Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate H281DRAFT_02675 H281DRAFT_02675 carbon-monoxide dehydrogenase small subunit
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__Burk376:H281DRAFT_02675 Length = 173 Score = 147 bits (372), Expect = 7e-41 Identities = 75/144 (52%), Positives = 91/144 (63%), Gaps = 1/144 (0%) Query: 9 VNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTLAHSV 68 VNG E V +L D+LR L LTGT GC+ G CGACTVL++G+ AC TLA V Sbjct: 10 VNGTAYEREVESRRMLGDFLRHDLELTGTHYGCEHGVCGACTVLIEGRTARACLTLAAQV 69 Query: 69 AGHSIETIEGLSH-EGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSRDEIR 127 G S+ T+EGL+H +G L+ LQ+AF E QCGFCTPGM+M LL PS EIR Sbjct: 70 NGRSLTTVEGLAHADGTLNELQKAFTETHALQCGFCTPGMLMTLTELLNETDSPSESEIR 129 Query: 128 AALAGNLCRCTGYVKIIESVEAAA 151 A+ GNLCRCTGY I+ + AA Sbjct: 130 EAITGNLCRCTGYQPIVAAALLAA 153 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: 143 Number of extensions: 13 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: 158 Length of database: 173 Length adjustment: 18 Effective length of query: 140 Effective length of database: 155 Effective search space: 21700 Effective search space used: 21700 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