Align Putative TRAP dicarboxylate transporter, DctQ subunit (characterized, see rationale)
to candidate GFF361 Psest_0362 TRAP-type C4-dicarboxylate transport system, small permease component
Query= uniprot:Q88NN9 (194 letters) >FitnessBrowser__psRCH2:GFF361 Length = 175 Score = 216 bits (549), Expect = 2e-61 Identities = 98/172 (56%), Positives = 136/172 (79%) Query: 20 MKSLFLSVNDTLYRSCIWIAGLSILAMTLIIPWGIFARYVLGTGSSWPEPVSILLMVVFT 79 MK+L L VND +YR+C+ +A +I+ M IIPWG+F+RY LG G WPEP++ILLMV+FT Sbjct: 1 MKNLVLGVNDAIYRACVIVAATAIVIMATIIPWGVFSRYALGQGLGWPEPIAILLMVLFT 60 Query: 80 FVGAAASYRAGAHMAVGMITDRLPPLQRQLVALLVQLLMIVVCVFMTYYGTRLCITTWNQ 139 FVGAAASYRAGAHMAV +++DRLPPL + + L V+L M + +FM +G +LC+ TWNQ Sbjct: 61 FVGAAASYRAGAHMAVQVLSDRLPPLAQPFIILFVRLAMAAISLFMLIWGYKLCVATWNQ 120 Query: 140 SLASLPGVRVGMTYAPIPVGGVLTLVFVLEKLLLGDQSNRKVVRFDLVEENE 191 L++L +RVG++YAPIP+GG +TL+FV+E+LL GDQS R+VV ++ EE++ Sbjct: 121 YLSTLTWMRVGISYAPIPLGGFITLLFVIEQLLYGDQSKRRVVDYEAREESK 172 Lambda K H 0.328 0.141 0.436 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: 113 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: 194 Length of database: 175 Length adjustment: 19 Effective length of query: 175 Effective length of database: 156 Effective search space: 27300 Effective search space used: 27300 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 (21.8 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