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_051184395.1 H567_RS0100390 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000422285.1:WP_051184395.1 Length = 339 Score = 316 bits (810), Expect = 5e-91 Identities = 163/336 (48%), Positives = 235/336 (69%), Gaps = 6/336 (1%) Query: 14 IGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYGAAAAGHRV 73 +GA+ AGC YFGYPITP ++I S++ P VG F+QAESE A+INM+ GA+A G R Sbjct: 1 MGAIEAGCRFYFGYPITPQNDIPEYMSKHLPAVGGTFIQAESEIASINMLLGASATGARA 60 Query: 74 MTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLVKGGGHGNY 133 MT+SS PG+SLKQEGIS+L G+++P VIV++ R+GPGLG I P Q DY Q +GGGHG+Y Sbjct: 61 MTSSSSPGISLKQEGISYLCGSQIPGVIVNMSRSGPGLGGISPSQGDYFQATRGGGHGDY 120 Query: 134 RNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRF-PERAVEHRPDT 192 R IVLAP+SVQE DLTM AF+LADKYRNPV+IL DA+LGQ+ EPL+ P R P+ Sbjct: 121 RTIVLAPSSVQEAYDLTMRAFDLADKYRNPVLILGDALLGQIKEPLKTRPYRGTP--PEK 178 Query: 193 SWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVEDAEIVLVA 252 W + G+ + ++ S++L EL + N++L KY + + E+R+E ++DA++++VA Sbjct: 179 DWILTGASGRPRRILKSLYLSEGELTDHNWFLYRKYQQM-KREIRFETQNLDDAKLLVVA 237 Query: 253 YGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMRE 312 +G +R+ KSAV AR G+ +GLLRPITL+PFP + +++ F++VE+S+GQM E Sbjct: 238 FGSLARIVKSAVGMAREKGMLIGLLRPITLYPFPYAALEKISRKIRNFMAVELSTGQMVE 297 Query: 313 DIKMASGCR--DVELVNRMGGNLIELRDILRKIREI 346 D+K+A G + V+ R G++ +I +I ++ Sbjct: 298 DVKLAVGHKKNQVDFYGRPPGSIPSPDEIFHEIAKV 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: 351 Number of extensions: 12 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: 339 Length adjustment: 29 Effective length of query: 323 Effective length of database: 310 Effective search space: 100130 Effective search space used: 100130 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