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 Ac3H11_3569 TRAP dicarboxylate transporter, DctQ subunit, unknown substrate 6
Query= TCDB::D5ATK0 (190 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3569 Length = 206 Score = 194 bits (492), Expect = 1e-54 Identities = 89/171 (52%), Positives = 126/171 (73%) Query: 1 MGALLALARVIDRINEFIGKSVSWLILVAVLVSATNAAIRKIFDISSNAWLEAQWYLFGA 60 M ALL L+R ID +N +GK V WLIL + ++S NA +RK F+ISSNA+LE QWYLF A Sbjct: 1 MQALLKLSRGIDWLNTQVGKYVVWLILASTVISGVNAVVRKAFNISSNAFLEVQWYLFAA 60 Query: 61 AFLMAAAYTLKQNEHIRIDIVYGAFSRRVQHWIDLFGHVFFLMPFLVLMLWLMFPWLMMS 120 +FL+AA YTL Q EH+++D++ FS+R Q WID+FG++ FL P + +LW P+ + Sbjct: 61 SFLLAAGYTLLQGEHVKVDVISSRFSKRTQIWIDVFGYIAFLTPMCLAVLWYGIPFFTRA 120 Query: 121 VRSGEVSTNSGGLIIWPAKSLLLIGFALLFAQGLSEIIKKIGVMRGLIADP 171 + SGE+S N+GGLI WP ++ +GFALL+ QG+SE+IK++G ++GLI DP Sbjct: 121 LASGEMSNNAGGLIRWPVYLMMPLGFALLWLQGISELIKRLGFLQGLIEDP 171 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: 137 Number of extensions: 3 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: 206 Length adjustment: 20 Effective length of query: 170 Effective length of database: 186 Effective search space: 31620 Effective search space used: 31620 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: 45 (21.9 bits)
This GapMind analysis is from Sep 17 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