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_067913121.1 AQZ52_RS15725 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_001519075.1:WP_067913121.1 Length = 403 Score = 255 bits (652), Expect = 1e-72 Identities = 165/415 (39%), Positives = 230/415 (55%), Gaps = 21/415 (5%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+IE + +P LGESV+E T+ +WL PG+ V +PIA + TDKV EVPS G + Sbjct: 1 MSIE-VKVPVLGESVSEATVGQWLKQPGEAVALDEPIASLETDKVAVEVPSPVAGIMGAH 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 V EG T+ VG ++ IET G A PA + AA A +A AAD + SPA Sbjct: 60 VAAEGDTVAVGALLGLIETSGVANA------PAPAPAAA--AAPAAVAAD--DAAALSPA 109 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 V R EHGID V GTG GR+T++D+ V +Q AAPAP A P Sbjct: 110 VRRAVLEHGIDPATVKGTGKDGRLTKEDVL----AAAVAKQAAPAPVVAAPAPAPA--PA 163 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P TS ++ + +T +R+ IA +K ++ T +VD++ ++ R KD Sbjct: 164 PVVSTS---GERREERVKMTRLRQTIAKRLKSAQETAAMLTTFNDVDMSAVMEARAKYKD 220 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K G L +FF KA ALK+ P +N+ GD+I+ ++IS+AV+ + L VP Sbjct: 221 VFEKKHGVKLGLMSFFAKASVLALKDIPSVNAQLQGDEIVYFDYVDISVAVSAPNGLVVP 280 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 V+++ D+ + GI K I KK RDG LT DM GGTFT++N G FG + S IIN PQ Sbjct: 281 VVRDVDKMSFAGIEKAIADYGKKARDGTLTMADMAGGTFTISNGGVFGGLMSTPIINPPQ 340 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +A+L + I RPVV D G I VR M+ + LS DHR++DG L +K+ +E Sbjct: 341 SAVLGLHRIEDRPVVRD-GQIVVRPMMYIALSYDHRIIDGREAVTALKTIKEAIE 394 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: 410 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 393 Effective length of database: 372 Effective search space: 146196 Effective search space used: 146196 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