Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate WP_004674373.1 RHE_RS29575 2Fe-2S iron-sulfur cluster-binding protein
Query= metacyc::MONOMER-17403 (163 letters) >NCBI__GCF_000092045.1:WP_004674373.1 Length = 94 Score = 74.7 bits (182), Expect = 4e-19 Identities = 41/89 (46%), Positives = 56/89 (62%), Gaps = 2/89 (2%) Query: 71 VLAVRCEGRYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLRRNPSPT 130 +LAV+ +G IET+ A+ L R+Q+ F + G QC F P +A LLR +P T Sbjct: 1 MLAVQADGSEIETMAREASI--LGRIQEAFRQHHGLQCEFVGPVSSLAIIDLLRHHPLET 58 Query: 131 DEEIRTALSGNLCRCTGYAKIVESVQAAA 159 D++IR ALSGN+CRCTGY IV +V+ A Sbjct: 59 DDKIREALSGNICRCTGYENIVNAVRELA 87 Lambda K H 0.322 0.138 0.425 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: 55 Number of extensions: 3 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: 163 Length of database: 94 Length adjustment: 14 Effective length of query: 149 Effective length of database: 80 Effective search space: 11920 Effective search space used: 11920 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 (21.9 bits) S2: 41 (20.4 bits)
This GapMind analysis is from Apr 09 2024. 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