Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 106 bits (264), Expect = 7e-28 Identities = 73/219 (33%), Positives = 118/219 (53%), Gaps = 14/219 (6%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 LE+++V K +G + A+ VS+EI GE + +G +G GKSTL+++I+G + G L+ + Sbjct: 4 LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLA---REVTNKIFLNKKKMMEES 121 G+ I P R L + ++Q AL P + + N+ A +V I K KM + Sbjct: 64 GRD-ITEVPPSQRDLAM--VFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAAL-SVVEARKV 180 L LQ R P + LSGGQRQ VA+ R++ S K+ L DEP + L + + Sbjct: 121 LNLTAYLQ-RTP------KALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTR 173 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI 219 +E+A ++ G + +TH+ ++ +ADR+ VL G I Sbjct: 174 VEIASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGII 212 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: 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: 348 Length adjustment: 26 Effective length of query: 225 Effective length of database: 322 Effective search space: 72450 Effective search space used: 72450 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: 48 (23.1 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