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= 0001.3705.p (296 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC tra... 560 e-161 gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transp... 203 2e-53 gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease ... 105 3e-24 gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease ... 101 8e-23 gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease ... 100 1e-22 >gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 560 bits (1443), Expect = e-161, Method: Compositional matrix adjust. Identities = 278/294 (94%), Positives = 290/294 (98%) Query: 3 VEKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALVQSMLLENPFGGYSEFVWFDNFKT 62 +EKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQAL QSMLL++ FGGYSEFVWFDNFKT Sbjct: 1 MEKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALYQSMLLQDAFGGYSEFVWFDNFKT 60 Query: 63 LFADPTYLEAFRTTAVFSALVAFFGLALSLLLAVFADRVRRGAALYKTFLIWPYAVSPVV 122 LF DPTYLE+FRTTA+FSALVAFFGLALSLLLAVFADRVRRGA++YKTFLIWPYAVSPVV Sbjct: 61 LFGDPTYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVV 120 Query: 123 VGVLWMFLLSPSLGILSHVLAWLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAGL 182 VGVLWMFLLSPSLGILSHVL+WLGLPWDYMINGTHAMILIV+AAIWKQISYNFLFFLAGL Sbjct: 121 VGVLWMFLLSPSLGILSHVLSWLGLPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGL 180 Query: 183 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLLSPTTFFLFVVNVVYAFFDTFVIVDATTHGG 242 QSIPKSLIEAAAIDGAGPVKRFFTIVFPL+SPTTFFLFVVNVVYAFFDTFVIVDATTHGG Sbjct: 181 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGG 240 Query: 243 PGKDTEILVYKVFVDGFRGGDLGGSAAQSVVLMAVVILLTVVQFKYVEKKVQYA 296 PGKDTEILVYKVF DGF+GGDLGGSAAQSVVLMA+VILLTVVQFKYVEKKVQYA Sbjct: 241 PGKDTEILVYKVFSDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQYA 294 >gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 203 bits (516), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 119/290 (41%), Positives = 174/290 (60%), Gaps = 2/290 (0%) Query: 3 VEKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALVQSMLLENPFGGYSEFVWFDNFKT 62 ++ R F ++W P LL PQ++I LFF WPAV+A+ S L PFG S FV DN+ Sbjct: 1 MDARPAFPTRWFPLLLATPQMLIVFLFFLWPAVKAIAWSFYLVRPFGNGSRFVGLDNYLR 60 Query: 63 LFADPTYLEAFRTTAVFSALVAFFGLALSLLLAVFADRVRRGAALYKTFLIWPYAVSPVV 122 + D ++ + R T VF+A + ++L LA + R L ++ IWPYAV+ VV Sbjct: 61 ILTDDSFYASLRATLVFTAGSTLLAVTIALALAACLELDVRAKRLLRSIFIWPYAVAGVV 120 Query: 123 VGVLWMFLLSPSLGILSHVLA-WLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAG 181 VG++ L++P G+L+ + W G+ W + G AM+ ++ A W Q+ NF+ F A Sbjct: 121 VGIVLKVLINPVTGLLAFLNQLWPGV-WAPHLIGAQAMLALIAAFAWTQVPLNFILFSAA 179 Query: 182 LQSIPKSLIEAAAIDGAGPVKRFFTIVFPLLSPTTFFLFVVNVVYAFFDTFVIVDATTHG 241 LQ IP L+ AAAIDGAGP +RF I P+++P V+NV+ AF F +VDA T G Sbjct: 180 LQRIPADLMGAAAIDGAGPWRRFIDIQLPMIAPALLLAGVINVIEAFTHGFGLVDALTQG 239 Query: 242 GPGKDTEILVYKVFVDGFRGGDLGGSAAQSVVLMAVVILLTVVQFKYVEK 291 GPG+ T IL Y+++ DGF G DL GS+A SVVLM ++ LT++Q ++ + Sbjct: 240 GPGRSTAILAYQIYSDGFIGLDLSGSSALSVVLMLFIVALTLLQLRFFRQ 289 >gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 105 bits (263), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 74/235 (31%), Positives = 119/235 (50%), Gaps = 8/235 (3%) Query: 54 FVWFDNFKTLFADPTYLEAFRTTAVFSALVAFFGLALSLLLAVFADRVRRGAALYKTFLI 113 FV +N+ L DP + + TA+ V + LLAV D+ RG + + +I Sbjct: 80 FVGLENYAFLLQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIARLLVI 139 Query: 114 WPYAVSPVVVGVLWM-FLLSPSLGILSHVLAWLGL-PWDYMINGTHAMILIVVAAIWKQI 