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= 0001.3987.p (350 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313406|ref|YP_003777498.1| branched-chain amino acid ABC t... 566 e-163 gi|300313299|ref|YP_003777391.1| branched-chain amino acid ABC t... 310 2e-85 gi|300310682|ref|YP_003774774.1| amino acid ABC transporter perm... 305 3e-84 gi|300310992|ref|YP_003775084.1| branched-chain aminoacid ABC tr... 82 6e-17 gi|300310521|ref|YP_003774613.1| branched-chain amino acid ABC t... 71 1e-13 >gi|300313406|ref|YP_003777498.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 350 Score = 567 bits (1460), Expect = e-163, Method: Compositional matrix adjust. Identities = 329/350 (94%), Positives = 340/350 (97%) Query: 1 VDTSILTVLIQDGITTGAIYALLSLALVLVFSVTRVIFLPQGEFVAFGALTLAAIQNGQA 60 +DTSILTVLIQDGITTGAIYALLSLALVLVFSVTRVIFLPQGEFVAFGALTLAAIQNGQA Sbjct: 1 MDTSILTVLIQDGITTGAIYALLSLALVLVFSVTRVIFLPQGEFVAFGALTLAAIQNGQA 60 Query: 61 PGTALLLVALGCVTLAVEAGTALRLAATRTRLLRRLPLLLATHVALPVALYAVTRYFDLQ 120 P TALLL+ALG VTLAVE G+ALRLA TR RLLRRLPLLLATH+ LP+A+ A+TR DLQ Sbjct: 61 PATALLLLALGAVTLAVETGSALRLAQTRARLLRRLPLLLATHLGLPLAILALTRCLDLQ 120 Query: 121 ALAMPWQILLALLIVVPMGPMIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPE 180 ALAMPWQILLALLIVVPMGPMIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPE Sbjct: 121 ALAMPWQILLALLIVVPMGPMIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPE 180 Query: 181 GTNTRPFTELQFNLGESPVSGQSVIVLVTVAALIAVIYVFFERTLTGKALRATAVNRLGA 240 GTNTRPFTE+QFNLGESPVSGQSVIVL+TVAALIAVIYVFFERTLTGKALRATAVNRLGA Sbjct: 181 GTNTRPFTEMQFNLGESPVSGQSVIVLITVAALIAVIYVFFERTLTGKALRATAVNRLGA 240 Query: 241 RLVGVGINQAGKLSFAMAAGIGALCGILIAPFTIVNYESGFIIALKGFVGAIFGGLASYP 300 RLVGVGINQAGKLSF MAAGIGALCGILIAPFTIVNYESGFIIALKGFVGAIFGGLASYP Sbjct: 241 RLVGVGINQAGKLSFGMAAGIGALCGILIAPFTIVNYESGFIIALKGFVGAIFGGLASYP 300 Query: 301 IAALGSVAVGLIESFSSFWASSYKELIVFTVIIPILLWRSLTSHHIDEEA 350 IAALGSV+VGLIESFSSFWAS+YKELIVFTVIIPILLWRSLTSHHIDEEA Sbjct: 301 IAALGSVSVGLIESFSSFWASAYKELIVFTVIIPILLWRSLTSHHIDEEA 350 >gi|300313299|ref|YP_003777391.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 346 Score = 310 bits (793), Expect = 2e-85, Method: Compositional matrix adjust. Identities = 185/351 (52%), Positives = 251/351 (71%), Gaps = 7/351 (1%) Query: 1 VDTSILTVLIQDGITTGAIYALLSLALVLVFSVTRVIFLPQGEFVAFGALTLAAIQNGQA 60 +D+SI +L DG+T G +Y L+++ALVLVF+VTR++F+PQGEFVA+GALTLA +Q GQ Sbjct: 1 MDSSIAAILTLDGLTNGIVYGLIAIALVLVFTVTRILFIPQGEFVAYGALTLAMLQQGQR 60 Query: 61 PGTALLLVALGCVTLAVEAGTALRLAATRTRLLRRLPLLLATHVALPVALYAVTRYFDLQ 