Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate 5209813 Shew_2266 2Fe-2S iron-sulfur cluster binding domain-containing protein (RefSeq)
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__PV4:5209813 Length = 168 Score = 123 bits (309), Expect = 1e-33 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 4/147 (2%) Query: 5 LTLSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTL 64 L L +NG+ N ++ +RD LGLTGTK GC G CGACT+ VDG+P AC T Sbjct: 6 LGLKINGKDYTLDADPNMPVLWAIRDLLGLTGTKYGCGAGLCGACTIHVDGEPARACLTS 65 Query: 65 AHSVAGHSIETIEGLSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSRD 124 V G + TIEGL+ +G L++A+ ++ QCG+C G +M+A ALL + PQP+ Sbjct: 66 LKQVQGKQVTTIEGLAADG----LKQAWRDNNVPQCGYCQAGQLMSAAALLSQYPQPNDA 121 Query: 125 EIRAALAGNLCRCTGYVKIIESVEAAA 151 +I A+ GNLCRC Y +I +++ A+ Sbjct: 122 QIEEAMVGNLCRCGTYTRIKAAIKQAS 148 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: 116 Number of extensions: 9 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: 168 Length adjustment: 18 Effective length of query: 140 Effective length of database: 150 Effective search space: 21000 Effective search space used: 21000 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