Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 179 bits (453), Expect = 1e-49 Identities = 94/246 (38%), Positives = 155/246 (63%), Gaps = 12/246 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ LT++ +V++D G I+ + L + GE L+GPSGCGK+T L+ +AGL+ + Sbjct: 1 MSTLTIE---QVHSDYQGQTIL--RGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPI 55 Query: 61 TEGELRLEDRVLNG----VSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEI 116 ++G + + R+L+G V ++ R++ M+FQ YAL+PH +V N+ FG++ GL Sbjct: 56 SQGRISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK---GLDKAAR 112 Query: 117 RQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176 + R+ E ++ + L R P +LSGGQQQRV++ RA+ +PE+ L+DEP SN+DAK+R Sbjct: 113 QARLGEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRG 172 Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236 EM E++ + + GV+ V+VTH + EA D++A+ DG + Q G+ Y P + +V Sbjct: 173 EMMVEIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYV 232 Query: 237 AGFIGE 242 A F+G+ Sbjct: 233 AEFLGQ 238 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: 352 Number of extensions: 18 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: 342 Length adjustment: 29 Effective length of query: 354 Effective length of database: 313 Effective search space: 110802 Effective search space used: 110802 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