Align glucose transporter, ATPase component (characterized)
to candidate WP_092481460.1 BM299_RS19625 dipeptide ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_900115975.1:WP_092481460.1 Length = 323 Score = 99.4 bits (246), Expect = 9e-26 Identities = 69/217 (31%), Positives = 106/217 (48%), Gaps = 6/217 (2%) Query: 28 IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRDA 87 +KAVD VS D++PGE +GL+G +G GKST +++ + AGE+ NG I + A Sbjct: 28 VKAVDGVSFDIHPGETLGLVGESGCGKSTTGRLILRLLEPTAGEVFFNGR--NIFDASAA 85 Query: 88 RSHNIETIYQTLALADNLDAASNLFLGRELVTP---FGLVDDSAMEAECRKIMNRLNPNF 144 N+ Q + + +G+ + P F L + +E R++++ + Sbjct: 86 EMRNLRREMQIIFQDPYASLNPRMTVGQIVAEPLRVFNLAAGAELEKRVRELLSCVGLAG 145 Query: 145 QKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLKAQ-G 203 SGGQRQ V IARA+ N K++I DEP +AL V L++ L+ + G Sbjct: 146 YHARRYPHEFSGGQRQRVGIARALATNPKLIICDEPVSALDVSIQSQVLNLLKDLQKEFG 205 Query: 204 IGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDV 240 I H +N V + DR VM GQLV D++ Sbjct: 206 FTYLFIAHGLNVVKHVSDRVGVMYLGQLVELAGDDEL 242 Lambda K H 0.317 0.135 0.373 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: 205 Number of extensions: 11 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: 260 Length of database: 323 Length adjustment: 26 Effective length of query: 234 Effective length of database: 297 Effective search space: 69498 Effective search space used: 69498 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: 48 (23.1 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