Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate Pf6N2E2_481 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
Query= reanno::pseudo6_N2E2:Pf6N2E2_481 (411 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_481 Length = 411 Score = 832 bits (2148), Expect = 0.0 Identities = 411/411 (100%), Positives = 411/411 (100%) Query: 1 MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD 60 MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD Sbjct: 1 MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD 60 Query: 61 DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ 120 DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ Sbjct: 61 DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ 120 Query: 121 ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180 ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT Sbjct: 121 ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180 Query: 181 ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240 ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV Sbjct: 181 ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240 Query: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP 300 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP Sbjct: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP 300 Query: 301 ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA 360 ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA Sbjct: 301 ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA 360 Query: 361 ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI 411 ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI Sbjct: 361 ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI 411 Lambda K H 0.319 0.134 0.404 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: 754 Number of extensions: 17 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:
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