Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_011939016.1 GURA_RS10785 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_000016745.1:WP_011939016.1 Length = 250 Score = 170 bits (431), Expect = 2e-47 Identities = 98/251 (39%), Positives = 147/251 (58%), Gaps = 6/251 (2%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +L V+ + +RFGG+ AL DV+ S+ ++ + IIGPNGAGK+TL N + G P +GSV+ Sbjct: 1 MLSVRQITQRFGGITALEDVSFSIGKDLITGIIGPNGAGKTTLFNIVTGIYTPTSGSVLL 60 Query: 63 DGKSVLGRAPYEIN-QMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISA--- 118 K + R P E +G+ R FQ E+FG ++VLEN+M+ +K F A Sbjct: 61 GDKDI-SRLPSEKRAYLGMVRTFQNIELFGKMTVLENVMVGLHSKSSSGFLACAFKMPWH 119 Query: 119 VSGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG 178 + +R I + A LE +AD AA++ G R LEI L+ EP++LL+DEP AG Sbjct: 120 LREERRIRDNAMRWLEFTGIADLAQQEAANLPFGKGRLLEIARALALEPKILLMDEPAAG 179 Query: 179 MARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKG 238 + +T+ L+++I+ E +T+ ++EHDM +V + D I VL G L E P+ I+ Sbjct: 180 LNSKETHELSLLIRKIR-EMGVTVVLVEHDMELVMDICDSIVVLNLGRKLAEGTPREIQE 238 Query: 239 NPKVREAYLGE 249 NP+V AYLGE Sbjct: 239 NPEVVAAYLGE 249 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: 178 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: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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