Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= SwissProt::Q921A2 (637 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 176 bits (446), Expect = 2e-48 Identities = 125/365 (34%), Positives = 183/365 (50%), Gaps = 25/365 (6%) Query: 45 AASLQGAELERAARRQFQRDETPAFVYAAAAFSALGGFLFGYDTGVVSGAMLLLRRQMRL 104 +AS GA E A T A + +AA +ALGG LFG+DT V+SGA L+ Q L Sbjct: 5 SASFAGAPDEEARA-------TVAIILSAAG-AALGGLLFGFDTAVISGATQALQLQFGL 56 Query: 105 GAMWQELLVSGAVGAAAVAALAGGALNGALGRRSAILLASALCTVGSAVLAAAANKETLL 164 V+ A+ + +L GA GR+ +L + V S A + L Sbjct: 57 TDAMLGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFL 116 Query: 165 AGRLVVGLGIGIASMTVPVYIAEVSPPNLRGRLVTINTLFITGGQFFA----SVVDGAFS 220 R + GL IG AS+ P+YIAEVSP RGRLV +N L I G A ++ G Sbjct: 117 VFRFMGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQ 176 Query: 221 YLQKDGWRYMLGLAAIPAVIQFLGFLFLPESPRWLIQKGQTQKARRILSQMRGNQTIDEE 280 Y WR+M G+ A+P+ I L L LPESPRWL GQ +AR ++ ++ D Sbjct: 177 Y--DVAWRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRL---GFADPR 231 Query: 281 YDSIRNSIEEEEKEASAAGPIICRMLSYPPTRRALAVGCGLQMFQQLSGINTIMYYSATI 340 + R + E +EA A P + + + P A+A+ MF QLSGIN ++YY+ I Sbjct: 232 AELARIELAEAREEA-AGKPRLFQRSHFTPVACAIAIA----MFNQLSGINALLYYAPRI 286 Query: 341 LQMSGVEDDRLAIWLASITAFTNFIFTLVGVWLVEKVGRRKLTFGSLAGTTVALTILALG 400 +++G D A+ + TN +FT+ ++L+++ GRR L F + A T+L +G Sbjct: 287 FELAGAGADS-ALLQSIAVGGTNLVFTVAALFLIDRFGRRPLLF--VGSVICAATLLLVG 343 Query: 401 FLLSA 405 + L + Sbjct: 344 WQLES 348 Score = 43.9 bits (102), Expect = 2e-08 Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 1/96 (1%) Query: 499 LVGLVLYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSAGINWIFNVLVSLTFLHTAEY 558 L GL+ ++ FA G + W SE++P R G A + +W+ ++ F A Sbjct: 357 LFGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAAS 416 Query: 559 LTYYGAFFLYAGFAAVGLLFVYGCLPETKGKKLEEI 594 + + F + + LL+ + +PET G LE++ Sbjct: 417 VGGW-VFAFFGAMMLLQLLWTWKFMPETNGIALEDM 451 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: 568 Number of extensions: 26 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: 637 Length of database: 458 Length adjustment: 35 Effective length of query: 602 Effective length of database: 423 Effective search space: 254646 Effective search space used: 254646 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