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= 0012.0046.p (338 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 676 0.0 gi|300310370|ref|YP_003774462.1| sugar ABC transporter periplasm... 174 1e-44 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 57 2e-09 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 676 bits (1744), Expect = 0.0, Method: Compositional matrix adjust. Identities = 336/338 (99%), Positives = 337/338 (99%) Query: 1 MKAMLKKTVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL 60 MKAMLKKTVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL Sbjct: 1 MKAMLKKTVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL 60 Query: 61 GAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120 GAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR Sbjct: 61 GAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120 Query: 121 LILNADVDAYISFDNEKVGEMQAEGILKVKNKGNFFLLGGSPTDNNAKMFREGQMKALKP 180 LILNADVDAYISFDNEKVGEMQAEGILKVKNKGNFFLLGGSPTDNNAKMFREGQMKALKP Sbjct: 121 LILNADVDAYISFDNEKVGEMQAEGILKVKNKGNFFLLGGSPTDNNAKMFREGQMKALKP 180 Query: 181 YIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK 240 YIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK Sbjct: 181 YIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK 240 Query: 241 LAGKVPVSGQDADLAAVKRVVAGTQTMTVYKPLKQIATEAANLSVQLARNEKPTYNAQYD 300 LAGKVPVSGQDADLAAVKRVVAGTQTMTVYKPLKQIATEAA LSV+LARNEKPTYNAQYD Sbjct: 241 LAGKVPVSGQDADLAAVKRVVAGTQTMTVYKPLKQIATEAAKLSVELARNEKPTYNAQYD 300 Query: 301 NGFKKVDSLLLKPILLTKENVKVLVDDGFYTQAQIDGR 338 NGFKKVDSLLLKPILLTKENVKVLVDDGFYTQAQIDGR Sbjct: 301 NGFKKVDSLLLKPILLTKENVKVLVDDGFYTQAQIDGR 338 >gi|300310370|ref|YP_003774462.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 357 Score = 174 bits (441), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 121/360 (33%), Positives = 199/360 (55%), Gaps = 31/360 (8%) Query: 1 MKAMLKKTVLALMTVTTLSMVAGSAMADAKNPK-IGFSIDDLRVERWARDRDFFTAAAEK 59 +K++L L L VT +S+ SA A++ + +G ++ RW D + ++ Sbjct: 3 IKSVLSGIALGL-GVTLMSI---SAQVSAQSKQLVGVAMPTKSSARWIADGNNMVKVLKE 58 Query: 60 LGAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYD 119 G + +Q A+ Q+SQIEN++++G V+VI + T LT+ +++A G+KV++YD Sbjct: 59 KGYQTDLQYAEDDIPNQLSQIENMLTKGAKVLVIAAIDGTTLTDVLQKAADKGVKVIAYD 118 Query: 120 RLILNA-DVDAYISFDNEKVGEMQAE------GILKVKNKGNFFLLGGSPTDNNAKMFRE 172 RLI + +VD Y +FDN +VG +QA+ G+ + K N L GGS DNNA F Sbjct: 119 RLIRGSKNVDYYATFDNFQVGVLQAQSLEKALGLKEGKGPFNIELFGGSSDDNNAFFFYN 178 Query: 173 GQMKALKPYIDKGDIKIVGQQW------VKEWNPTEALSIVENALTA--NNNKIDAIVAS 224 G M LKPYID G + + +Q W+P A + ++N L+A N K++A+++ Sbjct: 179 GAMSVLKPYIDSGKLVVRSKQMGMDKVATLRWDPATAQARMDNLLSAYYTNAKVNAVLSP 238 Query: 225 NDGTAGGAIQALAAQKLAGKVP------VSGQDADLAAVKRVVAGTQTMTVYKPLKQIAT 278 DG + G + +L + + P VSGQDA++ +VK ++ G Q T++K +++A Sbjct: 239 YDGLSIGILSSL--RGVGYGTPQQPFPYVSGQDAEVPSVKSIIRGEQYSTIFKDTRELAK 296 Query: 279 EAANLSVQLARNEKPTYN--AQYDNGFKKVDSLLLKPILLTKENVK-VLVDDGFYTQAQI 335 + + ++P N Y+NG K V S LLKP+++ K N K VLV G+YT+AQ+ Sbjct: 297 VTVGMVDAVLGGKQPQINDTKTYNNGVKVVPSYLLKPVVVDKSNWKEVLVGSGYYTEAQL 356 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 16/235 (6%) Query: 33 KIGFSIDDLRVERWARDRDFFTAAAEKLGAKVYVQSADASEQRQISQIENLISRGVDVIV 92 KIG S ++ + + AA+ LGAKV A + +QI+ IE+++ + +D+++ Sbjct: 27 KIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAHNVAKQIADIEDMLQQNIDILL 86 Query: 93 IVPFNATVLTNTIKEAKKAGIKVLSYDRLILNAD--VDAYISFDNEKVGEMQAEGIL-KV 149 I P ++ + +K AK + V++ D NA VD ++ N+ G + + Sbjct: 87 INPTDSAGVEAAVKAAKARNVIVVAVD---ANASGPVDMFVGSKNKDAGYQSCRALADAI 143 Query: 150 KNKGNFFLLGGSPTDNNAKMFREGQMKALKPYIDKGDIKIVGQQWVKEWNPTEALSIVEN 209 KG +L G P + EG +AL Y DIK+V Q ++ + + AL +VEN Sbjct: 144 GGKGEVAILDGIPVVPILQRV-EGCKQALAEY---KDIKLVATQNGRQ-DRSVALGVVEN 198 Query: 210 ALTANNNKIDAIVASNDGTAGGAIQALAAQKLAGK-VPVSGQDADLAAVKRVVAG 263 + + N + I + ND GGA+ ALAA + +GK + ++ D AVK + G Sbjct: 199 MIQSRPN-LKGIFSVND---GGAMGALAAIQGSGKDIKLTSVDGAPEAVKAIADG 249 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 0.315 0.131 0.356 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: 932,116 Number of extensions: 36313 Number of successful extensions: 156 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 7 Length of query: 338 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 252 Effective length of database: 1,212,660 Effective search space: 305590320 Effective search space used: 305590320 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)