Align Metapyrocatechase; MPC; EC 1.13.11.2; CatO2ase; Catechol 2,3-dioxygenase (uncharacterized)
to candidate RR42_RS31960 RR42_RS31960 biphenyl 2,3-dioxygenase
Query= curated2:Q53034 (318 letters) >FitnessBrowser__Cup4G11:RR42_RS31960 Length = 298 Score = 157 bits (396), Expect = 4e-43 Identities = 99/289 (34%), Positives = 146/289 (50%), Gaps = 9/289 (3%) Query: 4 VTGIGYIGIGVSDLPAWEEFAETIGFQIRERGEDGTLYLRMDKAHHRVAVHPTGEDDLTY 63 + +GYI + +D W + E + G LYL+MD+ +R + P +D Sbjct: 4 IRALGYIVVESTDTERWRHYGEQVLGMACTNAPHGALYLKMDERDYRYLIVPGKQDRYLA 63 Query: 64 VGWQVADENGFDELERTLRAAGVPVEMAGEDDAELRGVARLMRFEDPSGIKSEAYYGLVS 123 GW++A E F+ TLRAA V V A E + R + F DPSG + E ++G+ S Sbjct: 64 SGWELAGEAAFNHALATLRAANVEVTHASEAERIQRRAQAVAWFADPSGNRHEIFWGMRS 123 Query: 124 EPEVPYVSPYAVD-FVTEDQGFGHIVVMVDDYDETMRFYREVLGLQTSDLVK----VGAG 178 + + +VSP V FVT+ G GH V+ +DET F R+V+G SD+ + Sbjct: 124 D-FLRFVSPIGVSCFVTDPLGAGHSVLPAPAFDETYAFLRDVMGFGLSDIFRARFTTDPA 182 Query: 179 GVQTRMAFMRC-NPRQHSLAFWAGDSTTRLNHFMLQTQTLDQTGMTLDRC-FHGGIPATN 236 + R+ F+ C N R HSLA + + + H M + + + G LDR HG + Sbjct: 183 EPEKRIHFLHCGNGRHHSLAIFEAPAPSGCVHVMAEVPDMGEVGRALDRAQQHGVALSAT 242 Query: 237 LGRHVNDYAVSFYITTPSGFMIEYGWGVREV-VSDYPVDKYRSVSIWGH 284 LG+H ND VSFY+ TP GF +EYG+G V S + + VS+WGH Sbjct: 243 LGQHCNDRIVSFYMKTPGGFDLEYGYGGLVVDWSQHAAFEATRVSLWGH 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: 301 Number of extensions: 20 Number of successful extensions: 4 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