Align glucose transporter, ATPase component (characterized)
to candidate WP_083854810.1 C792_RS0100870 ATP-binding cassette domain-containing protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_000330705.1:WP_083854810.1 Length = 261 Score = 115 bits (288), Expect = 9e-31 Identities = 74/238 (31%), Positives = 133/238 (55%), Gaps = 21/238 (8%) Query: 11 GATPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQ 66 G L+++K + SF G KAVD +++ + E+ G++G +GAGKSTL++ ++ Sbjct: 13 GGCGLIDIKAATKSFAGKNGDFKAVDSITLSIQNKEIFGIIGESGAGKSTLMRFINALET 72 Query: 67 MDAGEIRVNGDKVEITNPRDARSH--NIETIYQTLALADNLDAASNLFLGREL---VTPF 121 D+G++ V+G V +D R H +I I+Q L N N+ L L TP Sbjct: 73 PDSGQVIVDGTDVVTLGKKDLRKHQKDISMIFQHFNLLGNKTVEDNIRLPLTLHKYKTPL 132 Query: 122 GLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPT 181 VD+ ++ + + ++ S P + LSGGQ+Q V IARA+ KIL+ DEPT Sbjct: 133 S-VDE---------VIEFVGLDDKRDSYP-AELSGGQKQRVGIARALVTRPKILLCDEPT 181 Query: 182 AALGPHETQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDID 238 +AL + T + +++ + + + + + ++ H++ + +LC RA+VM+ G+L+ T+D++ Sbjct: 182 SALDENTTDEIVDVLGRAQEEFDMTVVIVTHELGVIKQLCRRAAVMERGRLIDTIDVN 239 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: 176 Number of extensions: 13 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: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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 Sep 24 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