Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate HSERO_RS16320 HSERO_RS16320 FAD-binding molybdopterin dehydrogenase
Query= metacyc::MONOMER-18072 (282 letters) >FitnessBrowser__HerbieS:HSERO_RS16320 Length = 494 Score = 83.2 bits (204), Expect = 1e-20 Identities = 53/165 (32%), Positives = 83/165 (50%), Gaps = 2/165 (1%) Query: 103 MQVRNLGTIGGSAANADPSADIPTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRK 162 + VRN GT+GG+ AN P D L AL A+I+L S G R + DF+ + L+ Sbjct: 296 LPVRNAGTLGGNLANGSPIGDSMPWLIALGAQIVLYSVRGQRVMPLEDFYLAYQKSALQA 355 Query: 163 GEIIS--EIVLPNLEGYRTIYKKVVRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGER 220 E++ I LP E +YK R D + V A A++++ + I R+AYGG+ Sbjct: 356 DELVQAVRIPLPRKELRFRVYKLSKRFDQDISAVCAAFALQMQGDTIVQARIAYGGMAAT 415 Query: 221 PFRALEVEKSVMGKRLNDELVEEIVSKVSSQVNPPSDTRGSSWYR 265 P RA + E + G ++ + ++ ++ P SD R S+ YR Sbjct: 416 PKRAAQAEAVLQGGPWSEAQAQAAMAALAQDYAPLSDMRASAAYR 460 Lambda K H 0.317 0.134 0.367 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: 237 Number of extensions: 8 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: 282 Length of database: 494 Length adjustment: 30 Effective length of query: 252 Effective length of database: 464 Effective search space: 116928 Effective search space used: 116928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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