Align D-lactate transporter, ATP-binding component (characterized)
to candidate AO356_05335 AO356_05335 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05335 Length = 255 Score = 197 bits (501), Expect = 2e-55 Identities = 99/253 (39%), Positives = 162/253 (64%), Gaps = 7/253 (2%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 IL+V+N+ RFGGL A++ V L+V+E V A+IGPNGAGK+T+ NCL G P G+++ Sbjct: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRD-----GAFEMNAIS 117 DG+ + G + I + G+ R FQ +F D++ +EN++I + G F+ A Sbjct: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 Query: 118 AVSGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTA 177 +R+ +E AE+ L+++N+ + + A +++ G +RRLEI C+ PR+L+LDEP A Sbjct: 125 --KSEREAMEYAEYWLDKVNLTEFANRTAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 Query: 178 GMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIK 237 G+ +T + L+ ++ E ++T+ +IEHDM +V S++D I V+ QGTPL + P+ I+ Sbjct: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242 Query: 238 GNPKVREAYLGES 250 NP+V +AYLGE+ Sbjct: 243 DNPEVIKAYLGEA 255 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: 183 Number of extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 227 Effective length of database: 231 Effective search space: 52437 Effective search space used: 52437 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