Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= SwissProt::Q96QE2 (648 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 171 bits (432), Expect = 9e-47 Identities = 120/360 (33%), Positives = 183/360 (50%), Gaps = 33/360 (9%) Query: 80 FVYVVAVFSALGGFLFGYDTGVVSGAMLLLKRQLSL--DALWQELLVSSTVGAAAVSALA 137 FVY + + SA+GG LFGYD V+ GA + + Q L +S + + A+ Sbjct: 8 FVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTMQGLAMSVALLGCLIGAMV 67 Query: 138 GGALNGVFGRRAAILLASALFTAGSAVLAAANNKETLLAGRLVVGLGIGIASMTVPVYIA 197 G + +GR+ +L+++ +F + + A + LA R + G+GIGIAS P+YIA Sbjct: 68 AGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASGLSPMYIA 127 Query: 198 EVSPPNLRGRLVTINTLFITGGQFFASV---------------VDGAFSYLQKDGWRYML 242 EV+P ++RG+LV++N L I G A + D S+ + GWR+M Sbjct: 128 EVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQMGWRWMF 187 Query: 243 GLAAVPAVIQFFGFLFLPESPRWLIQKGQTQKARRILSQMRGNQTIDEEYDSIKNNIEEE 302 AA PA + F+PESPRWL KG+ +KA +LS++ GN+ ++E + E+ Sbjct: 188 WGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMV-----EQ 242 Query: 303 EKEVGSAGPVICRMLSYPPTRRALIVGCGLQMFQQLSGINTIMYYSATILQMSGVEDDRL 362 S G + ++L P R+ L++G + +FQQ G N I Y+ I Q +G + Sbjct: 243 TSASKSEGGL--KLLFSRPFRKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLGDV 300 Query: 363 AIWLASVTAFTNFIFTLVGVWLVEKVGRRKLTF---GSLAGTTVALIILALGFVLSAQVS 419 ++ VT N IFT V ++ VE++GRR L G LAG I L LG QVS Sbjct: 301 -LFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAG-----IYLVLGTCYFFQVS 354 Score = 63.2 bits (152), Expect = 3e-14 Identities = 31/94 (32%), Positives = 49/94 (52%) Query: 513 LILYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSSGINWIFNVLVSLTFLHTAEYLTY 572 ++L + +A +GP+ W + +EI+P R A + W+ + ++ TF L Sbjct: 362 VVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFPLLNTALGS 421 Query: 573 YGAFFLYAGFAAVGLLFIYGCLPETKGKKLEEIE 606 YG F++Y+ G LF LPETKGK LE +E Sbjct: 422 YGTFWIYSAICVFGFLFFLRALPETKGKSLETLE 455 Lambda K H 0.321 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: 697 Number of extensions: 32 Number of successful extensions: 6 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: 648 Length of database: 460 Length adjustment: 35 Effective length of query: 613 Effective length of database: 425 Effective search space: 260525 Effective search space used: 260525 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: 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