Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate GFF2055 PGA1_c20880 molybdenum hydroxylase family protein, small subunit
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__Phaeo:GFF2055 Length = 161 Score = 186 bits (471), Expect = 2e-52 Identities = 87/150 (58%), Positives = 114/150 (76%), Gaps = 1/150 (0%) Query: 10 IKIKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCT 69 +K+ + VNG V R LL FLREELGLTGT +GCDT+ CGAC V ++GK+VK+CT Sbjct: 2 VKVTMTVNGRTASGEVEGRTLLSGFLREELGLTGTHVGCDTSQCGACVVHVDGKAVKACT 61 Query: 70 LFAVQADGAEITTIEGLSV-DSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNP 128 + A +ADGA++ TIEG + D L+ IQ+AF+++ LQCGFCTPGM+M A LLK+NP P Sbjct: 62 MLAAEADGADVATIEGQAAPDGTLNTIQQAFQDHHGLQCGFCTPGMVMSAAALLKDNPKP 121 Query: 129 SEEEVRDGLHGNICRCTGYQNIVKAVLDAS 158 SE+E+R+ L GN+CRCTGY NIVKA++ AS Sbjct: 122 SEQEIREYLEGNLCRCTGYHNIVKAIMAAS 151 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: 133 Number of extensions: 4 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: 161 Length adjustment: 18 Effective length of query: 145 Effective length of database: 143 Effective search space: 20735 Effective search space used: 20735 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