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 GFF2445 Psest_2493 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component)
Query= curated2:P37942 (424 letters) >FitnessBrowser__psRCH2:GFF2445 Length = 406 Score = 243 bits (619), Expect = 1e-68 Identities = 154/419 (36%), Positives = 236/419 (56%), Gaps = 26/419 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAIE + P ESV +GT++ W PGD V + + I ++ TDKV EV + G +TE+ Sbjct: 1 MAIE-IKAPTFPESVADGTVATWHKQPGDAVKRDELIVDIETDKVVMEVLAEADGVLTEI 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 V EG T+ GE++ K+E A A Q AA+ AA P A ++ ++P +PA Sbjct: 60 VKNEGDTVLSGELLGKLEAGAAAAAAPAQ---AAAPAAAAPAAAASAGGEEPI---LAPA 113 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 +LA E+GID + + GTG GR+T++D+ +E K +APA +A+KP Sbjct: 114 ARKLAEENGIDPNSIRGTGKDGRVTKEDVVAAVEA-----------KKSAPA--AAAKPA 160 Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237 + P A GD K +P+T +R +A + +++ + T EV++ ++ R Sbjct: 161 APAAAA-PIFAEGDRVEKRVPMTRLRAKVAERLVEAQSSMAMLTTFNEVNMKPIMELRAK 219 Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296 KD F+KT G L F +FFVKA +ALK P +N+ G+ I+ +I +AV+++ Sbjct: 220 YKDLFEKTHNGVRLGFMSFFVKAAVEALKRQPGVNASIDGNDIVYHGYQDIGVAVSSDRG 279 Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356 L VPV++NA+ ++ I I KK + GKLT ++M GGTFT++N G FGS+ S I+ Sbjct: 280 LVVPVLRNAEHMSLAEIEGGINEFGKKAKAGKLTIEEMTGGTFTISNGGVFGSLLSTPIV 339 Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 N PQ AIL + I +RP+ + NG + + M+ L LS DHR++DG FL +K +LE Sbjct: 340 NPPQTAILGMHKIQERPMAV-NGQVVILPMMYLALSYDHRLIDGKEAVTFLVTMKDLLE 397 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: 417 Number of extensions: 23 Number of successful extensions: 4 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: 406 Length adjustment: 31 Effective length of query: 393 Effective length of database: 375 Effective search space: 147375 Effective search space used: 147375 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: 50 (23.9 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