171 P+ V P V ++W ++ P GIL++V+ LGL P D++ + M+ +++ W+ I Sbjct: 140 GPFFVMPTVAALIWKNMIMHPVYGILAYVMRHLGLEPIDWL--AEYPMLSVIIIVAWQWI 197 Query: 172 SYNFLFFLAGLQSIPKSLIEAAAIDGAGPVKRFFTIVFPLLSPTTFFLFVVNVVYAFFDT 231 + FL L LQS+ EAA +DGAGPV+ FF IV P L + ++ ++ Sbjct: 198 PFAFLILLTALQSLDTDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIF-LLSV 256 Query: 232 FVIVDATTHGGPGKDTEILVYKVFVDGFRGGDLGGSAAQSVVLMAVVILLTVVQF 286 F + TT GGPG T L + V+ G + D+G ++A + V+L +V F Sbjct: 257 FAEIFTTTAGGPGTATTNLTFLVYSIGLQQFDIGIASAGGIF---AVVLANIVSF 308 >gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 291 Score = 101 bits (251), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 88/292 (30%), Positives = 160/292 (54%), Gaps = 8/292 (2%) Query: 8 RFTSKWLPYLLVAPQIIITLLFFFWPAVQALVQSMLLENPFG-GYSEFVWFDNFKTLFAD 66 R S LP+LL++P +++ + F +PA+ L S P G S FV +N++ + D Sbjct: 3 RLPSSVLPWLLLSPAMVLLIAFTHYPALATLWHS-FFSTPKGVRPSVFVGLENYRLMADD 61 Query: 67 PTYLEAFRTTAVFSALVAFFGLALSLLLAVFADRVRRGAALYKTFLIWPYAVSPVVVGVL 126 P + +A F+ +AL++L+A++ + G + + P + + V + Sbjct: 62 PVFWQALCNNLWFALGTIPLAIALAILMALWVNEKLAGRGVLRLAYFTPTVLPMIAVANI 121 Query: 127 WMFLLSPSLGILSHVLAWLGLP-WDYMINGTHAMILIVVAAIWKQISYNFLFFLAGLQSI 185 W+F +P G+L + LGLP +++ N + ++V A+WK+ + +F+LA LQ I Sbjct: 122 WLFFYTPQYGLLEQITGALGLPSHNWLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQI 181 Query: 186 PKSLIEAAAIDGAGPVKRFFTIVFPLLSPTTFFLFVVNVVYAF--FDTFVIVDATTHGGP 243 L EAAA++GA + F+ + FPLL PTT F+ + ++ AF D V++ T GGP Sbjct: 182 SPVLAEAAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVM---TKGGP 238 Query: 244 GKDTEILVYKVFVDGFRGGDLGGSAAQSVVLMAVVILLTVVQFKYVEKKVQY 295 + +L+Y ++ GF D +AA +VVL+A++ L+ +V+F+ ++++ Y Sbjct: 239 DNASSLLLYYIYEVGFAFWDSSYAAALTVVLLALLGLIALVKFRVLDRRTHY 290 >gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 311 Score = 100 bits (250), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 77/271 (28%), Positives = 139/271 (51%), Gaps = 10/271 (3%) Query: 19 VAPQIIITLLFFFWPAVQALVQSMLLENPFGGYSE--FVWFDNFKTLFADPTYLEAFRTT 76 +AP ++TL++ +P + + S + G +E FV N+ LF PT+ A + Sbjct: 42 LAPACVMTLVYVLYPILYTIYLSFF---SWDGMTEPRFVGLANYVELFHAPTFYTALKNN 98 Query: 77 AVFSALVAFFGLALSLLLAVFADRVRRGAALYKTFLIWPYAVSPVVVGVLWMFLLSPSLG 136 V L+ + L +A++ ++ G + K+ P+ +S VVVG+++ + PS G Sbjct: 99 -VLWLLMFLLAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMYSWFYDPSFG 157 Query: 137 ILSHVLAWLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAGLQSIPKSLIEAAAID 196 +LS +L G+P + + +A I+ AA+W Q +Y + FL GL ++ +EAA ++ Sbjct: 158 LLS-LLFGQGVP--VLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARME 214 Query: 197 GAGPVKRFFTIVFPLLSPTTFFLFVVNVVYAFFDTFVIVDATTHGGPGKDTEILVYKVFV 256 GA ++ P L TTF FVV+++ A +F ++ T GGP + + +L Y + Sbjct: 215 GAKGWTMLRYVILPQLRSTTFMAFVVSIIGA-LRSFDLISVMTSGGPYESSTVLAYYAYD 273 Query: 257 DGFRGGDLGGSAAQSVVLMAVVILLTVVQFK 287 + G SAA +V L A++++ V Q + Sbjct: 274 QAIKYYRQGYSAAVAVTLFAIMLVYIVYQLR 304 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 0.331 0.144 0.450 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: 831,810 Number of extensions: 30786 Number of successful extensions: 166 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 150 Number of HSP's successfully gapped: 10 Length of query: 296 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 211 Effective length of database: 1,217,395 Effective search space: 256870345 Effective search space used: 256870345 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: 130 (54.7 bits)