Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate WP_057508464.1 ABB28_RS09875 protocatechuate 3,4-dioxygenase subunit alpha
Query= BRENDA::Q0SH27 (237 letters) >NCBI__GCF_001431535.1:WP_057508464.1 Length = 187 Score = 89.4 bits (220), Expect = 5e-23 Identities = 53/164 (32%), Positives = 85/164 (51%), Gaps = 9/164 (5%) Query: 70 AQGQRIIVHGRVLDSAGKPIPDTLIEVWQANAGGRYRHKMDSWPAPLDPHFNGVARCLTD 129 A G+R+ V G+V D G P+ D ++E+WQA+A G Y H D DP F+G R TD Sbjct: 32 ALGERVEVRGQVFDGTGLPVSDAVLEIWQADAQGIYAHAEDPRRDDHDPAFDGWGRVPTD 91 Query: 130 KQGHYEFTTIKPGAYPWGNHHNAWRPAHIHFSLFGQAFTQRLVTQMYFPDDPFFFQDPIY 189 + G + F+T+KPG+ G A P H+ +F + + ++YF D+P +DPI Sbjct: 92 ENGRFAFSTVKPGSVA-GPGGRAQAP-HLVVLVFMRGLLRAASARIYFSDEPRNDEDPIL 149 Query: 190 NSVPEAARERMISTFDYDHTRDNWAVGFKFDIVLRGRDATPFED 233 + VP R +++ D + +++ ++G D T F D Sbjct: 150 HLVPAERRGTLLAQAQGDGV-------YHWNVHMQGPDETVFFD 186 Lambda K H 0.322 0.140 0.458 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: 158 Number of extensions: 8 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: 237 Length of database: 187 Length adjustment: 21 Effective length of query: 216 Effective length of database: 166 Effective search space: 35856 Effective search space used: 35856 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 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 24 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