Align protocatechuate 3,4-dioxygenase α subunit (EC 1.13.11.3) (characterized)
to candidate CCNA_02492 CCNA_02492 protocatechuate 3,4-dioxygenase alpha chain
Query= metacyc::MONOMER-3186 (201 letters) >FitnessBrowser__Caulo:CCNA_02492 Length = 216 Score = 132 bits (331), Expect = 6e-36 Identities = 86/210 (40%), Positives = 120/210 (57%), Gaps = 26/210 (12%) Query: 5 LLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNR--------------LAKPDAPGEHI 50 L +TPSQT GP+ H GL + + D EI R AK + GE I Sbjct: 18 LFGQTPSQTVGPFFHYGLPWKGCADLIGDSEIGARPELFPAEHYVLASPTAKGEVAGEPI 77 Query: 51 LLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTV 110 ++ G V D +G V D+ +E+WQADA G Y D + + F +GR A+T + G + T+ Sbjct: 78 VIEGAVLDADGKAVSDAMIEIWQADAAGRYVDG-SSHSGFIGWGR-ASTGEDGVYRFVTI 135 Query: 111 KPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRET 170 +PG V++ APHI I +F RG+ L TRLYF+D+A ANA P+L L+ +RR+T Sbjct: 136 RPGRVDD----QQAPHIAIGVFGRGVIKRLATRLYFEDDA-ANAADPILALV-PAERRQT 189 Query: 171 LIAKRCEVDGKTAYRFDIRIQGEGETVFFD 200 LIA++ A+RFDI +QG+ ETVFFD Sbjct: 190 LIARKV----GQAWRFDIVLQGDRETVFFD 215 Lambda K H 0.319 0.137 0.423 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: 168 Number of extensions: 11 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: 201 Length of database: 216 Length adjustment: 21 Effective length of query: 180 Effective length of database: 195 Effective search space: 35100 Effective search space used: 35100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 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