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 3609500 Dshi_2884 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase (RefSeq)
Query= curated2:P37942 (424 letters) >FitnessBrowser__Dino:3609500 Length = 496 Score = 243 bits (620), Expect = 9e-69 Identities = 151/408 (37%), Positives = 219/408 (53%), Gaps = 28/408 (6%) Query: 8 MPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQT 67 +P LGESVTE T+S W GD V + + + E+ TDKV+ EVP+ G +TE++ EG T Sbjct: 108 VPTLGESVTEATVSTWFKKVGDTVVQDEMLCELETDKVSVEVPAPAAGVLTEILAPEGAT 167 Query: 68 LQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVLRLAGE 127 ++ + + GA A +PA + AA P A+ D P+ K+ L E Sbjct: 168 VEASAKLAVLGGAGAVAAPS---EPAPAPAA--PTAQGKDVEDAPSAKK-------LMAE 215 Query: 128 HGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPKEETSY 187 + + V GTG GR+ + D+ + K AAPAP +A + E Sbjct: 216 NNLASGDVQGTGRDGRVMKGDVLAALAAP----------KAAAPAPSAAPRAPVAAE--- 262 Query: 188 PASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDSFKKTEG 247 AA ++ + +T +R+ IA +K S+ T EVD+T +A R KD F+K G Sbjct: 263 --DAAREERVKMTKLRQTIAKRLKDSQNTAAMLTTYNEVDMTETMALRKEYKDLFEKKHG 320 Query: 248 FNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVPVIKNADE 307 L F +FF KA ALKE P++N+ G I+ K +++ IA T L VPVI++AD Sbjct: 321 VRLGFMSFFTKACCHALKEVPEVNAEIDGTDIVYKNFVHMGIAAGTPQGLVVPVIRDADR 380 Query: 308 KTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQAAILQVE 367 + I I ++ RDGKL+ +MQGGTFT++N G +GS+ S I+N PQ+ IL + Sbjct: 381 MSFAEIEAAIAEKGRRARDGKLSMAEMQGGTFTISNGGVYGSLMSSPILNPPQSGILGMH 440 Query: 368 SIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 I RP+V+ NG I +R M+ L LS DHR++DG FL RVK+ LE Sbjct: 441 KIQDRPMVI-NGEIKIRPMMYLALSYDHRIVDGKGAVTFLVRVKEALE 487 Score = 73.9 bits (180), Expect = 1e-17 Identities = 40/94 (42%), Positives = 54/94 (57%), Gaps = 1/94 (1%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P LGESVTE T++ W PGD V + + E+ TDKV EVPS GT+ E+V E Sbjct: 4 EVRVPTLGESVTEATVATWFKKPGDTVAVDEMLCELETDKVTVEVPSPAAGTLAEIVAAE 63 Query: 65 GQTLQVGEMICKI-ETEGANPAEQKQEQPAASEA 97 G T+ V ++ I E GA AE P A+ A Sbjct: 64 GSTVGVDALLASIGEGSGAAAAEAAPAAPKAAPA 97 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: 487 Number of extensions: 25 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: 496 Length adjustment: 33 Effective length of query: 391 Effective length of database: 463 Effective search space: 181033 Effective search space used: 181033 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