Align glucose transporter, ATPase component (characterized)
to candidate Ac3H11_3037 Fructose ABC transporter, ATP-binding component FrcA
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3037 Length = 268 Score = 169 bits (428), Expect = 5e-47 Identities = 96/243 (39%), Positives = 145/243 (59%), Gaps = 7/243 (2%) Query: 14 PLV-EMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 PLV + K + +G + A+D +L GE++ ++G NGAGKS+LIK LSGA D GEI Sbjct: 11 PLVMQAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKALSGATVPDEGEI 70 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTP------FGLVDD 126 ++G +++ +P +AR IET+YQ LA+A + A NLFLGREL P ++D Sbjct: 71 LLDGQRIQFKSPIEARRAGIETVYQDLAVAPAMTIAENLFLGRELRRPGLLGTALRMLDK 130 Query: 127 SAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGP 186 M E M L + ++ V LSGGQRQ VA+ARA F ++IMDEPTAALG Sbjct: 131 KKMLEESVARMAELKVGIRSMTQAVETLSGGQRQCVAVARAAAFARHVVIMDEPTAALGV 190 Query: 187 HETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLL 246 E MV ELI++++ +G+ + LI H++ V E+ DR + + G+ V+ ++ D + Sbjct: 191 KEGNMVLELIRRVRDKGLPVILISHNMPHVFEIADRIHIARLGKRAAVVNPKKISMSDTV 250 Query: 247 SMI 249 +++ Sbjct: 251 AVM 253 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: 168 Number of extensions: 5 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: 268 Length adjustment: 25 Effective length of query: 235 Effective length of database: 243 Effective search space: 57105 Effective search space used: 57105 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