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_011427082.1 RHE_RS19880 dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000092045.1:WP_011427082.1 Length = 418 Score = 257 bits (657), Expect = 4e-73 Identities = 152/418 (36%), Positives = 229/418 (54%), Gaps = 19/418 (4%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P LGESV+E T+ W GD + +PI E+ TDKV EVP+ +GT++E+V Sbjct: 4 EIRVPTLGESVSEATVGTWFKKVGDAIKADEPILELETDKVTIEVPAPVSGTLSEIVAAA 63 Query: 65 GQTLQVGEMICKI-ETEGANPAEQKQEQPAASE------AAENPVAKSAGAADQPNKKRY 117 G+T+ G ++ +I E GA A PAA+ AA P A ++ ++ + Sbjct: 64 GETVGPGALLGQIAEGAGAAAAAPAAAAPAAAPSQAVPAAAAQPAAAASSSSASVSTMPP 123 Query: 118 SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSAS 177 +PA ++ E + DQV G+G G++ + D+ + G +APA A+ Sbjct: 124 APAAAKMLAESNLSADQVDGSGKRGQVLKGDVIAAVAKG-----------ISAPAAAPAA 172 Query: 178 KPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237 P S A+ ++ + +T +R+ IA +K ++ T EVD+ ++ RN Sbjct: 173 APAAARGPSTVEDASREERVKMTRLRQTIAKRLKDAQNTAAMLTTYNEVDMKAVMDLRNK 232 Query: 238 IKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSL 297 KD F+K G L F FF KAV ALKE P +N+ G +I K ++ +AV T+ L Sbjct: 233 YKDIFEKKHGVKLGFMGFFTKAVTHALKELPAVNAEIDGTDVIYKNYCHVGMAVGTDKGL 292 Query: 298 FVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIIN 357 VPVI++AD+ +I I KD+ LAK RDG L+ DMQGGTFT+ N G +GS+ S I+N Sbjct: 293 VVPVIRDADQMSIAEIEKDLGRLAKAARDGSLSMADMQGGTFTITNGGVYGSLMSSPILN 352 Query: 358 YPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 PQ+ IL + I +RPV + G + +R M+ L LS DHR++DG FL RVK+ LE Sbjct: 353 APQSGILGMHKIQERPVAI-GGQVVIRPMMYLALSYDHRIVDGKEAVTFLVRVKESLE 409 Lambda K H 0.312 0.129 0.359 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: 421 Number of extensions: 16 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: 424 Length of database: 418 Length adjustment: 32 Effective length of query: 392 Effective length of database: 386 Effective search space: 151312 Effective search space used: 151312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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