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= 0003.0060.p (294 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... 573 e-165 gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transp... 201 8e-53 gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease ... 110 2e-25 gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease ... 108 8e-25 gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease ... 104 7e-24 >gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 573 bits (1478), Expect = e-165, Method: Compositional matrix adjust. Identities = 286/294 (97%), Positives = 293/294 (99%) Query: 1 VEKRARFTSKWLPYLLVAPQIIITLLFFFWPAIQALYQSMLLQDAFGGYSEFVWFDNFKT 60 +EKRARFTSKWLPYLLVAPQIIITLLFFFWPA+QALYQSMLLQDAFGGYSEFVWFDNFKT Sbjct: 1 MEKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALYQSMLLQDAFGGYSEFVWFDNFKT 60 Query: 61 LFADPTYLESFRTTALFSALVAFFGLALSLLLAVFADRVRRGASVYKTFLIWPYAVSPVV 120 LF DPTYLESFRTTA+FSALVAFFGLALSLLLAVFADRVRRGAS+YKTFLIWPYAVSPVV Sbjct: 61 LFGDPTYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVV 120 Query: 121 VGVLWMFLLSPSLGILSHVLAWLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAGL 180 VGVLWMFLLSPSLGILSHVL+WLGLPWDYMINGTHAMILIV+AAIWKQISYNFLFFLAGL Sbjct: 121 VGVLWMFLLSPSLGILSHVLSWLGLPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGL 180 Query: 181 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGG 240 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGG Sbjct: 181 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGG 240 Query: 241 PGKDTEILVYKVFTDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQYA 294 PGKDTEILVYKVF+DGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQYA Sbjct: 241 PGKDTEILVYKVFSDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQYA 294 >gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 201 bits (510), Expect = 8e-53, Method: Compositional matrix adjust. Identities = 117/290 (40%), Positives = 174/290 (60%), Gaps = 2/290 (0%) Query: 1 VEKRARFTSKWLPYLLVAPQIIITLLFFFWPAIQALYQSMLLQDAFGGYSEFVWFDNFKT 60 ++ R F ++W P LL PQ++I LFF WPA++A+ S L FG S FV DN+ Sbjct: 1 MDARPAFPTRWFPLLLATPQMLIVFLFFLWPAVKAIAWSFYLVRPFGNGSRFVGLDNYLR 60 Query: 61 LFADPTYLESFRTTALFSALVAFFGLALSLLLAVFADRVRRGASVYKTFLIWPYAVSPVV 120 + D ++ S R T +F+A + ++L LA + R + ++ IWPYAV+ VV Sbjct: 61 ILTDDSFYASLRATLVFTAGSTLLAVTIALALAACLELDVRAKRLLRSIFIWPYAVAGVV 120 Query: 121 VGVLWMFLLSPSLGILSHVLA-WLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAG 179 VG++ L++P G+L+ + W G+ W + G AM+ ++ A W Q+ NF+ F A Sbjct: 121 VGIVLKVLINPVTGLLAFLNQLWPGV-WAPHLIGAQAMLALIAAFAWTQVPLNFILFSAA 179 Query: 180 LQSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHG 239 LQ IP L+ AAAIDGAGP +RF I P+I+P V+NV+ AF F +VDA T G Sbjct: 180 LQRIPADLMGAAAIDGAGPWRRFIDIQLPMIAPALLLAGVINVIEAFTHGFGLVDALTQG 239 Query: 240 GPGKDTEILVYKVFTDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEK 289 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 = 110 bits (274), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 84/285 (29%), Positives = 139/285 (48%), Gaps = 12/285 (4%) Query: 3 KRARFTSKWLPYLLVAPQIIITLLFFFWPAIQALYQSMLLQDAFG-GYSEFVWFDNFKTL 61 ++ RF L+ P ++I L + P +Y S+ + + FV +N+ L Sbjct: 33 RKERFNPI---RLMQTPSVLILLAWMIVPLAMTIYFSVNRYNLMAPDQTGFVGLENYAFL 89 Query: 62 FADPTYLESFRTTALFSALVAFFGLALSLLLAVFADRVRRGASVYKTFLIWPYAVSPVVV 121 DP + S TAL V + LLAV D+ RG + + +I P+ V P V Sbjct: 90 LQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIARLLVIGPFFVMPTVA 149 Query: 