Align glucose transporter, ATPase component (characterized)
to candidate 6938852 Sama_2955 ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__SB2B:6938852 Length = 250 Score = 98.2 bits (243), Expect = 1e-25 Identities = 74/230 (32%), Positives = 117/230 (50%), Gaps = 17/230 (7%) Query: 13 TPLVEMKDISISF--GGIK--AVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMD 68 TP+V M++IS SF GG + +D++++D++PGE V L G +G+GKSTL+ +++G Q D Sbjct: 2 TPIVAMQEISKSFQDGGERHRVLDNLTLDIHPGETVALTGPSGSGKSTLLNLIAGFDQPD 61 Query: 69 AGEIRVNGDKVEITNPRD---ARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVD 125 G IR+ G + + D R + ++Q L + L+ +N+ P L + Sbjct: 62 DGHIRLLGRPSKHFSASDWDRFRRSELGMVFQQFNLLEPLNVQANIHF------PLAL-N 114 Query: 126 DSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG 185 + C + +RL + S PV +LSGGQ+Q VAIARA+ +L+ DEPT L Sbjct: 115 GKPWDDWCHTLTSRLGLT-ELLSRPVDSLSGGQQQRVAIARALSQRPPLLLADEPTGNLD 173 Query: 186 PHETQMVAELIQQL-KAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234 H V L+ L + I ++ H R + NGQ+ T Sbjct: 174 EHSGDEVMALLTSLARESNTAILMVTHSERCA-AFMQRRWHLCNGQIAET 222 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: 129 Number of extensions: 3 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: 250 Length adjustment: 24 Effective length of query: 236 Effective length of database: 226 Effective search space: 53336 Effective search space used: 53336 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