Align Ketoisovalerate oxidoreductase subunit VorC; VOR; 2-oxoisovalerate ferredoxin reductase subunit gamma; 2-oxoisovalerate oxidoreductase gamma chain; EC 1.2.7.7 (characterized)
to candidate 349861 BT0333 conserved hypothetical protein (NCBI ptt file)
Query= SwissProt::P80909 (79 letters) >FitnessBrowser__Btheta:349861 Length = 75 Score = 59.7 bits (143), Expect = 5e-15 Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 3/67 (4%) Query: 7 VINRVECKACERCIIACPRKVLYMSNKINERGYHYV-EYRGEGCNGCGNCYYTCPE--IN 63 V++ CK C C++ACP V+ ++ ++N +GY+Y + + + CNGC +C CP+ I+ Sbjct: 9 VVDTERCKGCNLCVVACPLDVIALNKEVNMKGYNYAWQVKEDTCNGCSSCAMVCPDGCIS 68 Query: 64 AIEVHIE 70 +V +E Sbjct: 69 VYKVKVE 75 Lambda K H 0.323 0.142 0.480 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: 34 Number of extensions: 2 Number of successful extensions: 1 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: 79 Length of database: 75 Length adjustment: 7 Effective length of query: 72 Effective length of database: 68 Effective search space: 4896 Effective search space used: 4896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 38 (20.5 bits) S2: 38 (19.2 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