Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 567 bits (1460), Expect = e-166 Identities = 281/537 (52%), Positives = 389/537 (72%), Gaps = 20/537 (3%) Query: 8 LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67 L +DI + +Y ++G+ LW+SR K ++ T+DYFLAGK+LPWWA+GASLIA+NISA Sbjct: 2 LETLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISA 61 Query: 68 EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127 EQ IGMSGSGY+IGLAIASYEWM+AITLI+VGKY LPIFI+ IYT+P+++E+RF+K++K Sbjct: 62 EQIIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRFDKRVK 121 Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVW 187 T LA+FW+S+YI VNLT+VL+LGGLA+ET+ GI +Y ++ LALF+L YS+YGGL AV + Sbjct: 122 TTLALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAY 181 Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLP 247 TD+IQV L+ GG + +Y+A+ + G AG ++ A P HFEMIL QSNP YM+LP Sbjct: 182 TDIIQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQSNPHYMSLP 241 Query: 248 GIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIA 307 GI+VL+GGLW+ N+ YWGFNQYIIQR LAAKSV+EAQKGI FAA+LKL++P +VVLPGIA Sbjct: 242 GISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLMPLIVVLPGIA 301 Query: 308 AYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLA 367 A ++ P + D+AYP + +P GVKG+VFAAL AAIVSSLA Sbjct: 302 AVLL-----------------YPGLESPDQAYPSMMALMPAGVKGLVFAALVAAIVSSLA 344 Query: 368 SMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIA-PMLGGIGQAFQY 426 SM NS +TIFTMDIY + P + V VGR +++++L+IA ++A P+LG QAFQY Sbjct: 345 SMTNSISTIFTMDIY-AMLRPAKSEGHYVLVGRLSSLISLLIALVMAQPLLGEFEQAFQY 403 Query: 427 IQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYT 486 IQE+TG+ +PGI+ +FL G+FW++ TS+GA+ + S F+ L+F +PFMD++ Sbjct: 404 IQEFTGVFTPGIVVIFLTGMFWRRATSQGALAAALGSAIFSFGLRFYWPELPFMDRIGLV 463 Query: 487 LLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543 L + + SL + ++ +++ F T R+FN++A G++++L LY +W Sbjct: 464 FLLCLALSVLVSL-MGRSLEEGASVALGGVSFKTGRAFNVSALGVVVILNFLYVTWW 519 Lambda K H 0.326 0.141 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 970 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 543 Length of database: 519 Length adjustment: 35 Effective length of query: 508 Effective length of database: 484 Effective search space: 245872 Effective search space used: 245872 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory