Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF3429 PS417_17545 2-oxoisovalerate dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_26635 (411 letters) >lcl|FitnessBrowser__WCS417:GFF3429 PS417_17545 2-oxoisovalerate dehydrogenase Length = 411 Score = 805 bits (2078), Expect = 0.0 Identities = 395/411 (96%), Positives = 404/411 (98%) Query: 1 MNQAYEPLRLHVPEPSGRPGCKTDFSYLRLTDAGTVRKPPIDVEPADTADLAKGLIRVLD 60 M Q YEPLRLHVPEPSGRPGCKTDF+YLRLTDAGTVRKP IDVEPADTADLAKGLIRVLD Sbjct: 1 MTQQYEPLRLHVPEPSGRPGCKTDFTYLRLTDAGTVRKPAIDVEPADTADLAKGLIRVLD 60 Query: 61 DQGNALGPWAEGVPVEILRKGMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ 120 DQG ALGPWAEGV VEI+R+GMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ Sbjct: 61 DQGQALGPWAEGVSVEIMRRGMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ 120 Query: 121 ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180 ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT Sbjct: 121 ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180 Query: 181 ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240 ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV Sbjct: 181 ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240 Query: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFVAVYAASAWAAERARRNLGP 300 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDF+AVYAASAWAAERARRNLGP Sbjct: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFIAVYAASAWAAERARRNLGP 300 Query: 301 TMIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLVKIGQWSEEEHVALSA 360 T+IEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHL+KIGQWSEEEH A+SA Sbjct: 301 TLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGQWSEEEHAAVSA 360 Query: 361 ELEAEIIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI 411 ELEAE++ AQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI Sbjct: 361 ELEAEVVKAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI 411 Lambda K H 0.319 0.134 0.403 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: 685 Number of extensions: 10 Number of successful extensions: 1 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: 411 Length of database: 411 Length adjustment: 31 Effective length of query: 380 Effective length of database: 380 Effective search space: 144400 Effective search space used: 144400 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 (21.8 bits) S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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