Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_091521216.1 BM253_RS06735 LPS export ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_900115115.1:WP_091521216.1 Length = 246 Score = 113 bits (283), Expect = 3e-30 Identities = 70/217 (32%), Positives = 118/217 (54%), Gaps = 6/217 (2%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 L ++ K++ K + GVS+E+N+GE+V LLG NGAGK+T +I G KP+ G++ + Sbjct: 3 LRAENLIKTYKGRKVVKGVSVEVNQGEIVGLLGPNGAGKTTSFYMIVGLVKPNSGNIFLD 62 Query: 65 GKKVIFNSPNDARSL-GIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 + N P R+ GI + Q+ ++ L I NI ++T L KK+ + + Sbjct: 63 NLNIT-NYPMYKRAQNGIGYLAQEASVFRKLSIEDNILSVLQLTT---LTKKEQEAKMES 118 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 L+D ++ N + + LSGG+R+ +ARA+ K IL+DEP A + V + + Sbjct: 119 LIDEFSLQHIRTN-RGDLLSGGERRRTEIARALATDPKFILLDEPFAGVDPVAVEDIQRI 177 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 LK K +G+LI HN+ + + D+ Y++ G I+ Sbjct: 178 VAQLKNKNIGILITDHNVQETLAITDKTYLMFEGGIL 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: 151 Number of extensions: 6 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: 246 Length adjustment: 24 Effective length of query: 227 Effective length of database: 222 Effective search space: 50394 Effective search space used: 50394 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 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