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_013258759.1 DEBA_RS09750 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000143965.1:WP_013258759.1 Length = 352 Score = 322 bits (825), Expect = 9e-93 Identities = 165/332 (49%), Positives = 235/332 (70%), Gaps = 7/332 (2%) Query: 5 MVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVY 64 ++KGN A+ +GA+ AGC YFGYPITP ++I S P VG F+QAESE A+INM+ Sbjct: 6 LIKGNEAIAMGAIEAGCRFYFGYPITPQNDIPEYMSATLPKVGGVFLQAESEVASINMLL 65 Query: 65 GAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQL 124 GA+A G R MT+SS PG+SLKQEGIS+LAG+E+PAV+V++ R+GPGLG I P Q DY Q Sbjct: 66 GASATGARAMTSSSSPGISLKQEGISYLAGSEIPAVVVNMSRSGPGLGGIHPSQGDYFQA 125 Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPER 184 +GGGHG+YR +VLAP++ QE DLT+ AF+LAD+YRNPV+IL DA++GQ+ EP+ E Sbjct: 126 TRGGGHGDYRTLVLAPSTAQENYDLTILAFDLADRYRNPVVILGDALIGQIKEPV---EL 182 Query: 185 AVEHR--PDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYM 242 H+ P WA+ G+ + ++ S++L EL E N+ L +KYA + + EVR+EEY+ Sbjct: 183 KPYHKKPPQKDWALTGNEGRPQRILKSLYLADGELTEQNWKLAKKYARMAK-EVRFEEYL 241 Query: 243 VEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFIS 302 +DAE+++ A+G +R+ K+++D R G K+GLLRPITL+PFPS +R AE + Sbjct: 242 TDDAEMIVAAFGSVARILKTSIDILREKGRKIGLLRPITLYPFPSAAVRRAAEKSGHLMV 301 Query: 303 VEMSSGQMREDIKMA-SGCRDVELVNRMGGNL 333 VE+++GQM ED+++A G V+ R G++ Sbjct: 302 VELNTGQMVEDVRLAVEGVAPVDFYGRPPGSI 333 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: 339 Number of extensions: 13 Number of successful extensions: 3 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: 352 Length adjustment: 29 Effective length of query: 323 Effective length of database: 323 Effective search space: 104329 Effective search space used: 104329 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