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_013843010.1 DESRU_RS15405 3-methyl-2-oxobutanoate dehydrogenase subunit VorB
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000215085.1:WP_013843010.1 Length = 355 Score = 345 bits (885), Expect = 1e-99 Identities = 182/349 (52%), Positives = 242/349 (69%), Gaps = 3/349 (0%) Query: 1 MATQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60 M+ ++KGN A+ GA+ AGC +FGYPITP SE+ H ++ P VG F+QAESE ++I Sbjct: 1 MSKVLMKGNEAIGEGAIRAGCRHFFGYPITPQSELPHYLAKRMPEVGGVFLQAESETSSI 60 Query: 61 NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120 NMVYGAA AG R MT+SS PG+SL QEGIS+L GAELP VIV+VMR GPGLGNI P Q+D Sbjct: 61 NMVYGAAGAGFRTMTSSSSPGISLMQEGISYLVGAELPCVIVNVMRGGPGLGNIAPAQSD 120 Query: 121 YNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR 180 Y Q VKGGGHG+YR IVLAP SVQE+ DL +F LAD+YR PV+++ D +LGQM EP+ Sbjct: 121 YFQSVKGGGHGDYRLIVLAPASVQEIIDLMGLSFGLADQYRTPVMVVGDGILGQMMEPVE 180 Query: 181 FPER-AVEHRPDTSWAVCGSR-ETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRY 238 E + P WA G + T N++ S+++ + E+ N L KY + + E R+ Sbjct: 181 LDEEVTLPEIPAKPWAAGGLKGRTAPNIINSLYIVPEACEDLNKKLFAKYETITQRETRW 240 Query: 239 EEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGC 298 EEY +EDAEIVL +G ++R+AKS VD ARA+GIK GL+RPITL+PFPSE + AE Sbjct: 241 EEYRLEDAEIVLTGFGTAARIAKSVVDKARAEGIKAGLIRPITLWPFPSEVYAKAAEQAG 300 Query: 299 TFISVEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREI 346 F+ VEMS GQM ED+K+A +G + V R GG + +D+ +++++ Sbjct: 301 QFLCVEMSMGQMVEDVKLAVNGRKPVGFYGRSGGMVPLAKDVFAEVKKL 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: 378 Number of extensions: 16 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: 355 Length adjustment: 29 Effective length of query: 323 Effective length of database: 326 Effective search space: 105298 Effective search space used: 105298 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