Align D-lactate transporter, ATP-binding component (characterized)
to candidate Dsui_2058 Dsui_2058 ABC-type branched-chain amino acid transport systems, ATPase component
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__PS:Dsui_2058 Length = 260 Score = 180 bits (456), Expect = 3e-50 Identities = 96/250 (38%), Positives = 149/250 (59%), Gaps = 4/250 (1%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +L ++NVGK FGGL L DV+ V +++ +IGPNGAGK+T+ N + G L P G + F Sbjct: 9 LLSIRNVGKHFGGLHVLQDVSFEVPAGSIYGLIGPNGAGKTTVFNLITGLLTPSAGQIDF 68 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRD-GAFE--MNAISAV 119 G++++G P+ I GI+R FQ IF ++ +LEN+M+ + G F +N+ + Sbjct: 69 QGQTLIGLEPHRITHQGIARTFQNIRIFKEMDLLENVMVGMHDHLNYGGFGIFLNSPACR 128 Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179 + ++ E+A +L + + K M A ++S GD+R+LE L+ EP+LLLLDEP AGM Sbjct: 129 AAEKKARERALELLSWVGLDHKADMLADNLSYGDQRKLEFARALATEPKLLLLDEPVAGM 188 Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGN 239 ++ ++ + I++ R + +IEHDM V L DRI VL G + E P ++ N Sbjct: 189 NPSEKTILMEEINNIRN-RGYGVFMIEHDMRFVMGLCDRIAVLNFGRIIAEGTPDEVRNN 247 Query: 240 PKVREAYLGE 249 P V EAYLG+ Sbjct: 248 PDVIEAYLGK 257 Lambda K H 0.318 0.135 0.379 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: 212 Number of extensions: 12 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: 251 Length of database: 260 Length adjustment: 24 Effective length of query: 227 Effective length of database: 236 Effective search space: 53572 Effective search space used: 53572 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