Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate WP_038019894.1 G579_RS17460 molybdopterin-dependent oxidoreductase
Query= metacyc::MONOMER-18073 (163 letters) >NCBI__GCF_000423825.1:WP_038019894.1 Length = 822 Score = 103 bits (256), Expect = 9e-27 Identities = 56/139 (40%), Positives = 76/139 (54%), Gaps = 1/139 (0%) Query: 16 VNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLFAVQA 75 VNGV P + L+ LR+ LGL G+K C CGAC V L+G V+ C A Sbjct: 6 VNGVRQMVEADPDMPLLWALRDRLGLMGSKPSCGIGACGACIVHLDGAPVRGCVTPLAAA 65 Query: 76 DGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEEEVRD 135 G E+TTIEGL+ D HP+ A+ QCG+C PG IM A LL +P P++ ++ Sbjct: 66 AGKEVTTIEGLAADPH-HPLLRAWLAEDVSQCGYCQPGQIMAAAALLAAHPQPTDLDIDA 124 Query: 136 GLHGNICRCTGYQNIVKAV 154 + +CRC YQ I +A+ Sbjct: 125 AMAHVLCRCGTYQRIRRAI 143 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: 266 Number of extensions: 6 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: 822 Length adjustment: 29 Effective length of query: 134 Effective length of database: 793 Effective search space: 106262 Effective search space used: 106262 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: 49 (23.5 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