Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate GFF1178 Psest_1211 xanthine dehydrogenase, small subunit
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__psRCH2:GFF1178 Length = 482 Score = 105 bits (261), Expect = 1e-27 Identities = 54/147 (36%), Positives = 80/147 (54%), Gaps = 11/147 (7%) Query: 22 ERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVL--------LNGKSVKSCTLFAV 73 ER + P ++ +LRE G TGTK GC + CGACTV+ L +++ SC F Sbjct: 13 ERALDPNTTVLQYLREHRGKTGTKEGCASGDCGACTVVVGELVDDRLRYRTLNSCLTFVS 72 Query: 74 QADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSE--- 130 G ++ ++E L +LH +Q+A + QCGFCTPG +M + L K +E Sbjct: 73 ALHGKQLISVEDLKDQGRLHSVQQAMVDCHGSQCGFCTPGFVMSLFALQKNAGAVNEYDP 132 Query: 131 EEVRDGLHGNICRCTGYQNIVKAVLDA 157 + + L GN+CRCTGY+ I++A A Sbjct: 133 HQTHEALAGNLCRCTGYRPILEAAEQA 159 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: 190 Number of extensions: 7 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: 482 Length adjustment: 25 Effective length of query: 138 Effective length of database: 457 Effective search space: 63066 Effective search space used: 63066 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: 47 (22.7 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