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 GFF348 PGA1_c03590 dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Query= curated2:P37942 (424 letters) >FitnessBrowser__Phaeo:GFF348 Length = 516 Score = 245 bits (626), Expect = 2e-69 Identities = 152/420 (36%), Positives = 218/420 (51%), Gaps = 23/420 (5%) Query: 2 AIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELV 61 A + +P LGESV+E T+S W GD V + + + E+ TDKV+ EVP+ G +TE+ Sbjct: 105 AATDVMVPTLGESVSEATVSTWFKKVGDSVAQDEMLCELETDKVSVEVPAPTAGILTEIT 164 Query: 62 GEEGQTLQVGEMICKI---ETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYS 118 EEG T+ + I E P K E ++ P + A D N + Sbjct: 165 AEEGSTVDATAKLGVISGGEAGAVTPTPSKGETAGGAQYTTPPAGQGGPAKDIAN----A 220 Query: 119 PAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASK 178 P+ + E G+ DQV G+G GRI + D+ R + AAPA S S Sbjct: 221 PSAEKAMAEAGLSADQVQGSGRDGRIMKDDVARAVAAAA-----------AAPAA-STSA 268 Query: 179 PEPKEETSYPASA---AGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYR 235 P P +A A ++ + +T +R+ IA +K S+ T EVD+T ++A R Sbjct: 269 PAAAAPVRAPVAADDAAREERVKMTRLRQTIAKRLKDSQNTAAMLTTYNEVDMTEVMALR 328 Query: 236 NSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATED 295 N KD F K G L F +FF KA AL E P++N+ G I+ K +++ IA T Sbjct: 329 NEYKDLFLKKHGVKLGFMSFFTKACVHALNEVPEVNAEIDGTDIVYKNFVHMGIAAGTPT 388 Query: 296 SLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGI 355 L VPVI++AD + I K I + RDGKL+ +MQGGTFT++N G +GS+ S I Sbjct: 389 GLVVPVIRDADAMSFADIEKAIAEKGARARDGKLSMAEMQGGTFTISNGGVYGSLMSSPI 448 Query: 356 INYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +N PQ+ IL + I RP+ + NG + +R M+ L LS DHR++DG FL RVK+ LE Sbjct: 449 LNPPQSGILGMHKIQDRPMAI-NGKVEIRPMMYLALSYDHRIVDGKGAVTFLVRVKEALE 507 Score = 71.2 bits (173), Expect = 7e-17 Identities = 39/105 (37%), Positives = 59/105 (56%), Gaps = 2/105 (1%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P LGESVTE T++ W PGD V + + E+ TDKV EVP+ GT+ E+V E Sbjct: 4 EVRVPTLGESVTEATVATWFKKPGDAVAADEMLCELETDKVTVEVPAPAAGTLGEIVAAE 63 Query: 65 GQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAA 109 G+T+ V ++ I G++ A +A A ++ AGAA Sbjct: 64 GETVGVDALLATIAEGGSDTA--AAPATSAPAATKDAAEGDAGAA 106 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: 494 Number of extensions: 26 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: 516 Length adjustment: 33 Effective length of query: 391 Effective length of database: 483 Effective search space: 188853 Effective search space used: 188853 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