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 8501322 DvMF_2055 2-ketoisovalerate ferredoxin reductase (RefSeq)
Query= SwissProt::P80908 (352 letters) >FitnessBrowser__Miya:8501322 Length = 361 Score = 313 bits (802), Expect = 4e-90 Identities = 169/345 (48%), Positives = 228/345 (66%), Gaps = 3/345 (0%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 +KGN A+ GA+ AGC CYFGYPITP ++I S P G +FVQAESE A+ NM+ G Sbjct: 16 IKGNEAIAHGALAAGCRCYFGYPITPQNDIPEMMSYALPDAGGEFVQAESEVASANMLLG 75 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125 AAAAG R +T+SS PG+SL QE IS++AG+ELP VIV++ R GPGLG+IGP Q DY Q V Sbjct: 76 AAAAGIRALTSSSSPGISLMQEAISYMAGSELPGVIVNMNRGGPGLGDIGPSQGDYFQSV 135 Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR-FPER 184 KGGGHG+Y+ VLAP + QE D+ + AF+LA KYRNPV++L DA++GQM EP+ + Sbjct: 136 KGGGHGDYKLFVLAPATCQECYDMMVQAFDLAFKYRNPVMVLGDAIVGQMKEPVTPWKPA 195 Query: 185 AVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVE 244 AV W + G++ L+ S+FL+ L N +LQ KYAA++ E + E ++ + Sbjct: 196 AVPATEAADWRLEGAKGRKPRLLKSLFLEDGALAGQNRHLQAKYAAMQA-EAKAESFLTD 254 Query: 245 DAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVE 304 DAE+++VAYG R+AKSA+ RA G KVGL+RP TLFPFP +R LAE G F+++E Sbjct: 255 DAELIVVAYGSIGRIAKSAIRKLRAQGHKVGLVRPQTLFPFPGPLLRGLAEQGKRFLTIE 314 Query: 305 MSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAG 348 + GQM ED++++ G D M G + D L I + G Sbjct: 315 HNCGQMVEDVRLSIRGIVDSAFYGHMPGEMPGSDDFLAPILDAMG 359 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: 375 Number of extensions: 15 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: 361 Length adjustment: 29 Effective length of query: 323 Effective length of database: 332 Effective search space: 107236 Effective search space used: 107236 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