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 352363 BT2836 2-oxoglutarate synthase subunit korA (NCBI ptt file)
Query= SwissProt::P80908 (352 letters) >FitnessBrowser__Btheta:352363 Length = 616 Score = 102 bits (254), Expect = 3e-26 Identities = 99/382 (25%), Positives = 164/382 (42%), Gaps = 42/382 (10%) Query: 6 VKGNTA----VIIGAMYAGCDCYFG-YPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60 + GN A +I A AG + Y G YPITPA++ILHE +++ L G K VQ E E A Sbjct: 239 INGNKATSYGLIAAAEKAGLELYLGSYPITPATDILHELAKHKSL-GVKTVQCEDEIAGC 297 Query: 61 NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120 GAA AG +T +SGPG+ LK E ++ ELP VIV+V R GP G P +++ Sbjct: 298 ASAVGAAFAGALAVTTTSGPGICLKSEAMNLAVIGELPLVIVNVQRGGPSTGL--PTKSE 355 Query: 121 YNQLVKG--GGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEP 178 L++ G +G V+A S D A ++A ++ PV++L DA + + Sbjct: 356 QTDLLQALYGRNGESPMPVIAATSPTNCFDAAYMAAKIALEHMTPVVLLTDAFVANGSAA 415 Query: 179 LRFPE--------------------RAVEHRPDTS---WAVCGSRETM--------KNLV 207 + P+ + +TS WA G+ M N Sbjct: 416 WKLPDLNDYPAINPPYVTPDMAGNWTPYQRNEETSARYWATPGTEGFMHRIGGLEKSNET 475 Query: 208 TSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTA 267 +I + + + Q K + + E EDA++++V +G + + A+D Sbjct: 476 GAISTEPENHNKMVHLRQAKVDKIADYIPELEVLGDEDADLLIVGWGGTYGHLRLAMDFM 535 Query: 268 RADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIKMASGCRDVELVN 327 R G KV + P P + ++ + E + GQ ++M ++ N Sbjct: 536 REHGKKVAFAHFQYINPLP-KNTADVLRKYKKIVVAEQNLGQFAGYLRMKVPGLNISQFN 594 Query: 328 RMGGNLIELRDILRKIREIAGE 349 ++ G R+++ ++ E Sbjct: 595 QVKGQPFVTRELIDAFTKLLEE 616 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: 457 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 616 Length adjustment: 33 Effective length of query: 319 Effective length of database: 583 Effective search space: 185977 Effective search space used: 185977 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