Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate RR42_RS10655 RR42_RS10655 pyruvate dehydrogenase
Query= BRENDA::Q72GU1 (367 letters) >FitnessBrowser__Cup4G11:RR42_RS10655 Length = 340 Score = 155 bits (391), Expect = 2e-42 Identities = 102/310 (32%), Positives = 148/310 (47%), Gaps = 3/310 (0%) Query: 41 LYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWVFPYYRDHG 99 L RDML R L+E+ L GK F+ G EA V + HA+ P D V YR+HG Sbjct: 26 LLRDMLRIRRLEEKCAELYDAGKIRGFLHLYIGEEAVGVGVLHALAPE-DNVVATYREHG 84 Query: 100 LALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAAGAAIS 159 AL G+ + L +M + +GR H +A F + + +P A G A++ Sbjct: 85 HALVRGMDMGVLMAEMYGKQQGCARGRGGSMHLFDRATRLFGGNAIVGGGLPLAVGLALA 144 Query: 160 MKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRHQTHSP 219 K+ +V C FGDGA +EG ++ +N A++ P +F CENN YA+ Sbjct: 145 EKMQAGQRVTACFFGDGAVAEGAFHESMNLASLWKLPVLFCCENNLYAMGTALERHESQT 204 Query: 220 TIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHSSADDD 279 + KA ++ + VDGMD++A + ++A R G GP +ELR YR+ HS D + Sbjct: 205 DLCAKAASYNMTAVAVDGMDIVAVHEAARDAAAHVRSGAGPVFLELRTYRFRAHSMYDAE 264 Query: 280 SRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEAEEAGPV 339 YR K EV W + PI F L+A G EE + AE+ + AE Sbjct: 265 -LYRQKAEVEAWEECGPIHTFTARLKAGGKLAEEEFLALDAAANAEVAKAEAFAEAGTWE 323 Query: 340 PPEWMFADVF 349 P E + DV+ Sbjct: 324 PVEDLLKDVY 333 Lambda K H 0.320 0.138 0.426 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: 319 Number of extensions: 19 Number of successful extensions: 3 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: 367 Length of database: 340 Length adjustment: 29 Effective length of query: 338 Effective length of database: 311 Effective search space: 105118 Effective search space used: 105118 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: 49 (23.5 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