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= 0001.1228.p (339 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312620|ref|YP_003776712.1| ABC transporter periplasmic pro... 67 2e-12 gi|300312970|ref|YP_003777062.1| nitrate/sulfonate/bicarbonate A... 64 2e-11 gi|300310977|ref|YP_003775069.1| alkanesulfonates ABC transporte... 60 3e-10 >gi|300312620|ref|YP_003776712.1| ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 333 Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 77/299 (25%), Positives = 124/299 (41%), Gaps = 31/299 (10%) Query: 47 RIGYWPVAAGLPFYAAVEAGYFKQAGLEVQAIKFAGAQQVMEAMLSGRADGSANGTGAGN 106 +IGY V AA EAG +K+ GL+V+ I+F +++A++ G+ D G Sbjct: 29 KIGYLRVMDDAQAMAAYEAGLYKKYGLDVELIEFKSGTDLVKAIVGGQLDSGVFGFSN-- 86 Query: 107 LAIGEIAQPGLFKIFATNPSNAKYVLDEFLVPQDSPVKSIADLKGKKVASGP--GIQNVT 164 A+ ++ K+ A+ + +DS + +ADLKGK +AS + Sbjct: 87 -AVAWASKGADLKVVG----GAQLGYHALVAREDSGINKVADLKGKTLASQAEGSTADTV 141 Query: 165 LAKTVLERAGATSATVVELPIGQHVA--SLAAGQVDAAYTLEPTGTVGRMSNSTRVLEAG 222 L VL AG + V + + VA SL +VDAA+ EP + + L A Sbjct: 142 LKGVVLRDAGIKADDVNVMGVSPQVAVQSLVGKRVDAAFLFEPQARIAQ-------LIAP 194 Query: 223 VIAKYILGDPMAPWHGGAAALTTEFIKKNPELARKYIAAYARGIELVRSKPDQARTYLKG 282 V Y +G+ + P+ + E +KK E K + A I L++ KP +A + G Sbjct: 195 VKQVYEIGE-VWPFPCMVVITSGETLKKKREAVWKSLDAQRDAITLLQKKPAEASKLIAG 253 Query: 283 Y--------TAIEGSLTNEVPLAAYMLYNEFKP----SDLAYFQKFYDLFVEKGVFSQR 329 Y T G + E + + F P D Q+ D+ +G R Sbjct: 254 YFIAEPTLKTLKHGEMLREDVIRDAIKSQTFTPKISKKDQDRMQEIADILQSQGSLKTR 312 >gi|300312970|ref|YP_003777062.1| nitrate/sulfonate/bicarbonate ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 60/223 (26%), Positives = 101/223 (45%), Gaps = 18/223 (8%) Query: 57 LPFYAAVEAGYFKQAGLEVQAIKFAGAQQVMEAMLSGRADGSANGTGAGNLAIGEIAQPG 116 LP A + GYFK GL+V+ FAG + ++AM+ G AD +G + + QP Sbjct: 49 LPLTIAEQLGYFKDEGLQVEISDFAGGAKALQAMVGGSAD-VVSGAYEHTINMQAKNQPI 107 Query: 117 LFKIFATNPSNAKYVLDEFLVPQDSPVKSIADLKGKKV-ASGPGIQNVTLAKTVLERAGA 175 + + ++ +P K++ADLKGKK+ + PG +A VL +AG Sbjct: 108 VAFVLQGRAPQIVLAVNNKTMPN---YKTVADLKGKKIGVTAPGSSTSVMASYVLAKAGL 164 Query: 176 TSATVVELPIGQHVASLAA---GQVDAAYTLEPTGTVGRMSNSTRVLEAGVIAK---YIL 229 + V + +G +++A GQ+DA L+P ++ S + + K + Sbjct: 165 KPSDVSFIGVGAAAGAISAVRSGQIDAIANLDPVISMLEQSKEIKTIADTRTLKDTNDVF 224 Query: 230 GDPM--APWHGGAAALTTEFIKKNPELARKYIAAYARGIELVR 270 G PM A + AA FI+K P + A R ++ ++ Sbjct: 225 GGPMPAATLYAPAA-----FIQKYPNTTQALTNAMVRALKWIQ 262 >gi|300310977|ref|YP_003775069.1| alkanesulfonates ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 327 Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 90/337 (26%), Positives = 135/337 (40%), Gaps = 25/337 (7%) Query: 10 TAHDAARRRFMA-KAGALTATAAITGAPAILRAQSVPIRIGYWPVAAGLPFYAA--VEAG 66 T H A RR A AL A GA + ++ +RIGY A L A Sbjct: 8 TVHQARRRAIQRLSAIALGALTIALGASPVQAQETKLLRIGYQKAANTLVLLKAHGTLEK 67 Query: 67 YFKQAGLEVQAIKFAGAQQVMEAMLSGRADGSANGTGAGNLAIGEIAQPGLFKIFATNPS 126 + G+EV+ +FA Q++EA+ G D G A A ++ + Sbjct: 68 RLQPLGVEVKWAEFAAGPQLLEALNVGSVDFGYVGEAPPVFAQAAGAD-FVYTAYEIPTP 126 Query: 127 NAKYVLDEFLVPQDSPVKSIADLKGKKVASGPGIQNVTLAKTVLERAGATSATV--VELP 184 +A + LV ++SP+KS+A+LKGKK+A G L +L++AG + + V L Sbjct: 127 DA----EGLLVQKNSPIKSVAELKGKKIAFNKGSDVHWLVVALLKKAGLQYSDIQPVYLA 182 Query: 185 IGQHVASLAAGQVDAAYTLEPTGTVGRMSNSTRVLEAGVIAKYILGDPMAPWHGGAAALT 244 A+ G VDA +P R L GV A H Sbjct: 183 PADARAAFERGAVDAWAIWDPFQAAAEKQVGARRLATGVGAVN---------HHQFFLSA 233 Query: 245 TEFIKKNPELARKYIAAYARGIELVRSKPDQARTYLKGYTAIEGSLTNEVPLAAYMLYNE 304 F KNP++ + + +R E VR+ QA L ++ + E L Y + Sbjct: 234 RPFAAKNPQVEKILLEEISREGEWVRTHTAQAAAQLAPIQGLDADII-ETGLKRYA--HV 290 Query: 305 FKPSD---LAYFQKFYDLFVEKGVFSQRIVVDNLIYK 338 +KP D LA QK D F E + + + V + + K Sbjct: 291 YKPVDAQVLAEQQKIADAFYELKLIPKPLKVSDAVLK 327 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 0.317 0.132 0.375 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: 985,767 Number of extensions: 41752 Number of successful extensions: 229 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 223 Number of HSP's successfully gapped: 6 Length of query: 339 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 253 Effective length of database: 1,212,660 Effective search space: 306802980 Effective search space used: 306802980 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 (21.7 bits) S2: 131 (55.1 bits)