Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Korea:Ga0059261_2542 Length = 258 Score = 104 bits (260), Expect = 2e-27 Identities = 65/224 (29%), Positives = 113/224 (50%), Gaps = 6/224 (2%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 L + + KS+ L VS+ + KGEVV LLG NGAGK+T + G KPD G ++ + Sbjct: 22 LAVVSIAKSYDKRVVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKPDAGRIMLD 81 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKL 124 G + LG+ + Q+ ++ L + NI E++ +K +L Sbjct: 82 GVDITPLPMYRRAILGLGYLPQETSIFRGLTVAKNISAVLELSEP---DKSARAARLDQL 138 Query: 125 LDSLQI-RIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 L+ + R+ D LSGG+R+ +ARA+ ++L+DEP A + + + +L Sbjct: 139 LEEFGLTRLRDAPAMA--LSGGERRRAEIARALAADPSIMLLDEPFAGIDPISIADIRDL 196 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227 + LK + +GVLI HN+ + ++ DR ++ G+++F E+ Sbjct: 197 VKELKTRNIGVLITDHNVRETLDIVDRASIIYDGRVLFAGSPED 240 Lambda K H 0.318 0.137 0.371 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: 159 Number of extensions: 8 Number of successful extensions: 3 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: 251 Length of database: 258 Length adjustment: 24 Effective length of query: 227 Effective length of database: 234 Effective search space: 53118 Effective search space used: 53118 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: 41 (21.7 bits) S2: 47 (22.7 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