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= 0001.3562.p (644 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312939|ref|YP_003777031.1| transmembrane nitrate/nitrite s... 1004 0.0 gi|300311886|ref|YP_003775978.1| multi-sensor signal transductio... 87 3e-18 gi|300311282|ref|YP_003775374.1| transmembrane sensor histidine ... 78 3e-15 gi|300310534|ref|YP_003774626.1| transmembrane sensor histidine ... 70 4e-13 >gi|300312939|ref|YP_003777031.1| transmembrane nitrate/nitrite sensor histidine kinase transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 650 Score = 1004 bits (2595), Expect = 0.0, Method: Compositional matrix adjust. Identities = 509/637 (79%), Positives = 562/637 (88%), Gaps = 6/637 (0%) Query: 14 HKRLTFRILLMTLVGLGLTMTAIGYTLLLSWQLEGGGTVINEAGSLRMRSYQLGLALEHQ 73 HKRLTFRILLMTL+GLGLTMTAIGYTLLLSWQLEGGGTVINEAGSLRMRSYQLGLALE Sbjct: 14 HKRLTFRILLMTLIGLGLTMTAIGYTLLLSWQLEGGGTVINEAGSLRMRSYQLGLALEMH 73 Query: 74 QARDTVQHDIERFSQILAMLQTGQTGQ------PSFVPSRGPIHEQLLQVQGQWQQRMQV 127 Q V +IERF QIL L TGQ Q PSFVP RGPIHEQLL+VQ W RMQV Sbjct: 74 QRDSAVLPEIERFDQILRSLHTGQGDQSGQGGQPSFVPPRGPIHEQLLRVQDGWTHRMQV 133 Query: 128 HARDVLQADDAQQRQQALAQYLQELPDFVGEINLLVALVEADLAGKTTWLRLCQTALIFL 187 HAR L+ D R+QA+ YLQELPDFV +INLLVALVEADLAGKTTWLRLCQTALIFL Sbjct: 134 HARAALETADPVLRRQAITLYLQELPDFVDDINLLVALVEADLAGKTTWLRLCQTALIFL 193 Query: 188 ALAASIAVLYLLYLWIVGPVRRLQVGIARMSQNDLDVRLAIDSEDEFGQLARGFNQMADH 247 ALAASIAVLYLLYLWIVGPVRR+Q GIARMS NDLDVRL I+S DEFGQLA FNQMADH Sbjct: 194 ALAASIAVLYLLYLWIVGPVRRMQAGIARMSMNDLDVRLPIESADEFGQLACAFNQMADH 253 Query: 248 VQGVHRTLEERVADKTARLREQNEEVGTLYEITDFLSGAHAIEALCSGFLRRIMQRIQAD 307 V+ VHRTLE+RVA+KTA+L+EQN+EV TLYE+T FLSGAHAIEALC GFL+RIM R+QAD Sbjct: 254 VRSVHRTLEQRVAEKTAQLQEQNDEVSTLYEVTGFLSGAHAIEALCGGFLQRIMARLQAD 313 Query: 308 GGTVRILDERGNLYIAVHEGISERIIDEERCLKVGDCLCGTATSQGIILVRDFRELDQQR 367 GGTVRILDERG+L++ VHEG+SE II+ ERCLKV DCLCG+AT QG+I+VRDF EL ++R Sbjct: 314 GGTVRILDERGHLHLTVHEGVSEAIIEAERCLKVDDCLCGSATQQGVIIVRDFHELGERR 373 Query: 368 RYRCQEEGAVSLGIFQIQVREQVIGSFSLHFSRERHISEEERRLLETLGRHLGSAIENQR 427 RYRC+EEGA S+GIFQI VREQVIGSFSLHFS R IS +ERRLLETLGRHLGSAIENQR Sbjct: 374 RYRCKEEGARSIGIFQILVREQVIGSFSLHFSHPREISADERRLLETLGRHLGSAIENQR 433 Query: 428 LIAREKEFAVSHERNLMAQGLHDSIAQGLNFLNLQVQMLEDSLAREDLAEIRDIAPLLRA 487 LIAREKEFA+++ERNL+AQGLHDSIAQGLNFLNLQVQMLEDSLAR+ L EIRDIAPLLR Sbjct: 434 LIAREKEFAIANERNLLAQGLHDSIAQGLNFLNLQVQMLEDSLARDRLDEIRDIAPLLRT 493 Query: 488 GVQENYEDVRELLLNFRSRLQDSDLESEMRKAVEKLQRQSGLQGDIEITGDGPPLAPEQQ 547 GVQENYEDVRELLLNFR+RLQDS+L+SEMRKA++KLQRQSGLQG I +TGDGPPLAPEQQ Sbjct: 494 GVQENYEDVRELLLNFRTRLQDSNLDSEMRKALDKLQRQSGLQGQITLTGDGPPLAPEQQ 553 Query: 548 LQVLFILQEALSNIRKHAQASRVRIEVDNGRDFCLTVSDDGHGFQLDQARAKGSEHVGLR 607 LQVLFILQEALSNIRKHA+A +V+I VDN +DF +TVSDDGHGF L+ ARAKG EHVGLR Sbjct: 554 LQVLFILQEALSNIRKHARAQQVQISVDNRQDFRMTVSDDGHGFTLESARAKGLEHVGLR 613 Query: 608 IMQERAERLGAHLDIASQPGAGTRITVRLMREERLVA 644 IMQERAERLGA+L+I SQPG GTRI + L+R+ERLVA Sbjct: 614 IMQERAERLGANLEIDSQPGHGTRIALTLLRQERLVA 650 >gi|300311886|ref|YP_003775978.1| multi-sensor signal transduction histidine kinase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 70/226 (30%), Positives = 115/226 (50%), Gaps = 13/226 (5%) Query: 417 RHLGSAIENQRLIAREKEFAVSHERNLMAQGLHDSIAQGLNFLNLQVQMLED--SLARED 