Align Metapyrocatechase; MPC; EC 1.13.11.2; CatO2ase; Catechol 2,3-dioxygenase (uncharacterized)
to candidate PfGW456L13_2530 2,3-dihydroxybiphenyl 1,2-dioxygenase
Query= curated2:Q53034 (318 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2530 Length = 298 Score = 166 bits (419), Expect = 8e-46 Identities = 103/290 (35%), Positives = 150/290 (51%), Gaps = 10/290 (3%) Query: 4 VTGIGYIGIGVSDLPAWEEFA-ETIGFQIRERGEDGTLYLRMDKAHHRVAVHPTGEDDLT 62 + G+GY+ + SDL W +A + +G + +D LYL+MD+ H+R+ V E+ Sbjct: 3 IRGLGYVTLLSSDLAQWRHYASQVLGMMVIGSDDDAHLYLKMDERHYRILVQKNVENGFG 62 Query: 63 YVGWQVADENGFDELERTLRAAGVPVEMAGEDDAELRGVARLMRFEDPSGIKSEAYYGLV 122 GW+VA + ++ L+ A V V +AELR V L+ F DP G + E ++G + Sbjct: 63 ACGWEVAGKAALEQAVSELQQADVQVTRGTAAEAELRKVQELVHFSDPDGNRHEIFWGPL 122 Query: 123 SEPEVPYVSPYAV-DFVTEDQGFGHIVVMVDDYDETMRFYREVLGLQTSDLVKV----GA 177 + +VSP V FVT + G GH+V+ ++ FY +VLG SDL+KV Sbjct: 123 QD-FARFVSPVGVKGFVTNELGMGHVVLPAPAFERCRDFYEQVLGFGLSDLMKVRFTPDP 181 Query: 178 GGVQTRMAFMRC-NPRQHSLAFWAGDSTTRLNHFMLQTQTLDQTGMTLDRCFHGGIP-AT 235 Q R+ F+ C N R HSLA + H M++ LD+ G LDR G+ + Sbjct: 182 AEPQKRIHFLHCNNGRHHSLAIFECPMPHGCVHMMVEVNALDEVGRALDRVHANGVKLSA 241 Query: 236 NLGRHVNDYAVSFYITTPSGFMIEYGWGVREVVSD-YPVDKYRSVSIWGH 284 LG+H ND +SFYI TPSGF +EYG V D + + VS WGH Sbjct: 242 TLGQHTNDQMISFYIKTPSGFDLEYGCDGLVVDWDRHTPFESTVVSHWGH 291 Lambda K H 0.320 0.137 0.420 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: 311 Number of extensions: 19 Number of successful extensions: 5 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: 318 Length of database: 298 Length adjustment: 27 Effective length of query: 291 Effective length of database: 271 Effective search space: 78861 Effective search space used: 78861 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: 48 (23.1 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