Align glucose transporter, ATPase component (characterized)
to candidate GFF1119 HP15_1097 branched-chain amino acid ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Marino:GFF1119 Length = 255 Score = 115 bits (289), Expect = 7e-31 Identities = 83/261 (31%), Positives = 138/261 (52%), Gaps = 26/261 (9%) Query: 15 LVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74 ++E + +S +GGIKA+D +S+ + G++G NGAGKSTL+ +L G + +G I Sbjct: 6 ILETESLSKHWGGIKALDDISLQFQDKHLHGVVGPNGAGKSTLLNMLCGTLKPTSGCIFH 65 Query: 75 NGDKVEITNPRD------ARSHNIETIYQTLALADNLDAAS--------NLFLGRELVTP 120 GD++E P + RS IY + +N A+ NLF R Sbjct: 66 KGDQIEGMKPWEFVHRGIGRSFQKTNIYVDVTCLENCAIAAQRRFTGSFNLFASRH---S 122 Query: 121 FGLVDDSAMEAECR-KIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDE 179 LV + A +A C+ + NR++ + +S G+++ + +A + + IL++DE Sbjct: 123 NKLVREGAEKALCQVGLENRVH-------TVAAEISYGEQRQLELAMVLATDPCILLLDE 175 Query: 180 PTAALGPHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDD 239 P A +G E+Q + EL+ QLK Q I L++HD++A+ EL D+ +V+ NG + T +D+ Sbjct: 176 PMAGMGHEESQRIIELMNQLK-QTYSIVLVEHDMDAIFELSDQLTVLDNGTHLITGTVDE 234 Query: 240 VTDDDLLSMIILGKRPGEAAA 260 V +D + LGK E AA Sbjct: 235 VRNDTRVKEAYLGKEKEEEAA 255 Lambda K H 0.317 0.135 0.373 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: 127 Number of extensions: 9 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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