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= 0001.4313.p (308 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311115|ref|YP_003775207.1| branched-chain amino acid ABC t... 86 5e-18 gi|300310287|ref|YP_003774379.1| branched-chain amino acid ABC t... 84 1e-17 gi|300313405|ref|YP_003777497.1| branched-chain amino acid ABC t... 80 2e-16 gi|300311879|ref|YP_003775971.1| amino acid ABC transporter perm... 79 3e-16 gi|300313300|ref|YP_003777392.1| branched-chain amino acid ABC t... 78 1e-15 >gi|300311115|ref|YP_003775207.1| branched-chain amino acid ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 655 Score = 85.5 bits (210), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 59/230 (25%), Positives = 117/230 (50%), Gaps = 4/230 (1%) Query: 5 VIALAWNLLAGFGGLIAIGQHAFIGVGAYSLFFLSNSLDCAPWLLLPLATLSALAFALLS 64 ++ +++ G+ G +++G G+G+Y+ L L ++ +P A F + Sbjct: 40 ILLFGLDIVVGYTGQVSLGHAGLFGIGSYAAGVLFFKLGMPIFVTVPAAIAVTAVFGAIL 99 Query: 65 AWPMFRLSGPYFAVGTWVLAEMLRIAAQNTDVLGAGS-GLSLDE-MNNIDRWTRNAGSYW 122 A P R++GPY A+ T +++I L G G+ L + M D+ + Y Sbjct: 100 ALPALRVTGPYLAMVTLAFGTIIQILINEMTFLTEGPLGIKLQKPMIGGDKMSEVQFFYL 159 Query: 123 AALALCISAVVVARMTLRGRIGLALMSVRDSEVAATACGVSVRKAKLWIWLIAAAMTGTA 182 A+ + +S +VV R+ L+ +G A ++RDS +A+ GVSV + K++ ++I+AA+ G + Sbjct: 160 VAVLMVLSMLVVHRI-LKSNLGRAFQALRDSPIASDCMGVSVYRYKVYAFIISAALAGLS 218 Query: 183 GALAYINTLQVTPDASFSLNWTAAAIFIAVLGGIGTLEGPFLGTLLYFFL 232 GAL + ++P+ +++ T + ++GG + G +G L+ L Sbjct: 219 GALYAYSEEYISPN-TYNFELTIMFLLAVIMGGRKSRIGSLIGALIVVML 267 >gi|300310287|ref|YP_003774379.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 84.3 bits (207), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 74/236 (31%), Positives = 117/236 (49%), Gaps = 23/236 (9%) Query: 7 ALAWNLLAGFGGLIAIGQHAFIGVGAYSLFFLSNSLDCAPWLL-LPLATLSALAFALLSA 65 A+ NLL G+ G +++G AF+ VGA++ + L+ + P L+ + LA L+A A L+ Sbjct: 59 AVGLNLLTGYAGQLSLGSAAFMAVGAFAAYNLNLRVAGLPLLVSIVLAGLAATAIGLVFG 118 Query: 66 WPMFRLSGPYFAVGT--------WVLAEMLRIAAQN-TDVLGAG----SGLSLDEMNNID 112 P RL G Y AV T WVL + + N + V+ A GL+ D Sbjct: 119 LPSLRLRGFYLAVSTLAAQFFVQWVLVKFSWFSNDNPSGVIDAPPLVVGGLAFDT----- 173 Query: 113 RWTRNAGSYWAALALCISAVVVARMTLRGRIGLALMSVRDSEVAATACGVSVRKAKLWIW 172 AG Y ALA+ ++ ++ + G ++VRD+E AA GV V + KL + Sbjct: 174 ----PAGRYLFALAIVTVLTLLCWRLVQSQTGHHFIAVRDNEQAARVIGVPVLRTKLLAF 229 Query: 173 LIAAAMTGTAGALAYINTLQVTPDASFSLNWTAAAIFIAVLGGIGTLEGPFLGTLL 228 I++ + G AG L L+ A F+L+ + +FI ++GG+ T+ G F G L Sbjct: 230 AISSFVIGVAGVLWGFVYLRTVEPAGFNLDRSLQILFIVIIGGLATIRGAFFGAAL 285 >gi|300313405|ref|YP_003777497.1| branched-chain amino acid ABC transporter ATP-binding protein/permease [Herbaspirillum seropedicae SmR1] Length = 596 Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 88/299 (29%), Positives = 137/299 (45%), Gaps = 26/299 (8%) Query: 5 VIALAWNLLAGFGGLIAIGQHAFIGVGAYSLFFLSNSLDCAPWL-LLPLATLSALAFALL 63 ++AL LL G GLI+ GQ AF+G+GAY+ +L+ +PW+ LL L+A + L+ Sbjct: 43 IVALGLVLLTGVAGLISFGQAAFVGMGAYTTAYLTTQFGLSPWIGLLAGIALTACSAFLI 102 Query: 64 SAWPMFRLSGPYFAVGTWVLAEMLRIAAQNTDVLGAGSGLSLDEMNNID--RWTRNAGSY 121 + M R+SG Y + T L N ++LG G++ + I + A Y Sbjct: 103 GSLTM-RISGHYLPLSTIAWGLSLYYLFGNLEMLGKHDGINGIPVITIGSVEFGNGASMY 161 Query: 122 ---WAALALCISAVVVARMTLRGRIGLALMSVRDSEVAATACGVSVRKAKLWIWLIAAAM 