474 R L AI+ Q+L++ ER +A+GLHD + Q L L + ++ ++ SL Sbjct: 248 RDLELAIQRQQLLSSRVIEVQERERQHLARGLHDDVGQSLTALKINLETIKKMGSLEGPS 307 Query: 475 LAEIRDIAPLLRAGVQENYEDVRELLLNFRS-RLQDSDLESEMRKAVEKLQRQSGLQGDI 533 L DI + A VR L L+ R +L + L + +R VE+ + + + G Sbjct: 308 LQNGIDIVTAVLA-------QVRSLSLDLRPPQLDNLGLIAALRSYVEQKSKLANVNGWF 360 Query: 534 EITGDGPPLAPEQQLQVLFILQEALSNIRKHAQASRVRIEVDNGRD-FCLTVSDDGHGFQ 592 E +G L + + I+QEA++NI +HA+ + +++D D L++ DDG GF Sbjct: 361 ESSGHDEQLHHDIENTAFRIVQEAVTNILRHARCQNIWVKIDRQHDQVYLSIRDDGRGFD 420 Query: 593 LDQARAKG--SEHVGLRIMQERAERLGAHLDIASQPGAGTRITVRL 636 +++AR+ GL M+ERA +G ++I S PGAGT I + L Sbjct: 421 IERARSNAISGTSFGLLNMEERAVLVGGSMEITSAPGAGTEIVMHL 466 >gi|300311282|ref|YP_003775374.1| transmembrane sensor histidine kinase transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 464 Score = 77.8 bits (190), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 74/228 (32%), Positives = 111/228 (48%), Gaps = 27/228 (11%) Query: 426 QRLIAREKEFAVSHERNLMAQGLHDSIAQGLNFLNLQVQMLEDSLAREDLAEIRDIAPLL 485 QR++ ++E ER +++ LHD I+Q L + LQ+ E +L R L + A Sbjct: 240 QRVVRSQEE-----ERARLSRDLHDGISQWLVSIKLQI---EAALVR--LNGTPEQAATA 289 Query: 486 RAGVQENYEDVRELLLNFR--------SRLQDSDLESEMRKAVEKLQRQSGLQGDIEI-- 535 RAG ++ + +L R + L D L + + + + +G +I Sbjct: 290 RAGFEKTATQINGVLAEVRRISHDLRPAILDDLGLAAALEHLCGEWRDAAGAGVEIVFEN 349 Query: 536 ---TGDGPPLAPEQQLQVLF-ILQEALSNIRKHAQASRVRIEVDNGRDF-CLTVSDDGHG 590 DG L P+ VLF I QEAL+NI +HA ASR+++ + G + L V D+GHG Sbjct: 350 QAQADDGATL-PDVVNTVLFRIAQEALTNIARHAGASRIKVRLYQGHNLLMLQVQDNGHG 408 Query: 591 FQLDQARAKGSEHVGLRIMQERAERLGAHLDIASQPGAGTRITVRLMR 638 F L Q +GLR M+ER E +G L I S P AGT I+ + R Sbjct: 409 FDLGQVDDHSRHGIGLRNMRERIEAVGGELGIDSSP-AGTSISAVIAR 455 >gi|300310534|ref|YP_003774626.1| transmembrane sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 677 Score = 70.5 bits (171), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 55/206 (26%), Positives = 103/206 (50%), Gaps = 6/206 (2%) Query: 440 ERNLMAQGLHDSIAQGLNFLNLQVQMLEDSLAREDLAEIRDIAPLLRAGVQENYEDVREL 499 E+ +A+ LHD++ L L++ ++ + L ++ R + ++ ++ R + Sbjct: 472 EKRAIARELHDNMGASLTALSMHLEGVYQILPPDEKWADRKVR--MQGLMKSLVATTRRI 529 Query: 500 LLNFRSRLQD-SDLESEMRKAVEKLQRQSGLQGDIEITGDGPPLAPEQQLQVLFILQEAL 558 R D L++ + + +++L ++G+ + + + E ++ + +LQE L Sbjct: 530 QTELRPNTLDLFGLKAAISEQLDELHERTGIACHASLPDEDVEVGHEMEIAIYRMLQEML 589 Query: 559 SNIRKHAQASRVRIEVDNGRD-FCLTVSDDGHGFQLDQARAKGSEHVGLRIMQERAERLG 617 +N+ KHA+AS+V + +D D LTV DDG G + + R + GLR ++ERA G Sbjct: 590 NNVTKHAKASKVDVILDIDEDHVALTVRDDGVG--IPEERRDNHKTYGLRGLRERATFFG 647 Query: 618 AHLDIASQPGAGTRITVRLMREERLV 643 +DI S PG G IT+ L LV Sbjct: 648 GEVDIRSTPGKGALITISLPIRPELV 673 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 0.388 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: 1,652,096 Number of extensions: 64061 Number of successful extensions: 328 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 325 Number of HSP's successfully gapped: 5 Length of query: 644 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 553 Effective length of database: 1,188,985 Effective search space: 657508705 Effective search space used: 657508705 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: 134 (56.2 bits)