Align D-lactate transporter, ATP-binding component (characterized)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Korea:Ga0059261_2703 Length = 313 Score = 95.9 bits (237), Expect = 9e-25 Identities = 69/230 (30%), Positives = 119/230 (51%), Gaps = 22/230 (9%) Query: 3 ILEVKNVGKRFG-GLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVM 61 IL V+ V K + G +AL V+L + + + A++GPNGAGK+TL++ + G + P +G+++ Sbjct: 4 ILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTIV 63 Query: 62 FDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSG 121 DG + ++G+ + ++F + +++R F A A Sbjct: 64 VDGHDAISEPRAARMKIGLVPQELSVDMFETVQATTR-----YSRR--LFGRPANDAYID 116 Query: 122 QRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMAR 181 Q +L+++++ DKR+ +S G KRR+ I L+ EP +L LDEPTAG+ Sbjct: 117 Q---------VLKDLSLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGV-- 165 Query: 182 ADTNNTIDLLKQIKS--ERDITIAIIEHDMHVVFSLADRITVLAQGTPLV 229 D + D+ K I S ER TI + H + +ADR+ V+ +G L+ Sbjct: 166 -DVSLRRDMWKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGELLL 214 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: 180 Number of extensions: 10 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: 313 Length adjustment: 26 Effective length of query: 225 Effective length of database: 287 Effective search space: 64575 Effective search space used: 64575 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