Align protocatechuate 4,5-dioxygenase α subunit (EC 1.13.11.8; EC 1.13.11.57) (characterized)
to candidate Ac3H11_1164 Protocatechuate 4,5-dioxygenase alpha chain (EC 1.13.11.8)
Query= metacyc::MONOMER-3165 (149 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1164 Length = 116 Score = 91.3 bits (225), Expect = 5e-24 Identities = 42/115 (36%), Positives = 66/115 (57%) Query: 3 LEKPYLDVPGTIIFDAEQSRKGYWLNQFCMSLMKAENRERFRADERAYLDEWAMTEEQKQ 62 + P +PGT FD Q+RKGY LN+ C S NR+ F ADE AY+ ++ + E+Q Sbjct: 1 MPSPLPPIPGTTPFDGNQARKGYALNKMCFSFNDEANRKAFVADEEAYMKQYGLNEQQAA 60 Query: 63 AVLARDLNWCMRTGGNIYFLAKIGATDGKSFQQMAGSMTGMTEEEYRAMMMGGGR 117 A+ A+++ + GG+ Y+LAK Q + TGMT++E++A ++ GR Sbjct: 61 AIRAKNVLQLIAAGGDAYYLAKFAGIFKLDMQDIGAQQTGMTKDEFKAKLVAAGR 115 Lambda K H 0.316 0.131 0.393 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: 64 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: 149 Length of database: 116 Length adjustment: 14 Effective length of query: 135 Effective length of database: 102 Effective search space: 13770 Effective search space used: 13770 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 41 (20.4 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