596), Expect = 1e-62, Method: Compositional matrix adjust. Identities = 117/229 (51%), Positives = 157/229 (68%) Query: 50 VFHDPVSVALLERVQRVAPSDANVVIIGATGTGKELIARHVHALSHRRDAPFVAVNCGAF 109 + P L++ + APSD V++ G TGTGKEL+A +HA S R P +++NC A Sbjct: 201 IGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAAL 260 Query: 110 SESLAESELFGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 169 ++L ESELFGH +GAF+GA+A + G FE A+GGTLFLDE+G+LPLA+Q KLLRVLQ + Sbjct: 261 PDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSGQ 320 Query: 170 VVRLGSRRSIPIDVRVIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPADILP 229 + R+GS R +DVR+IAATN L D V GHFR D Y+RL V + +P LRER D+L Sbjct: 321 LQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVLL 380 Query: 230 LAYHFLHEYRQRLGYGAPRIDAEGERKLREHDWPGNIRELENAIHHALL 278 LA +FL + R RLG + R+ A+ +R L ++ WPGNIRELE+ I + L Sbjct: 381 LAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSAL 429 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 227 bits (578), Expect = 1e-60, Method: Compositional matrix adjust. Identities = 113/251 (45%), Positives = 164/251 (65%), Gaps = 1/251 (0%) Query: 50 VFHDPVSVALLERVQRVAPSDANVVIIGATGTGKELIARHVHALSHRRDAPFVAVNCGAF 109 + D +A+ +++VAPS A+V+++G++GTGKE++AR +H LS R F+A+NC A Sbjct: 149 ITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAI 208 Query: 110 SESLAESELFGHEKGAFTGAIAHKAGWFEAANGGTLFLDEIGDLPLAIQVKLLRVLQERE 169 E+L ESELFG+EKGAFTGA G E A+GGT FLDE+GDLP+ +Q KLLR LQER Sbjct: 209 PENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERV 268 Query: 170 VVRLGSRRSIPIDVRVIAATNVRLQDAVAAGHFRQDLYYRLQVVQLAIPRLRERPADILP 229 + R+G IP+DVRVI AT+ L++ A+G FR+DLYYRL + + IP L+ER D + Sbjct: 269 IERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVL 328 Query: 230 LAYHFLHEYRQRLGYGAPRIDAEGERKLREHDWPGNIRELENAIHHALLICQEDSLRPEH 289 LA HF+ ++ + G + + + ++WPGN+RE+EN + A+++ + E Sbjct: 329 LARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMADGQQITAED 388 Query: 290 FHLSHVERRPA 300 LS VE R A Sbjct: 389 LGLS-VEGREA 398 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 0.136 0.401 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: 1,228,336 Number of extensions: 53486 Number of successful extensions: 233 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 219 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 131 (55.1 bits)