Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate PfGW456L13_3353 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-17403 (163 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3353 Length = 151 Score = 130 bits (328), Expect = 7e-36 Identities = 72/151 (47%), Positives = 96/151 (63%), Gaps = 2/151 (1%) Query: 12 LLGLNVNGRWREDAVTDDMLLVDYLRDIAGLTGVKTGCDGGECGACTVLIDGEAAPSCLV 71 +L LN+NG+ +E V DM L+ LRD+A LTG K GC +CGACTV +DG SC+ Sbjct: 1 MLTLNINGQDQELDVPADMPLLWVLRDVAHLTGTKFGCGIAQCGACTVHVDGAPLRSCIT 60 Query: 72 LAVR-CEGRYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLRRNPSPT 130 A G+ I T+EGL+A+G H +QQ + E QCG+C G IM+A LL + P PT Sbjct: 61 PATAVAHGQKILTIEGLSADGS-HPVQQAWAELDVVQCGYCQSGQIMSAAALLAKIPKPT 119 Query: 131 DEEIRTALSGNLCRCTGYAKIVESVQAAAEI 161 D +I ALSGN+CRC Y +I +V+ AAE+ Sbjct: 120 DSDIDQALSGNICRCGTYPRIRAAVKRAAEL 150 Lambda K H 0.322 0.138 0.425 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: 110 Number of extensions: 7 Number of successful extensions: 3 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: 163 Length of database: 151 Length adjustment: 17 Effective length of query: 146 Effective length of database: 134 Effective search space: 19564 Effective search space used: 19564 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 (21.9 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