Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 136 bits (343), Expect = 6e-37 Identities = 75/209 (35%), Positives = 121/209 (57%), Gaps = 12/209 (5%) Query: 26 EISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVL------NGVSAQD 79 +I L I GEF+ L GPSG GK++TLRM++GL T +G L + VS Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGR 79 Query: 80 RDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQ 139 R + +FQ Y+L+P+ +V+ N++F L+ + + + E + +G+ L D P Sbjct: 80 RKLGYLFQDYSLFPNMTVKENIAFALKNAKD------KAYLMELLESMGLLHLQDTLPKH 133 Query: 140 LSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHD 199 LSGGQQQRVAL RA+ P++ L+DEPLS LD +R +++ + + + +TT+ V+HD Sbjct: 134 LSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHD 193 Query: 200 QTEAMTMGDRVAVLDDGELQQVGTPLDCY 228 E + + DR+ LD G++ + TP + + Sbjct: 194 AGEIIKLSDRIIELDHGKVLRQCTPKEFF 222 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: 315 Number of extensions: 20 Number of successful extensions: 3 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: 290 Length adjustment: 28 Effective length of query: 355 Effective length of database: 262 Effective search space: 93010 Effective search space used: 93010 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: 49 (23.5 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