Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate CCNA_02353 CCNA_02353 membrane-bound aldehyde dehydrogenase iron-sulfur protein
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__Caulo:CCNA_02353 Length = 154 Score = 125 bits (313), Expect = 4e-34 Identities = 66/145 (45%), Positives = 88/145 (60%) Query: 7 LSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTLAH 66 L+VNG R V G+ L+ LRDTLGL GTK GC CGACTV +DG P AC T Sbjct: 5 LTVNGESRIADVDGDTPLLWVLRDTLGLVGTKYGCGAALCGACTVHLDGVPVRACVTPIS 64 Query: 67 SVAGHSIETIEGLSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSRDEI 126 V + TIEG+ +++Q A+ QCG+C G IM+A ALL P+P+ +EI Sbjct: 65 GVGEQKVTTIEGVGKTTVGAKVQAAWKAVDTPQCGYCQAGQIMSATALLATTPKPTDEEI 124 Query: 127 RAALAGNLCRCTGYVKIIESVEAAA 151 AA+ GNLCRC Y++I ++++ AA Sbjct: 125 DAAMNGNLCRCATYIRIKKAIKVAA 149 Lambda K H 0.320 0.135 0.412 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: 110 Number of extensions: 5 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: 158 Length of database: 154 Length adjustment: 17 Effective length of query: 141 Effective length of database: 137 Effective search space: 19317 Effective search space used: 19317 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: 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