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_013259162.1 DEBA_RS11800 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000143965.1:WP_013259162.1 Length = 366 Score = 327 bits (839), Expect = 2e-94 Identities = 174/333 (52%), Positives = 229/333 (68%), Gaps = 2/333 (0%) Query: 1 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60 MA ++++G+ + A+ AGC YFGYPITP +E+ S VG FVQAESE A+I Sbjct: 1 MAKKLMRGSHVLGEAAVRAGCRYYFGYPITPQNEVPEYMSGRLLEVGGTFVQAESELASI 60 Query: 61 NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120 NMV GA+ AG RVMT+SS PG+SLKQEGIS+LAG ELPAVI +++R GPGLGNI P Q+D Sbjct: 61 NMVIGASMAGGRVMTSSSSPGISLKQEGISYLAGLELPAVIANMVRGGPGLGNIAPAQSD 120 Query: 121 YNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR 180 Y Q +GGGHG+YR IVLAP S QE+CD+T+ AF+LADKYRNPV+IL D ++GQM EP+ Sbjct: 121 YFQATRGGGHGDYRCIVLAPASCQELCDMTIRAFDLADKYRNPVLILGDGMMGQMMEPVN 180 Query: 181 FPERA-VEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYE 239 FPE P W + G++ + S+ L+ LEE N+ L KY AV +NE+ +E Sbjct: 181 FPEPLDPAALPKKDWTLSGAKGRPPRALLSLLLNPKILEEHNYKLVRKYDAVVQNEIDWE 240 Query: 240 EYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCT 299 YM EDA +VLVAYG ++R+AK A+ R G+KVGLLRP TL+PFP + EL + Sbjct: 241 SYMTEDARLVLVAYGTAARIAKGAIARVRELGMKVGLLRPKTLWPFPKPALLELTKVVRH 300 Query: 300 FISVEMSSGQMREDIKMA-SGCRDVELVNRMGG 331 + +E+S+GQM ED+++A G +V R GG Sbjct: 301 LLVIELSAGQMVEDVELAVKGQAEVNFYGRPGG 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: 380 Number of extensions: 14 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: 366 Length adjustment: 29 Effective length of query: 323 Effective length of database: 337 Effective search space: 108851 Effective search space used: 108851 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