Align glucose transporter, ATPase component (characterized)
to candidate 3608605 Dshi_1998 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Dino:3608605 Length = 248 Score = 388 bits (997), Expect = e-113 Identities = 195/247 (78%), Positives = 220/247 (89%) Query: 13 TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 TPLVE+ DISISFGGI+AVD VS+DLYPGEVVGLLGHNGAGKSTLIK+L+GAY+ D+GEI Sbjct: 2 TPLVELDDISISFGGIRAVDGVSLDLYPGEVVGLLGHNGAGKSTLIKILAGAYRKDSGEI 61 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAE 132 R+NG K EI +PRDAR +NIETIYQTLALADNLDA+SNLFLGREL T G VDD+ MEAE Sbjct: 62 RINGKKAEINSPRDARRYNIETIYQTLALADNLDASSNLFLGRELTTRLGFVDDTRMEAE 121 Query: 133 CRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMV 192 R+IM RLNPNFQK SEPVSALSGGQRQSVAIARAVYFNA+ILIMDEPTAALG HETQMV Sbjct: 122 TRRIMARLNPNFQKLSEPVSALSGGQRQSVAIARAVYFNAQILIMDEPTAALGVHETQMV 181 Query: 193 AELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMIILG 252 A+LI++LKAQG+GIFLI HD ++ELCDR SVMKNG+LVGT ++DVT+DD+LSMIILG Sbjct: 182 ADLIKELKAQGLGIFLISHDTREMLELCDRVSVMKNGKLVGTERVEDVTEDDILSMIILG 241 Query: 253 KRPGEAA 259 K P A Sbjct: 242 KNPKAVA 248 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: 250 Number of extensions: 6 Number of successful extensions: 1 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: 248 Length adjustment: 24 Effective length of query: 236 Effective length of database: 224 Effective search space: 52864 Effective search space used: 52864 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 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