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_011386316.1 AMB_RS20045 dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000009985.1:WP_011386316.1 Length = 394 Score = 276 bits (707), Expect = 6e-79 Identities = 158/411 (38%), Positives = 231/411 (56%), Gaps = 29/411 (7%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P LGESVTE TI+KW GD V +P+ E+ TDKV EV + GT+T++V Sbjct: 4 EIKVPTLGESVTEATIAKWFKNVGDAVRADEPLVELETDKVTVEVNAPAAGTLTDIVAAA 63 Query: 65 GQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVLRL 124 G T++VG ++ + GA A PA AA P A A A P+ K+ + Sbjct: 64 GATVEVGALLGVLGAAGAAAA------PAPKAAAPAPAAAPAAAGVMPSAKK-------I 110 Query: 125 AGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPKEE 184 A + GID ++GTG GR+T+ D+ AAPAP +A P+P Sbjct: 111 AADAGIDTAAISGTGKDGRVTKGDVLAA---------------AAAPAP-AAPAPKPAAP 154 Query: 185 TSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDSFKK 244 + A A ++ + +T +RK IA +K ++ T EVD+T + RN KD F+K Sbjct: 155 SGPRAKADQEERVKMTRLRKTIAGRLKEAQNTAAMLTTFNEVDMTALFDVRNQYKDQFEK 214 Query: 245 TEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVPVIKN 304 G L F +FFVKA ALK++P +N+ GD ++ KK +I +AV T L VPV++ Sbjct: 215 RHGTKLGFMSFFVKACVAALKDWPAVNAEIDGDDLVYKKYYDIGVAVGTPQGLVVPVLRG 274 Query: 305 ADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQAAIL 364 AD+ + G+ + I L KK RDGKL+ +D+ GGTFT++N G +GS+ S I+N PQ+ IL Sbjct: 275 ADQLSFAGVEQGIANLGKKARDGKLSMEDLMGGTFTISNGGVYGSLMSTPILNTPQSGIL 334 Query: 365 QVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 + + +RP+VM +G I R M+ L LS DHR++DG FL RVK+ +E Sbjct: 335 GMHKVQQRPMVMPDGSIKARPMMYLALSYDHRIIDGREAVSFLVRVKECIE 385 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: 371 Number of extensions: 20 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 393 Effective length of database: 363 Effective search space: 142659 Effective search space used: 142659 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