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 207019 DVU1569 pyruvate ferredoxin oxidoreductase, alpha subunit
Query= SwissProt::P80908 (352 letters) >MicrobesOnline__882:207019 Length = 578 Score = 111 bits (277), Expect = 5e-29 Identities = 92/331 (27%), Positives = 143/331 (43%), Gaps = 47/331 (14%) Query: 5 MVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVY 64 M++GN A+ +GA+ AG YP+TPA+ + + +G QAE E AA+NMV Sbjct: 190 MLQGNEAIALGALAAGVKFCAFYPMTPATSVAQNLILHAERMGVVVEQAEDEIAAMNMVL 249 Query: 65 GAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQ 123 GA+ AG R + +SG G +L EG+S E P VIV R GP G EQAD + Sbjct: 250 GASYAGARALVPTSGGGFALMTEGVSLAGVMEQPVVIVLAQRPGPATGLPTRTEQADLD- 308 Query: 124 LVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLG---------- 173 L GHG + ++ AP + ++ LT AF+LA++++ P +L D L Sbjct: 309 LALYAGHGEFPRVIFAPATPEDCFHLTYAAFDLAERFQIPAFVLTDQYLADSYRPVAPFD 368 Query: 174 -QMAEPLRFPERAVEHRPDTSWAVCGSRETMKNLVTS--------------IFLDFDELE 218 PL P+ + + P+ G R L S + D E Sbjct: 369 LDALPPLAEPDFSTDKGPE------GDRYKRYELTKSGISPRRIPGFSKSLVLADCHEHT 422 Query: 219 EFNFYLQEKYAAVEENEVRYEE-------------YMVEDAEIVLVAYGISSRVAKSAVD 265 E + ++ + ++ R + + E +++L +G S A Sbjct: 423 EQGYITEDAGLRIAMSDKRLRKGDGLRSMALPPRCFGDEAPDLLLACWGSSEGAVVEAAQ 482 Query: 266 TARADGIKVGLLRPITLFPF-PSERIRELAE 295 RA G KVG+L ++P PS+ + E Sbjct: 483 RLRARGRKVGVLSFTQVWPLEPSQFLSRCGE 513 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: 489 Number of extensions: 33 Number of successful extensions: 2 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: 578 Length adjustment: 33 Effective length of query: 319 Effective length of database: 545 Effective search space: 173855 Effective search space used: 173855 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: 51 (24.3 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