Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate Ac3H11_3590 Carbon monoxide dehydrogenase small chain (EC 1.2.99.2)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3590 Length = 156 Score = 177 bits (449), Expect = 7e-50 Identities = 87/146 (59%), Positives = 107/146 (73%), Gaps = 1/146 (0%) Query: 10 IKIKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCT 69 ++++ VNG V P LLV LRE L LTGT +GCDT+ CGACTV +NG++VKSC Sbjct: 1 MQVQFTVNGRAASVDVPPNTLLVHALREHLLLTGTHVGCDTSQCGACTVHVNGRAVKSCA 60 Query: 70 LFAVQADGAEITTIEGLSV-DSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNP 128 + AVQA GAE+TTIEG++ D +HP+Q AFKE LQCGFCTPGM+M A L K +P Sbjct: 61 MLAVQAQGAEVTTIEGMAAADGTMHPMQAAFKECHGLQCGFCTPGMVMSAVDLCKNHPGA 120 Query: 129 SEEEVRDGLHGNICRCTGYQNIVKAV 154 SE E+R+ L GNICRCTGYQNIV+AV Sbjct: 121 SEGEIRELLEGNICRCTGYQNIVRAV 146 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: 113 Number of extensions: 4 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: 156 Length adjustment: 17 Effective length of query: 146 Effective length of database: 139 Effective search space: 20294 Effective search space used: 20294 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: 43 (21.2 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