Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_000021745.1:WP_012589117.1 Length = 265 Score = 157 bits (396), Expect = 3e-43 Identities = 87/250 (34%), Positives = 147/250 (58%), Gaps = 6/250 (2%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +L +K + R+GGL A+ D++L V E + A+IGPNGAGK++L N + G D G + Sbjct: 6 LLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDDGEIWL 65 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV--- 119 G + +P + + G++R FQ +F + + +EN+++ G+ + ++ Sbjct: 66 GGARIDRLSPSQRARRGLARTFQNLRLFTETTAIENVLVGMHLHVGGSL-LEILTRFGRF 124 Query: 120 -SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG 178 +R ++ A +L + ++ + A S+S GD+RRLEI L+ +P+LLLLDEP AG Sbjct: 125 RQAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARALAAKPKLLLLDEPAAG 184 Query: 179 MARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKG 238 M A+T LL+++++++ I++ ++EHDM +V L D+ITVL G + E P ++ Sbjct: 185 MNPAETAALRLLLEKLRAQK-ISMLLVEHDMSLVMRLCDKITVLNFGRKIAEGPPDAVRA 243 Query: 239 NPKVREAYLG 248 NP V EAYLG Sbjct: 244 NPAVIEAYLG 253 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: 155 Number of extensions: 7 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: 265 Length adjustment: 24 Effective length of query: 227 Effective length of database: 241 Effective search space: 54707 Effective search space used: 54707 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 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