120 PG LL+ L ++A + LR A + LL R LL T + +P+ + A+ + Q Sbjct: 61 PGPLWLLLVLALCAAGMQAASLLR--AGQAALLPRA--LLGT-LGVPLVIAALVWWAAPQ 115 Query: 121 ALAMPWQILLALLIVVPMGPMIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPE 180 A+P Q+LL LL++ +GP++Y+V Y+ +A +SVL LLIVS+G+HLAM GLGL+ FG E Sbjct: 116 QFALPVQVLLTLLLITALGPLMYQVVYESMADASVLQLLIVSVGIHLAMTGLGLVFFGAE 175 Query: 181 GTNTRPFTELQFNLGESPVSGQSVIVLVTVAALIAVIYVFFERTLTGKALRATAVNRLGA 240 G T F + ++NL +S Q+V+V+ AAL+ ++ F RTL GKALRATAVNRLGA Sbjct: 176 GFRTPAFWDERWNLASLTLSAQTVVVVAAAAALLVALWFFSGRTLYGKALRATAVNRLGA 235 Query: 241 RLVGVGINQAGKLSFAMAAGIGALCGILIAPFTIVNYESGFIIALKGFVGAIFGGLASYP 300 RL+G+ AGKLSFA+AA IGAL G+LI P + + Y+SGF+I LKGFV A G LAS+P Sbjct: 236 RLMGISTTLAGKLSFAVAAFIGALSGVLIGPMSTIFYDSGFLIGLKGFVAATIGALASFP 295 Query: 301 IAALGSVAVGLIESFSSFWASSYKELIVFTVIIPILLWRSLT--SHHIDEE 349 AA G++ VGL+ESFSSFWAS +KE+IVF ++PILLWRSL +H DEE Sbjct: 296 AAAGGALLVGLLESFSSFWASDFKEVIVFLALLPILLWRSLVIPAHDEDEE 346 >gi|300310682|ref|YP_003774774.1| amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 305 bits (782), Expect = 3e-84, Method: Compositional matrix adjust. Identities = 183/349 (52%), Positives = 249/349 (71%), Gaps = 6/349 (1%) Query: 1 VDTSILTVLIQDGITTGAIYALLSLALVLVFSVTRVIFLPQGEFVAFGALTLAAIQNGQA 60 ++ I+ +L QDGIT GAIYALL+L++VLVF+VTR++ +PQGEFV+FGALT+ +QNGQ Sbjct: 1 MNLQIVALLGQDGITNGAIYALLALSIVLVFTVTRILLIPQGEFVSFGALTMGMMQNGQP 60 Query: 61 PGTALLLVALGCVTLAVEAGTALRLAATRTRLLRRLPLLLATHVALPVALYAVTRYFDLQ 120 A LLVA+ A + R + RR L L +A + V + Sbjct: 61 LTVAWLLVAMCLGACAFDLYDMWRTSR------RRPSLWLPAKLAYAAVVGGVALSVNFA 114 Query: 121 ALAMPWQILLALLIVVPMGPMIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPE 180 L M QI + LL++VP+GP++YR+A+QP+A +S LVLLIVS+ VH+A+VG+ LL+FGPE Sbjct: 115 TLPMLVQIAMTLLLLVPLGPLMYRMAFQPIATASPLVLLIVSIAVHVALVGVALLVFGPE 174 Query: 181 GTNTRPFTELQFNLGESPVSGQSVIVLVTVAALIAVIYVFFERTLTGKALRATAVNRLGA 240 G T PFTE LG +S Q++ V+ LI +++ FERTL GKALRA A+NR+GA Sbjct: 175 GARTAPFTEAALELGSLRLSSQALWVICVSLLLIVGLFLMFERTLYGKALRAAALNRMGA 234 Query: 241 RLVGVGINQAGKLSFAMAAGIGALCGILIAPFTIVNYESGFIIALKGFVGAIFGGLASYP 300 RL+G+ AGK F +A+ IG + G+LIAP T + Y+SGF+I+LKGFVG+I GGL SYP Sbjct: 235 RLMGISPVFAGKAMFLLASLIGVMSGVLIAPITTIYYDSGFLISLKGFVGSIIGGLVSYP 294 Query: 301 IAALGSVAVGLIESFSSFWASSYKELIVFTVIIPILLWRSLTSHHIDEE 349 +AA G++A+GLIESFS+FWAS+YKE+IVF +IIPILLWRSLT+ H++EE Sbjct: 295 LAAAGALAIGLIESFSTFWASAYKEIIVFVLIIPILLWRSLTTRHVEEE 343 >gi|300310992|ref|YP_003775084.1| branched-chain aminoacid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 