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= 0028.0018.p (358 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311879|ref|YP_003775971.1| amino acid ABC transporter perm... 615 e-177 gi|300310287|ref|YP_003774379.1| branched-chain amino acid ABC t... 330 1e-91 gi|300311115|ref|YP_003775207.1| branched-chain amino acid ABC t... 126 3e-30 gi|300309520|ref|YP_003773612.1| branched-chain amino acid ABC t... 120 1e-28 gi|300310993|ref|YP_003775085.1| branched-chain amino acid ABC t... 114 1e-26 >gi|300311879|ref|YP_003775971.1| amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 358 Score = 615 bits (1587), Expect = e-177, Method: Compositional matrix adjust. Identities = 315/358 (87%), Positives = 340/358 (94%) Query: 1 MLYREAGQFKTSYIADSQIFPIRQDRIGMAILLAIAFVGIPLIGSEYWFSAILIPFLVFA 60 MLYREAGQFKTSYIADSQIFPIRQDRI + + AFVG+PL+GSEYWFSAIL+PFLVFA Sbjct: 1 MLYREAGQFKTSYIADSQIFPIRQDRIIFTLFMVFAFVGVPLLGSEYWFSAILVPFLVFA 60 Query: 61 LAALGLNILTGYAGQLSLGSAAFMAVGAYAAYNFQLRIEGIPIVLSFILAGGCAALVGIV 120 LAALGLN+LTGYAGQLSLGSAAFMAVGAYAAYNFQLR++GIPIV + +L+GGCAALVG++ Sbjct: 61 LAALGLNVLTGYAGQLSLGSAAFMAVGAYAAYNFQLRVDGIPIVATLLLSGGCAALVGVL 120 Query: 121 FGLPSLRIKGFYLAVATLAAQFFVVWALTKFSWFSNNSSSGVISTQKIDFFGIAINSPVK 180 FGLPSLRIKGFYLAVATLAAQFFVVWALTKF WFSNNSSSGVIST KIDFFGIAI++PV+ Sbjct: 121 FGLPSLRIKGFYLAVATLAAQFFVVWALTKFPWFSNNSSSGVISTPKIDFFGIAIDTPVR 180 Query: 181 KYLFVLGIVCVMAMLAKNLVRSSTGRAWMAVRDMDVAAEVIGIQLMRTKLLAFAVSSFFC 240 KYLFVL +V V+A++AKNLVRSSTGRAWMAVRDMDVAAEVIGI LMRTKL AFAVSSF+C Sbjct: 181 KYLFVLAVVSVLALVAKNLVRSSTGRAWMAVRDMDVAAEVIGIPLMRTKLTAFAVSSFYC 240 Query: 241 GVAGALYAFCYLGSVEPDGFSLDLSFRILFMIIIGGVGSILGAFLGSAFILLLPIFLDNV 300 GVAGALYAFCYLGSVEPDGFSLDLSFRILFMIIIGGVGSILG+FLGSAFILLLPIFLDN Sbjct: 241 GVAGALYAFCYLGSVEPDGFSLDLSFRILFMIIIGGVGSILGSFLGSAFILLLPIFLDNA 300 Query: 301 LPPLASLLHLPFTNATVSHIQLMLFGGLIIFFLIVEPHGLARLWQITKEKLRLWPFPH 358 LPPLA+LLHLPFTNATVSHIQ+M+FG LIIFFLI EPHGLARLWQI KEKLRLWPFPH Sbjct: 301 LPPLAALLHLPFTNATVSHIQMMVFGALIIFFLIAEPHGLARLWQIAKEKLRLWPFPH 358 >gi|300310287|ref|YP_003774379.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 330 bits (846), Expect = 1e-91, Method: Compositional matrix adjust. Identities = 179/319 (56%), Positives = 234/319 (73%), Gaps = 5/319 (1%) Query: 37 FVGIPLIGSEYWFSAILIPFLVFALAALGLNILTGYAGQLSLGSAAFMAVGAYAAYNFQL 96 +V +P I S Y A+LIPFL +LAA+GLN+LTGYAGQLSLGSAAFMAVGA+AAYN L Sbjct: 33 YVVVPWIASAYLIDALLIPFLALSLAAVGLNLLTGYAGQLSLGSAAFMAVGAFAAYNLNL 92 Query: 97 RIEGIPIVLSFILAGGCAALVGIVFGLPSLRIKGFYLAVATLAAQFFVVWALTKFSWFSN 156 R+ G+P+++S +LAG A +G+VFGLPSLR++GFYLAV+TLAAQFFV W L KFSWFSN Sbjct: 93 RVAGLPLLVSIVLAGLAATAIGLVFGLPSLRLRGFYLAVSTLAAQFFVQWVLVKFSWFSN 