Align Tripartite ATP-independent periplasmic transporter, DctQ-2 component, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate WP_086508064.1 BZY95_RS00590 C4-dicarboxylate ABC transporter permease
Query= TCDB::D5ATK0 (190 letters) >NCBI__GCF_002151265.1:WP_086508064.1 Length = 187 Score = 84.0 bits (206), Expect = 2e-21 Identities = 48/142 (33%), Positives = 75/142 (52%), Gaps = 1/142 (0%) Query: 19 GKSVSWLILVAVLVSATNAAIRKIFDISSNAWLEAQWYLFGAAFLMAAAYTLKQNEHIRI 78 G+++SWL LV + V TN R I S A E W+LFGA ++ AY + ++H+R+ Sbjct: 27 GRAISWLWLVTLAVVLTNVVNRFILGRGSIAVEELSWHLFGATMILTLAYAVVSDDHVRV 86 Query: 79 DIVYGAFSRRVQHWIDLFGHVFFLMPFLVLMLWLMFPWLMMSVRSGEVSTNSGGL-IIWP 137 D++ FS R Q WI+L V +P L LM+ ++ + S GE S GL + Sbjct: 87 DVIREKFSLRTQAWIELLAIVLLALPILYLMVEQLYQYGYRSYLRGERSQAPSGLPYRFI 146 Query: 138 AKSLLLIGFALLFAQGLSEIIK 159 K+L+ IG L+ S +++ Sbjct: 147 IKTLIPIGLTLVAVALFSRVLR 168 Lambda K H 0.330 0.142 0.444 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: 4 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: 190 Length of database: 187 Length adjustment: 20 Effective length of query: 170 Effective length of database: 167 Effective search space: 28390 Effective search space used: 28390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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