Align Catechol-2,3-dioxygenase; Catechol-induced ring cleavage extradiol dioxygenase; EC 1.13.11.2 (characterized)
to candidate WP_010529186.1 ON01_RS01220 VOC family protein
Query= SwissProt::P54721 (285 letters) >NCBI__GCF_000224785.1:WP_010529186.1 Length = 284 Score = 258 bits (659), Expect = 1e-73 Identities = 130/268 (48%), Positives = 178/268 (66%), Gaps = 5/268 (1%) Query: 8 THIGYAKLTIRSLERSLQFYCNVIGFQVLKKTDRQAELTADGKRVLLILEENPSAVVLPE 67 T++G + + L+++L FY +VIGF +L++TDR+A LTADGK LL L + P+A + E Sbjct: 11 TYVGEVNINVTDLDQALSFYQHVIGFNILEQTDRKAVLTADGKTPLLTLVQ-PAAPLPKE 69 Query: 68 RSVTGLYHFAILLPDRKELGIALARLIEHGIAIGHGDHAVSEALYLSDPDGNGIEMYADR 127 +GL+HFAILLP R +L L + + G +G DH VSEALYL+DPDGNGIE+Y DR Sbjct: 70 ERTSGLFHFAILLPSRADLSSFLRHIAKAGARLGASDHLVSEALYLNDPDGNGIEVYHDR 129 Query: 128 PRSTWQRDREGNYVMTTTAVDIEGLLEEAGDERKTSLPNDTIIGHIHLHVSDLKEAKAFY 187 P S W G M+T +D + LL E+ E K LP +T++GHIHLHV++LK + FY Sbjct: 130 PSSEWSWS-NGQVTMSTEPLDADSLLAESDQEWK-GLPEETVMGHIHLHVANLKSTEKFY 187 Query: 188 TDVLGFDIVGNYAGMSALFVSAGGYHHHIGLNIWAGRNAPPKPTNASGLDYYTVVLPHQE 247 D LGF +V NY G ALF S GGYHHHIGLNIW G NAP N++GL++Y+++ P E Sbjct: 188 ADGLGFQVVTNYPG--ALFTSTGGYHHHIGLNIWNGENAPVPSDNSAGLNWYSLIFPDNE 245 Query: 248 ELDLVANRVKHAGYSIEETENSFRVKDP 275 + N ++ AG SI++ N++ V DP Sbjct: 246 SREEKVNNLERAGVSIQQENNAYIVNDP 273 Score = 42.0 bits (97), Expect = 2e-08 Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%) Query: 159 ERKTSLPNDTIIGHIHLHVSDLKEAKAFYTDVLGFDIVGNYAGMSALFVSAGGYHHHIGL 218 E+K T +G ++++V+DL +A +FY V+GF+I+ A+ + G L Sbjct: 2 EKKFFEKRTTYVGEVNINVTDLDQALSFYQHVIGFNIL-EQTDRKAVLTADG----KTPL 56 Query: 219 NIWAGRNAP-PKPTNASGLDYYTVVLPHQEELDLVANRVKHAG 260 AP PK SGL ++ ++LP + +L + AG Sbjct: 57 LTLVQPAAPLPKEERTSGLFHFAILLPSRADLSSFLRHIAKAG 99 Score = 37.4 bits (85), Expect = 4e-07 Identities = 28/119 (23%), Positives = 55/119 (46%), Gaps = 5/119 (4%) Query: 6 EDTHIGYAKLTIRSLERSLQFYCNVIGFQVLKKTDRQAELTADGKRVLLILE-ENPSAVV 64 E+T +G+ L + +L+ + +FY + +GFQV+ + G + L N Sbjct: 166 EETVMGHIHLHVANLKSTEKFYADGLGFQVVTNYPGALFTSTGGYHHHIGLNIWNGENAP 225 Query: 65 LPERSVTGLYHFAILLPDRKELGIALARLIEHGIAIGHGDHAVSEALYLSDPDGNGIEM 123 +P + GL ++++ PD + + L G++I + A ++DP GN I + Sbjct: 226 VPSDNSAGLNWYSLIFPDNESREEKVNNLERAGVSI----QQENNAYIVNDPSGNEIHL 280 Lambda K H 0.318 0.137 0.402 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: 290 Number of extensions: 23 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 285 Length of database: 284 Length adjustment: 26 Effective length of query: 259 Effective length of database: 258 Effective search space: 66822 Effective search space used: 66822 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 (21.7 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