Align TRAP dicarboxylate transport system, small permease component (DctQ-like) (characterized, see rationale)
to candidate WP_086508844.1 BZY95_RS04840 TRAP transporter small permease
Query= uniprot:G8AR26 (179 letters) >NCBI__GCF_002151265.1:WP_086508844.1 Length = 173 Score = 63.5 bits (153), Expect = 2e-15 Identities = 50/152 (32%), Positives = 76/152 (50%), Gaps = 11/152 (7%) Query: 4 LVEALEMVTEWIMALMLAVMVALVFGNVVLRYGFNSGIVAAEELARLMFVWLVFLGATLA 63 L + L+ + M + +++ L VV RYGFNS I EE+ + + F+GA++ Sbjct: 5 LNKVLDFLESVAMVVFMSIATVLTTLQVVYRYGFNSSIFWVEEVVIYSIICMSFVGASMG 64 Query: 64 LRRHQHLGLDILQARLPARVRRACAVISHLLMI-YALWLFIQGSWFQL---LIGMETRST 119 +R H+ +D+L A +P V R +I+ LL I +A +L G FQL +G + Sbjct: 65 VRHGVHISVDVLNAFVPPAVNRWLHIIAALLGIAFAGYLAYYG--FQLYFNTLGRGQLTA 122 Query: 120 VLSFPMA-FYAAAGFFPAIAMALTIIANLWKI 150 L PMA FY G I+ L I+ LW I Sbjct: 123 ALRLPMAWFYLPIG----ISGILLILRYLWVI 150 Lambda K H 0.331 0.141 0.440 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: 83 Number of extensions: 5 Number of successful extensions: 1 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: 179 Length of database: 173 Length adjustment: 19 Effective length of query: 160 Effective length of database: 154 Effective search space: 24640 Effective search space used: 24640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 44 (21.6 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