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_111391064.1 CLV31_RS01310 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_003253485.1:WP_111391064.1 Length = 551 Score = 217 bits (552), Expect = 8e-61 Identities = 145/435 (33%), Positives = 217/435 (49%), Gaps = 45/435 (10%) Query: 6 MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65 +TMP++ +++ EGTI+ WL GD V + IAEV TDK E+ S G + + E G Sbjct: 130 ITMPKMSDTMQEGTIAAWLKKVGDTVKSGEIIAEVETDKATMELESYEDGVLLYIGVEAG 189 Query: 66 QTLQVGEMICKIETEGAN------------------------PAEQKQEQPAASEAAENP 101 ++ V +I I +GA+ PA +K E PAA Sbjct: 190 NSVAVDGVIAVIGEKGADYETLLKAHQSGSKSSAPAETPTTPPAAEKTEAPAAPAPQTAA 249 Query: 102 VAKSAGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQ 161 A +A A + + SP ++A E G+D+ QV G+G GGRI +KD++ + Sbjct: 250 PATTAVPATSGERVKASPLAKKIAAEKGLDIRQVPGSGEGGRIVKKDVETFV-------- 301 Query: 162 NPEELKTAAPAP-KSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHA 220 P AA AP SA+ P P +E V+ +RK IA + SK PH Sbjct: 302 -PAVSPMAAAAPVSSAAAPAPM------IGQESFREEKVSQMRKTIAKRLAESKYSAPHF 354 Query: 221 WTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKII 280 + ME+++ + R S+ + FN +KA A AL++ P++NS W GDKI Sbjct: 355 YLTMEINMDKAIEARKSMNEFSPVKISFN----DMVIKAAAAALRQHPKVNSSWLGDKIR 410 Query: 281 QKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFT 340 I+I +AVA E+ L VPVI+ AD ++ I+ L K ++ +L D +G TFT Sbjct: 411 YNDHIHIGMAVAVEEGLLVPVIRFADSLSLSQISNQAKTLGGKAKNKELQPKDWEGNTFT 470 Query: 341 VNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDG 400 ++N G FG + IIN P A IL V I K V++ +G + + +++ + LS DHRV+DG Sbjct: 471 ISNLGMFGIEEFTAIINPPDACILAVGGI-KETVIVKDGQMRIGNIMKVTLSCDHRVVDG 529 Query: 401 LVCGRFLGRVKQILE 415 V FL +K +LE Sbjct: 530 AVGSAFLQTLKGLLE 544 Score = 53.5 bits (127), Expect = 2e-11 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 10/106 (9%) Query: 4 EQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGE 63 E + MP++ +++ EG I+ WL GD V D +AEV TDK E+ S G + + + Sbjct: 3 EIIRMPKMSDTMEEGVIASWLKKVGDTVKPGDILAEVETDKATMELESYEEGVLLYIGVK 62 Query: 64 EGQTLQVGEMICKIETEG----------ANPAEQKQEQPAASEAAE 99 E ++ V +I I +G A +KQE+PAA ++ E Sbjct: 63 EKDSVPVNGIIAIIGEKGEEFQHLLNGSAEAPAKKQEEPAAPKSEE 108 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: 549 Number of extensions: 31 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 424 Length of database: 551 Length adjustment: 34 Effective length of query: 390 Effective length of database: 517 Effective search space: 201630 Effective search space used: 201630 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: 52 (24.6 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