Align chlorocatechol 1,2-dioxygenase 2 monomer (characterized)
to candidate H281DRAFT_03865 H281DRAFT_03865 protocatechuate 3,4-dioxygenase, beta subunit
Query= metacyc::MONOMER-14665 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_03865 Length = 234 Score = 68.6 bits (166), Expect = 1e-16 Identities = 42/117 (35%), Positives = 62/117 (52%), Gaps = 17/117 (14%) Query: 100 GDTLIFRGEVVDQEGAPLADVLLDMWQADAAGEY-----SFINPTLPDYLFRGKIRTDEN 154 G+ +I G V+D+ G P+ + L+++WQA+AAG Y P P++L G+ TD Sbjct: 73 GERIIVTGRVLDEGGRPVRNTLVEIWQANAAGRYVHKMDQHDAPLDPNFLGAGRCITDNE 132 Query: 155 GRFTLRTIVPAPYEIPKNGPTGALLAAAGWHAWRPAHLHWIIAKEGYES-LTTQLYF 210 GR+ TI P Y N P +AWRP H+H+ + E + S L TQ+YF Sbjct: 133 GRYRFLTIKPGAYPW-GNHP----------NAWRPNHIHFSLFGEHFGSRLVTQMYF 178 Lambda K H 0.316 0.134 0.410 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: 181 Number of extensions: 14 Number of successful extensions: 3 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: 254 Length of database: 234 Length adjustment: 24 Effective length of query: 230 Effective length of database: 210 Effective search space: 48300 Effective search space used: 48300 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: 46 (22.3 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