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 WP_018123272.1 B149_RS0100895 hypothetical protein
Query= SwissProt::P80909 (79 letters) >NCBI__GCF_000375485.1:WP_018123272.1 Length = 699 Score = 41.2 bits (95), Expect = 2e-08 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 7/76 (9%) Query: 5 YPVINRVECKACERCIIACPRKVLYMSNKINERGYHYVEYRGEGCNGCGNCYYTCP-EIN 63 YPV+N C AC C++ACPR V+ + + ++ + +E + C CP EIN Sbjct: 160 YPVVNPERCVACNGCVVACPRGVISLVSLSSKMIHLNLE-----TDCLAPCRQRCPGEIN 214 Query: 64 AIEVHIERCEDGDTDG 79 I +IE+ GD G Sbjct: 215 -IPRYIEQASRGDMAG 229 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: 190 Number of extensions: 11 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: 699 Length adjustment: 22 Effective length of query: 57 Effective length of database: 677 Effective search space: 38589 Effective search space used: 38589 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: 41 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 24 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