Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate 16948 b2868 xanthine dehydrogenase, Fe-S binding subunit (NCBI)
Query= metacyc::MONOMER-17403 (163 letters) >FitnessBrowser__Keio:16948 Length = 159 Score = 125 bits (313), Expect = 4e-34 Identities = 67/126 (53%), Positives = 80/126 (63%), Gaps = 3/126 (2%) Query: 32 LVDYLRDIAGLTGVKTGCDGGECGACTVLIDGEAAPSCLVLAVRCEGRYIETVEGLAANG 91 L + LR+ GL VK GC GECGACTVL+DG A SCL LA EG+ I T+EG A G Sbjct: 28 LSELLRE-QGLLSVKQGCCVGECGACTVLVDGTAIDSCLYLAAWAEGKEIRTLEGEAKGG 86 Query: 92 RLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLR--RNPSPTDEEIRTALSGNLCRCTGYA 149 +L +QQ + + QCGFCTPG+IMA +L R T EIR L+GNLCRCTGY Sbjct: 87 KLSHVQQAYAKSGAVQCGFCTPGLIMATTAMLAKPREKPLTITEIRRGLAGNLCRCTGYQ 146 Query: 150 KIVESV 155 IV +V Sbjct: 147 MIVNTV 152 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: 140 Number of extensions: 11 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: 163 Length of database: 159 Length adjustment: 17 Effective length of query: 146 Effective length of database: 142 Effective search space: 20732 Effective search space used: 20732 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: 43 (21.2 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