152 Query: 157 NSSSGVISTQKIDFFGIAINSPVKKYLFVLGIVCVMAMLAKNLVRSSTGRAWMAVRDMDV 216 ++ SGVI + G+A ++P +YLF L IV V+ +L LV+S TG ++AVRD + Sbjct: 153 DNPSGVIDAPPLVVGGLAFDTPAGRYLFALAIVTVLTLLCWRLVQSQTGHHFIAVRDNEQ 212 Query: 217 AAEVIGIQLMRTKLLAFAVSSFFCGVAGALYAFCYLGSVEPDGFSLDLSFRILFMIIIGG 276 AA VIG+ ++RTKLLAFA+SSF GVAG L+ F YL +VEP GF+LD S +ILF++IIGG Sbjct: 213 AARVIGVPVLRTKLLAFAISSFVIGVAGVLWGFVYLRTVEPAGFNLDRSLQILFIVIIGG 272 Query: 277 VGSILGAFLGSAFILLLPIFLDNVLPPLASLLHLPFTNATVSHIQLMLFGGLIIFFLIVE 336 + +I GAF G+A I++ P+ L + + LL F + + Q ++ G LIIFFLIVE Sbjct: 273 LATIRGAFFGAALIVVFPLLLSRL---GSLLLGQWFDSGVLEMSQRIVLGALIIFFLIVE 329 Query: 337 PHGLARLWQITKEKLRLWP 355 P GLA LWQ + + RLWP Sbjct: 330 PQGLAALWQ--RGRQRLWP 346 >gi|300311115|ref|YP_003775207.1| branched-chain amino acid ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 655 Score = 126 bits (316), Expect = 3e-30, Method: Compositional matrix adjust. Identities = 78/273 (28%), Positives = 158/273 (57%), Gaps = 7/273 (2%) Query: 29 MAILLAIAFVGIPLIGSEYWFSAILIPFLVFALAALGLNILTGYAGQLSLGSAAFMAVGA 88 +++L +A GIP++ ++ ++ L++A+ GL+I+ GY GQ+SLG A +G+ Sbjct: 8 LSLLGIVALAGIPMVVHNPYYLHLIETILIYAILLFGLDIVVGYTGQVSLGHAGLFGIGS 67 Query: 89 YAAYNFQLRIEGIPIVLSFILAGGCAALVGIVFGLPSLRIKGFYLAVATLAAQFFVVWAL 148 YAA ++ G+PI ++ A A+ G + LP+LR+ G YLA+ TLA + + Sbjct: 68 YAAGVLFFKL-GMPIFVTVPAAIAVTAVFGAILALPALRVTGPYLAMVTLAFGTIIQILI 126 Query: 149 TKFSWFSNNSSSGVISTQKIDFFGIAINSPVKKYLFVLGIVCVMAMLA-KNLVRSSTGRA 207 + ++ + I QK G ++ ++ +++ ++ V++ML +++S+ GRA Sbjct: 127 NEMTFLTEGPLG--IKLQKPMIGGDKMSE--VQFFYLVAVLMVLSMLVVHRILKSNLGRA 182 Query: 208 WMAVRDMDVAAEVIGIQLMRTKLLAFAVSSFFCGVAGALYAFCYLGSVEPDGFSLDLSFR 267 + A+RD +A++ +G+ + R K+ AF +S+ G++GALYA+ + P+ ++ +L+ Sbjct: 183 FQALRDSPIASDCMGVSVYRYKVYAFIISAALAGLSGALYAYSE-EYISPNTYNFELTIM 241 Query: 268 ILFMIIIGGVGSILGAFLGSAFILLLPIFLDNV 300 L +I+GG S +G+ +G+ +++LP L ++ Sbjct: 242 FLLAVIMGGRKSRIGSLIGALIVVMLPSLLSDI 274 >gi|300309520|ref|YP_003773612.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 404 Score = 120 bits (302), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 102/347 (29%), Positives = 170/347 (48%), Gaps = 57/347 (16%) Query: 57 LVFALAALGLNILTGYAGQLSLGSAAFMAVGAYAAY----------------------NF 94 L++ + ALGLN++ G+AG L LG AF A+GAY+A NF Sbjct: 48 LLYIMLALGLNVVVGFAGLLDLGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNF 107 Query: 95 QLRIEGIPIVLSFI---------LAGGCAALVGIVFGLPSLRIKGFYLAVATLAAQFFVV 145 + + G IV + I ++ AAL G + G P+L+++G YLA+ TL + Sbjct: 108 LVWLCGPEIVQNGIHLSLWLIVPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIR 167 Query: 146 WALTKFSWFSN--NSSSGVISTQKIDFFGIAINSP----------------VKKYLFVLG 187 + + N N G+ I FG+++ V Y F+ Sbjct: 168 IFMNNLNAPVNITNGPQGINLIDPIKVFGVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFL 227 Query: 188 IVCV-MAMLAKNLVRSSTGRAWMAVRDMDVAAEVIGIQLMRTKLLAFAVSSFFCGVAGAL 246 ++C+ + + L S GRAW+A+R+ ++AA+ +GI KLLAFA+ + F GVAGA+ Sbjct: 228 LLCIGVIFFSVRLQDSRLGRAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAM 287 Query: 247 YAFCYLGSVEPDGFSLDLSFRILFMIIIGGVGSILGAFLGSAFILLLPIFLDNVLPPLA- 305 + + G V P+ FSL S +L M+++GG+G I G LG + LP L +V+ P+ Sbjct: 288 FG-AFQGFVSPESFSLTESIAVLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQM 346 Query: 306 SLLHLPFTNATVSHIQLMLFGGLIIFFLIVEPHGLARLWQITKEKLR 352 ++ + +A V ++ +L+G ++ ++ P G LW + + R Sbjct: 347 AIFGKVWIDAEV--LRQLLYGLAMVVIMLTRPAG---LWPSPRHEDR 388 >gi|300310993|ref|YP_003775085.1| branched-chain amino acid ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 408 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 105/341 (30%), Positives = 160/341 (46%), Gaps = 45/341 (13%) Query: 23 RQDRIGMAILLAIAFVGIPLIGSEYWFSAILIPFLVFALAALGLNILTGYAGQLSLGSAA 82 RQ R + ILL A V P GS + + + L++ + LGLNI+ G+AG L LG Sbjct: 78 RQQRAAVMILLMAALV-WPFFGSRGYVDVMTLA-LIYVVLGLGLNIVVGFAGLLDLGYVG 135 Query: 83 FMAVGAYAAYNFQLRIEGIPIVLSFILAGGCAALVGIVFGLPSLRIKGFYLAVATLAAQF 142 F AVGAY Y + G+ LA +AL G + G P LR++G YLA+ TL Sbjct: 136 FYAVGAYT-YALCNQYFGLTFWECVPLAAAASALFGFLLGFPVLRLRGDYLAIVTLGFGE 194 Query: 143 FVVWALTKFSWFSNNSSSGVISTQKIDFFGIAI-NSPVKK-------------------- 181 + L + + GV K FG+ + +PV + Sbjct: 195 IIRLLLNNMTSITGGPD-GVSGIPKPTVFGLVMARNPVTEGGTTFHQLFGLSYQGGHMVI 253 Query: 182 --YLFVLGIVCVMAMLAKNLVRSSTGRAWMAVRDMDVAAEVIGIQLMRTKLLAFAVSSFF 239 Y L +V + L+R GRAW A+R+ ++A +GI + KL AF + + F Sbjct: 254 FLYFLALLMVLFTYFVTSRLLRMPMGRAWEALREDEIACRSLGINPTKVKLSAFTLGAAF 313 Query: 240 CGVAGALYAFCYLGSVEPDGFSLDLSFRILFMIIIGGVGSILGAFLGSAFILLLPIFLDN 299 G+AG+ +A G V P+ F+ S IL ++++GG+GS LG L A ILL Sbjct: 314 AGLAGSFFA-ARQGLVTPESFTFIESALILAIVVLGGMGSQLGVIL--AAILL------T 364 Query: 300 VLPPLASLLHLPFTNATVSHIQLMLFGGLIIFFLIVEPHGL 340 VLP LA + + ++++FG +++ ++ P GL Sbjct: 365 VLPELAR---------SFAEYRMLIFGLVMVLMMMWRPQGL 396 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 0.332 0.145 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: 1,033,066 Number of extensions: 41306 Number of successful extensions: 313 Number of sequences better than 1.0e-08: 23 Number of HSP's gapped: 277 Number of HSP's successfully gapped: 24 Length of query: 358 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 272 Effective length of database: 1,212,660 Effective search space: 329843520 Effective search space used: 329843520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 131 (55.1 bits)