178 W L L + +VV L R G A+ ++R V A GV + K+ I++ AA + Sbjct: 162 LLIWVVLILALVSVV---NFLDSRAGRAVRALRFGTVMPEAMGVDTARLKIVIFVYAAVL 218 Query: 179 TGTAGALAYINTLQVTPDASFSLNWTAAAIFIAVLGGIGTLEGPFLG----TLLYFFLRE 234 G +G L Y + Q F L + + + V+GG G + G LG +L FL+E Sbjct: 219 AGISGWL-YAHLQQAVNPTPFGLKYGIDYLLMVVVGGAGHVAGAILGAGLLAVLSNFLQE 277 Query: 235 ----SFSAYGAWYFIGLGSLAIFAMLFSPGGAWAPIKRRWDWDPLGLR--RLMPTDATP 287 G + I G + + F+ G W ++ R+ G R R +P DA P Sbjct: 278 WLPGVLGTGGNFEAIVFGIALVIFLQFANEGLWPRLQARF-----GRRRPRPLPADAAP 331 >gi|300311879|ref|YP_003775971.1| amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 358 Score = 79.3 bits (194), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 73/230 (31%), Positives = 114/230 (49%), Gaps = 15/230 (6%) Query: 7 ALAWNLLAGFGGLIAIGQHAFIGVGAYSLFFLSNSLDCAPWL-LLPLATLSALAFALLSA 65 AL N+L G+ G +++G AF+ VGAY+ + +D P + L L+ A +L Sbjct: 63 ALGLNVLTGYAGQLSLGSAAFMAVGAYAAYNFQLRVDGIPIVATLLLSGGCAALVGVLFG 122 Query: 66 WPMFRLSGPYFAVGTWVLAEMLRIAA-------QNTDVLGAGSGLSLDEMN-NIDRWTRN 117 P R+ G Y AV T + A+ + A N G S +D ID R Sbjct: 123 LPSLRIKGFYLAVAT-LAAQFFVVWALTKFPWFSNNSSSGVISTPKIDFFGIAIDTPVRK 181 Query: 118 AGSYWAALALCISAVVVARMTLRGRIGLALMSVRDSEVAATACGVSVRKAKLWIWLIAAA 177 Y LA+ +VA+ +R G A M+VRD +VAA G+ + + KL + +++ Sbjct: 182 ---YLFVLAVVSVLALVAKNLVRSSTGRAWMAVRDMDVAAEVIGIPLMRTKLTAFAVSSF 238 Query: 178 MTGTAGAL-AYINTLQVTPDASFSLNWTAAAIFIAVLGGIGTLEGPFLGT 226 G AGAL A+ V PD FSL+ + +F+ ++GG+G++ G FLG+ Sbjct: 239 YCGVAGALYAFCYLGSVEPDG-FSLDLSFRILFMIIIGGVGSILGSFLGS 287 >gi|300313300|ref|YP_003777392.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 597 Score = 77.8 bits (190), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 74/277 (26%), Positives = 123/277 (44%), Gaps = 13/277 (4%) Query: 5 VIALAWNLLAGFGGLIAIGQHAFIGVGAYSLFFLSNSLDCAPWLLLPLATLSALAFALLS 64 ++A+ LL G GG+ + GQ AF+G+GAY+ +L+ +PWL LP+ A + Sbjct: 40 LVAIGLVLLTGIGGMTSFGQAAFVGMGAYTTSYLTTVHGVSPWLTLPVGLFITGVSAYVL 99 Query: 65 AWPMFRLSGPYFAVGTWVLAEMLRIAAQNTDVLGAGSGLS---LDEMNNIDRWTRNAGSY 121 R+SG Y + T L D LG G+S ++ +D + Y Sbjct: 100 GRITLRMSGHYLPLATIAWGISLYFLFGKVDFLGKYDGISGIPALQLAGLD-LAKERHLY 158 Query: 122 WAALALCISAVVVARMTLRGRIGLALMSVRDSEVAATACGVSVRKAKLWIWLIAAAMTGT 181 + A+ ++A V+ L R G A+ +++ A A GV + K+ I++ AA + Sbjct: 159 YLIWAIVLAAAWVSLNLLDSRAGRAIRALKGGRSMAEAMGVDTGRYKILIFVFAALLASV 218 Query: 182 AGALAYINTLQVTPDASFSLNWTAAAIFIAVLGGIGTLEGPFLGTLLYFFLRESFSAY-- 239 +G L V P + FSL +FI V+GGI + G LG + L + Sbjct: 219 SGWLFAHMQRTVNP-SPFSLAMGIEYLFIVVVGGIAHIWGALLGAGVLKLLSDQLQVLLP 277 Query: 240 ------GAWYFIGLGSLAIFAMLFSPGGAWAPIKRRW 270 G++ I G + I + ++ GG W ++ W Sbjct: 278 ALLGDGGSYESIVFGLILILLLKYAGGGLWPWVRALW 314 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 0.326 0.138 0.444 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: 876,684 Number of extensions: 33897 Number of successful extensions: 207 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 188 Number of HSP's successfully gapped: 20 Length of query: 308 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 223 Effective length of database: 1,217,395 Effective search space: 271479085 Effective search space used: 271479085 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 130 (54.7 bits)