Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate WP_012759947.1 RLEG_RS32870 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-18073 (163 letters) >NCBI__GCF_000023185.1:WP_012759947.1 Length = 174 Score = 122 bits (307), Expect = 2e-33 Identities = 59/145 (40%), Positives = 85/145 (58%) Query: 10 IKIKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCT 69 + + + VN L+ P L+ LR +L L G K GC CGAC VL++G+ V+SCT Sbjct: 5 VSVSLNVNDALWRVSAKPETPLLYILRNDLCLNGPKYGCGLGECGACAVLVDGRPVRSCT 64 Query: 70 LFAVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPS 129 + + T+EGL+VD LHP+Q+AF E A QCG+C GMI+ LL+ N +P Sbjct: 65 VPLGAIGKRRVITLEGLAVDGLLHPVQQAFIEEAAAQCGYCLNGMIIATVGLLQRNTDPD 124 Query: 130 EEEVRDGLHGNICRCTGYQNIVKAV 154 E ++RD L ++CRC + I+ AV Sbjct: 125 ESDIRDALRHHLCRCGTHVEILAAV 149 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: 96 Number of extensions: 5 Number of successful extensions: 1 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: 174 Length adjustment: 18 Effective length of query: 145 Effective length of database: 156 Effective search space: 22620 Effective search space used: 22620 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 Apr 09 2024. 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