Align D-lactate transporter, ATP-binding component (characterized)
to candidate GFF3453 PS417_17675 ABC transporter
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__WCS417:GFF3453 Length = 249 Score = 184 bits (468), Expect = 1e-51 Identities = 99/251 (39%), Positives = 158/251 (62%), Gaps = 7/251 (2%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +LE K++ +G A++ VNL V T+H IIGPNGAGK++L +CL G+ G++ F Sbjct: 4 LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAIHF 63 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 DGK+++ + + +G++R FQ +F +LSV EN+ + RDGA +N V + Sbjct: 64 DGKNLMRKPAHGRVGLGMARSFQLTSLFQNLSVRENLRLAA-QGRDGARALNFWRRVDSK 122 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 R+ LE A+ +LE + + + A +S G +R LE+GM + +P+LL+LDEPT+GM Sbjct: 123 REHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLLMLDEPTSGMGID 182 Query: 183 DTNNTIDLLKQIKSE--RDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNP 240 D I ++ Q+ S+ RD T+ +IEH+M +V S++ RITV++ G LVE P+ ++ + Sbjct: 183 D----IPIMTQLISDLGRDHTVLLIEHNMSIVMSISQRITVMSHGQILVEGTPEFVRADE 238 Query: 241 KVREAYLGESA 251 +VR AYLGE+A Sbjct: 239 RVRTAYLGEAA 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: 176 Number of extensions: 10 Number of successful extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 227 Effective length of database: 225 Effective search space: 51075 Effective search space used: 51075 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 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