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= 0001.0425.p (308 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease ... 584 e-168 gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC tra... 116 3e-27 gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease ... 98 8e-22 gi|300310302|ref|YP_003774394.1| sugar ABC transporter permease ... 93 3e-20 gi|300312691|ref|YP_003776783.1| sugar ABC transporter permease ... 86 5e-18 >gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 584 bits (1505), Expect = e-168, Method: Compositional matrix adjust. Identities = 295/309 (95%), Positives = 299/309 (96%), Gaps = 1/309 (0%) Query: 1 MPSPSQLAARSLR-SPPRKERFNPIRLMQAPSVLLLLAWMIVPLVMTIYFSVNRYNLMAP 59 M S SQ A+R + SPPRKERFNPIRLMQ PSVL+LLAWMIVPL MTIYFSVNRYNLMAP Sbjct: 16 MQSTSQPASRRQQTSPPRKERFNPIRLMQTPSVLILLAWMIVPLAMTIYFSVNRYNLMAP 75 Query: 60 DQTGFVGLENYRFLLQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIAR 119 DQTGFVGLENY FLLQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIAR Sbjct: 76 DQTGFVGLENYAFLLQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIAR 135 Query: 120 LLVIGPFFVMPTVAALIWKNMIMHPVYGILAYVMRHLGLEPIDWLAEYPMLSVIIIVAWQ 179 LLVIGPFFVMPTVAALIWKNMIMHPVYGILAYVMRHLGLEPIDWLAEYPMLSVIIIVAWQ Sbjct: 136 LLVIGPFFVMPTVAALIWKNMIMHPVYGILAYVMRHLGLEPIDWLAEYPMLSVIIIVAWQ 195 Query: 180 WIPFAFLILLTALQSLDHDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLS 239 WIPFAFLILLTALQSLD DQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLS Sbjct: 196 WIPFAFLILLTALQSLDTDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLS 255 Query: 240 IFAEIFTTTAGGPGTATTNLTFLVYSIGLQQFDIGIASAGGIFAVVLANIVSFFLVRMLA 299 +FAEIFTTTAGGPGTATTNLTFLVYSIGLQQFDIGIASAGGIFAVVLANIVSFFLVRMLA Sbjct: 256 VFAEIFTTTAGGPGTATTNLTFLVYSIGLQQFDIGIASAGGIFAVVLANIVSFFLVRMLA 315 Query: 300 RNLKGVNEK 308 RNLKGVNEK Sbjct: 316 RNLKGVNEK 324 >gi|300313088|ref|YP_003777180.1| sn-glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 294 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 87/285 (30%), Positives = 142/285 (49%), Gaps = 12/285 (4%) Query: 17 RKERFNPI---RLMQAPSVLLLLAWMIVPLVMTIYFSVNRYNLMAPDQTGFVGLENYRFL 73 ++ RF L+ AP +++ L + P V +Y S+ + + FV +N++ L Sbjct: 3 KRARFTSKWLPYLLVAPQIIITLLFFFWPAVQALYQSMLLQDAFG-GYSEFVWFDNFKTL 61 Query: 74 LQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFDQPFRGRGIARLLVIGPFFVMPTVA 133 DP + S TA+ V + LLAV D+ RG I + +I P+ V P V Sbjct: 62 FGDPTYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVVV 121 Query: 134 ALIWKNMIMHPVYGILAYVMRHLGLEPIDWL--AEYPMLSVIIIVAWQWIPFAFLILLTA 191 ++W ++ P GIL++V+ LGL P D++ + M+ ++I W+ I + FL L Sbjct: 122 GVLWM-FLLSPSLGILSHVLSWLGL-PWDYMINGTHAMILIVIAAIWKQISYNFLFFLAG 179 Query: 192 LQSLDHDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIF-LLSIFAEIFTTTAG 250 LQS+ EAA +DGAGPV+ FF IV P + + ++ ++ F + TT G Sbjct: 180 LQSIPKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHG 239 Query: 251 GPGTATTNLTFLVYSIGLQQFDIGIASAGGIF---AVVLANIVSF 292 GPG T L + V+S G + D+G ++A + V+L +V F Sbjct: 240 GPGKDTEILVYKVFSDGFKGGDLGGSAAQSVVLMALVILLTVVQF 284 >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 = 79/273 (28%), Positives = 140/273 (51%), Gaps = 11/273 (4%) Query: 29 APSVLLLLAWMIVPLVMTIYFSVNRYNLMAPDQTGFVGLENYRFLLQDPAFWPSIGNTAL 88 AP+ ++ L +++ P++ TIY S ++ M + FVGL NY L P F+ ++ N L Sbjct: 43 APACVMTLVYVLYPILYTIYLSFFSWDGMTEPR--FVGLANYVELFHAPTFYTALKNNVL 100 Query: 89 -LIGSVLAISVIGGTLLAVLFDQPFRGRGIARLLVIGPFFVMPTVAALIWKNMIMHPVYG 147 L+ +LA + G +A+ +Q G + + L PF + V L++ + P +G Sbjct: 101 WLLMFLLAPPM--GLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMY-SWFYDPSFG 157 Query: 148 ILAYVMRHLGLEPIDWLAEYPMLSVIIIVAWQWIPFAFLILLTALQSLDHDQKEAAQLDG 207 +L+ + G+ P+ A Y +I W + ++ LT L +L+HDQ EAA+++G Sbjct: 158 LLSLLFGQ-GV-PVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARMEG 215 Query: 208 AGPVRIFFYIVLPHLKRAITVVIMIETIFLLSIFAEIFTTTAGGPGTATTNLTFLVYSIG 267 A + Y++LP L+ + ++ I L F I T+GGP ++T L + Y Sbjct: 216 AKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYESSTVLAYYAYDQA 275 Query: 268 LQQFDIGIASAGGI--FAVVLANIVSFFLVRML 298 ++ + G ++A + FA++L IV + L RML Sbjct: 276 IKYYRQGYSAAVAVTLFAIMLVYIV-YQLRRML 307 >gi|300310302|ref|YP_003774394.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 296 Score = 92.8 bits (229), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 70/247 (28%), Positives = 125/247 (50%), Gaps = 18/247 (7%) Query: 40 IVPLVMTIYFSVNRYNLMAPDQTGFVGLENYRFLLQDPAFWPSIGNTALLIGSVLAISVI 99 I+PL+ + +SV ++++P+Q FVGL+ +R +++D ++ + VL + + Sbjct: 25 IIPLMTVVNYSVQ--DIISPEQKVFVGLDWFREVMRDGELHAALLRQLIFSFCVLLVQIP 82 Query: 100 GGTLLAVLFDQPFRGRGIARLLVI--GPFFVMPTVAALIWKNMIMHPVYGILAYVMRHLG 157 G LA+ P +G + LVI P + V IW+ + G+ YV+ LG Sbjct: 83 LGIGLALAM--PHKGWKSSATLVILAMPLLIPWNVVGTIWQ-IFGRADIGLGGYVLNLLG 139 Query: 158 LE------PIDWLAEYPMLSVIIIVAWQWIPFAFLILLTALQSLDHDQKEAAQLDGAGPV 211 ++ P+D L+V+++ W W P L+ L+S+ +AAQ+DGA Sbjct: 140 IDYNYASNPLD-----AWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQAAQIDGASRW 194 Query: 212 RIFFYIVLPHLKRAITVVIMIETIFLLSIFAEIFTTTAGGPGTATTNLTFLVYSIGLQQF 271 +F YI LP ++ + + +++ + I+ E F T GGPG +TT L+ + + QF Sbjct: 195 AVFRYIQLPKMRGVLVIAVLLRFMDSFMIYTEPFVLTGGGPGNSTTFLSQYLTQKAVGQF 254 Query: 272 DIGIASA 278 D+G A+A Sbjct: 255 DLGPAAA 261 >gi|300312691|ref|YP_003776783.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 292 Score = 85.5 bits (210), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 76/247 (30%), Positives = 128/247 (51%), Gaps = 6/247 (2%) Query: 26 LMQAPSVLLLLAWMIVPLVMTIYFSVNRYNLMAPDQTGFVGLENYRFLLQDPAFWPSIGN 85 L PS+L++L +VP V I ++ L PD + +V L N L+ D F +I Sbjct: 12 LFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPD-SDYVWLRNLERLMSDRRFLNAIEV 70 Query: 86 TALL-IGSVLAISVIGGTLLAVLFDQPF-RGRGIARLLVIGPFFVMPTVAALIWKNMIMH 143 +A+ + +VL ++G + LF+ + R +L+I P + AA IWK M Sbjct: 71 SAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSAAFIWKFM-YS 129 Query: 144 PVYGILAYVMRHLGLEPIDWLAE--YPMLSVIIIVAWQWIPFAFLILLTALQSLDHDQKE 201 P+ GIL +++ +G+ +L++ + +V ++ WQW F +I+L L++L + E Sbjct: 130 PLTGILGWLLGLVGIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLLETLPPEPLE 189 Query: 202 AAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLSIFAEIFTTTAGGPGTATTNLTF 261 AA+LD A +++ YI LP LK + ++ I+ + L F I+ T GGPG AT L Sbjct: 190 AARLDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGPGVATETLDM 249 Query: 262 LVYSIGL 268 Y+ G+ Sbjct: 250 YAYAQGI 256 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 0.330 0.144 0.439 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: 920,272 Number of extensions: 37815 Number of successful extensions: 205 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 189 Number of HSP's successfully gapped: 11 Length of query: 308 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 223 Effective length of database: 1,217,395 Effective search space: 271479085 Effective search space used: 271479085 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)