Align Putative TRAP dicarboxylate transporter, DctQ subunit (characterized, see rationale)
to candidate GFF3395 PS417_17375 C4-dicarboxylate ABC transporter
Query= uniprot:Q88NN9 (194 letters) >FitnessBrowser__WCS417:GFF3395 Length = 175 Score = 276 bits (705), Expect = 2e-79 Identities = 124/175 (70%), Positives = 158/175 (90%) Query: 20 MKSLFLSVNDTLYRSCIWIAGLSILAMTLIIPWGIFARYVLGTGSSWPEPVSILLMVVFT 79 MK+L L +ND +Y +CIW+AGLS+L + LIIPWGIFARYVLGTGSSWPEP +ILLM+VFT Sbjct: 1 MKNLLLRINDRIYMTCIWVAGLSVLGVALIIPWGIFARYVLGTGSSWPEPTAILLMLVFT 60 Query: 80 FVGAAASYRAGAHMAVGMITDRLPPLQRQLVALLVQLLMIVVCVFMTYYGTRLCITTWNQ 139 F+GAAASYRAGAHM+V M+TDRLPP QRQ++ ++ QLLM +C+FMT +GT+LC++TWNQ Sbjct: 61 FIGAAASYRAGAHMSVAMVTDRLPPRQRQIIGVVSQLLMGTICLFMTIWGTKLCLSTWNQ 120 Query: 140 SLASLPGVRVGMTYAPIPVGGVLTLVFVLEKLLLGDQSNRKVVRFDLVEENEGAA 194 ++++P +RVG+TY PIP+GG+LTL+FV+EKLLLGDQSNR+VVRFDLVEE+EGAA Sbjct: 121 FMSAIPTLRVGITYMPIPIGGLLTLIFVVEKLLLGDQSNRRVVRFDLVEESEGAA 175 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: 146 Number of extensions: 2 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