Align Putative TRAP dicarboxylate transporter, DctQ subunit (characterized, see rationale)
to candidate AO356_23050 AO356_23050 C4-dicarboxylate ABC transporter
Query= uniprot:Q88NN9 (194 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23050 Length = 175 Score = 269 bits (687), Expect = 2e-77 Identities = 122/175 (69%), Positives = 156/175 (89%) Query: 20 MKSLFLSVNDTLYRSCIWIAGLSILAMTLIIPWGIFARYVLGTGSSWPEPVSILLMVVFT 79 MK+L L +ND +Y +CIW+AGLS+LA++L+IPWG+FARYVLG+GSSWPEP +ILLM+VFT Sbjct: 1 MKNLLLRINDKIYMTCIWVAGLSVLAISLMIPWGVFARYVLGSGSSWPEPTAILLMMVFT 60 Query: 80 FVGAAASYRAGAHMAVGMITDRLPPLQRQLVALLVQLLMIVVCVFMTYYGTRLCITTWNQ 139 F+GAAASYRAGAHMAV M+TDR+PP + ++ QLLM ++C+FMT +G +LC++TWNQ Sbjct: 61 FIGAAASYRAGAHMAVAMLTDRMPPHLKSAASIFSQLLMALICIFMTVWGFKLCMSTWNQ 120 Query: 140 SLASLPGVRVGMTYAPIPVGGVLTLVFVLEKLLLGDQSNRKVVRFDLVEENEGAA 194 +ASLPG+RVG+TY PIP+GG+LTLVFVLEKLLLGDQS R+VV+FDLVEE+EGAA Sbjct: 121 FMASLPGLRVGVTYLPIPLGGLLTLVFVLEKLLLGDQSKRRVVQFDLVEESEGAA 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: 148 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