Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 351063 BT1535 ABC transporter ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Btheta:351063 Length = 221 Score = 132 bits (331), Expect = 1e-35 Identities = 81/223 (36%), Positives = 126/223 (56%), Gaps = 10/223 (4%) Query: 4 LTLDDVTKVY-TDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTE 62 +TL ++K+Y TDE + VA+E ++L +D GEFL ++GPSGCGKST L +M L+ T Sbjct: 2 ITLTSLSKIYRTDEI--ETVALENVNLTVDRGEFLSIMGPSGCGKSTLLNIMGLLDAPTT 59 Query: 63 GELRLEDRVLNGV------SAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEI 116 G + + G+ + +++ + VFQS+ L +V N+ L + E Sbjct: 60 GTVEINGTHTEGMKDKQLAAFRNKTLGFVFQSFHLINSLNVMDNVELPLLYRR-IGSGER 118 Query: 117 RQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176 ++ +E + +G+S ++ P QLSGGQ QRV + RAI+ PE+ L DEP NLD+K+ A Sbjct: 119 KRLAKEVLEKVGLSHRMNHFPTQLSGGQCQRVTIARAIIGHPEIILADEPTGNLDSKMGA 178 Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQ 219 E+ L RL E G T V VTH++ +A + D ++Q Sbjct: 179 EVMELLHRLNKEDGRTIVMVTHNEEQAKQTSRTIRFFDGRQVQ 221 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: 187 Number of extensions: 7 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: 221 Length adjustment: 26 Effective length of query: 357 Effective length of database: 195 Effective search space: 69615 Effective search space used: 69615 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