Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate Ac3H11_793 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_793 Length = 298 Score = 129 bits (325), Expect = 6e-35 Identities = 84/268 (31%), Positives = 141/268 (52%), Gaps = 10/268 (3%) Query: 16 PAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTFFL 75 P +I +A I PL+ + S+ ++ R F+G E + V+ DE A+ R Sbjct: 18 PVIICVAFSAILPLMTVVNYSVQ--DIISPERRVFVGTEWFAAVMRDEELHAALWRQLTF 75 Query: 76 LGTALPLQIALGLGIALVLHQPGL--TLVKTLARLSLVLPMATTYAVVGLLGQVMFNQKF 133 L ++I LG+ +AL + G + V + LSL++P + VVG + Q+ Sbjct: 76 SLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIP----WNVVGTIWQIYGRADI 131 Query: 134 GVVNQLLG--GADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAARL 191 G++ ++L G + ++ G+ A+ ++ DVW WTP VAL+ AGL +P +AAR+ Sbjct: 132 GLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQAARI 191 Query: 192 ETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMIQR 251 + SK+ V RY+QLP + L+ ++LR D+ ++ F LT GGPG++T F+S + Sbjct: 192 DGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFLSQYLTT 251 Query: 252 VGFRGFDQGLASAQAIILLIITIVLAQI 279 FD G A+A ++I I ++L I Sbjct: 252 KAVGQFDLGPAAAFSLIYFFIILLLCFI 279 Lambda K H 0.329 0.144 0.440 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: 245 Number of extensions: 14 Number of successful extensions: 3 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: 288 Length of database: 298 Length adjustment: 26 Effective length of query: 262 Effective length of database: 272 Effective search space: 71264 Effective search space used: 71264 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: 48 (23.1 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