Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Synpcc7942_1718 Synpcc7942_1718 glycolate oxidase subunit GlcE
Query= reanno::psRCH2:GFF3771 (353 letters) >FitnessBrowser__SynE:Synpcc7942_1718 Length = 425 Score = 99.8 bits (247), Expect = 1e-25 Identities = 57/158 (36%), Positives = 95/158 (60%), Gaps = 3/158 (1%) Query: 37 LGLQADGVLLDTREHRGIVSYDPTELVVTVRAGTPLTELETALDEAGQMLPCEPPHFGEG 96 LG D V+ R ++ + +L VTV AG L +L+T L E GQ LP +P GE Sbjct: 72 LGHPVDAVISTAACDR-LIEHAAADLTVTVEAGMTLGQLQTILAETGQWLPFDPIA-GES 129 Query: 97 ATVGGMIAAGLSGPRRPWSGSVRDFVLGSRVITGQGKHLRFGGEVMKNVAGYDLSRLMAG 156 +++G +++ G+SG R GS+RDF++G + G+ + GG V+KNVAGYD+ +L+ G Sbjct: 130 SSLGALVSTGMSGSLRHRYGSLRDFLIGITFLRHDGQWAKGGGRVVKNVAGYDMMKLLHG 189 Query: 157 SFGCLGVLTEVSLKVLPKPRLCTSLRLEIDLERALLKL 194 ++G LG++ +++ + P P ++ + D E A+L+L Sbjct: 190 AWGSLGLIGKLTFRTYPLPNAWGTIACQGDRE-AILQL 226 Lambda K H 0.319 0.137 0.417 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: 399 Number of extensions: 25 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: 353 Length of database: 425 Length adjustment: 30 Effective length of query: 323 Effective length of database: 395 Effective search space: 127585 Effective search space used: 127585 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 (21.7 bits) S2: 50 (23.9 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