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= 0001.4056.p (783 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313473|ref|YP_003777565.1| transcription accessory protein... 1570 0.0 gi|300312983|ref|YP_003777075.1| 30s ribosomal protein S1 [Herba... 59 2e-09 >gi|300313473|ref|YP_003777565.1| transcription accessory protein [Herbaspirillum seropedicae SmR1] Length = 783 Score = 1570 bits (4065), Expect = 0.0, Method: Compositional matrix adjust. Identities = 768/783 (98%), Positives = 780/783 (99%) Query: 1 MLPSIEQRLALELAAKPVQVAAAIALLDEGATVPFIARYRKEVTGGLDDVQLRLLEERLR 60 MLPSIEQRLALELAAKPVQVAAAIALLDEGATVPFIARYRKEVTGGLDDVQLRLLEERLR Sbjct: 1 MLPSIEQRLALELAAKPVQVAAAIALLDEGATVPFIARYRKEVTGGLDDVQLRLLEERLR 60 Query: 61 YLRELESRRAAIIASIEEQGKMTPVLLDAITHAEDKTRLEDLYLPYKPKRRTKAQIAAEA 120 YLRELESRRAAIIASIEEQGKMTPVLLDAITHAEDKTRLEDLYLPYKPKRRTKAQIAAEA Sbjct: 61 YLRELESRRAAIIASIEEQGKMTPVLLDAITHAEDKTRLEDLYLPYKPKRRTKAQIAAEA 120 Query: 121 GLTELADALLNDPSLNPEEEAAKYIKPAFTTDNGDNPGVPDTKAALDGARQILMERFSED 180 GLTELADALLNDP+LNPEEEAAK+IKPAFTTDNGDNPGVPDTKAALDGARQILMERFSED Sbjct: 121 GLTELADALLNDPTLNPEEEAAKFIKPAFTTDNGDNPGVPDTKAALDGARQILMERFSED 180 Query: 181 AELLQSLREYITEHGVVESKVVEGKQDAGEKFADYFDYSETYSTIPSHRALALFRGRREE 240 AELLQSLREY+TEHGVVESKV+EGKQDAGEKFADYFDYSETYSTIPSHRALALFRGRREE Sbjct: 181 AELLQSLREYLTEHGVVESKVIEGKQDAGEKFADYFDYSETYSTIPSHRALALFRGRREE 240 Query: 241 MLNVVLRLDTEEEKPKWDAPHNPCEGRIASRFGVSNKGRPADKWLSDTVRWAWRVKVFMH 300 MLNV+LRLD+EEEKPKWDAPHNPCEGRIASRFGVSNKGR ADKWLSDTVRWAWRVKVFMH Sbjct: 241 MLNVILRLDSEEEKPKWDAPHNPCEGRIASRFGVSNKGRAADKWLSDTVRWAWRVKVFMH 300 Query: 301 LETELMTNLREKAEAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVAIVDATGK 360 LETELMTNLREKAEAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVAIVDATGK Sbjct: 301 LETELMTNLREKAEAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVAIVDATGK 360 Query: 361 VVATDTIYPHQPRNDWNGSLHTLSQLAEKHNVSLISIGNGTASRETDKLAQDLIKLRPEL 420 VVATDTIYPHQPRNDWNGSLHTLSQLAEKHNVSLISIGNGTASRETDKLAQDLIKLRPEL Sbjct: 361 VVATDTIYPHQPRNDWNGSLHTLSQLAEKHNVSLISIGNGTASRETDKLAQDLIKLRPEL 420 Query: 421 KLTKIVVSEAGASVYSASEFASKELPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVG 480 KLTKIVVSEAGASVYSASEFASKELPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVG Sbjct: 421 KLTKIVVSEAGASVYSASEFASKELPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVG 480 Query: 481 QYQHDVSQSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG 540 QYQHDVSQSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG Sbjct: 481 QYQHDVSQSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG 540 Query: 541 MFNSRAALREVPRLGDKTFEQAAGFLRVMNGENPLDASAVHPESYPLVEKILADIKKDVK 600 MF+SRAALREVPRLG+KTFEQAAGFLRVMNGENPLDASAVHPESYPLVEKILADIKKDVK Sbjct: 541 MFSSRAALREVPRLGEKTFEQAAGFLRVMNGENPLDASAVHPESYPLVEKILADIKKDVK 600 Query: 601 SVLGQTSLLKGLSPSKYADEKFGVPTVTDILKELDKPGRDPRPEFTTATFKDGVEEIKDL 660 SVLGQTSLLKGLSP+KYADEKFGVPTVTDILKELDKPGRDPRPEFTTATFK+GVEEIKDL Sbjct: 601 SVLGQTSLLKGLSPAKYADEKFGVPTVTDILKELDKPGRDPRPEFTTATFKEGVEEIKDL 660 Query: 661 RVDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNSYVKDPHTVVKAGQVVKVKVLEV 720 R DMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSN+YVKDPHTVVKAGQVVKVKVLEV Sbjct: 661 RPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNTYVKDPHTVVKAGQVVKVKVLEV 720 Query: 721 DEKRKRIALTMRLNDTAPAPGARNEQRGDRTDSHRLSQHQNQRGREQAPANNAMAAAFAK 780 DEKRKRIALTMRLNDTAPAPGARNEQRGDRTDS RLSQHQNQRGREQAPANNAMAAAFAK Sbjct: 721 DEKRKRIALTMRLNDTAPAPGARNEQRGDRTDSRRLSQHQNQRGREQAPANNAMAAAFAK 780 Query: 781 LKG 783 L+G Sbjct: 781 LRG 783 >gi|300312983|ref|YP_003777075.1| 30s ribosomal protein S1 [Herbaspirillum seropedicae SmR1] Length = 585 Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 37/90 (41%), Positives = 57/90 (63%), Gaps = 8/90 (8%) Query: 666 LEGVVTNVAAFGAFVDIGVHQDGLVHISAL--SNSYVKDPHTVVKAGQVVKVKVLEVDEK 723 L G VTN+ +GAFV++ +GLVH+S + +N V P+ VV+ G V+V VLE+DE+ Sbjct: 306 LFGKVTNLTDYGAFVEVEQGIEGLVHVSEMDWTNKNVA-PNKVVQLGDEVEVMVLEIDEE 364 Query: 724 RKRIALTMRLNDTAPAPG---ARNEQRGDR 750 R+RI+L M+ P P A + ++GD+ Sbjct: 365 RRRISLGMK--QCKPNPWDDFAMSHKKGDK 392 Score = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 32/95 (33%), Positives = 57/95 (60%), Gaps = 2/95 (2%) Query: 657 IKDLRVDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNSYVKDPHTVVKAGQVVKVK 716 ++ L+ ++ G+V N+ +GAFVD+G DGL+HI+ L+ V+ P V+ GQ + K Sbjct: 212 METLKEGTVVTGIVKNITDYGAFVDLG-GIDGLLHITDLAWRRVRHPSEVLSVGQEITAK 270 Query: 717 VLEVDEKRKRIALTMRLNDTAPAPG-ARNEQRGDR 750 VL+ D+++ R++L ++ P G +R +G R Sbjct: 271 VLKYDQEKNRVSLGVKQLGDDPWTGLSRRYPQGTR 305 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 0.315 0.132 0.367 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: 2,165,004 Number of extensions: 85451 Number of successful extensions: 320 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 320 Number of HSP's successfully gapped: 3 Length of query: 783 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 690 Effective length of database: 1,179,515 Effective search space: 813865350 Effective search space used: 813865350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 134 (56.2 bits)