Align 2-oxoisovalerate dehydrogenase subunit alpha; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_012403064.1 BPHY_RS18995 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::Q5SLR4 (367 letters) >NCBI__GCF_000020045.1:WP_012403064.1 Length = 327 Score = 159 bits (403), Expect = 8e-44 Identities = 103/323 (31%), Positives = 164/323 (50%), Gaps = 4/323 (1%) Query: 33 LEGEKLRRLYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWV 91 L EKL YR M R +ER + TG+ F+ AG EA+ V + D+V Sbjct: 7 LSREKLLDAYRLMRTIREFEERLHVEFATGEIPGFVHLYAGEEASAVGTMLHLNDK-DYV 65 Query: 92 FPYYRDHGLALALGIPLKELLGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVP 151 +R HG +A G+ + ++ ++ + KG+ H + + + P Sbjct: 66 ATTHRGHGHCIAKGVDVHGMMAEIYGRQTGVCKGKGGSMHIADLSKGMLGANGIVGAGGP 125 Query: 152 PAAGAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFIAENNFYAISVD 211 GAA++ KL +TG V VC FGDGA+++G + +N A+V PA+F+AENN YA + Sbjct: 126 LVCGAALAAKLKKTGGVGVCFFGDGASNQGVIFESMNLASVWRLPAIFVAENNGYAEATS 185 Query: 212 YRHQTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYG 271 S IAD+A FG+PG +VDG D A + + EA+ERAR G GP+LVE+++ RY Sbjct: 186 STWSVSSDNIADRASGFGMPGVIVDGFDFFAVHEALGEAIERARGGGGPTLVEVKLSRYF 245 Query: 272 PHSSADDDSRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLK 331 H D + P E +KD + RF+ + + N + + +++A ++ + Sbjct: 246 GHFEGDAQTYRAPGEVQKLREEKDCLKRFQERVVRAEMLNTDDLRKIDSDVKALIDDSVL 305 Query: 332 EAEEAGPVPPEW-MFEDVFAEKP 353 +A +A P+P E + DV+ P Sbjct: 306 KA-KAAPLPAEADLLTDVYVSYP 327 Lambda K H 0.320 0.137 0.421 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: 267 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: 367 Length of database: 327 Length adjustment: 29 Effective length of query: 338 Effective length of database: 298 Effective search space: 100724 Effective search space used: 100724 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 Apr 09 2024. 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