Align Catechol 1,2-dioxygenase; EC 1.13.11.1; 1,2-CTD (uncharacterized)
to candidate WP_086511962.1 BZY95_RS21655 catechol 1,2-dioxygenase
Query= curated2:P31019 (302 letters) >NCBI__GCF_002151265.1:WP_086511962.1 Length = 247 Score = 350 bits (897), Expect = e-101 Identities = 168/224 (75%), Positives = 184/224 (82%) Query: 78 LGFDHYMDMRMDAADAEAKRTGGTPRTIEGPLYVAGAPEAEGFARMDDDPDTDGETMWLH 137 LGFDHY+DMR DA DAEAKR GGTPRTIEGPLYVAGAPEAEGFARMDD D +GETMWL Sbjct: 1 LGFDHYLDMRQDAIDAEAKRVGGTPRTIEGPLYVAGAPEAEGFARMDDGQDQNGETMWLT 60 Query: 138 GQVRDTAGKPIPGAKVEIWHCNSKGGYSFFDKSQTPYNLRRTIIADNEGYYRARSVIPSG 197 GQVRD G PI GAKVEIWH NSKGGYSFFD +Q+ YNLRRTI D EG Y ARS+IPSG Sbjct: 61 GQVRDVDGTPIAGAKVEIWHANSKGGYSFFDPTQSEYNLRRTIYTDAEGRYTARSIIPSG 120 Query: 198 YGVPEGAPTDQVLKLLGRHGERPAHIHYFISAPGHQHLTTQINLAGDPYTYDDFAFATRQ 257 YGVPEGAPTD VLK LGRHGERPAHIHYFISAPGHQHLTTQINLAGDPYT+DDFAFATR+ Sbjct: 121 YGVPEGAPTDVVLKSLGRHGERPAHIHYFISAPGHQHLTTQINLAGDPYTFDDFAFATRE 180 Query: 258 DLAAEGKRVENHPAAQQYGVEGTVTEVIFNIELSPTAEEELQAR 301 +L +R+E Q ++G +EV+F+IEL+ T ELQ R Sbjct: 181 ELVVPAERIEAQDVIAQRELDGPFSEVVFDIELAKTDVAELQTR 224 Lambda K H 0.317 0.136 0.411 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: 340 Number of extensions: 11 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: 302 Length of database: 247 Length adjustment: 25 Effective length of query: 277 Effective length of database: 222 Effective search space: 61494 Effective search space used: 61494 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: 47 (22.7 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