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= 0003.0043.p (394 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC t... 201 7e-53 gi|300312236|ref|YP_003776328.1| amino acid ABC transporter peri... 104 1e-23 gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 87 2e-18 gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC t... 83 3e-17 gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmi... 81 1e-16 >gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 201 bits (512), Expect = 7e-53, Method: Compositional matrix adjust. Identities = 131/381 (34%), Positives = 205/381 (53%), Gaps = 14/381 (3%) Query: 15 ATLAAALSPLAL---AADPIKIGLVTALSGQSAQAGEALTRGMSIAIDEINAKGGLLGGR 71 A +AAAL LAL AADPIKIG+ +G SA G ++ G+ +A+ EINA GGLLG R Sbjct: 7 AFVAAALMSLALTSQAADPIKIGVSGPYTGGSAPMGVSMRDGVKLAVAEINAAGGLLG-R 65 Query: 72 KLELVRRDDEGNPAKGVVAARELIFKEKVTVLFGGLDTPVSMAIVPIINQEKVPFVGPWA 131 +++L+ RDDE +GV A+ELI KEKV G ++T V++A + K+P + A Sbjct: 66 QIQLIERDDEAKNERGVQIAQELINKEKVVATVGFINTGVALASQRFYQEAKIPVINNVA 125 Query: 132 AGTGVTKN--GANPNYAFRVSAVDELVDKAMLNYAQKTFKSSKAGLILVNNPWGESNEKG 189 GT +TK NY FR SA D++ K + + A K +K ++ + +G+ + Sbjct: 126 TGTVITKQFEKEKDNYVFRTSAADKIQAKMIADEAVDKQKFTKVAILADSTNYGQLGRED 185 Query: 190 IVAALAEKGLKPAGIEKFEASDVDVVPQLSRLKAAGADTLYLVGNVGPS-AQVVKSLDRM 248 + LA+K + P +EK+ DVD+ QL + K GA + G +GP AQ+ ++++ Sbjct: 186 LEKVLADKKVTPVAVEKYNIKDVDMTAQLLKSKQGGAQAVLTYG-IGPELAQIANGMEKL 244 Query: 249 GWKVPVVSHWGPAGGRFTELAGPNAKNVHFIQTFSFFGKLSPVGEKVVAELKAKYPAIKG 308 W VP++ W + G F + +G N QTF G +P + + + Y + Sbjct: 245 NWHVPIIGSWPLSMGNFIDNSGKNGNGARMPQTFIQDGN-TPKRKAFIEAYQKAYKVDRM 303 Query: 309 PDDITPAVGVANAYDGMQLAALAIAKAGSTNGDAVREGFYKID-RYEGLIKTYVKPFSPT 367 P AV A YD + L A AI +AG+T+GD VR ++ + EG++ TY KPF+ Sbjct: 304 P----SAVSAAQGYDSILLLAAAIKQAGTTDGDKVRAALENLNTKVEGVVTTYDKPFTHD 359 Query: 368 VHDALQADDYVWAQFIDNRIL 388 H+A++ V + + R++ Sbjct: 360 DHEAIKPAMVVMGEVKNGRVI 380 >gi|300312236|ref|YP_003776328.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 104 bits (260), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 95/317 (29%), Positives = 148/317 (46%), Gaps = 14/317 (4%) Query: 17 LAAALSPLALAADPIKIGLVTALSGQSAQAGEALTRGMSIAIDEINAKGGLLGGRKLELV 76 + A LS ALAAD IK+G+ AL+G +A+ G A+ G ++A +EINAKGG + G KL LV Sbjct: 15 IGATLSQAALAAD-IKLGVAEALTGPAAKYGVAIKNGFTLASEEINAKGG-VNGDKLALV 72 Query: 77 