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 208876 DVU3349 pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-binding domain protein
Query= SwissProt::P80908 (352 letters) >MicrobesOnline__882:208876 Length = 357 Score = 301 bits (772), Expect = 1e-86 Identities = 165/347 (47%), Positives = 227/347 (65%), Gaps = 6/347 (1%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 +KGN A+ GA+ AGC CYFGYPITP ++I S P G +FVQAESE AA NM+ G Sbjct: 11 IKGNEAIAHGALAAGCRCYFGYPITPQNDIPEMMSSAIPAAGGEFVQAESEVAAANMLLG 70 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125 AAA G R T+SS PG+SL QE IS++AG+ELP VIV++ R GPGLG+IGP Q DY Q V Sbjct: 71 AAACGVRAFTSSSSPGVSLMQEAISYMAGSELPGVIVNMNRGGPGLGDIGPSQGDYFQSV 130 Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPERA 185 KGGGHG+YR VLAP + QE D+ +AF++A ++R PV++L DA++GQM EP+ P + Sbjct: 131 KGGGHGDYRTYVLAPATCQECYDMMFEAFDVAYRFRTPVLVLGDAIVGQMKEPVT-PWKR 189 Query: 186 VEHRPDT---SWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYM 242 + P T W + G++ L+ S+FL+ L N LQ KY A++E R E + Sbjct: 190 DDLDPATEGADWRLQGAKGRPARLLKSLFLEDGALAGQNRNLQAKYEAMKE-LARAECFE 248 Query: 243 VEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFIS 302 EDA++V+VA+G R+AKSA+ RA G KVGL+RP+TLFPFP + +++LA G F++ Sbjct: 249 TEDADLVVVAFGSIGRIAKSAIRKLRAQGHKVGLVRPVTLFPFPEKVLQDLAAKGKRFLT 308 Query: 303 VEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAG 348 +E + GQM +D+++A D + M G L D L+ I + G Sbjct: 309 IEHNCGQMVDDVRLAVRAYCDSDFYGHMPGELPGSDDFLKPILDALG 355 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: 378 Number of extensions: 16 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: 357 Length adjustment: 29 Effective length of query: 323 Effective length of database: 328 Effective search space: 105944 Effective search space used: 105944 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 17 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