Align D-lactate transporter, ATP-binding component (characterized)
to candidate Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Korea:Ga0059261_2542 Length = 258 Score = 122 bits (305), Expect = 9e-33 Identities = 76/248 (30%), Positives = 128/248 (51%), Gaps = 17/248 (6%) Query: 4 LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63 L V ++ K + LSDV+LSV + V ++GPNGAGK+T ++G + PD G +M D Sbjct: 22 LAVVSIAKSYDKRVVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKPDAGRIMLD 81 Query: 64 GKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQR 123 G + Y +G+ + Q IF L+V +N ++A+ +S Sbjct: 82 GVDITPLPMYRRAILGLGYLPQETSIFRGLTVAKN--------------ISAVLELSEPD 127 Query: 124 DILEKA--EHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMAR 181 A + +LEE + R A ++S G++RR EI L+ +P ++LLDEP AG+ Sbjct: 128 KSARAARLDQLLEEFGLTRLRDAPAMALSGGERRRAEIARALAADPSIMLLDEPFAGIDP 187 Query: 182 ADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPK 241 + DL+K++K+ R+I + I +H++ + DR +++ G L P+++ + Sbjct: 188 ISIADIRDLVKELKT-RNIGVLITDHNVRETLDIVDRASIIYDGRVLFAGSPEDLVADAN 246 Query: 242 VREAYLGE 249 VR YLGE Sbjct: 247 VRRLYLGE 254 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: 165 Number of extensions: 8 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: 258 Length adjustment: 24 Effective length of query: 227 Effective length of database: 234 Effective search space: 53118 Effective search space used: 53118 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