Align chlorocatechol 1,2-dioxygenase 2 monomer (characterized)
to candidate CCNA_02491 CCNA_02491 protocatechuate 3,4-dioxygenase beta chain
Query= metacyc::MONOMER-14665 (254 letters) >FitnessBrowser__Caulo:CCNA_02491 Length = 235 Score = 70.5 bits (171), Expect = 3e-17 Identities = 51/160 (31%), Positives = 83/160 (51%), Gaps = 22/160 (13%) Query: 100 GDTLIFRGEVVDQEGAPLADVLLDMWQADAAGEY-----SFINPTLPDYLFRGKIRTDEN 154 G +I G V+D++G P+ + ++++WQA+AAG Y + P P++ G++ TD+ Sbjct: 70 GQRIIVSGRVLDEDGRPVPNTVMEIWQANAAGRYIHKKDQWDAPLDPNFTGAGRVITDDE 129 Query: 155 GRFTLRTIVPAPYEIPKNGPTGALLAAAGWHAWRPAHLHWIIAKEGYES-LTTQLYFENG 213 GR+ +I P Y P G +AWRPAH+H + + + L TQ+YF + Sbjct: 130 GRYQFVSIRPGAY------PWG-----NHHNAWRPAHIHLSLLGPAFATRLVTQMYFPDD 178 Query: 214 QWTGSD-VANAVK---PELLLSLDKIEAQSGPHFETSYKF 249 D +ANAV + L+S IEA + P++ Y F Sbjct: 179 PLIEIDPIANAVPLPYRQRLVSRFDIEA-TKPNWALGYLF 217 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: 194 Number of extensions: 13 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: 235 Length adjustment: 24 Effective length of query: 230 Effective length of database: 211 Effective search space: 48530 Effective search space used: 48530 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