Align Anthranilate 1,2-dioxygenase ferredoxin subunit (characterized)
to candidate Pf1N1B4_5586 Probable vanillate O-demethylase oxygenase subunit oxidoreductase protein (EC 1.14.13.-)
Query= SwissProt::Q84BZ1 (108 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5586 Length = 348 Score = 40.4 bits (93), Expect = 2e-08 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 1/67 (1%) Query: 9 WHPLGAIDEFTEDEPAARVAGQKPIAVFRIGDELFAMHDLCSHGHARLSEGYVEDGCVEC 68 W+ DE E ++ G+K + + ++ A+ D C H A LS GYVE+G + C Sbjct: 7 WYVACTPDEIAEKPLGRQICGEKMVFYRGLEGKVAAVEDFCPHRGAPLSLGYVENGNLVC 66 Query: 69 PLHQGLI 75 H GL+ Sbjct: 67 GYH-GLV 72 Lambda K H 0.321 0.140 0.441 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: 100 Number of extensions: 4 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: 108 Length of database: 348 Length adjustment: 20 Effective length of query: 88 Effective length of database: 328 Effective search space: 28864 Effective search space used: 28864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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