Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085126658.1 B9O00_RS29715 ATP-binding cassette domain-containing protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_900177295.1:WP_085126658.1 Length = 260 Score = 200 bits (508), Expect = 3e-56 Identities = 104/231 (45%), Positives = 157/231 (67%), Gaps = 1/231 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 L+E+R + +FG VKA+DGVS+++ GEVV LLG NGAGKSTLIK++SG G+++ Sbjct: 8 LVEMRGIEVAFGGVKAVDGVSLDLYAGEVVGLLGHNGAGKSTLIKVLSGAVPARAGEILI 67 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122 +G V SP DAR IETIYQ LAL +L N+FL RE+T L++++M E++ Sbjct: 68 DGAAVRIASPQDARRHRIETIYQTLALADNLNAAANLFLGRELTTPTGLLDEERMEAETR 127 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 ++L L + V +LSGGQRQ++A+ARAV+F A++++MDEPTAAL V E V E Sbjct: 128 RILARLNRNFDRFSTPVRSLSGGQRQSIAIARAVHFDARILIMDEPTAALGVQETAMVAE 187 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233 L R LK +G+G+ +I+H+I ++++DR+ VL G+++ ++ ET +E+ Sbjct: 188 LVRQLKAEGIGIFLISHDIHDVFDLSDRVTVLKNGRLVGTRRVAETTQDEV 238 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: 138 Number of extensions: 5 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: 260 Length adjustment: 24 Effective length of query: 227 Effective length of database: 236 Effective search space: 53572 Effective search space used: 53572 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 Apr 09 2024. 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