Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 349883 BT0355 Na+/glucose cotransporter (NCBI ptt file)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Btheta:349883 Length = 564 Score = 296 bits (757), Expect = 2e-84 Identities = 172/522 (32%), Positives = 296/522 (56%), Gaps = 43/522 (8%) Query: 11 IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70 +D +V ++ +IG+ +WV R K Q + DYFL G+ W A+GAS+ A+NI +E Sbjct: 4 LDWLVIGVFFLALIGIIVWVVRQK---QNDSADYFLGGRDATWLAIGASIFASNIGSEHL 60 Query: 71 IGMSGSGYSIGLAIASYE---WMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127 IG++G+G S G+A+A +E WM ++I+G F+P + +YT+PEF+E+R+N + + Sbjct: 61 IGLAGAGASSGMAMAHWEIQGWM----ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSR 116 Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSI-------LGLALFALVYSIYG 180 TIL+V + Y+ + +Y GGL + + GI ++ I +GL + +Y+I+G Sbjct: 117 TILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFG 176 Query: 181 GLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSN 240 G+ +V++T V+Q L+LG + + +GG D + G L +SN Sbjct: 177 GMKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSN 236 Query: 241 PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFL 300 N P + LIG + +YW +Q+I+QR L+ K+ EA++G +F A+LKL+ FL Sbjct: 237 DD-ANFPWLGALIGSA-IIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFL 294 Query: 301 VVLPGIAAYVITSDPQLMASLGDIAATNLPS-AANADKAYPWL-TQFLPVGVKGVVFAAL 358 ++PG+ A+ + + + + G+ L + ANAD A+P L + LP GVKG+V + Sbjct: 295 FLIPGMIAFAL--HQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGI 352 Query: 359 AAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLG 418 AA++SSLAS+ NS+A +FT+D YK + P++ + KLV +G+ A VV +I+ L P++ Sbjct: 353 LAALMSSLASLFNSSAMLFTIDFYKRF-RPETPEKKLVGIGQIATVVIVILGILWIPIMR 411 Query: 419 GIGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFAL--------- 468 +G + Y+Q+ +++PGI A FLLG+ WK+T+++G + G++A + L Sbjct: 412 SVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYY 471 Query: 469 ---------FLKFMPLSMPFMDQMLYTLLFTMVVIAFTSLST 501 K++ M ++ + LF ++V+ SL+T Sbjct: 472 SNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLAT 513 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: 973 Number of extensions: 61 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: 564 Length adjustment: 36 Effective length of query: 507 Effective length of database: 528 Effective search space: 267696 Effective search space used: 267696 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: 53 (25.0 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