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_2446 Echvi_2446 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes
Query= curated2:P37942 (424 letters) >FitnessBrowser__Cola:Echvi_2446 Length = 427 Score = 288 bits (738), Expect = 2e-82 Identities = 178/445 (40%), Positives = 256/445 (57%), Gaps = 50/445 (11%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MA +M MP++GES+ EGTI WL G+ + + + + EV TDKV+ EVPSS G + ++ Sbjct: 1 MATVEMVMPKMGESIIEGTILTWLKKEGESIEEDESVLEVATDKVDTEVPSSHAGVLKKI 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQP-----------------AASEAAE--NP 101 + +EG + VG I IETEG + K +P A S+ A NP Sbjct: 61 LAKEGDVVAVGAPIALIETEGEEEDDTKATEPKEVDTDSSSEKEDLLAAAPSQTATIINP 120 Query: 102 VA-KSAGAADQPNKKRYSPAVLRLAGEHGI---DLDQVTGTGAGGRITRKDIQRLIETGG 157 V KS G +K+ YSP VL +A E GI +L + GTG GR+T+ D+ +++ Sbjct: 121 VTEKSTG-----DKRFYSPLVLSIAKEEGISKAELATIPGTGKEGRVTKHDMLDYLKSRS 175 Query: 158 VQEQNPEELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEI 217 + P PK+A+ + +AGD+ I + +RK I+ M SK Sbjct: 176 TAT-------SGTPMPKAAA-----------SVSAGDEIIEMDRMRKMISERMVASKQIS 217 Query: 218 PHAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGD 277 PH + +E DVTN+V +RN +K+++K G LTF FFV+AVA+A+++FP +N GD Sbjct: 218 PHVTSFVEADVTNIVLWRNKVKEAYKNKMGEPLTFTPFFVEAVAKAIQDFPMINISVDGD 277 Query: 278 KIIQKKDINISIAVA-TEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQG 336 +II+KKDINI +AVA +L VPVIK A+E + G++K I LA + R KL AD++ G Sbjct: 278 RIIKKKDINIGVAVALPSGNLIVPVIKKANELNLTGLSKKINDLAARARTNKLAADELSG 337 Query: 337 GTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMD---NGMIAVRDMVNLCLSL 393 GT+T++N GSFG++ II PQ AIL V +I K+P VM+ +IAVR + L S Sbjct: 338 GTYTISNVGSFGNLMGTPIIMQPQVAILAVGAITKKPAVMETPTGDVIAVRHKMFLSHSY 397 Query: 394 DHRVLDGLVCGRFLGRVKQILESID 418 DHRV+DG + G F+ RV LE+ D Sbjct: 398 DHRVVDGSLGGMFVKRVADYLEAFD 422 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: 419 Number of extensions: 20 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: 427 Length adjustment: 32 Effective length of query: 392 Effective length of database: 395 Effective search space: 154840 Effective search space used: 154840 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 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