Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 5210844 Shew_3270 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__PV4:5210844 Length = 474 Score = 222 bits (565), Expect = 3e-62 Identities = 147/486 (30%), Positives = 250/486 (51%), Gaps = 41/486 (8%) Query: 11 IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70 I + +F ++ + R + DYFLAG L W V SL+ NISAEQ Sbjct: 5 IQVAIFVALTTLVALITYLKCRKVTRDANDSRDYFLAGGGLSWIVVAGSLMMTNISAEQI 64 Query: 71 IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKK-LKTI 129 +GM+G+ L +A +E +AI LII+ K+ +PI+ T E +E+++ K ++ + Sbjct: 65 VGMNGAQT---LLVAWWEIAAAIGLIILAKWLIPIYYRYNCTTTTELLERKYQDKGIRAM 121 Query: 130 LAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGL--ALFALVYSIYGGLSAVVW 187 +++ ++ Y F+ L VLY G L ++++ G+ + ++L + A+ +Y+I+GGL A+ Sbjct: 122 VSLLFMLGYAFILLPVVLYTGSLFMKSMFGLSISVTVLAIIFAVVGAIYAIFGGLRAIAI 181 Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLP 247 +D + L+L G +Y+A+ + D +G+ +I D + ++P Sbjct: 182 SDTLNGLGLILMGLAVSYLAMHAV---DWDLSGIPLE------RLTLIGDSQS----DIP 228 Query: 248 GIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIA 307 +L G +++ ++YWG N I QR LAAKSV EAQKG+ A +KLI+P +VVLPGI Sbjct: 229 WSTLLTGMIFI-QIFYWGTNMVITQRALAAKSVKEAQKGLYAAVVMKLIIPVIVVLPGIV 287 Query: 308 AYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLA 367 A+ +L +GD+A L + LP + G A +A A++SS Sbjct: 288 AF------KLYGDVGDVAYGKL------------VGDLLPSWLSGAFAAVIAGAVLSSFN 329 Query: 368 SMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAFQYI 427 S LNS A ++T DI++ YI+ D+ K +G A++ +I+ + P+ + Sbjct: 330 SCLNSAAALYTCDIHQNYINADADVRK---IGSRVALLFTLISVALVPLFARSESIIALL 386 Query: 428 QEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYTL 487 Q+ GL S +LA F+ L +K ++K G+V + F+ + F+ M TL Sbjct: 387 QQLNGLYSMPVLAAFICALVFKNVSAKAIKWGLVFGVLLYALFTFIWSPLHFIHLMAITL 446 Query: 488 LFTMVV 493 L T++V Sbjct: 447 LATILV 452 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: 708 Number of extensions: 51 Number of successful extensions: 7 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: 474 Length adjustment: 34 Effective length of query: 509 Effective length of database: 440 Effective search space: 223960 Effective search space used: 223960 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