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_035253234.1 H567_RS0102590 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000422285.1:WP_035253234.1 Length = 355 Score = 296 bits (757), Expect = 7e-85 Identities = 161/350 (46%), Positives = 221/350 (63%), Gaps = 3/350 (0%) Query: 5 MVKGNTAVIIGAMYAGCDCYFGYPITPASEIL-HEASRYFPLVGRKFVQAESEEAAINMV 63 +++G+ + A+ AGC Y GYPITP +E+ + A L F+QAESE AA+NMV Sbjct: 2 LMRGSHVIGEAAVRAGCRFYAGYPITPQNELTEYMAGAMARLEDGTFIQAESELAAVNMV 61 Query: 64 YGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQ 123 GAA AG R MT+SS PG+SLKQEGIS+LA ELPAVIV+ MR GPGLGNI P Q DY Q Sbjct: 62 IGAAMAGARAMTSSSSPGVSLKQEGISYLAAQELPAVIVNTMRGGPGLGNIAPSQGDYFQ 121 Query: 124 LVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPE 183 +GGGHG+YR IVLAP S QE+ D+T AF+ AD YR PV+IL D ++GQM EP+ FPE Sbjct: 122 ATRGGGHGDYRTIVLAPASGQELADITRKAFDYADTYRTPVMILGDGMIGQMMEPVVFPE 181 Query: 184 RA-VEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYM 242 ++ P W + G++ ++ S+ LD E+ N+ L KY + E+Y+ Sbjct: 182 PLDLKKLPPKPWILDGAKGRPSRIIRSLLLDVSVEEDQNWKLVRKYEQITREIPAAEKYL 241 Query: 243 VEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFIS 302 +DA +V+VAYG ++R+AK A+ R G+KVGLLRPITL+PFP+ + E++ F+ Sbjct: 242 TDDARLVVVAYGTAARIAKGAIKRMRDIGLKVGLLRPITLWPFPNRILVEMSRWVRHFLV 301 Query: 303 VEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAGESN 351 EMS+GQM ED+++ G V R GG + ++ + I + N Sbjct: 302 YEMSTGQMVEDVRLGLEGRSQVHFYGRPGGVVSTPEELSKVINTLYHRQN 351 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: 385 Number of extensions: 10 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: 355 Length adjustment: 29 Effective length of query: 323 Effective length of database: 326 Effective search space: 105298 Effective search space used: 105298 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