Align Catechol 1,2-dioxygenase; EC 1.13.11.1 (characterized)
to candidate BPHYT_RS20450 BPHYT_RS20450 6-chlorohydroxyquinol-1,2-dioxygenase
Query= SwissProt::P86029 (303 letters) >FitnessBrowser__BFirm:BPHYT_RS20450 Length = 287 Score = 178 bits (451), Expect = 1e-49 Identities = 89/253 (35%), Positives = 145/253 (57%), Gaps = 6/253 (2%) Query: 6 TESVKTSLGPNATPRAKKLIASLVQHVHDFARENHLTTEDWLWGVDFINRIGQMSDSRRN 65 TE+V + R K ++ SLV+H+HDFARE +LT +W G+ F+ +G ++D +R Sbjct: 10 TEAVLARHAHSGDERLKTIVTSLVRHLHDFAREVNLTESEWEQGIRFLTDVGLITDDKRQ 69 Query: 66 EGILVCDIIGLETLVDALTNESEQSNHTSSAILGPFYLPDSPVYPNGGSIVQKAIPTDVK 125 E IL+ D +GL LV A+ N + T + + GPF++ +P Y NG + A Sbjct: 70 EFILLSDTLGLSMLVTAMANR-KPPGCTEATVFGPFFVEGAPAYRNGDDVSNGA--RGEP 126 Query: 126 CFVRGKVTDTEGKPLGGAQLEVWQCNSAGFYSQQADHDGPEFN-LRGTFITDDEGNYSFE 184 CFV G V +G+ + A++EVWQ ++ GFY Q H G + + RG + +G Y F Sbjct: 127 CFVSGTVKGADGEAVANARIEVWQADADGFYDVQ--HAGDDTHRARGVLHSLADGRYHFR 184 Query: 185 CLRPTSYPIPYDGPAGDLLKIMDRHPNRPSHIHWRVSHPGYHTLITQIYDAECPYTNNDS 244 + YPIP+DGP G +L + RHP RP+H+H+ ++ PGY L+T ++ Y ++D+ Sbjct: 185 SIVAEPYPIPHDGPVGRMLAALGRHPWRPAHLHFMITAPGYERLVTHVFREGDQYLDSDA 244 Query: 245 VYAVKDDIIVHFE 257 V+ V+ ++ ++ Sbjct: 245 VFGVRSSLVAQWK 257 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: 233 Number of extensions: 13 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: 287 Length adjustment: 26 Effective length of query: 277 Effective length of database: 261 Effective search space: 72297 Effective search space used: 72297 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