Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate WP_065398092.1 BBI00_RS07000 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P09062 (423 letters) >NCBI__GCF_001684965.1:WP_065398092.1 Length = 417 Score = 239 bits (611), Expect = 9e-68 Identities = 146/418 (34%), Positives = 236/418 (56%), Gaps = 27/418 (6%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 +K+P GE I +VE+ W VK GD + +DQ +A+V +DKAT+E+P+ SG V+ L + G Sbjct: 6 MKVPSPGESITEVEIATWLVKDGDYVEKDQPIAEVDSDKATLELPAEQSG-VITLKAEEG 64 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 +V+ VG + I+++ + P A+ + AP AA+P Q+ KPAA A+A A Sbjct: 65 DVVQVGQVVCLIDMDAAKPEGAAPAAEAPKQEEAPKAAEPAKQEAPKPAA-PAAAPQTYA 123 Query: 126 PIVPRQPGDKPLASPAVRKRALDAGIELRYVHGSGPAGRILHEDLD-----AFMSKPQSA 180 P SPA +K + G++ V G+G GRI D + A P +A Sbjct: 124 TGAP---------SPAAKKILDEKGMDAAQVSGTGRDGRITKTDAELAAVPALGGNPLTA 174 Query: 181 AGQTPNGYARRTDSEQVPVIGLRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALRQQLNS 240 G +R T + ++ V LRRKIAQR+ K A + E+D++ + LR+Q Sbjct: 175 TG------SRSTTTTKLSV--LRRKIAQRLVSVKNETAMLTTFNEVDMSEIFRLRKQYKE 226 Query: 241 KHGDSRGK-LTLLPFLVRALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQGDNGLM 299 + G L + F +A+ AL+ +P +NA+ D + ++ + + IA G GLM Sbjct: 227 EFAQKHGVGLGFMSFFTKAVTRALQMYPDVNASIDGDFKV--NYDFCDISIAVSGPKGLM 284 Query: 300 VPVLRHAEAGSLWANAGEISRLANAARNNKASREELSGSTITLTSLGALGGIVSTPVVNT 359 VPVLR+AE S A I LA R+ K + +E++G T T+T+ G G ++STP++N Sbjct: 285 VPVLRNAENMSFSAIEANIKDLATKVRDGKITVDEMTGGTFTITNGGTFGSMMSTPIINP 344 Query: 360 PEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGLLEQP 417 P+ AI+G++ +++RPV +DGQ+V+R MM ++ S+DHR++DG ++ F+ AV+ ++ P Sbjct: 345 PQSAILGMHNIIQRPVAVDGQVVIRPMMYVAMSYDHRIIDGKESVGFLVAVKEGIDNP 402 Lambda K H 0.316 0.133 0.376 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: 406 Number of extensions: 17 Number of successful extensions: 4 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: 423 Length of database: 417 Length adjustment: 32 Effective length of query: 391 Effective length of database: 385 Effective search space: 150535 Effective search space used: 150535 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 (21.6 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