Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 5209419 Shew_1890 glucose/galactose transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__PV4:5209419 Length = 421 Score = 415 bits (1066), Expect = e-120 Identities = 221/415 (53%), Positives = 289/415 (69%), Gaps = 17/415 (4%) Query: 1 MAFVSSTTPQNGSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQA 60 MA + ++ G ++++ L ++TSLFF+WGFIT LNDILIPHLK F L+Y +A Sbjct: 1 MAMMQQSSTATGVGGEQENYRFALV-SLTSLFFMWGFITCLNDILIPHLKAAFSLNYAEA 59 Query: 61 MLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLA 120 ML+QFCFFGAYFLVS AG L+ +GY +GI+ GL A GC LFYPA++L Y LFL A Sbjct: 60 MLIQFCFFGAYFLVSMPAGKLVKALGYQKGIVTGLLIAALGCALFYPAAALATYGLFLGA 119 Query: 121 LFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAG 180 LFVLASGITILQV+ANP+V LG TA+SRLNL QA N+LG T+ P FG++LI A Sbjct: 120 LFVLASGITILQVAANPYVNALGSVETASSRLNLTQAFNALGTTVAPYFGAVLILSVAVE 179 Query: 181 THEA----------VQLPYLLLAAVIGIIAVGFIFLG-GKVK-HADMG----VDHRHKGS 224 E V+LPYL+LA +G++A+ F L ++K H G V H K S Sbjct: 180 ASETLTQAQAEAEVVKLPYLILATALGVLALVFAKLDLPQIKEHCQSGEQGEVVHNGKTS 239 Query: 225 LLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGR 284 L L+LGA+ IF+YVGAEVSIGSFLVN+ A+ I GL E SAA +++YWGGAM+GR Sbjct: 240 ALQSLHLVLGAVGIFVYVGAEVSIGSFLVNFLAQDDIAGLSEASAASYITYYWGGAMVGR 299 Query: 285 FAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLA 344 F G+A+ ++ VL NA+ A LL+ L + S+G +A+ A+LAVG FNSIMFPTIF+LA Sbjct: 300 FIGSAVMQKVPAGTVLGFNALMAALLVALAMTSTGTVAMWAILAVGLFNSIMFPTIFSLA 359 Query: 345 IEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWY 399 + LG TS+GSG+LC AIVGGA+LP++QGV+ADN+G+Q +F +P CY +I +Y Sbjct: 360 LRDLGPHTSQGSGVLCLAIVGGAILPLLQGVLADNIGIQHAFFLPIICYLFIMFY 414 Lambda K H 0.329 0.142 0.425 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: 506 Number of extensions: 22 Number of successful extensions: 2 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: 413 Length of database: 421 Length adjustment: 31 Effective length of query: 382 Effective length of database: 390 Effective search space: 148980 Effective search space used: 148980 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 (21.8 bits) S2: 50 (23.9 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