308 Score = 82.0 bits (201), Expect = 6e-17, Method: Compositional matrix adjust. Identities = 72/213 (33%), Positives = 115/213 (53%), Gaps = 23/213 (10%) Query: 142 IYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPEGTNTRPFT-------ELQFNL 194 + RVAY+PL LV LI ++G+ + L + G R + L+F + Sbjct: 91 VERVAYRPLRGGPRLVPLISAIGMSIF-----LQNYVQIGQGARDMSVPVLISGALEFQM 145 Query: 195 GES-----PVSGQSVIVLVTVAALIAVIYVFFERTLTGKALRATAVNRLGARLVGVGINQ 249 G P S + VIV VT+ ++A+ +F R+ G+A RA A + A L+G+ N+ Sbjct: 146 GSDFTVTIPYS-RMVIVGVTLVLMVALT-LFIARSRMGRACRACAEDMGMANLLGIDTNK 203 Query: 250 AGKLSFAMAAGIGALCGILIAPFTI--VNYESGFIIALKGFVGAIFGGLASYPIAALGSV 307 +F + A + A+ G+LIA TI +N GFI +K F A+ GG+ S P A LG V Sbjct: 204 VISFTFVLGAMLAAVGGVLIA-LTIGKLNPYIGFIAGIKAFTAAVLGGIGSIPGAMLGGV 262 Query: 308 AVGLIESFSS-FWASSYKELIVFTVIIPILLWR 339 +GL E+F++ + S YK+++ F +++ ILL+R Sbjct: 263 LLGLAETFAAGYLPSEYKDVVSFGLLVLILLFR 295 >gi|300310521|ref|YP_003774613.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 309 Score = 70.9 bits (172), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 67/216 (31%), Positives = 118/216 (54%), Gaps = 23/216 (10%) Query: 141 MIYRVAYQPLAHSSVLVLLIVSLGVHLAMVGLGLLMFGPEGTNTRPFTELQFNLGESPVS 200 +I R+AY+PL ++ L LI ++GV + + L ++++G + PF ++ + PV Sbjct: 87 LIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMIWG---RSPLPFPQV---MPSDPVH 140 Query: 201 ------GQSVIVLVTVAALIAV-IYVFFERTLTGKALRATAVNRLGARLVGVGINQAGKL 253 + I+L+ +A L V + + E+T G+A+RATA N A L+GV N+ + Sbjct: 141 IAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAENPRIAGLMGVDANKVIVV 200 Query: 254 SFAMAAGIGALCGIL-IAPFTIVNYESGFIIALKGFVGAIFGGLASYPIAALGSVAVGLI 312 +FA+ AG+ A+ G++ A ++ + GF+ LK F A+ GG+ + A LG + +GLI Sbjct: 201 TFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLGGIGNIYGAMLGGILLGLI 260 Query: 313 ESF---------SSFWASSYKELIVFTVIIPILLWR 339 ES +F S+Y+++ F V+I +L R Sbjct: 261 ESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLR 296 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 0.328 0.142 0.406 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: 876,871 Number of extensions: 30845 Number of successful extensions: 251 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 239 Number of HSP's successfully gapped: 12 Length of query: 350 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 264 Effective length of database: 1,212,660 Effective search space: 320142240 Effective search space used: 320142240 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: 131 (55.1 bits)