Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_05701 Length = 362 Score = 302 bits (773), Expect = 1e-86 Identities = 174/369 (47%), Positives = 229/369 (62%), Gaps = 17/369 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA LTL V K Y G + I +D++DGEF+V+VGPSGCGKST LRM+AGLE + Sbjct: 1 MAALTLQGVKKTYD----GKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 +EG + + +V+N + +DR+IAMVFQ+YALYPH SV NM + L+ + G+ +I QRV Sbjct: 57 SEGTISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIA-GVDRAQIAQRV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +L + LL RKP +LSGGQ+QRVA+GRAIVR+P VFL DEPLSNLDA+LR +MR Sbjct: 116 NAAAQILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRL 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+QRL L T++YVTHDQ EAMT+ RV V++ G +Q+G P + Y RP +FVAGFI Sbjct: 176 EIQRLHARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFI 235 Query: 241 GEPSMNLFDGSLS--GDTF--RGDGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGER 294 G P MNL +G +S G TF G+G PL+G A G TLGIRPE ++ G+ Sbjct: 236 GSPGMNLLEGRVSDDGSTFDVAGNGPQLPLAGVASIGREVAKGREWTLGIRPEHMSPGQA 295 Query: 295 RSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDA 354 + T + E G +N H R+ D TA R AG+ V+ P Sbjct: 296 DAPHTTLTVD--SCELLGADNLAHGRWGKHD----VTARLPHAHRPAAGEALQVALPARH 349 Query: 355 IHLFDGETG 363 +H FD +G Sbjct: 350 LHFFDPASG 358 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: 382 Number of extensions: 21 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: 362 Length adjustment: 30 Effective length of query: 353 Effective length of database: 332 Effective search space: 117196 Effective search space used: 117196 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