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_043537207.1 SACCYDRAFT_RS10825 2-oxo acid dehydrogenase subunit E2
Query= curated2:P37942 (424 letters) >NCBI__GCF_000244975.1:WP_043537207.1 Length = 404 Score = 236 bits (602), Expect = 9e-67 Identities = 135/416 (32%), Positives = 228/416 (54%), Gaps = 27/416 (6%) Query: 8 MPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQT 67 MP+L +++ EG I W GD++ + D +AE+ TDK E+ + G + ++ EG Sbjct: 1 MPRLSDTMEEGVIVTWRKQVGDELRRGDVVAEIETDKALMELEAYDDGVLERVLVAEGDR 60 Query: 68 LQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPN-------KKRYSPA 120 +G I + +G+ A + + P ++ A + A A PN + + SP Sbjct: 61 APIGTPIAVVG-DGSGTAPETEPVPVSAPARDTTPASLRPAPGAPNAPGASSPRPKSSPL 119 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 ++A EHGIDL+ V G+G GGRI RKD++ + T +PAP ++P Sbjct: 120 ARKIAREHGIDLNTVEGSGPGGRIIRKDVEAAV--------------TTSPAP---ARPA 162 Query: 181 PKEETSYPASAAGDK-EIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIK 239 P + A + D EIP+T VR+ A + SK + PH + +DVT+++ +R ++ Sbjct: 163 PAATSPADAVSTTDADEIPLTTVRRVAARRLTESKQQAPHFYLTTAIDVTDLLTFRTTLN 222 Query: 240 DSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFV 299 D+ + +G ++ V+AVA L+ P +N +AGD +++ + +++ +AVA D L V Sbjct: 223 DTLRAADGPKVSLNDLIVRAVAVTLRADPSVNVSFAGDTLLRHRGVHLGVAVAVPDGLVV 282 Query: 300 PVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYP 359 PV+++AD K++ IA + A + R+G+L AD+M GGTFT++N G +G Q +IN P Sbjct: 283 PVVRDADRKSVSEIAAETREKASRAREGRLRADEMSGGTFTISNLGMYGIEQFAAVINPP 342 Query: 360 QAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +AAIL V + + ++D G + R ++ + LS DHR +DG RFL ++ +LE Sbjct: 343 EAAILAVGAASEELRLVD-GEVVARSILRVTLSADHRAVDGATGARFLRQLTALLE 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: 388 Number of extensions: 20 Number of successful extensions: 5 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: 404 Length adjustment: 31 Effective length of query: 393 Effective length of database: 373 Effective search space: 146589 Effective search space used: 146589 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 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