Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 17739 b3679 predicted transporter (NCBI)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Keio:17739 Length = 571 Score = 225 bits (573), Expect = 4e-63 Identities = 159/549 (28%), Positives = 272/549 (49%), Gaps = 47/549 (8%) Query: 8 LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67 ++ + I+ F + ++ + W R K S + YFLAG+SL + ASL+ N+S Sbjct: 1 MNSLQILSFVGFTLLVAVITWWKVR--KTDTGSQQGYFLAGRSLKAPVIAASLMLTNLST 58 Query: 68 EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127 EQ +G+SG Y G+++ +E SA+TLI + FLP ++++GI TIP+F+E+R++K + Sbjct: 59 EQLVGLSGQAYKSGMSVMGWEVTSAVTLIFLALIFLPRYLKRGIATIPDFLEERYDKTTR 118 Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETIL----------GIPLMYSILGLALFALVYS 177 I+ ++ L VLY G LAL ++ G + ++ L L ++Y+ Sbjct: 119 IIIDFCFLIATGVCFLPIVLYSGALALNSLFHVGESLQISHGAAIWLLVILLGLAGILYA 178 Query: 178 IYGGLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILD 237 + GGL A+ D I LV+GG M + + G + G+ ++ I Sbjct: 179 VIGGLRAMAVADSINGIGLVIGGLMVPVFGLIAM-GKGSFMQGIEQLTTVHAEKLNSIGG 237 Query: 238 QSNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIV 297 ++P LP I GL + N +YW NQ I+QRTLA+KS++E QKG + A LK++ Sbjct: 238 PTDP----LP-IGAAFTGLILVNTFYWCTNQGIVQRTLASKSLAEGQKGALLTAVLKMLD 292 Query: 298 PFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWL-TQFLPVGVKGVVFA 356 P ++VLPG+ A+ + D LP AD AYP L LPV + G A Sbjct: 293 PLVLVLPGLIAFHLYQD--------------LP---KADMAYPTLVNNVLPVPMVGFFGA 335 Query: 357 ALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPM 416 L A++S+ LNS +T+F+M IY+ I+ ++ +LV VGR I++ L+AP Sbjct: 336 VLFGAVISTFNGFLNSASTLFSMGIYRRIINQNAEPQQLVTVGRKFGFFIAIVSVLVAPW 395 Query: 417 LGGIGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPL 475 + Q + ++++ G+ + ++ + ++G F+ + + A + + I + + ++ Sbjct: 396 IANAPQGLYSWMKQLNGIYNVPLVTIIIMGFFFPRIPALAAKVAMGIGIISYITINYL-- 453 Query: 476 SMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVT-SSMFVTD----RSFNIAAYG 530 + F LY L T + L I P+ T F D ++ IA+ G Sbjct: 454 -VKFDFHFLYVLACTFCINVVVML--VIGFIKPRATPFTFKDAFAVDMKPWKNVKIASIG 510 Query: 531 IMIVLAVLY 539 I+ + +Y Sbjct: 511 ILFAMIGVY 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: 857 Number of extensions: 60 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: 571 Length adjustment: 36 Effective length of query: 507 Effective length of database: 535 Effective search space: 271245 Effective search space used: 271245 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