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_015739364.1 ADEG_RS06995 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000024605.1:WP_015739364.1 Length = 353 Score = 346 bits (887), Expect = e-100 Identities = 183/349 (52%), Positives = 243/349 (69%), Gaps = 3/349 (0%) Query: 1 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60 M ++KGN A GA+ AGC +FGYPITP SE+ H +R P VG ++QAESE AAI Sbjct: 1 MPRVLMKGNEAFGEGAIRAGCRYFFGYPITPQSELPHYLARRLPEVGGVYLQAESEVAAI 60 Query: 61 NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120 NMVYGAAAAG RVMT+SS PG+SL QEGIS+LAGAELP VIV+VMR GPGLGNI P Q+D Sbjct: 61 NMVYGAAAAGARVMTSSSSPGISLMQEGISYLAGAELPCVIVNVMRGGPGLGNIAPAQSD 120 Query: 121 YNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR 180 Y Q VKGGGHG+YR + LAP+SVQE+ DL AF+LADKYRNPV++L D +LGQM EP+ Sbjct: 121 YFQAVKGGGHGDYRLLCLAPSSVQEILDLMGLAFDLADKYRNPVMVLGDGILGQMMEPVE 180 Query: 181 FPERAVEHR-PDTSWAVCGSR-ETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRY 238 P + E + P WA G+ +N++ S++++ +ELEE N L+ KY +EE E R+ Sbjct: 181 LPPYSGELKLPPKPWATTGTAGRGTRNIINSLYIEPEELEEVNLRLKAKYRRMEEEEKRW 240 Query: 239 EEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGC 298 E Y++E+AE+VLVA+G +RVA++AV+ R +GI GL+RPITL+PFP Sbjct: 241 ETYLLEEAELVLVAFGTMARVARAAVERLREEGIAAGLIRPITLYPFPDAPFHAAFSRAR 300 Query: 299 TFISVEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREI 346 F+ VEM+ GQM ED+++A G V R GG + + +++ +E+ Sbjct: 301 AFLVVEMNLGQMVEDVRLAVEGRCPVHFYGRTGGVVPTVAEVVSFAKEV 349 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: 356 Number of extensions: 9 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: 353 Length adjustment: 29 Effective length of query: 323 Effective length of database: 324 Effective search space: 104652 Effective search space used: 104652 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