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_011939118.1 GURA_RS11370 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000016745.1:WP_011939118.1 Length = 351 Score = 318 bits (814), Expect = 2e-91 Identities = 166/320 (51%), Positives = 222/320 (69%), Gaps = 1/320 (0%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 VKGN AV + A+ AGC YFGYPITP S+I SR P +G +F+QAESE A+INM+ G Sbjct: 7 VKGNEAVAMAAIEAGCRYYFGYPITPQSDIPEYLSRELPKLGGEFIQAESEIASINMLLG 66 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125 A+A G R MT+SS PG+SLKQEGIS++AG+ELP VIV++ R+GPGLG I QADY Q V Sbjct: 67 ASATGVRAMTSSSSPGISLKQEGISYMAGSELPGVIVNISRSGPGLGGIDASQADYFQSV 126 Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPERA 185 KGGGHG Y +VLAP SVQEM DLTM AF+LAD YR P ++L D+V+GQM E L R Sbjct: 127 KGGGHGGYHIVVLAPASVQEMYDLTMLAFDLADIYRMPAMVLGDSVVGQMKEALVANRRP 186 Query: 186 VEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVED 245 P WAV G + + +V S+FL ELE N+ L KY ++E E R+EE+ D Sbjct: 187 ETKLPPKDWAVRGKGDGEQRVVKSLFLGDGELEAHNWRLHAKYQELKERETRWEEFETAD 246 Query: 246 AEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEM 305 A++++ A+G ++R+ K+AV AR G+KVGLLRP+TLFPFP + + + + + +E+ Sbjct: 247 AQLLVTAFGSTARIVKTAVLMARDAGLKVGLLRPVTLFPFPEKALLQATQQCKKVLDIEL 306 Query: 306 SSGQMREDIKMASGCRDVEL 325 ++GQM ED+++ S RD E+ Sbjct: 307 NTGQMVEDVRL-SVARDAEV 325 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: 336 Number of extensions: 11 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: 351 Length adjustment: 29 Effective length of query: 323 Effective length of database: 322 Effective search space: 104006 Effective search space used: 104006 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 Apr 09 2024. 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