Align Catechol-2,3-dioxygenase; Catechol-induced ring cleavage extradiol dioxygenase; EC 1.13.11.2 (characterized)
to candidate SMc00115 SMc00115 hypothetical protein
Query= SwissProt::P54721 (285 letters) >FitnessBrowser__Smeli:SMc00115 Length = 296 Score = 181 bits (458), Expect = 2e-50 Identities = 101/268 (37%), Positives = 142/268 (52%), Gaps = 5/268 (1%) Query: 9 HIGYAKLTIRSLERSLQFYCNVIGFQVLKKTDRQAELTADGKRVLLILEENPSAVVLPER 68 ++ + L + LE +Y +IG ++ L G R LL L + +AV P R Sbjct: 24 YVDRSHLVVSDLETVSSWYQRIIGLSPIEANISGVTLGVAG-RPLLTLTSDGNAVRAP-R 81 Query: 69 SVTGLYHFAILLPDRKELGIALARLIEHGIAI-GHGDHAVSEALYLSDPDGNGIEMYADR 127 + GL+H A L+PDR ELG L E G+ + G DH VSEA+YL+DP+GNGIE+Y DR Sbjct: 82 NAPGLFHHAFLVPDRTELGRWLVHAAESGVQLQGASDHLVSEAIYLADPEGNGIEIYRDR 141 Query: 128 PRSTWQRDREGNYVMTTTAVDIEGLLEEAGDERKTSLPNDTIIGHIHLHVSDLKEAKAFY 187 PR W +G M T +D++ L EE LP T IGHIHL VSD+ +A AF+ Sbjct: 142 PREEWNYGADGMVAMNTLPLDLQALYEEVPKNGWDGLPAGTTIGHIHLQVSDIPQADAFF 201 Query: 188 TDVLGFDIVGNYAGMSALFVSAGGYHHHIGLNIWAGRNAPPKPTNASGLDYYTVVLPHQE 247 D LG D++ Y G S F + G YHHH+ NIW R AP + N +GL YT+ Sbjct: 202 RDALGLDLMARYPGAS--FFATGKYHHHVAANIWNSRGAPKRQGNMTGLADYTIRFREPA 259 Query: 248 ELDLVANRVKHAGYSIEETENSFRVKDP 275 L ++ +++ ++ + DP Sbjct: 260 ALAAAIRKLDALEIAVDRQGDAHSLTDP 287 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: 241 Number of extensions: 19 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: 285 Length of database: 296 Length adjustment: 26 Effective length of query: 259 Effective length of database: 270 Effective search space: 69930 Effective search space used: 69930 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: 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