Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF61 HP15_61 chain A, alpha-keto acid dehydrogenase-like protein
Query= reanno::pseudo3_N2E3:AO353_26635 (411 letters) >FitnessBrowser__Marino:GFF61 Length = 409 Score = 488 bits (1257), Expect = e-142 Identities = 239/406 (58%), Positives = 300/406 (73%), Gaps = 1/406 (0%) Query: 6 EPLRLHVPEPSGRPGCKTDFSYLRLTDAGTVRKPPIDVEPADTADLAKGLIRVLDDQGNA 65 +PL LHVPEP RPG K FS+L + +AG RKP + +D DL GL+RVLDD G A Sbjct: 5 KPLHLHVPEPPARPGDKPSFSHLVIPEAGETRKPDVTDSESDMRDLPYGLVRVLDDNGAA 64 Query: 66 LGPWAEGVPVEILRKGMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQALALN 125 +GPW G+ ++LRKG+R+ML TR+FD R+ RQ K SFYM+S GEEAIG+AQ+LAL+ Sbjct: 65 IGPWDPGLSPDVLRKGLRSMLLTRVFDERLFRVHRQGKTSFYMKSTGEEAIGAAQSLALS 124 Query: 126 IDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFTISGNL 185 DMCFPTYR S LMAR+ PL+D++ Q+ SNE+DPLKGRQLPI++S +D GF+++SGN+ Sbjct: 125 QGDMCFPTYRVMSWLMARDYPLIDMVNQIFSNEKDPLKGRQLPILFSARDYGFYSLSGNV 184 Query: 186 ATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVVNNQW 245 ++F VGW MASA KGD KIA +IG+G TAE DFH ALTFA VYRAPVIL V NNQW Sbjct: 185 GSRFGHAVGWAMASAYKGDDKIALGYIGEGTTAEGDFHEALTFASVYRAPVILCVTNNQW 244 Query: 246 AISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFVAVYAASAWAAERARRNLGPTMIEW 305 AIS++ IAG EATTFA + + G+ LRVDGNDF+AV++A+ WAAERAR NLG T+IE+ Sbjct: 245 AISSYSGIAGAEATTFAAKALAYGLPGLRVDGNDFLAVWSATKWAAERARNNLGATLIEF 304 Query: 306 VTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLVKIGQWSEEEHVALSAELEAE 365 TYRA HSTSDDP+KYRPAD+ H+PLGDP+ RLK HL+ +G+W +E H AL+ EL Sbjct: 305 FTYRAAGHSTSDDPTKYRPADEAEHWPLGDPLERLKHHLISLGEWDDERHEALTDELSET 364 Query: 366 IIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI 411 + AA KE E GTL G PS MFE V+ E + QR+E+GI Sbjct: 365 VRAAVKEGEAVGTL-GQSKPSVREMFEGVFAEPDWRVLEQRREVGI 409 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: 512 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: 411 Length of database: 409 Length adjustment: 31 Effective length of query: 380 Effective length of database: 378 Effective search space: 143640 Effective search space used: 143640 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