122 GVLWM-FLLSPSLGILSHVLAWLGL-PWDYMINGTHAMILIVVAAIWKQISYNFLFFLAG 179 ++W ++ P GIL++V+ LGL P D++ + M+ +++ W+ I + FL L Sbjct: 150 ALIWKNMIMHPVYGILAYVMRHLGLEPIDWL--AEYPMLSVIIIVAWQWIPFAFLILLTA 207 Query: 180 LQSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHG 239 LQS+ EAA +DGAGPV+ FF IV P + + ++ ++ F + TT G Sbjct: 208 LQSLDTDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIF-LLSVFAEIFTTTAG 266 Query: 240 GPGKDTEILVYKVFTDGFKGGDLGGSAAQSVVLMALVILLTVVQF 284 GPG T L + V++ G + D+G ++A + V+L +V F Sbjct: 267 GPGTATTNLTFLVYSIGLQQFDIGIASAGGIF---AVVLANIVSF 308 >gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 311 Score = 108 bits (269), Expect = 8e-25, Method: Compositional matrix adjust. Identities = 79/271 (29%), Positives = 141/271 (52%), Gaps = 10/271 (3%) Query: 17 VAPQIIITLLFFFWPAIQALYQSMLLQDAFGGYSE--FVWFDNFKTLFADPTYLESFRTT 74 +AP ++TL++ +P + +Y S D G +E FV N+ LF PT+ + + Sbjct: 42 LAPACVMTLVYVLYPILYTIYLSFFSWD---GMTEPRFVGLANYVELFHAPTFYTALKNN 98 Query: 75 ALFSALVAFFGLALSLLLAVFADRVRRGASVYKTFLIWPYAVSPVVVGVLWMFLLSPSLG 134 L+ L+ + L +A++ ++ G V K+ P+ +S VVVG+++ + PS G Sbjct: 99 VLW-LLMFLLAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMYSWFYDPSFG 157 Query: 135 ILSHVLAWLGLPWDYMINGTHAMILIVVAAIWKQISYNFLFFLAGLQSIPKSLIEAAAID 194 +LS +L G+P + + +A I+ AA+W Q +Y + FL GL ++ +EAA ++ Sbjct: 158 LLS-LLFGQGVP--VLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARME 214 Query: 195 GAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGGPGKDTEILVYKVFT 254 GA ++ P + TTF FVV+++ A +F ++ T GGP + + +L Y + Sbjct: 215 GAKGWTMLRYVILPQLRSTTFMAFVVSIIGA-LRSFDLISVMTSGGPYESSTVLAYYAYD 273 Query: 255 DGFKGGDLGGSAAQSVVLMALVILLTVVQFK 285 K G SAA +V L A++++ V Q + Sbjct: 274 QAIKYYRQGYSAAVAVTLFAIMLVYIVYQLR 304 >gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 291 Score = 104 bits (260), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 86/291 (29%), Positives = 159/291 (54%), Gaps = 6/291 (2%) Query: 6 RFTSKWLPYLLVAPQIIITLLFFFWPAIQALYQSMLLQDAFGGYSEFVWFDNFKTLFADP 65 R S LP+LL++P +++ + F +PA+ L+ S S FV +N++ + DP Sbjct: 3 RLPSSVLPWLLLSPAMVLLIAFTHYPALATLWHSFFSTPKGVRPSVFVGLENYRLMADDP 62 Query: 66 TYLESFRTTALFSALVAFFGLALSLLLAVFADRVRRGASVYKTFLIWPYAVSPVVVGVLW 125 + ++ F+ +AL++L+A++ + G V + P + + V +W Sbjct: 63 VFWQALCNNLWFALGTIPLAIALAILMALWVNEKLAGRGVLRLAYFTPTVLPMIAVANIW 122 Query: 126 MFLLSPSLGILSHVLAWLGLP-WDYMINGTHAMILIVVAAIWKQISYNFLFFLAGLQSIP 184 +F +P G+L + LGLP +++ N + ++V A+WK+ + +F+LA LQ I Sbjct: 123 LFFYTPQYGLLEQITGALGLPSHNWLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQIS 182 Query: 185 KSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAF--FDTFVIVDATTHGGPG 242 L EAAA++GA + F+ + FPL+ PTT F+ + ++ AF D V++ T GGP Sbjct: 183 PVLAEAAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVM---TKGGPD 239 Query: 243 KDTEILVYKVFTDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQY 293 + +L+Y ++ GF D +AA +VVL+AL+ L+ +V+F+ ++++ Y Sbjct: 240 NASSLLLYYIYEVGFAFWDSSYAAALTVVLLALLGLIALVKFRVLDRRTHY 290 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 0.449 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: 879,144 Number of extensions: 34962 Number of successful extensions: 162 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 10 Length of query: 294 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 210 Effective length of database: 1,222,130 Effective search space: 256647300 Effective search space used: 256647300 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)