Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate 7024304 Shewana3_1496 2Fe-2S iron-sulfur cluster binding domain-containing protein (RefSeq)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__ANA3:7024304 Length = 165 Score = 109 bits (273), Expect = 2e-29 Identities = 55/139 (39%), Positives = 81/139 (58%), Gaps = 4/139 (2%) Query: 16 VNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLFAVQA 75 +NG + P + ++ LR+ LGLTGTK GC CGACTV L+G+ V++C QA Sbjct: 23 INGRSFTLNADPNMPILWALRDILGLTGTKYGCGAGLCGACTVHLDGQPVRACLTSVSQA 82 Query: 76 DGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEEEVRD 135 G ++TTIEGL ++ A+ E+ QCG+C G +M A L+ ++P PS E++ Sbjct: 83 QGKQLTTIEGLDNQK----LKNAWAEHNVPQCGYCQAGQLMSAAALVTQHPKPSAEQIDA 138 Query: 136 GLHGNICRCTGYQNIVKAV 154 + GN+CRC Y I A+ Sbjct: 139 AMSGNLCRCGTYPRIKAAL 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: 96 Number of extensions: 3 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: 165 Length adjustment: 18 Effective length of query: 145 Effective length of database: 147 Effective search space: 21315 Effective search space used: 21315 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