RRDDEGNPAKGVVAARELIFKEKVTVLFGGLDTPVSMAIVPIINQEKVPFVGPWAAGTGV 136 D++G + + ++LIF++KV +FG + + A PI N KV G G+ Sbjct: 73 IEDEQGKKEEAINVFKKLIFQDKVLAVFGPTLSNSAFAADPIANAAKVVVFGTSNTADGI 132 Query: 137 TKNGANPNYAFRVSAVDELVDKAMLNYAQKTFKSSKAGLILVN-NPWGESNEKGIVAALA 195 T G + FR S ++ V + A K F K +I N + + +S A L Sbjct: 133 TAMGP---FTFRNSVMEADVLPVTVKAAVKHFGIKKVAVIYGNDDAFTKSGYDVFKATLE 189 Query: 196 EKGLKPAGIEKFEASDVDVVPQLSRLKAAGADTLYLVGNVGPSAQVVKSLDRMGWKVPVV 255 + + E + DVD QL+++KA D + +A ++ +G K P + Sbjct: 190 HQKIPVTTTEAYAKGDVDFKAQLTKIKAGNPDAIVCSCLAEEAANIILQTRALGMKQPFI 249 Query: 256 SHWGPAGGRFTELAGPNAKNVHFIQTFSFFGKLSPVGEKVVAELKAKYPAIKGPDDITPA 315 G + E+A N +S + +P + + KAK+ A PD Sbjct: 250 GGNGLNSPKLFEIAKDAGDNTLMGSPWSAENQ-TPANKAFITAYKAKFGA--DPDQFA-- 304 Query: 316 VGVANAYDGMQLAALAI 332 A AYD M + A A+ Sbjct: 305 ---AQAYDAMYIVADAL 318 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 93/342 (27%), Positives = 152/342 (44%), Gaps = 24/342 (7%) Query: 7 RTLIAAAAATLAAALSPLALAADPIKIGLVTALSGQSAQAGEALTRGMSIAIDEINAKGG 66 ++ I A + A + A + + +KI V LSG +A G+ G +A+DE+NAKG Sbjct: 4 KSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGF 63 Query: 67 LLGGR--KLELVRRDDEGNPAKGVVAARELIFKEKVTVLFGGLDTPVSMAIVPIINQEKV 124 +GG+ K ELV DD +P + A +L+ +KV + G L++ ++ I + + Sbjct: 64 TIGGKKVKFELVGEDDASDPKQATAVATKLV-DQKVAAVIGHLNSGTTIPASKIYSDAGI 122 Query: 125 PFVGPWAAGTGVTKNGANPNYAFRVSAVDELVDKAMLNYAQKTFKSSKAGLILVNNPWGE 184 P V P A T+ G AFRV A D + A+ YA + + + +I +G+ Sbjct: 123 PQVSPSATNPKYTQQGFKT--AFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ 180 Query: 185 SNEKGIVAALAEKGLKPAG-------IEKFEASDVDVVPQLSRLKAAGADTLYLVGNVGP 237 VA KG K AG +A+D + + L+ LK D ++ G Sbjct: 181 G-----VADEFAKGAKAAGGTIVGTQYTNDKATDFNAI--LTSLKGKKPDVVFFGGMDAV 233 Query: 238 SAQVVKSLDRMGWKVPVVSHWGPAGGRFTELAGPNAKNVHFIQTFSFFGKLSPVGEKVVA 297 +++ + ++G + G G LAG + I + G + G+K + Sbjct: 234 GGPMLRQMKQLGISAKFMGGDGICTGSLPGLAGDGLGDDQVICAEA--GGVDEAGKKGMD 291 Query: 298 ELKAKYPAIKGPDDITPAVGVANAYDGMQLAALAIAKAGSTN 339 + +A Y G D + A A AYD A A+AKAGS + Sbjct: 292 DFRAAYKKKFGIDVVYNA---AYAYDATMTVADAMAKAGSAD 330 >gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 83.2 bits (204), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 53/161 (32%), Positives = 84/161 (52%), Gaps = 4/161 (2%) Query: 25 ALAADPIKIGLVTALSGQSAQAGEALTRGMSIAIDEINAKGGLLGGRKLELVRRDDEGNP 84 A A D I+IG + + Q A E RG +A+DEINA GG+LG +KLE++ RDD GNP Sbjct: 