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= 0001.3355.p (292 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312691|ref|YP_003776783.1| sugar ABC transporter permease ... 535 e-153 gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease ... 96 4e-21 gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease ... 94 1e-20 gi|300310302|ref|YP_003774394.1| sugar ABC transporter permease ... 91 9e-20 gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease ... 88 6e-19 >gi|300312691|ref|YP_003776783.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 292 Score = 535 bits (1378), Expect = e-153, Method: Compositional matrix adjust. Identities = 272/292 (93%), Positives = 285/292 (97%) Query: 1 MFNRGKTSLPYLFLGPPLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRNIERLLS 60 MFNRGKTSLPYLFLGP LLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRN+ERL+S Sbjct: 1 MFNRGKTSLPYLFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRNLERLMS 60 Query: 61 DRRFLNAIEVSAIWEVVTVLGALVVGVLVAIYLFEQVHGKWRHAMCLLLITPVLLPRVSA 120 DRRFLNAIEVSA+WEVVTVLGA++VG+ +A+YLFE VHGKWR AMC+LLITPVLLPRVSA Sbjct: 61 DRRFLNAIEVSAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSA 120 Query: 121 AFIWKFMYSPLTGILGWLLGLLGIHDTAFLSDPVLALYAVAAVDIWQWGLFFAVIVLKLL 180 AFIWKFMYSPLTGILGWLLGL+GIHDTAFLSDP LALYAVA VDIWQWGLFFAVIVLKLL Sbjct: 121 AFIWKFMYSPLTGILGWLLGLVGIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLL 180 Query: 181 ETLPPEPLEAARLDYARTWQVYAYIALPMLKAPIISLVFIKMVESLRSFDLIYVMTKGGP 240 ETLPPEPLEAARLDYARTWQVYAYIALPMLK P+ISLVFIKMVESLRSFDLIYVMTKGGP Sbjct: 181 ETLPPEPLEAARLDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGP 240 Query: 241 GVATETLDMYAYAQGIGLSGKVSYASTMAVLMMVATTLIFTLIWKRVSQWED 292 GVATETLDMYAYAQGIGLSGKVSYASTMAVLMM+ATTLIFTLIWKRVS+WED Sbjct: 241 GVATETLDMYAYAQGIGLSGKVSYASTMAVLMMIATTLIFTLIWKRVSKWED 292 >gi|300309782|ref|YP_003773874.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 95.5 bits (236), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 81/244 (33%), Positives = 128/244 (52%), Gaps = 8/244 (3%) Query: 16 PPLLVMLVLGLVPTVAAINLALKNRVLRYPD-SDYVWLRNIERLLSDRRFLNAIEVSAIW 74 P +L++L +VP I ++ L PD + +V L N LL D F +I +A+ Sbjct: 46 PSVLILLAWMIVPLAMTIYFSVNRYNLMAPDQTGFVGLENYAFLLQDPAFWPSIGNTALL 105 Query: 75 EVVTVLGALVVGVLVAIYLFEQVHGKWRHAMCLLLITPVLLPRVSAAFIWKFM-YSPLTG 133 + +VL V+G + LF+Q + R LL+I P + AA IWK M P+ G Sbjct: 106 -IGSVLAISVIGGTLLAVLFDQPF-RGRGIARLLVIGPFFVMPTVAALIWKNMIMHPVYG 163 Query: 134 ILGWLLGLLGIHDTAFLSD-PVLALYAVAAVDIWQWGLFFAVIVLKLLETLPPEPLEAAR 192 IL +++ LG+ +L++ P+L++ + A WQW F +I+L L++L + EAA+ Sbjct: 164 ILAYVMRHLGLEPIDWLAEYPMLSVIIIVA---WQWIPFAFLILLTALQSLDTDQKEAAQ 220 Query: 193 LDYARTWQVYAYIALPMLKAPIISLVFIKMVESLRSFDLIYVMTKGGPGVATETLDMYAY 252 LD A +++ YI LP LK I ++ I+ + L F I+ T GGPG AT L Y Sbjct: 221 LDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLSVFAEIFTTTAGGPGTATTNLTFLVY 280 Query: 253 AQGI 256 + G+ Sbjct: 281 SIGL 284 >gi|300312388|ref|YP_003776480.