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 YP_427805.1 Rru_A2721 2-oxoglutarate synthase, subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000013085.1:YP_427805.1 Length = 595 Score = 117 bits (292), Expect = 1e-30 Identities = 73/196 (37%), Positives = 104/196 (53%), Gaps = 10/196 (5%) Query: 2 ATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAIN 61 A ++ GN A GA+ G YPITPA+EIL + P VG VQAE E A+IN Sbjct: 204 ARWLISGNEASAFGALKGGIRFVAAYPITPATEILEWLAPELPKVGGCLVQAEDELASIN 263 Query: 62 MVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQAD 120 M+ G + G +TA+SGPG++L E + +E P V+ +VMR GP G EQ D Sbjct: 264 MILGGSFGGVPALTATSGPGLALMTESLGLGVASETPIVVCNVMRGGPSTGIPTKSEQVD 323 Query: 121 YNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR 180 N + G HG+ ++V APN + + T + LA+ + PVI+L+D +GQ Sbjct: 324 LN-IALYGLHGDAPHVVTAPNGIGDCAATTQWSVHLAEAMQVPVIVLSDQAMGQ------ 376 Query: 181 FPERAVEHRPDTSWAV 196 RA+ +P T +V Sbjct: 377 --SRAIIDKPATRASV 390 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: 495 Number of extensions: 22 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: 595 Length adjustment: 33 Effective length of query: 319 Effective length of database: 562 Effective search space: 179278 Effective search space used: 179278 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 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