Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 182 bits (461), Expect = 2e-50 Identities = 107/293 (36%), Positives = 172/293 (58%), Gaps = 12/293 (4%) Query: 23 ALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNI 82 A+ + + + G +GPSGCGK+T+L +++GL G ++ DGRD+T +R++ Sbjct: 18 AIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLDGRDITDQPSSKRDL 77 Query: 83 AQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAAD 142 A VFQ +Y M+V EN++F L+ KV + I ++V A +L ++ L + L+ Sbjct: 78 AMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNLTQYLQRTPKELSGG 137 Query: 143 AKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVE 202 +Q++++GR +VRA LFDEPL+ +D L+ Q R ++ ++H +L T IYVTHDQVE Sbjct: 138 QRQRVAIGRAIVRAP-KVFLFDEPLSNLDAALRGQTRVEIAKLHRDLGATTIYVTHDQVE 196 Query: 203 ALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGH 262 A+T AD+VVV+ G QVG+ L+++PA+ FV FIG+P MN +P D V Sbjct: 197 AMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNVVPV--DKLPQPVQQQ 254 Query: 263 RLASPVGRALPAGALQVGIRPEYLALAQPQQAGALP--GTVVQVQDIGTYQML 313 A+P G A+ A +G+RPE + + + GA P G V ++ +G ++ Sbjct: 255 APAAPAGAAVGA----IGLRPENITV---RTTGATPVGGQVDLIEALGAETLI 300 Lambda K H 0.320 0.136 0.395 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: 290 Number of extensions: 11 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: 358 Length of database: 350 Length adjustment: 29 Effective length of query: 329 Effective length of database: 321 Effective search space: 105609 Effective search space used: 105609 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