Align D-lactate transporter, ATP-binding component (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 123 bits (309), Expect = 6e-33 Identities = 69/223 (30%), Positives = 121/223 (54%), Gaps = 10/223 (4%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +LE+ + K F G++AL +VNL VR +++HA++G NGAGKSTLL CL G D+G+++F Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 GK + + E + GIS V Q + SV++NM + + + G F Q Sbjct: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMF--------VDQ 123 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 + + + + +E+++ ++S + +EI S +++++DEPT+ + Sbjct: 124 DKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183 Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225 + N+ +++++K ER I I H M +F L D +TVL G Sbjct: 184 EVNHLFTIIRKLK-ERGCGIVYISHKMEEIFQLCDEVTVLRDG 225 Score = 54.3 bits (129), Expect = 5e-12 Identities = 51/227 (22%), Positives = 101/227 (44%), Gaps = 13/227 (5%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ILEV+N+ ++ DV+ + + + I G GA ++ ++ L G G++ Sbjct: 265 ILEVRNLTSL--RQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITL 322 Query: 63 DGKSVLGRAPYEINQMGISRVFQ---TPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV 119 GK + E G + V + + I+ L + N +I N + + Sbjct: 323 HGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK-----NKVGLL 377 Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNA-ASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG 178 R + + +++ M + H S+S G+++++ IG L +P +L+LDEPT G Sbjct: 378 DNSR-MKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRG 436 Query: 179 MARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225 + L+ ++ +++ I II +M + + DRI V++ G Sbjct: 437 IDVGAKFEIYQLIAEL-AKKGKGIIIISSEMPELLGITDRILVMSNG 482 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: 271 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 506 Length adjustment: 29 Effective length of query: 222 Effective length of database: 477 Effective search space: 105894 Effective search space used: 105894 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: 49 (23.5 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