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 Echvi_3886 Echvi_3886 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form
Query= curated2:P37942 (424 letters) >FitnessBrowser__Cola:Echvi_3886 Length = 547 Score = 217 bits (553), Expect = 6e-61 Identities = 140/439 (31%), Positives = 228/439 (51%), Gaps = 52/439 (11%) Query: 6 MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65 +TMP++ +++ EGTI+ WL GD+V D +AEV TDK E+ S G + + +EG Sbjct: 125 ITMPKMSDTMQEGTIASWLKKEGDEVKSGDILAEVETDKATMELESYDDGVLLHIGVQEG 184 Query: 66 QTLQVGEMICKIETEGAN-------------------PAEQKQEQPAASEAAENPVAK-- 104 ++ + +I I +GA+ PA +++E+ A + A P K Sbjct: 185 DSVPIDGVIAVIGEKGADYEKLLKAHEQKSNGGSDEKPAAKEEEKKEAPKEASKPAPKKE 244 Query: 105 --------SAGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETG 156 S+ A+ + + SP +LA + G+D+ + G+G GGRI ++D++ Sbjct: 245 ETAKQTTSSSSASSDNGRIKASPLAKKLAEDKGVDIALIKGSGEGGRIIKRDVESF---- 300 Query: 157 GVQEQNPEELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTE 216 +P ++ AA + +A P + SY E V+ +RK IA + SK Sbjct: 301 -----DPASVQPAAQSGVAA--PAAVGQESYT-------EEKVSQMRKTIAKRLAESKFS 346 Query: 217 IPHAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAG 276 PH + ME+++ + R S+ + FN +KAVA +LK+ P++NS W G Sbjct: 347 APHFYLTMEINMDKAIEARKSMNEIAPVKISFN----DMVIKAVAASLKQHPKVNSSWLG 402 Query: 277 DKIIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQG 336 DKI + ++I +AVA E+ L VPVI+ AD KT+ I+++ L K ++ +L D +G Sbjct: 403 DKIRYNEHVHIGMAVAVEEGLLVPVIRFADSKTLSQISQEAKTLGGKAKNKELQPKDWEG 462 Query: 337 GTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHR 396 TFT++N G FG + I+N P A IL V I K V++ +G + V +++ + LS DHR Sbjct: 463 NTFTISNLGMFGIEEFTAIVNPPDACILAVGGI-KETVIVKDGQMQVGNVMKVTLSCDHR 521 Query: 397 VLDGLVCGRFLGRVKQILE 415 V+DG V FL +K +LE Sbjct: 522 VVDGAVGSGFLKTLKGLLE 540 Score = 43.5 bits (101), Expect = 2e-08 Identities = 30/110 (27%), Positives = 51/110 (46%), Gaps = 1/110 (0%) Query: 11 LGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQTLQV 70 + +++ EG I+ WL GD V D +AEV TDK E+ S G + + EE + V Sbjct: 1 MSDTMEEGVIAAWLKKVGDDVKAGDILAEVETDKATMELESYDEGVLLHIGVEEKDAVPV 60 Query: 71 GEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 +I I +G + + ++ + + AKS A+ ++ S A Sbjct: 61 NGVIAIIGEKGEDIDDLLKDLDGGG-SGDADAAKSEAPAEDKKEESSSEA 109 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: 579 Number of extensions: 39 Number of successful extensions: 7 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: 547 Length adjustment: 34 Effective length of query: 390 Effective length of database: 513 Effective search space: 200070 Effective search space used: 200070 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 17 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