Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate PfGW456L13_4084 Xanthine dehydrogenase iron-sulfur subunit (EC 1.17.1.4) / Xanthine dehydrogenase, FAD binding subunit (EC 1.17.1.4)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4084 Length = 484 Score = 108 bits (269), Expect = 2e-28 Identities = 51/145 (35%), Positives = 80/145 (55%), Gaps = 13/145 (8%) Query: 22 ERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNG-------------KSVKSC 68 E + P + ++++LR+ +G GTK GC + CGACTV++ +S+ SC Sbjct: 13 EHALDPNLTVLNYLRDHVGKPGTKEGCASGDCGACTVVVGELQTDDDGREHIRYRSLNSC 72 Query: 69 TLFAVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNP 128 F G ++ ++E L +LH +Q+A E QCGFCTPG +M + L K + P Sbjct: 73 LTFVSSLHGKQLISVEDLKHKGELHSVQKAMVECHGSQCGFCTPGFVMSLFALQKNSDAP 132 Query: 129 SEEEVRDGLHGNICRCTGYQNIVKA 153 + + L GN+CRCTGY+ I++A Sbjct: 133 DHAKAHEALAGNLCRCTGYRPILEA 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: 160 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: 484 Length adjustment: 25 Effective length of query: 138 Effective length of database: 459 Effective search space: 63342 Effective search space used: 63342 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