Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= SwissProt::Q921A2 (637 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 147 bits (372), Expect = 8e-40 Identities = 113/373 (30%), Positives = 180/373 (48%), Gaps = 56/373 (15%) Query: 69 FVYAAAAFSALGGFLFGYDTGVVSGAMLLLRRQMRLGAMWQELLVSGAV--GAAAVAALA 126 ++Y+ + + LGG LFGYDT V+SGA L + +Q V + +A + + Sbjct: 12 YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVL 71 Query: 127 GGALNGA----LGRRSAILLA------SALCTVGSAVLA---AAANKETLLAG---RLVV 170 GGAL+G LGRR+++ LA SAL + VL N + L+A R++ Sbjct: 72 GGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLIAFNLYRVLG 131 Query: 171 GLGIGIASMTVPVYIAEVSPPNLRGRLVTINTLFITGGQFFASVVD-------------- 216 G+G+G+AS P+YIAE++P N+RG LV+ N I G V+ Sbjct: 132 GIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIILK 191 Query: 217 ---GAFS-------YLQKDGWRYMLGLAAIPAVIQFLGFLFLPESPRWLIQKGQTQKARR 266 G S + ++GWRYM G A PA L F+P++PR+L+ Q +KA Sbjct: 192 DAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAYT 251 Query: 267 ILSQMRGNQTIDEEYDSIRNSIEEEEKEASAAGPIICRMLSYPPTRRALAVGCGLQMFQQ 326 IL ++ G + E + I+ + +E+ + ++ +Y T + +G L +FQQ Sbjct: 252 ILEKINGKKKAQEILNDIKATAQEKTE----------KLFTYGVT--VIVIGILLSVFQQ 299 Query: 327 LSGINTIMYYSATILQMSGVEDDRLAIWLASITAFTNFIFTLVGVWLVEKVGRRKLTFGS 386 GIN ++YY+ I + +G E + I N IFTLV ++ V++ GR+ L Sbjct: 300 AIGINAVLYYAPRIFENAGAEGG--GMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIG 357 Query: 387 LAGTTVALTILAL 399 G V +A+ Sbjct: 358 SIGMAVGAFAVAM 370 Score = 67.8 bits (164), Expect = 1e-15 Identities = 34/100 (34%), Positives = 54/100 (54%), Gaps = 1/100 (1%) Query: 499 LVGLVLYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSAGINWIFNVLVSLTFLHTAEY 558 ++ +++Y FF GP+ W + SEI+P R A + WIFN +VS TF ++ Sbjct: 382 VLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDF 441 Query: 559 LTYYGAFFLYAGFAAVGLLFVYGCLPETKGKKLEEIESLF 598 + A+ LY +FV+ +PETKGK LE++ L+ Sbjct: 442 SPMF-AYSLYGIICVAAAIFVWRWVPETKGKTLEDMSKLW 480 Lambda K H 0.322 0.136 0.410 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: 594 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 637 Length of database: 484 Length adjustment: 36 Effective length of query: 601 Effective length of database: 448 Effective search space: 269248 Effective search space used: 269248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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