Align 2-oxoisovalerate dehydrogenase subunit alpha 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_047092924.1 AAV99_RS06245 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::Q84JL2 (472 letters) >NCBI__GCF_001013305.1:WP_047092924.1 Length = 330 Score = 147 bits (370), Expect = 7e-40 Identities = 94/296 (31%), Positives = 147/296 (49%), Gaps = 7/296 (2%) Query: 146 IFYEAQRQGRLSFYATAIGEEAINIASAAALTPQDVIFPQYREPGVLLWRGFTLQEFANQ 205 ++ + + +G L Y IGEEA+ + AL PQD + YRE G L RG + + Sbjct: 35 LYTQEKIRGFLHLY---IGEEAVAVGVMEALAPQDAVVATYREHGHALVRGVSAGAIMAE 91 Query: 206 CFGNKSDYGKGRQMPVHYGSNKLNYFTVSATIATQLPNAVGAAYSLKMDKKDACAVTYFG 265 +G + GR +H ++ +A + LP A G A + K+ + +V +FG Sbjct: 92 MYGKQEGCSGGRGGSMHLFDAATRFYGGNAIVGGGLPLAAGLALADKLAGRSNVSVCFFG 151 Query: 266 DGGTSEGDFHAALNIAAVMEAPVLFICRNNGWAISTPTSDQFRSDGVVVKGRAYGIRSIR 325 +G +EG+FH LN+AA+ + PVLF+C NN +A+ T + K Y ++S Sbjct: 152 EGAVAEGEFHETLNLAALWQLPVLFVCENNLYAMGTALDISESETDISAKAACYRMQSDA 211 Query: 326 VDGNDALAMYSAVHTAREMAIREQ-RPILIEALTYRVGHHSTSDDSTRYRSAGEIEWWNK 384 VDG + + + +A A AIRE RP +E TYR HS D YR+ E+E W K Sbjct: 212 VDGMNVVNVEAAARRA-VAAIRETGRPYFLECRTYRFRAHSMFDPQL-YRAKAEVEEW-K 268 Query: 385 ARNPLSRFRTWIESNGWWSDKTESDLRSRIKKEMLEALRVAEKTEKPNLQNMFSDV 440 R P++RF+TW G +D + + E+ EA+ AE + ++F +V Sbjct: 269 GRGPITRFKTWALEAGELNDPDIEAIEQEVAHEIAEAVAFAEAGTWEPVGHLFHNV 324 Lambda K H 0.318 0.132 0.394 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: 335 Number of extensions: 10 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: 472 Length of database: 330 Length adjustment: 31 Effective length of query: 441 Effective length of database: 299 Effective search space: 131859 Effective search space used: 131859 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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