Align protocatechuate 3,4-dioxygenase (subunit 1/2) (EC 1.13.11.3) (characterized)
to candidate RR42_RS32060 RR42_RS32060 protocatechuate 3,4-dioxygenase
Query= BRENDA::I0DHJ1 (239 letters) >FitnessBrowser__Cup4G11:RR42_RS32060 Length = 192 Score = 90.5 bits (223), Expect = 2e-23 Identities = 57/141 (40%), Positives = 76/141 (53%), Gaps = 10/141 (7%) Query: 45 SETTGPDFSHLGFGAHDH-DLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQA 103 S+T GP + H+G D DL + GERI++ GRV+D G PVP+ +VE+WQA Sbjct: 7 SQTVGP-YLHIGLSGLDRADLTAEASE---LTGERIVIEGRVIDGKGDPVPDGMVEIWQA 62 Query: 104 NAGGRYRHKNDR---YLAPLDPNFGGVGRCLTDRDGYYSFRTIKPGPYPWRNGPNDWRPA 160 N GRYRH +D L P F G GR T DG + F T+KPGP P +G + Sbjct: 63 NPAGRYRHPDDARDGAETALVPGFTGFGRLPTGPDGSFRFVTVKPGPVPGPDGQP--QAP 120 Query: 161 HIHFAISGPSIATKLITQLYF 181 HI ++ + L T+LYF Sbjct: 121 HIVVSLFMRGLLKHLSTRLYF 141 Lambda K H 0.322 0.140 0.450 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: 176 Number of extensions: 12 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: 239 Length of database: 192 Length adjustment: 22 Effective length of query: 217 Effective length of database: 170 Effective search space: 36890 Effective search space used: 36890 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 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