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= 0001.0829.p (340 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310369|ref|YP_003774461.1| sugar ABC transporter permease ... 540 e-155 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 137 1e-33 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 129 4e-31 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 114 1e-26 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 114 1e-26 >gi|300310369|ref|YP_003774461.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 340 Score = 540 bits (1392), Expect = e-155, Method: Compositional matrix adjust. Identities = 313/340 (92%), Positives = 324/340 (95%) Query: 1 MMLASSLRRVSHAPWFTSMVTVLLLVVMLLAGAFGYDGFLSPQVMLNLLIDNAFLLVVAI 60 MML SSLRR SHAPWFTSMVTV+LLVVML+AGA GYDGFLSPQVMLNLLIDNAFLLVVAI Sbjct: 1 MMLVSSLRRASHAPWFTSMVTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAI 60 Query: 61 GMSFVILSGGIDLSVGSVLALTTMVAAFLLQSWHWPPLLVVAVVLLMGAGFGAVMGAMIH 120 GM+FVILSGGIDLSVGSVLALTTMVAAFLLQ+WHW PLLV+ VLLMGAGFGA MGAMIH Sbjct: 61 GMTFVILSGGIDLSVGSVLALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIH 120 Query: 121 YFKLQAFIVTLAGMFLARGLCYLISINSITIDDPLFVAMSQTRLEFAGLFISPSVVIALL 180 YFKLQAFIVTLAGMFLARGLCYLISINSITIDDPLF +SQTRLE AGLFISPSVVIAL Sbjct: 121 YFKLQAFIVTLAGMFLARGLCYLISINSITIDDPLFTTLSQTRLELAGLFISPSVVIALF 180 Query: 181 VLVAAIWMAHGTRFGRAVYAIGGSEQSAMLMGLPVGRTKVLVYAFSGFCASVAGVLFSFY 240 +L AIWMAH TRFGRAVYAIGG+E SA+LMGLPVGRTKVLVYAFSG CA+VAGVLFSFY Sbjct: 181 MLALAIWMAHCTRFGRAVYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFY 240 Query: 241 MLSGYGLHAQGVELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGSLSSW 300 MLSGYGLHAQGVELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDG+LSSW Sbjct: 241 MLSGYGLHAQGVELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSW 300 Query: 301 WTKIFIGALLFVFCVAQRVISLGALRGKPAGSAKAAPAGA 340 WTKIFIGALLFVFCVAQRVISLGALRGKPAGSAKAAPAGA Sbjct: 301 WTKIFIGALLFVFCVAQRVISLGALRGKPAGSAKAAPAGA 340 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 137 bits (345), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 107/293 (36%), Positives = 165/293 (56%), Gaps = 12/293 (4%) Query: 4 ASSLRRVSHAPWFTSMVTVL------LLVVMLLAGAFGYDGFLSPQVMLNLLIDNAFLLV 57 A+SL + A W + + + L L+VV LL G D F + N+L + + + Sbjct: 10 AASLHTAASARWRSLIHSPLALPLAGLVVVSLLMG-LASDNFFTLSNWFNVLRQVSIVGI 68 Query: 58 VAIGMSFVILSGGIDLSVGSVLALTTMVAAFLLQSWHWPPLLVVAVVLLMGAGFGAVMGA 117 +A+GMSFVIL+GGIDLSVG+ +AL ++A L+ + P L + + + G + GA Sbjct: 69 LAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGA 128 Query: 118 MIHYFKLQAFIVTLAGMFLARGLCYLISINSITIDDPLFVAMSQTRLEFAGLFISPSVVI 177 ++ + ++ A IVTLA M +ARG+ + S P +++ + + P VI Sbjct: 129 LVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISW----FGVGRIGMVPVPVI 184 Query: 178 ALLVLVAAIWMA-HGTRFGRAVYAIGGSEQSAMLMGLPVGRTKVLVYAFSGFCASVAGVL 236 +L++ A W+ T FGR VYAIGG+E +A L G+ R K+ VYA SGF + +A ++ Sbjct: 185 LMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAII 244 Query: 237 FSFYMLSGYGLHAQGVELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQT 289 + ++SG G ELDAIAAVV+GGT + GG G V GTL G ++LG++ Sbjct: 245 LTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNN 297 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 129 bits (323), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 102/286 (35%), Positives = 153/286 (53%), Gaps = 9/286 (3%) Query: 35 GYDGFLSPQVMLNLLIDNAFLLVVAIGMSFVILSGGIDLSVGSVLALTTMVAAFLLQSWH 94 G F S + +N+L A LV+A GM+FVIL+ GIDLSVGSVLA++ ++ + S Sbjct: 56 GTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLG--MQVSLG 113 