Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF3116 HP15_3059 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Marino:GFF3116 Length = 233 Score = 125 bits (314), Expect = 8e-34 Identities = 68/220 (30%), Positives = 125/220 (56%), Gaps = 7/220 (3%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L + DVH +G ++AL GVS+E+ KGE+V+L+G NGAGK+TL+ + G + G + Sbjct: 1 MLVLEDVHTHYGKIEALHGVSVEVKKGEIVSLIGANGAGKTTLLMTVCGNPRASSGRIFL 60 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 EG+++ S GI + + + L + N+ + F N K + +S++ Sbjct: 61 EGREITNESTAQIMRSGIAIVPEGRRVFSGLTVEENLHMGG------FFNTKAEIRKSQE 114 Query: 124 LLDSLQIRIPD-INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 + L R+ + + + +SGG++Q +A+ RA+ +MI++DEP+ L+ + +++ E Sbjct: 115 HVYELFPRLKEREHQRAGTMSGGEQQMLAIGRALMSRPEMIILDEPSLGLAPLIIKQIFE 174 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFH 222 + L+++G+ V ++ N Q +ADR YVL+ GKI H Sbjct: 175 IIGQLREEGITVFLVEQNAHQALNLADRGYVLETGKIRLH 214 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: 127 Number of extensions: 4 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: 251 Length of database: 233 Length adjustment: 23 Effective length of query: 228 Effective length of database: 210 Effective search space: 47880 Effective search space used: 47880 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: 46 (22.3 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