Align protocatechuate 3,4-dioxygenase (subunit 1/2) (EC 1.13.11.3) (characterized)
to candidate PP_4656 PP_4656 protocatechuate 3,4-dioxygenase beta chain
Query= BRENDA::Q0SH26 (213 letters) >FitnessBrowser__Putida:PP_4656 Length = 239 Score = 63.5 bits (153), Expect = 3e-15 Identities = 46/146 (31%), Positives = 69/146 (47%), Gaps = 16/146 (10%) Query: 29 SQTVGP-YVHIG-------LFPTWENSGDAVPEDAPGRIDVSFSVIDGAGQPIGDAMIET 80 S+T GP + H+G L + N G + E RI V+ V+D G+P+ + ++E Sbjct: 45 SETTGPDFSHLGFGAHDHDLLLNFNNGGLPIGE----RIIVAGRVVDQYGKPVPNTLVEM 100 Query: 81 WQADAAGRFNSPTDPRGAAEATPAGFRSLARVFADESGTIVVHTVKPGALPAEDGAVE-- 138 WQA+A GR+ D R A P F + R D G T+KPG P +G + Sbjct: 101 WQANAGGRYRHKND-RYLAPLDP-NFGGVGRCLTDRDGYYSFRTIKPGPYPWRNGPNDWR 158 Query: 139 APHINVGLFARGMLERLYTRLYFPED 164 HI+ + + +L T+LYF D Sbjct: 159 PAHIHFAISGPSIATKLITQLYFEGD 184 Lambda K H 0.317 0.136 0.412 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: 161 Number of extensions: 13 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: 213 Length of database: 239 Length adjustment: 22 Effective length of query: 191 Effective length of database: 217 Effective search space: 41447 Effective search space used: 41447 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: 46 (22.3 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