Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate 207007 DVU1559 aldehyde oxidoreductase (TIGR)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__DvH:207007 Length = 906 Score = 139 bits (349), Expect = 2e-37 Identities = 70/156 (44%), Positives = 96/156 (61%), Gaps = 3/156 (1%) Query: 10 IKIKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCT 69 IK V +NG P L +LRE LGLT K+GC CG+C V+++GK V+SC+ Sbjct: 2 IKRMVTINGAPRMAITRPDTTLATYLRESLGLTSVKVGCGQGHCGSCNVIVDGKLVRSCS 61 Query: 70 L-FAVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNP 128 + +GA ITT+EG+ LHP+Q A+ + A QCGFC+PG I+ A L+ NP P Sbjct: 62 YKMSRLTEGATITTLEGIGTPDNLHPLQVAWMAHGAAQCGFCSPGFIVSAKALIDTNPKP 121 Query: 129 SEEEVRDGL--HGNICRCTGYQNIVKAVLDASRRLR 162 S ++VRD H N CRCTGY+ +V AV+DA+ +R Sbjct: 122 SRDDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVVR 157 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: 360 Number of extensions: 20 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: 906 Length adjustment: 30 Effective length of query: 133 Effective length of database: 876 Effective search space: 116508 Effective search space used: 116508 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