Align D-lactate transporter, ATP-binding component (characterized)
to candidate 5210884 Shew_3310 ABC transporter-related protein (RefSeq)
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__PV4:5210884 Length = 243 Score = 117 bits (292), Expect = 3e-31 Identities = 72/247 (29%), Positives = 129/247 (52%), Gaps = 12/247 (4%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 IL+ +N+ K + + DV+L+V+ + ++GPNGAGK+T +VG + D G + Sbjct: 5 ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRIFI 64 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 D + + + GI + Q IF LSV +N+M + D +N G+ Sbjct: 65 DDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQTRSD----LNN----DGR 116 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 E+ EH+LEE ++ R + ++S G++RR+EI L+ P+ +LLDEP AG+ Sbjct: 117 E---EELEHLLEEFHITHIRDSHGMALSGGERRRVEIARALAANPKFILLDEPFAGVDPI 173 Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKV 242 + +++Q+K+ R + + I +H++ + ++ +++ G + E P I N +V Sbjct: 174 SVIDIKKIIEQLKN-RGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDNQQV 232 Query: 243 REAYLGE 249 R YLGE Sbjct: 233 RAVYLGE 239 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: 152 Number of extensions: 14 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: 243 Length adjustment: 24 Effective length of query: 227 Effective length of database: 219 Effective search space: 49713 Effective search space used: 49713 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