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 RR42_RS15930 RR42_RS15930 sugar transporter
Query= TCDB::D5ATK0 (190 letters) >FitnessBrowser__Cup4G11:RR42_RS15930 Length = 180 Score = 160 bits (406), Expect = 9e-45 Identities = 80/166 (48%), Positives = 116/166 (69%), Gaps = 1/166 (0%) Query: 4 LLALARVIDRINEFIGKSVSWLILVAVLVSATNAAIRKIFDISSNAWLEAQWYLFGAAFL 63 LL L+R IDR+N+ G+ + +IL++ L+SA NA +R F++S N LE QWY+F A + Sbjct: 4 LLGLSRQIDRLNQHTGRLANIMILLSCLISAGNALLRYGFNLSDNWPLELQWYMFAIAVM 63 Query: 64 MAAAYTLKQNEHIRIDIVYGAFSRRVQHWIDLFGHVFFLMPFLVLMLWLMFPWLMM-SVR 122 A+YT ++NEH+R+D++YG S R QHWID+FG +FFL+P VL WL + L + S R Sbjct: 64 FGASYTFQRNEHVRVDLIYGNVSERAQHWIDIFGIIFFLLPSCVLFAWLSWESLFLPSWR 123 Query: 123 SGEVSTNSGGLIIWPAKSLLLIGFALLFAQGLSEIIKKIGVMRGLI 168 E S NSGGL +P K ++ +GFALL QG+SE+IK+I ++GL+ Sbjct: 124 ILEQSGNSGGLPRYPIKLVVPLGFALLALQGVSELIKRIAALKGLV 169 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: 118 Number of extensions: 3 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: 190 Length of database: 180 Length adjustment: 19 Effective length of query: 171 Effective length of database: 161 Effective search space: 27531 Effective search space used: 27531 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 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