Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_01451 H281DRAFT_01451 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_01451 Length = 415 Score = 281 bits (718), Expect = 3e-80 Identities = 165/364 (45%), Positives = 217/364 (59%), Gaps = 21/364 (5%) Query: 18 GGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSA 77 GG+ V +E + LD+ GEF+VL+GPSGCGKST L +AGL VT+G + + + Sbjct: 58 GGNTV-IENLDLDVQPGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGEDMTWADP 116 Query: 78 QDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKP 137 +DR IA+VFQSYALYP SV N+SF L + G P EI +RV +ML + LL RKP Sbjct: 117 KDRRIALVFQSYALYPTMSVERNLSFALRIN-GTPKAEIARRVARAAEMLQLGPLLKRKP 175 Query: 138 GQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVT 197 QLSGGQ+QRVA+GRAIVR+ +VFL DEPLSNLDAKLR E+R EL++L LG T +YVT Sbjct: 176 AQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGATMIYVT 235 Query: 198 HDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLS---- 253 HDQ EAM + R+AV+ G +QQ GTP + Y RP NLFVA F+G P+MNL +G+L Sbjct: 236 HDQVEAMMLATRMAVMRGGAIQQFGTPAEVYARPANLFVATFLGTPAMNLVNGTLEQRDG 295 Query: 254 -----GDTFRGDGFDYPL---SGATRDQLGGAS---GLTLGIRPEDVTVGERRSGQRTFD 302 + +R D +Y SG ++ Q S LG+R EDV +G + Sbjct: 296 ALHFCTEQWRLDVSNYAFVDRSGESQPQSQPQSPPRPCVLGVRAEDVRIGPTQGEGAGEH 355 Query: 303 AEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGET 362 A++ +VEP GN V L + G Q + ++ V GD S + LFD + Sbjct: 356 AKISLVEPMGNHRVVWLDY----HGVQIASIDQSKTPVMPGDTLAFSLDSTHVSLFDAAS 411 Query: 363 GDAL 366 G L Sbjct: 412 GARL 415 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: 431 Number of extensions: 23 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: 415 Length adjustment: 31 Effective length of query: 352 Effective length of database: 384 Effective search space: 135168 Effective search space used: 135168 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