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_011384715.1 AMB_RS11715 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000009985.1:WP_011384715.1 Length = 427 Score = 221 bits (564), Expect = 3e-62 Identities = 146/428 (34%), Positives = 225/428 (52%), Gaps = 28/428 (6%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 Q+ MP L ++TEG ++KWL GD V D + E+ TDK E + G + +++ Sbjct: 4 QILMPALSPTMTEGNLAKWLKNEGDAVKSGDILCEIETDKATMEFEAVDEGVLGKILVAG 63 Query: 65 GQT-----------LQVGE---MICKIETEGANPAEQKQEQPAASEA---AENPVAKSAG 107 G + L+ GE I I A PA K PAA+ A A PVA +G Sbjct: 64 GTSGVAVNTPIAVLLEEGEDASAISAISAISAAPAP-KAAAPAAAAAPVTAAAPVAAPSG 122 Query: 108 AADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELK 167 A ++ SP R+A + +DL V G+G GRI + D++ I+ G + P Sbjct: 123 PAHGGDRVVASPLAKRIAKDGNVDLKAVKGSGPHGRIVKADVEAAIKAGPAK---PAAAP 179 Query: 168 TAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVD 227 A AP + S P P + + + +EIP + +RK IA + +K+ IPH + ++ + Sbjct: 180 AAIVAPAAKSAPAPAAASPFEPAF---EEIPNSSMRKVIARRLTEAKSTIPHFYLSIDCE 236 Query: 228 VTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINI 287 + ++ R + +++ + L+ F V+AVA ALK+ P N+ W + I + DI+I Sbjct: 237 LDALLKVRADLNG---RSDAYKLSVNDFVVRAVALALKKAPAANASWGEEAIKRYTDIDI 293 Query: 288 SIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSF 347 S+AVAT L P++ +AD K + I+ ++ LA K RDGKL ++ QGG FT++N G F Sbjct: 294 SVAVATPSGLITPIVHHADHKGLAEISNEMKSLAAKARDGKLKPEEFQGGGFTISNLGMF 353 Query: 348 GSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFL 407 G + IIN PQ IL V + +RPVV G +AV ++ LS+DHRV+DG V FL Sbjct: 354 GIKEFAAIINPPQGCILAVGAGEQRPVV-KAGALAVATVMTCTLSVDHRVVDGAVGAEFL 412 Query: 408 GRVKQILE 415 K+++E Sbjct: 413 AAFKKLIE 420 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: 411 Number of extensions: 25 Number of successful extensions: 6 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