Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate YP_004140096.1 Mesci_0881 3-methyl-2-oxobutanoate dehydrogenase
Query= reanno::Smeli:SMc03201 (410 letters) >NCBI__GCF_000185905.1:YP_004140096.1 Length = 410 Score = 711 bits (1835), Expect = 0.0 Identities = 343/409 (83%), Positives = 371/409 (90%) Query: 1 MDEFSRLSLHVPEPAVRPGDLPDFSNVKIPKAGSVPRPDVDVDPEEIRDLAYSIIRVLNR 60 M + L HVPEP VRPG PDFSNV IPKAGSVPRP++DVDP IRD A+SIIRVLNR Sbjct: 1 MADAGMLRFHVPEPEVRPGGTPDFSNVPIPKAGSVPRPEIDVDPRTIRDHAFSIIRVLNR 60 Query: 61 EGEAVGPWAGFLSDEELLTGLRHMMLLRAFDARMLMAQRQGKTSFYMQHLGEEAVSCAFR 120 GEAVGPWAG LS +ELLTGLRHMM LR FDARM MAQRQGKTSFYMQHLGEEAV+CAFR Sbjct: 61 TGEAVGPWAGLLSSDELLTGLRHMMTLRTFDARMQMAQRQGKTSFYMQHLGEEAVACAFR 120 Query: 121 KALRKGDMNFPTYRQAGLLIADDYPMVEMMNQIFSNELDPCHGRQLPVMYTSKEHGFFTI 180 KAL GDMNFPTYRQAGLLIAD YPMV MMNQI+SNE DP GRQLPVMY+SKEHGFF+I Sbjct: 121 KALAPGDMNFPTYRQAGLLIADGYPMVTMMNQIYSNEADPLKGRQLPVMYSSKEHGFFSI 180 Query: 181 SGNLATQYVQAVGWAMASAIKNDTRIAAGWIGDGSTAESDFHSALVFASTYKAPVILNIV 240 SGNLATQY+QAVGWAMASAI ND+RIAA WIGDGSTAESDFHSALVFASTYKAPV+LN+V Sbjct: 181 SGNLATQYIQAVGWAMASAISNDSRIAAAWIGDGSTAESDFHSALVFASTYKAPVVLNVV 240 Query: 241 NNQWAISTFQGIARGGSGTFAARGLGFGIPALRVDGNDYLAVYAVARWAAERARLNLGPT 300 NNQWAISTFQGIARGGSGTFAARGLGFGIP+LRVDGNDYLAV+AVA+WAAERAR NLGPT Sbjct: 241 NNQWAISTFQGIARGGSGTFAARGLGFGIPSLRVDGNDYLAVHAVAKWAAERARSNLGPT 300 Query: 301 LIEYVTYRVGAHSTSDDPSAYRPKTESEAWPLGDPVLRLKKHLILRGAWSEERHAQAEAE 360 L+EYVTYR GAHS+SDDPSAYRPKTES+AWPLGDP++RLK HLI G WS+ERHAQAEAE Sbjct: 301 LVEYVTYRAGAHSSSDDPSAYRPKTESDAWPLGDPIVRLKNHLIALGVWSDERHAQAEAE 360 Query: 361 IMDEVIQAQKEAERHGTLHAGGRPSVRDIFEGVYAEMPPHIRRQRQKAG 409 I+D VI AQKEAE HGTLHAGG+PS RD+FEG+YAEMPPH+RRQRQ+AG Sbjct: 361 ILDTVIAAQKEAEGHGTLHAGGKPSTRDMFEGLYAEMPPHLRRQRQQAG 409 Lambda K H 0.320 0.135 0.410 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: 701 Number of extensions: 21 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: 410 Length of database: 410 Length adjustment: 31 Effective length of query: 379 Effective length of database: 379 Effective search space: 143641 Effective search space used: 143641 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 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