Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate 8499876 DvMF_0641 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__Miya:8499876 Length = 905 Score = 146 bits (369), Expect = 8e-40 Identities = 75/150 (50%), Positives = 99/150 (66%), Gaps = 3/150 (2%) Query: 16 VNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLFAVQA 75 VNG+ V P L D LRE+L LTG K+GC CGAC+V+L+GK V+SC + Sbjct: 8 VNGIPRNLVVDPEATLADVLREQLLLTGVKVGCGEGQCGACSVILDGKVVRSCAYKMRRL 67 Query: 76 -DGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEEEVR 134 DGA +TTIEG+ LHP+Q A+ + QCGFCTPG I+ A LL+EN +PS ++VR Sbjct: 68 PDGASVTTIEGVGSPDCLHPLQLAWTAHGGAQCGFCTPGFIVSARQLLEENKSPSRDDVR 127 Query: 135 DGL--HGNICRCTGYQNIVKAVLDASRRLR 162 D H N+CRCTGY+ +V AV+DA++ LR Sbjct: 128 DWFQKHRNVCRCTGYKPLVDAVMDAAKVLR 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: 368 Number of extensions: 23 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: 905 Length adjustment: 30 Effective length of query: 133 Effective length of database: 875 Effective search space: 116375 Effective search space used: 116375 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 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