Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate WP_086511962.1 BZY95_RS21655 catechol 1,2-dioxygenase
Query= BRENDA::P07773 (311 letters) >NCBI__GCF_002151265.1:WP_086511962.1 Length = 247 Score = 278 bits (711), Expect = 9e-80 Identities = 133/217 (61%), Positives = 161/217 (74%), Gaps = 2/217 (0%) Query: 78 LGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILH 137 LGFDHYLDMR DA DA TPRTIEGPLYVAGAPE+ G+ARMDDG D NG T+ L Sbjct: 1 LGFDHYLDMRQDAIDAEAKRVGGTPRTIEGPLYVAGAPEAEGFARMDDGQDQNGETMWLT 60 Query: 138 GTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILP 197 G + D DG P+ AKVEIWHAN+KG YS FDPT Q +N+RR+I TD G+Y R+I+P Sbjct: 61 GQVRDVDGTPIAGAKVEIWHANSKGGYSFFDPT--QSEYNLRRTIYTDAEGRYTARSIIP 118 Query: 198 AGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYAT 257 +GYG P PT +L LGRHG RPAHIHYF+SA GH+ LTTQIN+AGDPYT+DDFA+AT Sbjct: 119 SGYGVPEGAPTDVVLKSLGRHGERPAHIHYFISAPGHQHLTTQINLAGDPYTFDDFAFAT 178 Query: 258 REGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTR 294 RE LVV A + I +++GPF+E+VFD++L + Sbjct: 179 REELVVPAERIEAQDVIAQRELDGPFSEVVFDIELAK 215 Lambda K H 0.317 0.138 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: 340 Number of extensions: 14 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: 311 Length of database: 247 Length adjustment: 25 Effective length of query: 286 Effective length of database: 222 Effective search space: 63492 Effective search space used: 63492 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)
Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate WP_306766583.1 BZY95_RS20335 dioxygenase
Query= BRENDA::P07773 (311 letters) >NCBI__GCF_002151265.1:WP_306766583.1 Length = 84 Score = 117 bits (292), Expect = 1e-31 Identities = 52/84 (61%), Positives = 67/84 (79%) Query: 1 MEVKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVA 60 M VKIF+T +VQDFL+ +G +QEGGN R KQI+HR+LSDL+K I+D ++T +EYW+ V+ Sbjct: 1 MTVKIFDTPEVQDFLKTVAGFDQEGGNERAKQIMHRLLSDLFKLIDDFDVTPEEYWSAVS 60 Query: 61 YLNQLGANQEAGLLSPGLGFDHYL 84 LN LG + GLLSPGLGFDHYL Sbjct: 61 LLNALGGQTQFGLLSPGLGFDHYL 84 Lambda K H 0.317 0.138 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: 111 Number of extensions: 4 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: 311 Length of database: 84 Length adjustment: 17 Effective length of query: 294 Effective length of database: 67 Effective search space: 19698 Effective search space used: 19698 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: 43 (21.2 bits)
This GapMind analysis is from Apr 09 2024. 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