Align protocatechuate 4,5-dioxygenase α subunit (EC 1.13.11.8; EC 1.13.11.57) (characterized)
to candidate WP_011382704.1 AMB_RS01305 protocatechuate 4,5-dioxygenase subunit alpha
Query= metacyc::MONOMER-3165 (149 letters) >NCBI__GCF_000009985.1:WP_011382704.1 Length = 117 Score = 96.7 bits (239), Expect = 1e-25 Identities = 43/108 (39%), Positives = 67/108 (62%) Query: 10 VPGTIIFDAEQSRKGYWLNQFCMSLMKAENRERFRADERAYLDEWAMTEEQKQAVLARDL 69 +PGT +FD + +RKGY LN+ C S ENR+ F D AY D++ + E+QK+AV++ + Sbjct: 9 IPGTTLFDGDMARKGYALNKMCFSFNSEENRQEFLKDPGAYCDKFGLNEQQKKAVISLQV 68 Query: 70 NWCMRTGGNIYFLAKIGATDGKSFQQMAGSMTGMTEEEYRAMMMGGGR 117 + GGN YF+AK+G Q + TG+T+EE++A ++ GR Sbjct: 69 LDMLAAGGNAYFIAKLGGIYKLDMQDVGAQQTGVTKEEFQAKLVAAGR 116 Lambda K H 0.316 0.131 0.393 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: 76 Number of extensions: 1 Number of successful extensions: 1 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: 149 Length of database: 117 Length adjustment: 15 Effective length of query: 134 Effective length of database: 102 Effective search space: 13668 Effective search space used: 13668 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: 41 (20.4 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