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= 0001.3719.p (411 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 579 e-166 gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio... 261 6e-71 gi|300313916|ref|YP_003778008.1| two component response regulato... 223 2e-59 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 205 6e-54 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 201 7e-53 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 579 bits (1493), Expect = e-166, Method: Compositional matrix adjust. Identities = 300/403 (74%), Positives = 326/403 (80%), Gaps = 15/403 (3%) Query: 18 ASHKKAVRQETDMPTSLPDQPRADSQIHAASTAFSTPLSPRCAHGRQVPRYRDIDQLAGG 77 A K + RQET MPT+ +QP A+++ A + T + R A R PRYRDIDQLA G Sbjct: 41 ARQKSSPRQETIMPTTPVEQPLAEAE---ADSDVRTSTAARSASSRHAPRYRDIDQLAAG 97 Query: 78 DALMQALVERGKRLIERGIPVLILGQTGTGKEYLSRALHDYSARRQAGWIAVNCASIPES 137 DA M L+ERGKRLI+RGIPVLILG+TGTGKEYLSRALHDYSARR+A WIAVNCASIPES Sbjct: 98 DACMHDLIERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPES 157 Query: 138 LAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVT 197 LAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREV Sbjct: 158 LAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVI 217 Query: 198 PLGALRPVPVDVQLICATHQDLPNLIAQGRFREDLYYRIAGGVLRLPALRERADLGRLVL 257 PLGA PVPVDVQLICATHQDL LIA+GRFREDLYYR+AGGVLRLPALRER+D RLV+ Sbjct: 218 PLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVM 277 Query: 258 QMMADELGVQADEQLIAPAAWQRLLAYPWPGNLRQMHAVIRYSCAVMNGTRIEVSDLPEE 317 QM+ +ELG AD+ +I AA QRLLAYPWPGNLRQMHAVIRYSCAVMNG RIEV DLPEE Sbjct: 278 QMITEELGRPADDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRDLPEE 337 Query: 318 LMQSQGPVLAQVHPLAPRMAERPPSAVV---------TGGPWPDERTRVIAALNGSRWNI 368 LMQ Q LA+VHP+ RP ++ +G P+ DERTRVI ALNGSRWNI Sbjct: 338 LMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNI 397 Query: 369 SAASRQLGMCRASLYRKLRQLDIPHVRDQGVSVMDAMGTYAVA 411 SAASRQLGMCRASLYRKLRQLDIPHVRDQ M A YAVA Sbjct: 398 SAASRQLGMCRASLYRKLRQLDIPHVRDQA---MPAYPAYAVA 437 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 261 bits (668), Expect = 6e-71, Method: Compositional matrix adjust. Identities = 152/327 (46%), Positives = 207/327 (63%), Gaps = 15/327 (4%) Query: 70 DIDQLAGGDALMQALVERGKRLIERGIPVLILGQTGTGKEYLSRALHDYSAR---RQ--- 123 D+ L GD M A++ + +R+I+R IP+LI G+TGTGKE+L++A+H SAR RQ Sbjct: 351 DLQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRA 410 Query: 124 --AGWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPL 181 A ++AVNC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGDMPL Sbjct: 411 GAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPL 470 Query: 182 ALQTRLLRVLSEREVTPLGALRPVPVDVQLICATHQDLPNLIAQGRFREDLYYRIAGGVL 241 ALQ RLLRVL ER VTPLG+ R +PVD L+CAT+Q L + A+ FREDLYYRI G + Sbjct: 471 ALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQV 530 Query: 242 RLPALRERADLGRLVLQMMADELGVQADEQLIAPAAWQRLLAYPWPGNLRQMHAVIRYSC 301 +LPALR+R+DL +L+ +++ DE G A A LLA WPGNLRQ+ ++R S Sbjct: 531 KLPALRDRSDLPQLIERILEDEGGPHAPR--FDAQAQALLLASHWPGNLRQLANLVRTSL 588 Query: 302 AVMNGTR-IEVSDLPEELMQSQGPVLAQVHPLAPRMAERPPSAVVTGGPWPDERTRVIAA 360 A+ G I LP++ ++ G A + A R + W + A Sbjct: 589 AMAEGEEAIGPHHLPDDFLEEAGAPGALHDGMHTMHAVRSDCLSIQDNEW----AAIERA 644 Query: 361 LNGSRWNISAASRQLGMCRASLYRKLR 387 L N+SAA++ LG+ R ++YR+L+ Sbjct: 645 LRTHAGNVSAAAKALGVSRNTIYRRLK 671 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 223 bits (568), Expect = 2e-59, Method: Compositional matrix adjust. Identities = 139/329 (42%), Positives = 193/329 (58%), Gaps = 22/329 (6%) Query: 72 DQLAGGDALMQALVERGKRLIERGIPVLILGQTGTGKEYLSRALHDYSARRQAGWIAVNC 131 +QL G M+ + ++ R VL+LG+TGTGKE ++RALH AR ++AVNC Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNC 193 Query: 132 ASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVL 191 A+IP L ESELFG+ KGAFSGA + G+ Q+ADGGTLFLDEIGDM LA Q ++LRVL Sbjct: 194 AAIPAELIESELFGHVKGAFSGATSPRL-GRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 192 SEREVTPLGALRPVPVDVQLICATHQDLPNLIAQGRFREDLYYRIAGGVLRLPALRERAD 251 ERE+TP+G + V VDV++I ATH+DL + I QGRFREDL+YR+ + +PALRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 252 LGRLVLQMMADELGVQADEQLIAPAAWQRLLAYPWPGNLRQMHAVIRYSCAVMNGTRIEV 311 + + +LG A ++ I+PAA + LL + WPGN+R++ + + + +G IE Sbjct: 313 DILTIAEHFLRQLGGDAPKR-ISPAAARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEA 371 Query: 312 SDLPEELMQSQGPVLAQVH-------PLAPRMAERPPSAVVTGGPWPDERTRVIAALNGS 364 D+ G A PLA +AE ER + AL G+ Sbjct: 372 EDIGLSARPPAGAASAASAPAIDWDGPLAVALAEV-------------ERVMIERALQGA 418 Query: 365 RWNISAASRQLGMCRASLYRKLRQLDIPH 393 N + A+R+LG+ R LYR+L + H Sbjct: 419 AGNRAEAARRLGISRQQLYRRLEEAGKSH 447 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 205 bits (521), Expect = 6e-54, Method: Compositional matrix adjust. Identities = 130/334 (38%), Positives = 184/334 (55%), Gaps = 36/334 (10%) Query: 73 QLAGGDALMQALVERGK------RLIERGIP----VLILGQTGTGKEYLSRALHDYSARR 122 Q AGG + L+ R R IE+ P V++LG +GTGKE L+RALH S R Sbjct: 137 QQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRS 196 Query: 123 QAGWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLA 182 ++A+NCA+IPE+L ESELFGY KGAF+GA + GKV+ A GGT FLDE+GD+P+ Sbjct: 197 GRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTI-GKVELAHGGTFFLDEVGDLPMP 255 Query: 183 LQTRLLRVLSEREVTPLGALRPVPVDVQLICATHQDLPNLIAQGRFREDLYYRIAGGVLR 242 LQ +LLR L ER + +G +PVDV++ICATHQ+L L A G FREDLYYR+ +++ Sbjct: 256 LQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIK 315 Query: 243 LPALRERADLGRLVLQMMADELGVQADEQLI-----APAAWQRLLAYPWPGNLRQMHAVI 297 +PAL+ER L+ + + + + A AA +R Y WPGN+R+M + Sbjct: 316 IPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIER---YEWPGNVREMENCV 372 Query: 298 RYSCAVMNGTRIEVSDLPEELMQSQGPVLAQVHPLAPRMAERPPSAVVTGGPWPDERTRV 357 + + +G +I DL + +G + PL R ER V Sbjct: 373 MRAVIMADGQQITAEDLG---LSVEG---REAEPLNLRQVRDEA-----------ERKAV 415 Query: 358 IAALNGSRWNISAASRQLGMCRASLYRKLRQLDI 391 + AL NI A+ LG+ R +LY + + +I Sbjct: 416 VKALTRMDGNILKAAELLGVSRPTLYDLMSRHEI 449 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 201 bits (512), Expect = 7e-53, Method: Compositional matrix adjust. Identities = 109/246 (44%), Positives = 162/246 (65%), Gaps = 7/246 (2%) Query: 81 MQALVERGKRLIERGIPVLILGQTGTGKEYLSRALHDYSARRQAGWIAVNCASIPESLAE 140 MQ + RL + + VLI G++G+GKE ++RALH +S R ++A+N A+IP+ L E Sbjct: 143 MQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTAAIPKDLLE 202 Query: 141 SELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVTPLG 200 SELFG+ +GAF+GA +G+ +QA+GGTLFLDEIGDMPL LQTRLLRVLS+ +G Sbjct: 203 SELFGHERGAFTGA-QAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVG 261 Query: 201 ALRPVPVDVQLICATHQDLPNLIAQGRFREDLYYRIAGGVLRLPALRERAD----LGRLV 256 + + +V++I ATHQ+L + +G FREDLY+R+ LRLP+LRER++ L R Sbjct: 262 GHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILARYF 321 Query: 257 LQMMADELGVQADEQLIAPAAWQRLLAYPWPGNLRQMHAVIRYSCAVMNGTRIEVSDLPE 316 L A +LGV+A ++P A Q L +PGN+RQ+ + + + G +E+ DLP+ Sbjct: 322 LAQSARQLGVEAKR--LSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTVEIKDLPQ 379 Query: 317 ELMQSQ 322 +L++ + Sbjct: 380 DLVEER 385 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 0.320 0.135 0.403 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: 1,432,033 Number of extensions: 65948 Number of successful extensions: 292 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 262 Number of HSP's successfully gapped: 12 Length of query: 411 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 323 Effective length of database: 1,203,190 Effective search space: 388630370 Effective search space used: 388630370 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 (21.8 bits) S2: 132 (55.5 bits)