Align protocatechuate 4,5-dioxygenase (subunit 1/2) (EC 1.13.11.8) (characterized)
to candidate WP_011382705.1 AMB_RS01310 protocatechuate 3,4-dioxygenase subunit beta
Query= BRENDA::G2IQQ3 (302 letters) >NCBI__GCF_000009985.1:WP_011382705.1 Length = 278 Score = 253 bits (646), Expect = 4e-72 Identities = 126/284 (44%), Positives = 177/284 (62%), Gaps = 13/284 (4%) Query: 1 MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60 MA++ GI +H+P +G AI + YW P F G+ P+ W+ + PDV ++VYND Sbjct: 1 MAKIVGGINVTHVPYIGRAIAGNLQQDAYWKPFFDGFPPVHAWLDKV--KPDVAVVVYND 58 Query: 61 HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120 H F ++ +PTF+IG A + ADEGWG V KG DL+WH+ SLI EFD+T Sbjct: 59 HGLNFFLDKMPTFSIGAAAEYSNADEGWGIPTVAPFKGDQDLSWHLIDSLIEAEFDLTTC 118 Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCK-----VIPFPVNVVTYPPPSGKRCFALGDSIRAA 175 +M VDH T+PL ++ WP + +P N V +P PS KRC A G +I A Sbjct: 119 QEMLVDHAFTLPLELL------WPTRNAALRTVPICQNTVQFPLPSAKRCLAFGRAINKA 172 Query: 176 VESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRE 235 +ES+ D V V GTGG+SHQL+G RAG INK+FDL F+DKL+SDP+ +++ + + Sbjct: 173 IESWDSDARVVVLGTGGLSHQLEGTRAGFINKKFDLEFMDKLVSDPDWVTQYSNEDLVEL 232 Query: 236 SGSEGIELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQ 279 +G++GIEL+ WL RGAL KV+ ++T YHIP SNTA G + ++ Sbjct: 233 TGTQGIELLNWLTCRGALGGKVKAVHTNYHIPISNTAAGLLAME 276 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: 278 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: 302 Length of database: 278 Length adjustment: 26 Effective length of query: 276 Effective length of database: 252 Effective search space: 69552 Effective search space used: 69552 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