Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate GFF2055 PGA1_c20880 molybdenum hydroxylase family protein, small subunit
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__Phaeo:GFF2055 Length = 161 Score = 161 bits (407), Expect = 5e-45 Identities = 81/154 (52%), Positives = 105/154 (68%), Gaps = 2/154 (1%) Query: 5 LTLSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTL 64 +T++VNGR V G LL +LR+ LGLTGT GCD +CGAC V VDG+ AC L Sbjct: 4 VTMTVNGRTASGEVEGRTLLSGFLREELGLTGTHVGCDTSQCGACVVHVDGKAVKACTML 63 Query: 65 AHSVAGHSIETIEG-LSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSR 123 A G + TIEG + +G L+ +Q+AF +H G QCGFCTPGM+M+A ALL+ NP+PS Sbjct: 64 AAEADGADVATIEGQAAPDGTLNTIQQAFQDHHGLQCGFCTPGMVMSAAALLKDNPKPSE 123 Query: 124 DEIRAALAGNLCRCTGYVKIIESVEAAACGSEVS 157 EIR L GNLCRCTGY I++++ AA+ G +VS Sbjct: 124 QEIREYLEGNLCRCTGYHNIVKAIMAAS-GQDVS 156 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: 147 Number of extensions: 12 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: 161 Length adjustment: 17 Effective length of query: 141 Effective length of database: 144 Effective search space: 20304 Effective search space used: 20304 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