26 ARAQDTIRIGEINSYKAQPAFL-EPYRRGWEMALDEINASGGVLG-KKLEVIARDDNGNP 83 Query: 85 AKGVVAARELIFKEKVTVLFGGLDTPVSMAIVPIINQEKVPFVGPWAAGTGVTKNGANPN 144 V A EL+ +E+V +LFGG + +A+ Q +V F+ + N Sbjct: 84 GDSVRVAEELMARERVALLFGGFLSNTGLALTDYAKQHRVFFLAAEPLTDKIVWQNGN-K 142 Query: 145 YAFRVSAVDELVDKAMLNYAQKTFKSSKAGLILVNNPWGES 185 Y +R+ ++ +++ A K K + ++ N +G+S Sbjct: 143 YTYRLRPSTSMLVASVVKEAVK-LKKKRWAIVYPNYEYGQS 182 >gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 417 Score = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 103/361 (28%), Positives = 170/361 (47%), Gaps = 34/361 (9%) Query: 4 LTRRTLIAAAA----ATLAAALSPLALAADPIKIGLVTALSGQSAQAGEALTRGMSIAID 59 ++RRT++ A A A A++ P A AAD IK+G++ +LSG A + +L + ID Sbjct: 1 MSRRTVLKATALGAFALAASSWLPSAFAADTIKVGILHSLSGTMAISETSLKDVALMTID 60 Query: 60 EINAKGGLLGGRKLELVRRDDEGNPAKGVVAARELIFKEKVTVLFGGLDTPVSMAIVPII 119 EINA GG++ G+KLE V D N AR+LI ++KV+V+FG + +++P+ Sbjct: 61 EINAAGGVM-GKKLEPVVVDPASNWPLFAEKARQLISQDKVSVVFGCWTSVSRKSVLPVF 119 Query: 120 NQ-EKVPFVGPWAAGTGVTKN----GANPNYAFRVSAVDELVDKAMLNYAQKTFKSSKAG 174 + + F G + KN GA PN + AV+ L+ K + + + Sbjct: 120 KELNSLLFYPVQYEGEELEKNVFYTGAAPNQQ-AIPAVEYLMSK-------EGGGAKRFV 171 Query: 175 LILVNNPWGESNEKGIVAALAEKGLKPAGIEK----FEASDVD-VVPQLSRLKAAGADTL 229 L+ + + + K + A L KG+K + I++ F SD +V + + A G + Sbjct: 172 LLGTDYVYPRTTNKILRAFLHSKGVKDSDIDEVYTPFGHSDYQTIVANIKKFSAGGKTAV 231 Query: 230 YLVGNVGPSAQVVKSLDRMGWK---VPVVSHWGPAGGRFTELAGPNAKN-VHFIQTFSFF 285 N + K L G K VPVV+ + G EL G + K V + +++F Sbjct: 232 ISTINGDSNVPFYKELGNAGLKATDVPVVAF---SVGE-EELRGVDTKPLVGHLAAWNYF 287 Query: 286 GKL-SPVGEKVVAELK--AKYPAIKGPDDITPAVGVANAYDGMQLAALAIAKAGSTNGDA 342 + +PV + + K AK + D + + Y G+ + A A+ KA ST+ D Sbjct: 288 ESVKNPVNTAFIKKWKEYAKAKNLPNADTVVTNDPMEATYVGIHMWAQAVEKAKSTDTDK 347 Query: 343 V 343 V Sbjct: 348 V 348 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 0.134 0.387 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: 1,159,307 Number of extensions: 50305 Number of successful extensions: 196 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 176 Number of HSP's successfully gapped: 20 Length of query: 394 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 307 Effective length of database: 1,207,925 Effective search space: 370832975 Effective search space used: 370832975 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 (21.6 bits) S2: 131 (55.1 bits)