Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_050656427.1 C1M55_RS25425 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::P12694 (445 letters) >NCBI__GCF_002893965.1:WP_050656427.1 Length = 327 Score = 131 bits (329), Expect = 4e-35 Identities = 95/301 (31%), Positives = 143/301 (47%), Gaps = 15/301 (4%) Query: 116 DRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFM 175 D + + G F+ G+EG G+ AA+ + D +F Q R A + + + + Sbjct: 38 DAVQIHIRDHGFAGFWHPGKGQEGAVAGAVAAMRDDDYLFYQGRGATWPLAKGMTMGPII 97 Query: 176 AQCYGNI--SDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVI 233 G + S GKG +P H+ + + L + P A GAA +A+ +V + Sbjct: 98 GDLLGKVTGSTGGKGAGVP-HWADPALGIMGEGATLGSVYPVAAGAALSAQMRGTGQVAL 156 Query: 234 CYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGI 293 FG+G A+ G H A+ + P+++FC NNG +++TP IA R YGI Sbjct: 157 ADFGDGTAARGTFHETLLEASRWKLPLVYFCENNGISVTTPFESVSPTRTIAERATAYGI 216 Query: 294 MSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVN- 352 +RVDG+D AVY+ATK A RA P LIEA+ R+G H D+ YR D ++ Sbjct: 217 PGVRVDGHDAVAVYHATKAAIDRARDGQGPSLIEAVVTRVGGH-WEGDAQKYRPEDFLST 275 Query: 353 YWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDV 412 Y D D SRL L Q +R +V EA +AE P P+P+++ DV Sbjct: 276 YRDPLDIMRSRLDALLADQ----------IVAAARAEVAEALAEAEAAPLPDPSVIMKDV 325 Query: 413 Y 413 + Sbjct: 326 F 326 Lambda K H 0.320 0.135 0.405 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: 353 Number of extensions: 20 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: 445 Length of database: 327 Length adjustment: 30 Effective length of query: 415 Effective length of database: 297 Effective search space: 123255 Effective search space used: 123255 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