Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate 6939345 Sama_3438 isoquinoline 1-oxidoreductase, alpha subunit, putative (RefSeq)
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__SB2B:6939345 Length = 151 Score = 124 bits (312), Expect = 5e-34 Identities = 64/145 (44%), Positives = 90/145 (62%), Gaps = 4/145 (2%) Query: 4 LLTLSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCT 63 + +L +NGR L+ LRD +GLTGTK GC G CGACTV VDG+P AC T Sbjct: 1 MTSLKINGRLFTLDADPKMPLLWALRDLMGLTGTKYGCGAGLCGACTVHVDGEPMRACLT 60 Query: 64 LAHSVAGHSIETIEGLSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSR 123 S+ G S+ TIEGL+ E +L+ ++ H QCGFC G +M+A AL+ ++P+PS Sbjct: 61 SIKSLEGKSVTTIEGLADE----QLKDSWRRHKVPQCGFCQAGQLMSAAALVSKHPRPSD 116 Query: 124 DEIRAALAGNLCRCTGYVKIIESVE 148 +I A+AGN+CRC Y +I +++ Sbjct: 117 SQIDEAMAGNICRCGTYTRIRAAIK 141 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: 118 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: 151 Length adjustment: 17 Effective length of query: 141 Effective length of database: 134 Effective search space: 18894 Effective search space used: 18894 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