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 GFF1040 Psest_1073 TRAP-type mannitol/chloroaromatic compound transport system, small permease component
Query= TCDB::D5ATK0 (190 letters) >FitnessBrowser__psRCH2:GFF1040 Length = 200 Score = 85.5 bits (210), Expect = 6e-22 Identities = 51/154 (33%), Positives = 83/154 (53%), Gaps = 1/154 (0%) Query: 7 LARVIDRINEFIGKSVSWLILVAVLVSATNAAIRKIFDISSNAWLEAQWYLFGAAFLMAA 66 ++R +DR+ IG++ +WL L +LV N R S A E W+LFGAA ++A Sbjct: 21 ISRPLDRLLVAIGEASAWLWLAVLLVVLANVFSRFALSRGSIALEELSWHLFGAALMLAL 80 Query: 67 AYTLKQNEHIRIDIVYGAFSRRVQHWIDLFGHVFFLMPFLVLMLWLMFPWLMMSVRSGEV 126 AY + +++H+R+D++ FS R Q WI+L + +P +VLM+ + P+ + E Sbjct: 81 AYAVVRDDHVRVDVLRERFSLRSQAWIELIAILLLALPVIVLMIDALIPYAYKAYLYNER 140 Query: 127 STNSGGL-IIWPAKSLLLIGFALLFAQGLSEIIK 159 S GL + KS+L IG L+ LS ++ Sbjct: 141 SQAPSGLPYRFIFKSVLPIGLVLVALALLSRALR 174 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: 88 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: 190 Length of database: 200 Length adjustment: 20 Effective length of query: 170 Effective length of database: 180 Effective search space: 30600 Effective search space used: 30600 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