Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate SMc01980 SMc01980 sugar transport system ATP-binding ABC transporter protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Smeli:SMc01980 Length = 355 Score = 307 bits (786), Expect = 3e-88 Identities = 179/365 (49%), Positives = 226/365 (61%), Gaps = 18/365 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + + ++ K Y G + ++ L I DGEF+VLVGPSGCGKST LRM+AGLE+V Sbjct: 1 MASIDIANIKKSY-----GTHPVLHDVDLKISDGEFVVLVGPSGCGKSTLLRMIAGLESV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T GE+R+ R +N ++ +DRDIAMVFQSYALYPH SV NMS+ L D I V Sbjct: 56 TGGEIRIAGRRVNELAPKDRDIAMVFQSYALYPHMSVARNMSYSLRLRK-TAKDRITTVV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 LG+ LLDR+P LSGGQ+QRVA+GRAIVR P+ FL DEPLSNLDA+LR +MR Sbjct: 115 AGAAAKLGLDPLLDRRPKALSGGQRQRVAMGRAIVRQPKAFLFDEPLSNLDARLREQMRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+++L +LG T++YVTHDQ EAMT+ DR+ ++ G +QQVG+PLD Y RP NLFVAGFI Sbjct: 175 EIKKLHKDLGATSIYVTHDQIEAMTLADRIVAMNGGVVQQVGSPLDLYDRPANLFVAGFI 234 Query: 241 GEPSMNLFDGSL-SGDTFR---GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRS 296 G P MN F+G+ +GD R D PL A + S +TLGIRPE V + Sbjct: 235 GSPGMNFFEGAYHAGDAPRFEMSDEIGIPLDAAA--PVSNNSKVTLGIRPEHVVLAGH-- 290 Query: 297 GQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIH 356 G T A V +VEP G +HL F T +S + A V FP +H Sbjct: 291 GPETLLAGVDLVEPTGFGIILHLSL----GRAAFKVFTNDRSFLTASGTIPVHFPAHHLH 346 Query: 357 LFDGE 361 FD E Sbjct: 347 FFDAE 351 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: 434 Number of extensions: 29 Number of successful extensions: 4 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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