Align protocatechuate 4,5-dioxygenase (subunit 1/2) (EC 1.13.11.8) (characterized)
to candidate Ga0059261_0529 Ga0059261_0529 Catalytic LigB subunit of aromatic ring-opening dioxygenase
Query= BRENDA::G2IQQ3 (302 letters) >FitnessBrowser__Korea:Ga0059261_0529 Length = 297 Score = 421 bits (1083), Expect = e-123 Identities = 196/285 (68%), Positives = 229/285 (80%), Gaps = 2/285 (0%) Query: 1 MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60 MAR+T G+ SSH+P LG A G +DY+GP+F GY R+W K PDVV+LVYND Sbjct: 1 MARITAGVASSHVPLLGVAHDLGKDRDDYFGPIFAGYDWTREWEK--AEKPDVVVLVYND 58 Query: 61 HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120 HASAFDM IIPTFAIGC E + PADEGWGPR VPDV GHPDLAWHIAQSLILDEFDMTI+ Sbjct: 59 HASAFDMKIIPTFAIGCGERYAPADEGWGPRKVPDVHGHPDLAWHIAQSLILDEFDMTII 118 Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFP 180 N+MDVDHG TVPLSM+FG EWPCKVIP VNVVTYPPPSG RC+ALG++I AV SFP Sbjct: 119 NEMDVDHGLTVPLSMMFGHVPEWPCKVIPLAVNVVTYPPPSGNRCWALGEAIARAVASFP 178 Query: 181 EDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEG 240 E+LNV VWGTGGMSHQLQGPRAGLIN+E+D NF+D L+ E L +PHI+YLRE+GSEG Sbjct: 179 EELNVQVWGTGGMSHQLQGPRAGLINREWDNNFLDGLVGASEHLRHVPHIEYLRETGSEG 238 Query: 241 IELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAG 285 IE+VMWLIMRGAL ++ L+ YH+P SNTA+G ++L+P+ G Sbjct: 239 IEMVMWLIMRGALGKRTAMLHRHYHVPCSNTAIGHLVLRPDNGEG 283 Lambda K H 0.319 0.138 0.439 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: 425 Number of extensions: 8 Number of successful extensions: 2 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: 302 Length of database: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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 (21.8 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