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 291 Score = 94.4 bits (233), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 72/253 (28%), Positives = 126/253 (49%), Gaps = 2/253 (0%) Query: 6 KTSLPYLFLGPPLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRNIERLLSDRRFL 65 + LP+L L P +++++ P +A + + + S +V L N + D F Sbjct: 6 SSVLPWLLLSPAMVLLIAFTHYPALATLWHSFFSTPKGVRPSVFVGLENYRLMADDPVFW 65 Query: 66 NAIEVSAIWEVVTVLGALVVGVLVAIYLFEQVHGKWRHAMCLLLITPVLLPRVSAAFIWK 125 A+ + + + T+ A+ + +L+A+++ E++ G R + L TP +LP ++ A IW Sbjct: 66 QALCNNLWFALGTIPLAIALAILMALWVNEKLAG--RGVLRLAYFTPTVLPMIAVANIWL 123 Query: 126 FMYSPLTGILGWLLGLLGIHDTAFLSDPVLALYAVAAVDIWQWGLFFAVIVLKLLETLPP 185 F Y+P G+L + G LG+ +L +P L A+ V +W+ FF + L L+ + P Sbjct: 124 FFYTPQYGLLEQITGALGLPSHNWLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQISP 183 Query: 186 EPLEAARLDYARTWQVYAYIALPMLKAPIISLVFIKMVESLRSFDLIYVMTKGGPGVATE 245 EAA L+ A WQ + + P+L + ++ ++ + R D I VMTKGGP A+ Sbjct: 184 VLAEAAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVMTKGGPDNASS 243 Query: 246 TLDMYAYAQGIGL 258 L Y Y G Sbjct: 244 LLLYYIYEVGFAF 256 >gi|300310302|ref|YP_003774394.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 296 Score = 91.3 bits (225), Expect = 9e-20, Method: Compositional matrix adjust. Identities = 62/256 (24%), Positives = 127/256 (49%), Gaps = 6/256 (2%) Query: 3 NRGKTSLPYLFLGPPLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRNIERLLSDR 62 N+ + + F+ P L + ++P + +N ++++ ++ +V L ++ D Sbjct: 2 NKPYNNKAWFFILPVFLTVAFSAIIPLMTVVNYSVQD-IISPEQKVFVGLDWFREVMRDG 60 Query: 63 RFLNAIEVSAIWEVVTVLGALVVGVLVAIYLFEQVHGKWRHAMCLLLIT-PVLLPRVSAA 121 A+ I+ +L + +G+ +A+ + H W+ + L+++ P+L+P Sbjct: 61 ELHAALLRQLIFSFCVLLVQIPLGIGLALAM---PHKGWKSSATLVILAMPLLIPWNVVG 117 Query: 122 FIWKFMYSPLTGILGWLLGLLGIHDTAFLSDPVLALYAVAAVDIWQWGLFFAVIVLKLLE 181 IW+ G+ G++L LLGI D + S+P+ A V +D+W W A++ L Sbjct: 118 TIWQIFGRADIGLGGYVLNLLGI-DYNYASNPLDAWLTVLLMDVWHWTPLVALLAFAGLR 176 Query: 182 TLPPEPLEAARLDYARTWQVYAYIALPMLKAPIISLVFIKMVESLRSFDLIYVMTKGGPG 241 ++P +AA++D A W V+ YI LP ++ ++ V ++ ++S + +V+T GGPG Sbjct: 177 SIPDAYYQAAQIDGASRWAVFRYIQLPKMRGVLVIAVLLRFMDSFMIYTEPFVLTGGGPG 236 Query: 242 VATETLDMYAYAQGIG 257 +T L Y + +G Sbjct: 237 NSTTFLSQYLTQKAVG 252 >gi|300309613|ref|YP_003773705.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 311 Score = 88.2 bits (217), Expect = 6e-19, Method: Compositional matrix adjust. Identities = 73/258 (28%), Positives = 124/258 (48%), Gaps = 9/258 (3%) Query: 13 FLGPPLLVMLVLGLVPTVAAINLALKNRVLRYPDSDYVWLRNIERLLSDRRFLNAIEVSA 72 FL P ++ LV L P + I L+ + + +V L N L F A++ + Sbjct: 41 FLAPACVMTLVYVLYPILYTIYLSFFSWD-GMTEPRFVGLANYVELFHAPTFYTALKNNV 99 Query: 73 IWEVVTVLGALVVGVLVAIYLFEQVHGKWRHAMCLLLITPVLLPRVSAAFIWKFMYSPLT 132 +W ++ +L A +G+ +A+YL ++V G + L P +L V ++ + Y P Sbjct: 100 LWLLMFLL-APPMGLAIALYLNQKVIGM--RVVKSLFFAPFVLSGVVVGLMYSWFYDPSF 156 Query: 133 GILGWLLGLLGIHDTAFLSDPVLALYAVAAVDIWQWGLFFAVIVLKLLETLPPEPLEAAR 192 G+L L G L D A + + +W + ++ L L L + +EAAR Sbjct: 157 GLLSLLFG----QGVPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAAR 212 Query: 193 LDYARTWQVYAYIALPMLKAPIISLVFIKMVESLRSFDLIYVMTKGGPGVATETLDMYAY 252 ++ A+ W + Y+ LP L++ + ++ +LRSFDLI VMT GGP ++ L YAY Sbjct: 213 MEGAKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYESSTVLAYYAY 272 Query: 253 AQGIGLSGKVSYASTMAV 270 Q I + Y++ +AV Sbjct: 273 DQAIKYY-RQGYSAAVAV 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 0.142 0.443 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: 686,523 Number of extensions: 19915 Number of successful extensions: 143 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 141 Number of HSP's successfully gapped: 9 Length of query: 292 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 208 Effective length of database: 1,222,130 Effective search space: 254203040 Effective search space used: 254203040 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)