Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS27980 AZOBR_RS27980 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__azobra:AZOBR_RS27980 Length = 360 Score = 304 bits (778), Expect = 3e-87 Identities = 177/370 (47%), Positives = 224/370 (60%), Gaps = 20/370 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + + D+ K Y G + +S+DI DGEF+ LVGPSGCGKST LRM+AGLE Sbjct: 1 MASVIIRDLRKSY-----GGTPVLHGVSVDIADGEFVALVGPSGCGKSTLLRMIAGLEEA 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 EGE+R+ R++N V +DRDIAMVFQ+YALYPH +V N+ F L + EI RV Sbjct: 56 GEGEIRIGGRLVNDVPPKDRDIAMVFQNYALYPHMTVAQNLGFALTLKD-VDRGEIAARV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 ++LG+S LLDR+PGQLSGGQ+QRVA+GRAIVRDP +FL DEPLSNLDAKLR +MR Sbjct: 115 ARAAEVLGLSALLDRRPGQLSGGQRQRVAMGRAIVRDPRLFLFDEPLSNLDAKLRVQMRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L L + +YVTHDQ EAMTM DR+ V+ DG ++Q G PLD Y RP N FVAGFI Sbjct: 175 EIKALHQRLRTSAIYVTHDQIEAMTMADRIVVMRDGRVEQAGAPLDLYDRPANRFVAGFI 234 Query: 241 GEPSMNLFDGSLSGD---TFRGDGF-DYPLSGATRDQLGGASGLTLGIRPEDVTVGERRS 296 G P+MN G ++ + +FR DG D PLS + G + LG+RPE + Sbjct: 235 GSPAMNFLTGRIAVNGRASFRLDGGPDLPLSAVPLEADGRPA--VLGLRPEHALI----D 288 Query: 297 GQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIH 356 + V VVEP G+E V V G F + GD + P + H Sbjct: 289 PEEGVPLHVAVVEPTGSETQV----VGQLAGQPFVGVFRERVAARPGDILPLRLPAASAH 344 Query: 357 LFDGETGDAL 366 LFD G L Sbjct: 345 LFDAGEGRRL 354 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: 493 Number of extensions: 35 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: 360 Length adjustment: 30 Effective length of query: 353 Effective length of database: 330 Effective search space: 116490 Effective search space used: 116490 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