Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_156167385.1 AAV99_RS05200 LPS export ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_001013305.1:WP_156167385.1 Length = 258 Score = 112 bits (281), Expect = 6e-30 Identities = 69/228 (30%), Positives = 118/228 (51%), Gaps = 4/228 (1%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 LE+ + KS+ L +S+ + KGEV+ LLG NGAGK+T I G KPD G ++ + Sbjct: 22 LEVVSIAKSYDKRSVLSDISLSVGKGEVLGLLGPNGAGKTTCFYSIMGLVKPDSGRILMD 81 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKL 124 G V LG+ + Q+ ++ + + NI E+ +K E ++L Sbjct: 82 GVDVTRLPMYRRAILGLGYLPQETSIFRGMTVEQNINCVLEMVEP---DKATRARELERL 138 Query: 125 LDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELA 184 LD + + + LSGG+R+ +ARA+ S ++L+DEP A + + + +L Sbjct: 139 LDEFGLTRLRSSPAMA-LSGGERRRCEIARALAASPSIMLLDEPFAGIDPLSISDIRDLV 197 Query: 185 RNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEE 232 +LK +G+GVLI HN+ + E+ DR ++ G+++F +E +E Sbjct: 198 ADLKNRGIGVLITDHNVRETLEIVDRACIIYGGQVLFAGSPQELVADE 245 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: 156 Number of extensions: 9 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: 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 24 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