Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate 3609274 Dshi_2660 (2Fe-2S)-binding domain protein (RefSeq)
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__Dino:3609274 Length = 162 Score = 164 bits (416), Expect = 5e-46 Identities = 82/156 (52%), Positives = 107/156 (68%), Gaps = 2/156 (1%) Query: 3 TLLTLSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACC 62 T +T++VNG+ R V G LL +LRD L LTGT GCD +CGAC V VDG+ AC Sbjct: 2 TSVTMTVNGKARSGEVEGRTLLSSFLRDQLHLTGTHVGCDTSQCGACVVHVDGEAVKACT 61 Query: 63 TLAHSVAGHSIETIEGLSH-EGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQP 121 LA G + TIEG+++ +G+LS +Q AF EH G QCGFCTPGM+M+A ALL+ NP+P Sbjct: 62 VLAADADGAEVTTIEGMANADGSLSAIQAAFQEHHGLQCGFCTPGMVMSAAALLKDNPKP 121 Query: 122 SRDEIRAALAGNLCRCTGYVKIIESVEAAACGSEVS 157 S EIR L GN+CRCTGY I++++ AA G +V+ Sbjct: 122 SEHEIREYLEGNICRCTGYHNIVKAI-LAASGQQVA 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: 146 Number of extensions: 8 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: 162 Length adjustment: 17 Effective length of query: 141 Effective length of database: 145 Effective search space: 20445 Effective search space used: 20445 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