Align D-lactate transporter, ATP-binding component (characterized)
to candidate CCNA_03714 CCNA_03714 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Caulo:CCNA_03714 Length = 252 Score = 130 bits (327), Expect = 3e-35 Identities = 81/250 (32%), Positives = 130/250 (52%), Gaps = 19/250 (7%) Query: 4 LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63 L V +VGK FG + +V+L ++ V ++GPNGAGK+T + G + D G++ D Sbjct: 11 LFVDSVGKSFGDRPVVKNVSLRLKRGEVAGLLGPNGAGKTTCFYMVTGLIAADYGAIYLD 70 Query: 64 GKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQR 123 G+++ + ++ ++G+ + Q IF ++V +N+M EM R Sbjct: 71 GENITAQPMFQRARLGVGYLPQEASIFRGMTVEQNVM--------AVVEMRE----RDPR 118 Query: 124 DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG---MA 180 E+ +LEE+ + R A ++S G++RR+EI L+ EP +LLDEP AG +A Sbjct: 119 KAREQVTSILEELRITHIRKSPAVALSGGERRRVEIARALASEPSFMLLDEPFAGIDPLA 178 Query: 181 RADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNP 240 AD I LK R I I I +H++ + DR +++ G L E P+ I NP Sbjct: 179 IADIREVIGYLK----GRGIGILITDHNVRETLDIIDRASIIHAGEVLFEGSPREIVENP 234 Query: 241 KVREAYLGES 250 +V+ YLGES Sbjct: 235 EVKRVYLGES 244 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: 171 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: 251 Length of database: 252 Length adjustment: 24 Effective length of query: 227 Effective length of database: 228 Effective search space: 51756 Effective search space used: 51756 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