Align Ketoisovalerate oxidoreductase subunit VorB; VOR; 2-oxoisovalerate ferredoxin reductase subunit beta; 2-oxoisovalerate oxidoreductase beta chain; EC 1.2.7.7 (characterized)
to candidate WP_013450413.1 CALNI_RS01395 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000183405.1:WP_013450413.1 Length = 349 Score = 301 bits (771), Expect = 2e-86 Identities = 159/345 (46%), Positives = 226/345 (65%), Gaps = 2/345 (0%) Query: 5 MVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVY 64 ++KGN A+ A+ AG YFGYPITP +E+ S+ +GR FVQAESE AAINMVY Sbjct: 6 LMKGNEAIAEAAVRAGVKGYFGYPITPQNEVTAYMSKRMVELGRAFVQAESEVAAINMVY 65 Query: 65 GAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQL 124 GAA+ G MT SS PG++L QEGIS++ GAE+PAVIV++ R GPGLGNIGP Q DYNQ Sbjct: 66 GAASTGELAMTTSSSPGIALMQEGISYMCGAEVPAVIVNISRGGPGLGNIGPSQGDYNQS 125 Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPER 184 +GGG+G+Y IV P+++QE D+T AF++A++YRNPV+IL D LGQMAE + P Sbjct: 126 TRGGGNGDYFLIVYTPSTLQEAVDITYKAFDVANRYRNPVLILGDGALGQMAETVVLPPF 185 Query: 185 AVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVE 244 D W + G + V S+ L L+ NF+L+EK+ V+ NEV Y E + + Sbjct: 186 KELESKDKGWELNGCKGREPRSVKSLRLAEGMLKLHNFHLKEKFEQVKRNEVEY-ELIGD 244 Query: 245 DAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVE 304 D +I++VA+G ++RV+KSA+ A G+KVG+ RPI ++P+P ++ E A+ + VE Sbjct: 245 DYDILIVAFGTAARVSKSAIKEAAKHGVKVGMFRPILIWPYPYAQLTEAAKKAKKVLVVE 304 Query: 305 MSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAG 348 M++GQM D+ +A +E + + GG +++ +IL KI I G Sbjct: 305 MNNGQMLFDVMLAVKDDNKIEFLGKPGGEVVDPDEILEKILSIKG 349 Lambda K H 0.319 0.136 0.390 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: 295 Number of extensions: 12 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: 352 Length of database: 349 Length adjustment: 29 Effective length of query: 323 Effective length of database: 320 Effective search space: 103360 Effective search space used: 103360 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: 49 (23.5 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