Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate Ac3H11_3428 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3428 Length = 168 Score = 123 bits (308), Expect = 2e-33 Identities = 62/136 (45%), Positives = 87/136 (63%), Gaps = 4/136 (2%) Query: 31 LVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLFAVQADGAEITTIEGL---- 86 L+ LR +L L G K GC CGACTVL++G + ++C + A G E+TT+EGL Sbjct: 29 LLHVLRNDLLLNGPKYGCGLGQCGACTVLVDGIAARACVIPAQGVAGREVTTLEGLPGRC 88 Query: 87 SVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEEEVRDGLHGNICRCTG 146 S + LHP+Q+AF + A QCG+C GM+M A LL+ NP+P E VR L GN+CRC Sbjct: 89 SRTAGLHPVQQAFVDEQAAQCGYCLNGMVMMAVALLERNPDPDEAAVRRELSGNLCRCGT 148 Query: 147 YQNIVKAVLDASRRLR 162 + I++AVL A++ +R Sbjct: 149 HVEIIRAVLRAAQLMR 164 Lambda K H 0.322 0.138 0.409 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: 5 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: 163 Length of database: 168 Length adjustment: 18 Effective length of query: 145 Effective length of database: 150 Effective search space: 21750 Effective search space used: 21750 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