Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_002117405.1:WP_085770502.1 Length = 293 Score = 141 bits (356), Expect = 1e-38 Identities = 83/249 (33%), Positives = 133/249 (53%), Gaps = 5/249 (2%) Query: 4 LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63 L + N+ FGG+QALS+++ SV + +IIGPNGAGKS+L+N + G PD G + D Sbjct: 35 LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94 Query: 64 GKSVLGRAPYE-INQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 K+ R P E + +G++R FQ +F LSV +N+ + + + + Sbjct: 95 -KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRAR 153 Query: 123 RDILEK---AEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179 D L E ML + + R+ A ++ G ++R+E+ L+ PRLLLLDEP AGM Sbjct: 154 ADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGM 213 Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGN 239 + + ++ + +I +IEHD+ VV L+DR+ VL G + + P ++ + Sbjct: 214 TAGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMND 273 Query: 240 PKVREAYLG 248 V +AYLG Sbjct: 274 EAVIDAYLG 282 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: 175 Number of extensions: 5 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: 251 Length of database: 293 Length adjustment: 25 Effective length of query: 226 Effective length of database: 268 Effective search space: 60568 Effective search space used: 60568 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 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