Align D-lactate transporter, ATP-binding component (characterized)
to candidate BWI76_RS05980 BWI76_RS05980 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Koxy:BWI76_RS05980 Length = 260 Score = 159 bits (403), Expect = 4e-44 Identities = 91/254 (35%), Positives = 143/254 (56%), Gaps = 11/254 (4%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ILEV++V +FGGL+A+ V+ V E + +IGPNGAGK+T+ N + P +GSV Sbjct: 7 ILEVQDVTMQFGGLRAIDSVSFHVDEAEIFGLIGPNGAGKTTMFNVITANYKPTSGSVTL 66 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV--- 119 GKS+ G P + GI+R FQ +F ++VLEN+M+ D A + + A Sbjct: 67 AGKSLKGLKPNRVVNAGIARTFQNIRLFNSMTVLENVMVGL----DSASRYSLLEAALHI 122 Query: 120 ----SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEP 175 +R KA +L+++ +A + A ++S G++R++EI L+ P+LLLLDEP Sbjct: 123 GRYFPAERAAKAKAMAILDDIGIAHFADVQATNLSYGNQRKVEIARALATSPKLLLLDEP 182 Query: 176 TAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQN 235 AGM +T DL+ +++++ +++ +IEHDM V L +R+ VL G PL Sbjct: 183 AAGMNPKETEELADLIFRMRNDYRLSVLLIEHDMPFVNKLCERVMVLEYGKPLFSGLMSE 242 Query: 236 IKGNPKVREAYLGE 249 +P V AYLG+ Sbjct: 243 AIQDPDVISAYLGD 256 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: 166 Number of extensions: 4 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: 260 Length adjustment: 24 Effective length of query: 227 Effective length of database: 236 Effective search space: 53572 Effective search space used: 53572 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