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_011651832.1 RL_RS11615 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000009265.1:WP_011651832.1 Length = 451 Score = 212 bits (540), Expect = 2e-59 Identities = 141/445 (31%), Positives = 223/445 (50%), Gaps = 38/445 (8%) Query: 6 MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65 +TMP L ++ EG +SKWLV GDKV D IAE+ TDK EV + GT+ +LV G Sbjct: 5 ITMPALSPTMEEGNLSKWLVKEGDKVKSGDVIAEIETDKATMEVEAVDEGTVAKLVVAAG 64 Query: 66 -QTLQVGEMICKIETEG----------------------ANPAEQKQEQPAASE--AAEN 100 + ++V +I + +G A P + PA S AA Sbjct: 65 TEGVKVNALIAVLAADGEDVAAAASAAGSAAPAPKADGAAAPKAEAAPAPAQSTPAAAPA 124 Query: 101 PVAKSAGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQE 160 P A A + N+ SP RLA E GIDL V GTG GR+ + DI+ + G + Sbjct: 125 PAAAPASVSADGNRTFSSPLARRLAKEAGIDLSAVAGTGPHGRVVKSDIEAAVAGGAAKA 184 Query: 161 QNPEELKTAAPAPKSASKPE--PK---EETSYPASAAGDKE-IPVTGVRKAIASNMKRSK 214 P AA AP++++ P PK EE G E +P G+RK IA + SK Sbjct: 185 AAPA---AAASAPQASAAPAAAPKGASEEAVLKLFEPGSYELVPHDGMRKTIARRLVESK 241 Query: 215 TEIPHAWTMMEVDVTNMVAYRNSIKDSFKKTEG---FNLTFFAFFVKAVAQALKEFPQMN 271 IPH + ++ ++ ++A R + D+ + + + L+ +KA+A +L++ P N Sbjct: 242 QTIPHFYVSVDCELDALLALRAQLNDAAPRKDNAPAYKLSVNDMVIKAMALSLRDVPDAN 301 Query: 272 SMWAGDKIIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTA 331 W +++ K ++ +AV+ L P+I+ A+EKT+ I+ ++ L K+ +D KL Sbjct: 302 VSWTDSNMVKHKHADVGVAVSIPGGLITPIIRKAEEKTLSTISNEMRDLGKRAKDRKLKP 361 Query: 332 DDMQGGTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCL 391 ++ QGGT +V+N G G ++N P A IL V + +R VV+ G +A+ ++++ L Sbjct: 362 EEYQGGTSSVSNMGMMGVKNFAAVVNPPHATILAVGAGEQR-VVVKKGEMAIATVMSVTL 420 Query: 392 SLDHRVLDGLVCGRFLGRVKQILES 416 S DHR +DG + L K +E+ Sbjct: 421 STDHRCVDGALGAELLQAFKGYIEN 445 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: 429 Number of extensions: 21 Number of successful extensions: 7 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: 451 Length adjustment: 32 Effective length of query: 392 Effective length of database: 419 Effective search space: 164248 Effective search space used: 164248 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: 51 (24.3 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