Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 6938983 Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__SB2B:6938983 Length = 270 Score = 122 bits (307), Expect = 9e-33 Identities = 86/267 (32%), Positives = 137/267 (51%), Gaps = 22/267 (8%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G+ V E+ISL I G+ ++GPSG GK+T L+++AG GE+ + ++ +S Sbjct: 19 GERVIYEDISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVPDHGEVLFDGVNIHDISRS 78 Query: 79 D-----RDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLL 133 + + ++M+FQS AL+ +V N++F L E +GL + IR+ V + +G+ Sbjct: 79 ELFELRKRMSMLFQSGALFTDMNVFDNIAFALREHSGLDEAIIRRIVLMKLEAVGLRGAA 138 Query: 134 DRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTT 193 P +LSGG Q+RVAL RAI +PE+ + DEP + D + ++ L L +T+ Sbjct: 139 MLMPSELSGGMQRRVALARAIALEPEMVMYDEPFAGQDPISMGVLVKLIRELSDALNLTS 198 Query: 194 VYVTHDQTEAMTMGDRVAVLDDGELQQVGTP--LDCYHRPNNLFVAGFIGEPSMNLFDGS 251 V V+HD E + + D V V+ + + GTP L H P G GEP DG Sbjct: 199 VVVSHDVGEVLGIADYVYVIAEKRIIAQGTPAQLKSSHDPRLRQFIG--GEP-----DGP 251 Query: 252 LSGDTFRGDGFDYPLSGATRDQLGGAS 278 + F YP + ++ GGA+ Sbjct: 252 VP--------FHYPANDYMKELTGGAN 270 Lambda K H 0.316 0.136 0.384 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: 279 Number of extensions: 15 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: 383 Length of database: 270 Length adjustment: 28 Effective length of query: 355 Effective length of database: 242 Effective search space: 85910 Effective search space used: 85910 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: 42 (22.0 bits) S2: 48 (23.1 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