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_048060884.1 MTH_RS03295 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000008645.1:WP_048060884.1 Length = 352 Score = 659 bits (1700), Expect = 0.0 Identities = 322/352 (91%), Positives = 345/352 (98%) Query: 1 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFP+VGRKFVQAESEEAAI Sbjct: 1 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPMVGRKFVQAESEEAAI 60 Query: 61 NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120 NMVYGAAAAGHRVMTASSGPG+SLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQ D Sbjct: 61 NMVYGAAAAGHRVMTASSGPGISLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQGD 120 Query: 121 YNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR 180 YNQ+VKGGGHGNYRN+VLAP+SVQEMCDLTM+AFELADKYRNPV++L DAVLGQMAEPLR Sbjct: 121 YNQIVKGGGHGNYRNMVLAPSSVQEMCDLTMEAFELADKYRNPVVVLTDAVLGQMAEPLR 180 Query: 181 FPERAVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEE 240 FPE AVEHRPDTSWAVCG+RETMKNLVTSIFLDFDELEEFNFYLQEKYA +EENEVRYEE Sbjct: 181 FPEEAVEHRPDTSWAVCGNRETMKNLVTSIFLDFDELEEFNFYLQEKYARIEENEVRYEE 240 Query: 241 YMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTF 300 Y+V+DAEIV+VAYGISSRVA+SAV+TARA+GI VGLLRPITLFPFPS+RIRELA+GGC F Sbjct: 241 YLVDDAEIVMVAYGISSRVARSAVETARAEGINVGLLRPITLFPFPSDRIRELADGGCRF 300 Query: 301 ISVEMSSGQMREDIKMASGCRDVELVNRMGGNLIELRDILRKIREIAGESND 352 ISVEMSSGQMREDI+MASGCRDVELVNRMGGNLIELRD+L KIRE+AG+S+D Sbjct: 301 ISVEMSSGQMREDIRMASGCRDVELVNRMGGNLIELRDVLEKIREVAGDSSD 352 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: 545 Number of extensions: 13 Number of successful extensions: 1 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