Align Catechol 1,2-dioxygenase; EC 1.13.11.1 (characterized)
to candidate RR42_RS32880 RR42_RS32880 hydroxyquinol 1,2-dioxygenase
Query= SwissProt::P86029 (303 letters) >FitnessBrowser__Cup4G11:RR42_RS32880 Length = 295 Score = 194 bits (492), Expect = 3e-54 Identities = 108/282 (38%), Positives = 153/282 (54%), Gaps = 9/282 (3%) Query: 3 QAFTESVKTSLGPNATPRAKKLIASLVQHVHDFARENHLTTEDWLWGVDFINRIGQMSDS 62 + T++V R K+++ SLVQH+H FARE HLT +W G+ F+ +G S Sbjct: 7 ETITQAVLARHADMPNGRMKEIMTSLVQHLHAFAREVHLTEAEWAEGIKFLTEVGHTCTS 66 Query: 63 RRNEGILVCDIIGLETLVDALTNESEQSNHTSSAILGPFYLPDSPVYPNGGSIVQKAIPT 122 R E IL+ D +GL TLV A N + T + + GPFY+ D+P Y G + T Sbjct: 67 SRQEFILLSDTLGLSTLVTA-QNHKKPRGCTEATVFGPFYVDDAPEYELGADVANGM--T 123 Query: 123 DVKCFVRGKVTDTEGKPLGGAQLEVWQCNSAGFYS-QQADHDGPEFNLRGTFITDDEGNY 181 C+V GKV G+ + A+LEVWQ +S GFY QQA DG + RGT D+ G + Sbjct: 124 GEPCYVSGKVKSVTGEAVPNARLEVWQADSEGFYDVQQAGLDGHQG--RGTLTADERGGF 181 Query: 182 SFECLRPTSYPIPYDGPAGDLLKIMDRHPNRPSHIHWRVSHPGYHTLITQIYDAECPYTN 241 F+ + YPIP+DGP G +L M RHP RP+H+H+ +S PG+ TLIT ++ Y + Sbjct: 182 HFKSIVAECYPIPHDGPVGRMLDAMGRHPWRPAHLHFMISAPGFETLITHVFREGGEYLD 241 Query: 242 NDSVYAVKDDII---VHFEKVDNKDKDLVGKVEYKLDYDISL 280 +D+V+ V+ +I V E D Y LD+D L Sbjct: 242 SDAVFGVRSSLIGDWVRHEAGTAPDGTSSATPFYTLDFDFIL 283 Lambda K H 0.316 0.134 0.407 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: 280 Number of extensions: 16 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: 303 Length of database: 295 Length adjustment: 27 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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: 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