Align glucose transporter, ATPase component (characterized)
to candidate Ga0059261_3276 Ga0059261_3276 ABC-type multidrug transport system, ATPase and permease components
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Korea:Ga0059261_3276 Length = 595 Score = 95.1 bits (235), Expect = 3e-24 Identities = 69/208 (33%), Positives = 109/208 (52%), Gaps = 6/208 (2%) Query: 28 IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRDA 87 + A+ ++ + PGE V ++G +GAGKSTL +++ Y + GEIRV+G V +P + Sbjct: 368 VSALHQFTLSVAPGETVAVVGPSGAGKSTLFQLVQRFYDPEGGEIRVDGIPVRSADPGEV 427 Query: 88 RSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKIMNRLNPNFQKF 147 R+ +T+ A A NL GR T + +A A + + L + F Sbjct: 428 RARMAMVPQETVIFA--ATARDNLRYGRWDATE-EQIWQAAEAANAAEFLRELPQGLETF 484 Query: 148 -SEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLKAQGIGI 206 E + LSGGQRQ +AIARA+ +A IL++DE T+AL ++V + ++ L QG Sbjct: 485 LGEDGARLSGGQRQRLAIARALLRDAPILLLDEATSALDAESERLVQDALEHL-MQGRTT 543 Query: 207 FLIDHDVNAVMELCDRASVMKNGQLVGT 234 +I H + A + R VM G++V T Sbjct: 544 LVIAHRL-ATVRAAKRIIVMDEGRIVET 570 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: 255 Number of extensions: 11 Number of successful extensions: 2 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: 595 Length adjustment: 31 Effective length of query: 229 Effective length of database: 564 Effective search space: 129156 Effective search space used: 129156 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: 50 (23.9 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