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= 0003.0002.p (311 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... 470 e-134 gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transp... 177 7e-46 gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease ... 112 5e-26 gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease ... 99 5e-22 gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease ... 98 8e-22 >gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 470 bits (1210), Expect = e-134, Method: Compositional matrix adjust. Identities = 230/270 (85%), Positives = 251/270 (92%) Query: 1 VEKRARFTSSWLPYALVAPQILITILFFFWPAVQALYQSVLLQDAFGGYSEFVWFDNFAA 60 +EKRARFTS WLPY LVAPQI+IT+LFFFWPAVQALYQS+LLQDAFGGYSEFVWFDNF Sbjct: 1 MEKRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALYQSMLLQDAFGGYSEFVWFDNFKT 60 Query: 61 LFGDPSYLAAFGTTAIFSVLVAVGGMVLSLILAVFADRVVKGAAIYKTFLIWPYAVSPVV 120 LFGDP+YL +F TTAIFS LVA G+ LSL+LAVFADRV +GA+IYKTFLIWPYAVSPVV Sbjct: 61 LFGDPTYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVV 120 Query: 121 VGVLWMFLLSPSLGLLSHVLAWLGINWNYMVNGNQAMTLIVIAAIWKQISYNFLFFLAGL 180 VGVLWMFLLSPSLG+LSHVL+WLG+ W+YM+NG AM LIVIAAIWKQISYNFLFFLAGL Sbjct: 121 VGVLWMFLLSPSLGILSHVLSWLGLPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGL 180 Query: 181 QSIPKSLIEAAAIDGAGPVKRFFTIIFPMISPTTFFLMVVNIVYAFFDTFAIVEATTHGG 240 QSIPKSLIEAAAIDGAGPVKRFFTI+FP+ISPTTFFL VVN+VYAFFDTF IV+ATTHGG Sbjct: 181 QSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGG 240 Query: 241 PGKDTEILVYKVFSDGFKGGDLGSAAAXAV 270 PGKDTEILVYKVFSDGFKGGDLG +AA +V Sbjct: 241 PGKDTEILVYKVFSDGFKGGDLGGSAAQSV 270 >gi|300311926|ref|YP_003776018.1| glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 177 bits (450), Expect = 7e-46, Method: Compositional matrix adjust. Identities = 110/271 (40%), Positives = 159/271 (58%), Gaps = 2/271 (0%) Query: 1 VEKRARFTSSWLPYALVAPQILITILFFFWPAVQALYQSVLLQDAFGGYSEFVWFDNFAA 60 ++ R F + W P L PQ+LI LFF WPAV+A+ S L FG S FV DN+ Sbjct: 1 MDARPAFPTRWFPLLLATPQMLIVFLFFLWPAVKAIAWSFYLVRPFGNGSRFVGLDNYLR 60 Query: 61 LFGDPSYLAAFGTTAIFSVLVAVGGMVLSLILAVFADRVVKGAAIYKTFLIWPYAVSPVV 120 + D S+ A+ T +F+ + + ++L LA + V+ + ++ IWPYAV+ VV Sbjct: 61 ILTDDSFYASLRATLVFTAGSTLLAVTIALALAACLELDVRAKRLLRSIFIWPYAVAGVV 120 Query: 121 VGVLWMFLLSPSLGLLSHV-LAWLGINWNYMVNGNQAMTLIVIAAIWKQISYNFLFFLAG 179 VG++ L++P GLL+ + W G+ W + G QAM ++ A W Q+ NF+ F A Sbjct: 121 VGIVLKVLINPVTGLLAFLNQLWPGV-WAPHLIGAQAMLALIAAFAWTQVPLNFILFSAA 179 Query: 180 LQSIPKSLIEAAAIDGAGPVKRFFTIIFPMISPTTFFLMVVNIVYAFFDTFAIVEATTHG 239 LQ IP L+ AAAIDGAGP +RF I PMI+P V+N++ AF F +V+A T G Sbjct: 180 LQRIPADLMGAAAIDGAGPWRRFIDIQLPMIAPALLLAGVINVIEAFTHGFGLVDALTQG 239 Query: 240 GPGKDTEILVYKVFSDGFKGGDLGSAAAXAV 270 GPG+ T IL Y+++SDGF G DL ++A +V Sbjct: 240 GPGRSTAILAYQIYSDGFIGLDLSGSSALSV 270 >gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 112 bits (279), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 81/270 (30%), Positives = 134/270 (49%), Gaps = 13/270 (4%) Query: 3 KRARFTSSWLPYALVAPQILITILFFFWPAVQALYQSVLLQDAFG-GYSEFVWFDNFAAL 61 ++ RF L + P +LI + + P +Y SV + + FV +N+A L Sbjct: 33 RKERFNPIRL---MQTPSVLILLAWMIVPLAMTIYFSVNRYNLMAPDQTGFVGLENYAFL 89 Query: 62 FGDPSYLAAFGTTAIFSVLVAVGGMVLSLILAVFADRVVKGAAIYKTFLIWPYAVSPVVV 121 DP++ + G TA+ V ++ +LAV D+ +G I + +I P+ V P V Sbjct: 90 LQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIARLLVIGPFFVMPTVA 