Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 348 bits (892), Expect = e-100 Identities = 184/345 (53%), Positives = 235/345 (68%), Gaps = 7/345 (2%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA +++ I KF+G +A+ I+L I+ GEF+VFVGPSGCGKSTLLR +AGLE + G + Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 + GRD+T + RDLAMVFQSYALYPHM+V ENM F +K+ + + E++ AAR+ Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 L L YL R P +LSGGQRQRVAIGRAIV+ P VFLFDEPLSNLDA LR Q RVE+ LH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 + LGAT IYVTHDQVEAMT+AD++VVL G IEQVG+P++LY KP ++FVA+FIG+P MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 VFSSDVGLQDISLDASAA-------FVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLL 293 V D Q + A AA +G RPE+I + G + V + E LG E+L+ Sbjct: 241 VVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETLI 300 Query: 294 YLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 Y+ GG Q V+R + +VG AVSL + H FD AGR + Sbjct: 301 YVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVV 345 Lambda K H 0.320 0.139 0.396 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: 388 Number of extensions: 15 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: 338 Length of database: 350 Length adjustment: 29 Effective length of query: 309 Effective length of database: 321 Effective search space: 99189 Effective search space used: 99189 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 (21.8 bits) S2: 49 (23.5 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