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_011780776.1 MVAN_RS17970 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000015305.1:WP_011780776.1 Length = 580 Score = 248 bits (632), Expect = 5e-70 Identities = 163/443 (36%), Positives = 236/443 (53%), Gaps = 41/443 (9%) Query: 8 MPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQT 67 MP+LGESVTEGT+++WL GD V+ +P+ EV TDKV+ E+PS GT+ + EE T Sbjct: 134 MPELGESVTEGTVTRWLKKVGDSVDVDEPLVEVSTDKVDTEIPSPVAGTLLSITAEEDDT 193 Query: 68 LQVGEMICKIETEGANPAEQKQEQP----------------AASEAAENP---------- 101 ++VG + KI GA A + + +P A EAA P Sbjct: 194 VEVGGELAKIGDAGAEAAPEPEPEPEPQPEPEPKTTTPSAKPAEEAAPEPKPEPTPQPKP 253 Query: 102 -VAKSAGAADQPNKKRY-SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQ 159 A +A A + Y +P V +LAGEH +DL V GTG GGRI ++D+ E Sbjct: 254 EPAPAAAAESSGDSSPYVTPLVRKLAGEHSVDLASVKGTGVGGRIRKQDVLAAAEA---- 309 Query: 160 EQNPEELKTAAPAPKSASK-PEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIP 218 + P+E AAPA ++ +K P P E + A G + +R+ A + S Sbjct: 310 SKAPKEAPKAAPAAEAPAKVPTPAPEGAL-AHLRGTTQ-KANRIRQITAKKTRESLQTTA 367 Query: 219 HAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGD- 277 + EVD+T +VA R K F + EG NLT+ F +AV ALK P +N+ + D Sbjct: 368 QLTQVHEVDMTKIVALRAKAKAKFAEREGVNLTYLPFIARAVIDALKIHPNVNASYNEDS 427 Query: 278 -KIIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQG 336 +I ++ +AV TE L PVI NA + ++ G+A+ I+ +A + R G L D++ G Sbjct: 428 KEITYYDAEHLGVAVDTEQGLLSPVIHNAGDLSLGGLARAISDIAARARSGDLKPDELSG 487 Query: 337 GTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRP-VVMD---NGMIAVRDMVNLCLS 392 GTFT+ N GS G++ I+ PQAA+L +IVKRP V++D N I VR + L L+ Sbjct: 488 GTFTITNIGSQGALFDTPILVPPQAAMLGTGAIVKRPRVIVDDYGNESIGVRSVSYLPLT 547 Query: 393 LDHRVLDGLVCGRFLGRVKQILE 415 DHR++DG GRF+ +K+ LE Sbjct: 548 YDHRLIDGADAGRFVTTIKRRLE 570 Score = 77.8 bits (190), Expect = 8e-19 Identities = 66/243 (27%), Positives = 106/243 (43%), Gaps = 47/243 (19%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAI + MP LGESVTEGT+++WL GD V + +P+ EV TDKV+ E+PS G + ++ Sbjct: 1 MAIS-VQMPALGESVTEGTVTRWLKQEGDTVEEDEPLLEVSTDKVDTEIPSPAAGVLKKI 59 Query: 61 VGEEGQTLQVGEMIC--------------KIETEGANPAEQKQEQPAASEAAENPVAKSA 106 V +E T++VG + K E E E + E A E P AK Sbjct: 60 VAQEDDTVEVGGELAVIGDADDSDAGGDEKPEPEPEPEPEAEAEPEPAPEPEPEPEAKPK 119 Query: 107 GAADQPNKKRYSPAVLRLAGE---------------HGIDLD-------------QVTGT 138 Q + +P ++ GE +D+D ++ Sbjct: 120 AKPAQSSGSA-TPVLMPELGESVTEGTVTRWLKKVGDSVDVDEPLVEVSTDKVDTEIPSP 178 Query: 139 GAGGRIT-RKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPKEE--TSYPASAAGDK 195 AG ++ + +E GG + + AAP P+ +P+P+ E T+ P++ ++ Sbjct: 179 VAGTLLSITAEEDDTVEVGGELAKIGDAGAEAAPEPEPEPEPQPEPEPKTTTPSAKPAEE 238 Query: 196 EIP 198 P Sbjct: 239 AAP 241 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: 598 Number of extensions: 35 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: 580 Length adjustment: 34 Effective length of query: 390 Effective length of database: 546 Effective search space: 212940 Effective search space used: 212940 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