149 Query: 122 GVLWM-FLLSPSLGLLSHVLAWLG---INWNYMVNGNQAMTLIVIAAIWKQISYNFLFFL 177 ++W ++ P G+L++V+ LG I+W M ++I W+ I + FL L Sbjct: 150 ALIWKNMIMHPVYGILAYVMRHLGLEPIDWL----AEYPMLSVIIIVAWQWIPFAFLILL 205 Query: 178 AGLQSIPKSLIEAAAIDGAGPVKRFFTIIFPMISPTTFFLMVVNIVYAFFDTFAIVEATT 237 LQS+ EAA +DGAGPV+ FF I+ P + ++++ ++ FA + TT Sbjct: 206 TALQSLDTDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIF-LLSVFAEIFTTT 264 Query: 238 HGGPGKDTEILVYKVFSDGFKGGDLGSAAA 267 GGPG T L + V+S G + D+G A+A Sbjct: 265 AGGPGTATTNLTFLVYSIGLQQFDIGIASA 294 >gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 291 Score = 98.6 bits (244), Expect = 5e-22, Method: Compositional matrix adjust. Identities = 72/257 (28%), Positives = 134/257 (52%), Gaps = 2/257 (0%) Query: 6 RFTSSWLPYALVAPQILITILFFFWPAVQALYQSVLLQDAFGGYSEFVWFDNFAALFGDP 65 R SS LP+ L++P +++ I F +PA+ L+ S S FV +N+ + DP Sbjct: 3 RLPSSVLPWLLLSPAMVLLIAFTHYPALATLWHSFFSTPKGVRPSVFVGLENYRLMADDP 62 Query: 66 SYLAAFGTTAIFSVLVAVGGMVLSLILAVFADRVVKGAAIYKTFLIWPYAVSPVVVGVLW 125 + A F++ + L++++A++ + + G + + P + + V +W Sbjct: 63 VFWQALCNNLWFALGTIPLAIALAILMALWVNEKLAGRGVLRLAYFTPTVLPMIAVANIW 122 Query: 126 MFLLSPSLGLLSHVLAWLGI-NWNYMVNGNQAMTLIVIAAIWKQISYNFLFFLAGLQSIP 184 +F +P GLL + LG+ + N++ N + +++ A+WK+ + +F+LA LQ I Sbjct: 123 LFFYTPQYGLLEQITGALGLPSHNWLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQIS 182 Query: 185 KSLIEAAAIDGAGPVKRFFTIIFPMISPTTFFLMVVNIVYAFFDTFAIVEATTHGGPGKD 244 L EAAA++GA + F+ + FP++ PTT F+++ ++ AF IV T GGP Sbjct: 183 PVLAEAAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIV-VMTKGGPDNA 241 Query: 245 TEILVYKVFSDGFKGGD 261 + +L+Y ++ GF D Sbjct: 242 SSLLLYYIYEVGFAFWD 258 >gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 311 Score = 98.2 bits (243), Expect = 8e-22, Method: Compositional matrix adjust. Identities = 73/256 (28%), Positives = 129/256 (50%), Gaps = 10/256 (3%) Query: 17 VAPQILITILFFFWPAVQALYQSVLLQDAFGGYSE--FVWFDNFAALFGDPSYLAAFGTT 74 +AP ++T+++ +P + +Y S D G +E FV N+ LF P++ A Sbjct: 42 LAPACVMTLVYVLYPILYTIYLSFFSWD---GMTEPRFVGLANYVELFHAPTFYTALKNN 98 Query: 75 AIFSVLVAVGGMVLSLILAVFADRVVKGAAIYKTFLIWPYAVSPVVVGVLWMFLLSPSLG 134 ++ +L+ + + L +A++ ++ V G + K+ P+ +S VVVG+++ + PS G Sbjct: 99 VLW-LLMFLLAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMYSWFYDPSFG 157 Query: 135 LLSHVLAWLGINWNYMVNGNQAMTLIVIAAIWKQISYNFLFFLAGLQSIPKSLIEAAAID 194 LLS + G + + A I+ AA+W Q +Y + FL GL ++ +EAA ++ Sbjct: 158 LLSLLF---GQGVPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARME 214 Query: 195 GAGPVKRFFTIIFPMISPTTFFLMVVNIVYAFFDTFAIVEATTHGGPGKDTEILVYKVFS 254 GA +I P + TTF VV+I+ A +F ++ T GGP + + +L Y + Sbjct: 215 GAKGWTMLRYVILPQLRSTTFMAFVVSIIGA-LRSFDLISVMTSGGPYESSTVLAYYAYD 273 Query: 255 DGFKGGDLGSAAAXAV 270 K G +AA AV Sbjct: 274 QAIKYYRQGYSAAVAV 289 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 0.328 0.143 0.448 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: 917,708 Number of extensions: 36356 Number of successful extensions: 181 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 163 Number of HSP's successfully gapped: 10 Length of query: 311 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 226 Effective length of database: 1,217,395 Effective search space: 275131270 Effective search space used: 275131270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 130 (54.7 bits)