Align protocatechuate 3,4-dioxygenase, beta chain; EC 1.13.11.3 (characterized)
to candidate AO356_04920 AO356_04920 protocatechuate 3,4-dioxygenase
Query= CharProtDB::CH_121290 (241 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04920 Length = 188 Score = 99.0 bits (245), Expect = 6e-26 Identities = 55/159 (34%), Positives = 90/159 (56%), Gaps = 10/159 (6%) Query: 75 IGERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPNFGGCGRMLTDD 134 +G+RV + G V D G+ V +A++EVWQANA+G+Y HP D +DP+F G GR+ D Sbjct: 33 LGQRVAITGQVVDGNGQFVNDAMLEVWQANAAGKYAHPEDDQDKPLDPHFEGFGRVPVDA 92 Query: 135 NGYYVFRTIKPGPYPWRNRINEWRPAHIHFSLIADGWAQRLISQFYFEGDTLIDSCPILK 194 G + F TIKPG P + H+ + A G + L+++ YF+G+ ++ P+L Sbjct: 93 EGRFRFTTIKPGTVP--GLAGTTQAPHLVVLVFARGLVKHLLTRIYFDGEQANETDPLLA 150 Query: 195 TIPSEQQRRALIALEDKSNFIEADSRCYRFDITLRGRRA 233 +P E++R ++A D S Y++++ L+G A Sbjct: 151 CVP-EERRGTIVAKPDASG-------VYQWNVILQGTDA 181 Lambda K H 0.321 0.139 0.439 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: 143 Number of extensions: 6 Number of successful extensions: 2 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: 241 Length of database: 188 Length adjustment: 21 Effective length of query: 220 Effective length of database: 167 Effective search space: 36740 Effective search space used: 36740 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: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. 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