Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 258 bits (659), Expect = 2e-73 Identities = 151/350 (43%), Positives = 209/350 (59%), Gaps = 28/350 (8%) Query: 24 VEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRDIA 83 +++I LDI GEF +GPSGCGK+T LR++AG T G + + R ++G+ A RD+ Sbjct: 34 LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIGGRDISGLPAHKRDVG 93 Query: 84 MVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSGG 143 MVFQSYAL+PH +VR N++FGLEE +P EI +RV+ D++G+ L DR+P QLSGG Sbjct: 94 MVFQSYALWPHMTVRRNVAFGLEERR-VPRAEIERRVDAALDLVGLKHLADRRPSQLSGG 152 Query: 144 QQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTEA 203 QQQRVAL R IV +P+V L+DEPLSNLDAKLR +MR EL LQ +LG+TT++VTHDQ EA Sbjct: 153 QQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKLGLTTIFVTHDQEEA 212 Query: 204 MTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFRGDGFD 263 T+ DR+AV++DG +QQVGTP + Y P NLFVAGF+G + N+ +G + Sbjct: 213 NTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLG--TANVLEGQVRA--------- 261 Query: 264 YPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGN-ENAVHLRFV 322 + G T +GG + L P V G +G+ F + + + G A H+R + Sbjct: 262 --VDGGTAFVMGGGVPIPL---PHGVEPG--AAGKLMFRPQNLFIRQDGGPPRAGHVRLM 314 Query: 323 DGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGETGDALKNRELP 372 +F + + G + V P A GDAL + P Sbjct: 315 GVVRHREFLGASIRYAVDIGGQQVQVDAPHQA--------GDALLPTDTP 356 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: 417 Number of extensions: 18 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: 371 Length adjustment: 30 Effective length of query: 353 Effective length of database: 341 Effective search space: 120373 Effective search space used: 120373 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: 50 (23.9 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