Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate WP_011937928.1 GURA_RS05055 molybdopterin cofactor-binding domain-containing protein
Query= metacyc::MONOMER-17403 (163 letters) >NCBI__GCF_000016745.1:WP_011937928.1 Length = 931 Score = 121 bits (303), Expect = 4e-32 Identities = 65/148 (43%), Positives = 87/148 (58%), Gaps = 3/148 (2%) Query: 17 VNGRWREDAVTDDMLLVDYLRDIAGLTGVKTGCDGGECGACTVLIDGEAAPSCLVLAVRC 76 VNG R V + LL D LR LTG K GC G+CGAC V++DG+ SC+V + Sbjct: 8 VNGIERTLIVDQEALLSDVLRKQLHLTGTKVGCGTGQCGACNVIMDGKLVRSCVVKMKKV 67 Query: 77 EG-RYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLRRNPSPTDEEIR 135 E I T+EG+ LH +Q+ F QCGFCTPG I++ + LL NP+PT E++R Sbjct: 68 ENLAKITTIEGIGTPLNLHPIQKAFIFHGALQCGFCTPGFIVSTKALLDENPNPTREDVR 127 Query: 136 TALS--GNLCRCTGYAKIVESVQAAAEI 161 N CRCTGY+ IV++V AA++ Sbjct: 128 DWFQKYRNACRCTGYSMIVDAVMDAAKV 155 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: 374 Number of extensions: 21 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: 163 Length of database: 931 Length adjustment: 30 Effective length of query: 133 Effective length of database: 901 Effective search space: 119833 Effective search space used: 119833 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: 50 (23.9 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