Align D-lactate transporter, ATP-binding component (characterized)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Pedo557:CA265_RS16020 Length = 250 Score = 117 bits (294), Expect = 2e-31 Identities = 72/237 (30%), Positives = 120/237 (50%), Gaps = 15/237 (6%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ++E+K++ K F G L ++ E + IIG +G+GK+TLL C+VG PD+GSV++ Sbjct: 1 MIEIKDIYKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGSVLY 60 Query: 63 DGKSVLGRAPYEIN---QMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV 119 DG+ YE + I +FQ +F ++V EN+M P D Sbjct: 61 DGRDFTPMT-YEQRIEVRKEIGMLFQGSALFDSMTVEENIMFPLNMFTD----------- 108 Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179 +++ LE+ + LE +N+A K + A +S G K+R+ I +S P+ L DEP +G+ Sbjct: 109 QSRKEKLERVDFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNSGL 168 Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNI 236 + +L+++I E T ++ HDM+ V + D I L +G E + I Sbjct: 169 DPKTSIVIDELIQEITEEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEGSNKEI 225 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: 159 Number of extensions: 3 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: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 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