Query: 95 WPPLLVVAVVLLMGAGFGAVMGAMIHYFKLQAFIVTLAGMFLARGLCYLISINSITIDD- 153 P + + + G G V GAM+ + AF+VTL M RG YL++ + +++ Sbjct: 114 AAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNND 173 Query: 154 -PLFVAMSQTRLEFAGLFISPSVVIALLVLVAAIWMAHGTRFGRAVYAIGGSEQSAMLMG 212 P F + I +V + LL V + T G +YAIGG+ Q+A L G Sbjct: 174 IPSFEWIGNGDFLHVPWLIWVAVAVVLLSWV----ILRKTVLGMHIYAIGGNLQAARLTG 229 Query: 213 LPVGRTKVLVYAFSGFCASVAGVLFSFYMLSGYGLHAQGVELDAIAAVVIGGTLLTGGYG 272 + VG + VY+ SG + +AG + + + G G ELDAIAAVV+GGT L GG G Sbjct: 230 IRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVG 289 Query: 273 YVAGTLTGVLILGVIQTLIAFDGSLSSWWTKIFIGALLFVFCVAQR 318 + GT+ G LI+GV+ + G LSS+W + GA++ + + + Sbjct: 290 SIWGTVVGALIIGVMNNGLTILG-LSSFWQYVAKGAVIVLAVILDK 334 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 104/284 (36%), Positives = 152/284 (53%), Gaps = 19/284 (6%) Query: 39 FLSPQVMLNLLIDNAFLLVVAIGMSFVILSGGIDLSVGSVLALTTMVAAFLLQSWHWPPL 98 FLS Q M NLL D+A +++A+ VIL+ GIDLSV S LAL+ M++A L + H+P L Sbjct: 49 FLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLALSGMMSALL--AMHFPAL 106 Query: 99 LV---VAVVLLMGAGFGAVMGAMIHYFKLQAFIVTLAGMFLARGLCYLIS----INSITI 151 V + + +L+G G + G +I Y +L +VTL M + RG+ +++S ++S + Sbjct: 107 PVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGGAWVSSRNM 166 Query: 152 DDPLFVAMSQTRLEFAGLFISPSVVIALLVLVAAIWMAHGTRFGRAVYAIGGSEQSAMLM 211 F+A RL GL + V + L +VA ++A TRFGR +YAIG +A + Sbjct: 167 PAD-FIAFPLARL--GGL--THLVWLGALAVVAIWFLARHTRFGRDLYAIGNDPAAAAYV 221 Query: 212 GLPVGRTKVL-VYAFSGFCASVAGVLFSFYMLSGYGLHAQGVELDAIAAVVIGGTLLTGG 270 G+ R ++L Y SG A +AG L+ Y A G EL IAA VIGG + GG Sbjct: 222 GI-ASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIGGVSIAGG 280 Query: 271 YGYVAGTLTGVLILGVIQTLIAFDGSLSSWWTKIFIGALLFVFC 314 G V+G + G L L VI + +S +W G L + C Sbjct: 281 VGQVSGAVLGALFLSVINNALPIM-RISPFWQSALTG--LVILC 321 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 101/298 (33%), Positives = 155/298 (52%), Gaps = 25/298 (8%) Query: 25 LVVMLLAGAFGYDGFLSPQVMLNLLIDNAFLLVVAIGMSFVILSGGIDLSVGSVLALTTM 84 L+ M + AF + FLS + L D L+V+++GM+F+++ GGIDLSVGSV+AL Sbjct: 30 LLAMCVMFAFLSENFLSAATFITLSNDIPPLVVMSVGMTFILIIGGIDLSVGSVMALAAS 89 Query: 85 VAAFLLQSWHWPPLLVVAVVLLMGAGFGAVMGAMIHYFKLQAFIVTLAGMFLARGLCYLI 144 + + + W WP + +++ A G + G + ++++ +FIV+L + +ARGL Y + Sbjct: 90 MLSMAMVRWGWPLYAAAPLGVVVAALCGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQV 149 Query: 145 SINSIT---------IDDPLFVAMSQTRLEFAGLFISPSVVIALLVLVAAIWMAHGTRFG 195 + NS T I P+ MS L + V+IA LVL T G Sbjct: 150 T-NSRTEYIGSAVDVISSPILFGMSPAFLSAIAI-----VIIAQLVLTR-------TVLG 196 Query: 196 RAVYAIGGSEQSAMLMGLPVGRTKVLVYAFSGFCASVAGVLFSFYMLSGYGLHAQ-GVEL 254 R IG +E++ L G+ +K+L +A G A +A LF L + G+EL Sbjct: 197 RYWIGIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAA-LFQVSRLEAADPNGGVGMEL 255 Query: 255 DAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGSLSSWWTKIFIGALLFV 312 IAAVVIGGT L GG G + T GVLI+ V++ +A G +S +I GA++ V Sbjct: 256 QVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVG-VSEPMKRIITGAVIVV 312 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 0.142 0.427 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: 762,440 Number of extensions: 25049 Number of successful extensions: 269 Number of sequences better than 1.0e-08: 23 Number of HSP's gapped: 256 Number of HSP's successfully gapped: 26 Length of query: 340 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,212,660 Effective search space: 308015640 Effective search space used: 308015640 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 (21.9 bits) S2: 131 (55.1 bits)