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_013074672.1 BTUS_RS03125 2-oxo acid dehydrogenase subunit E2
Query= curated2:P37942 (424 letters) >NCBI__GCF_000092905.1:WP_013074672.1 Length = 459 Score = 272 bits (696), Expect = 1e-77 Identities = 161/449 (35%), Positives = 248/449 (55%), Gaps = 38/449 (8%) Query: 3 IEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVG 62 I Q +P +GE + E I +W V PG+ V + + EV TDK E+PS G + E+ G Sbjct: 2 IYQWRLPDVGEGIHEAEIVRWRVQPGEVVTEDQVLLEVQTDKATVEIPSPVAGKVVEVHG 61 Query: 63 EEGQTLQVGEMICKIETE------GANPAEQKQEQPAAS--------EAAENPVAKSAGA 108 +EGQ + VG ++ +IETE G + PA S E+ S G Sbjct: 62 DEGQVVPVGTVLVEIETEEGQVSPGLRGVAAESGMPAGSATSGVVGRESERQVPPGSPGT 121 Query: 109 ADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQE-----QNP 163 + + + +P V RLA E GID++QV GTG GGR+ +D++ GG ++ P Sbjct: 122 GNGLQRAKAAPVVRRLARELGIDINQVPGTGPGGRVLEEDVRAFAARGGDRDLGGGTSGP 181 Query: 164 E----ELKTAAPAPKSASKPEPKEETSYPASA------------AGDKEIPVTGVRKAIA 207 E E ++ A + ++ K+ET P A A ++ IP+ GVR+ IA Sbjct: 182 EVQVGEGRSETGAQRLSTAEPKKQETVSPVGAREAEGSFAEGQDADEQRIPLRGVRRVIA 241 Query: 208 SNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEF 267 +M +SK IPH M E DVT +VA+R +++S + + +T+ F VKAV LK + Sbjct: 242 EHMVQSKFTIPHVTGMDEADVTELVAFRRQVEESAAEGQ-VKITYLPFIVKAVVAGLKAY 300 Query: 268 PQMNSMWAGDK--IIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVR 325 P N+ ++ I+ K+ +I IAV D L VP++ +AD K++ IA++I L +K R Sbjct: 301 PYFNAGLDDERREIVLKRRYHIGIAVDAPDGLLVPIVHDADRKSVLEIAEEIEELKEKAR 360 Query: 326 DGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRD 385 G L+ D+M+GGTFT++N GSFG + + II+YPQAAIL IV+RPV++++ + R Sbjct: 361 SGSLSPDEMRGGTFTISNIGSFGGLFATPIIHYPQAAILATGKIVRRPVMLEDDRVVGRW 420 Query: 386 MVNLCLSLDHRVLDGLVCGRFLGRVKQIL 414 M+ + L+ DHR++DG RF+G + Q+L Sbjct: 421 MMPISLTFDHRIIDGAAATRFMGYIMQLL 449 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: 473 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: 459 Length adjustment: 32 Effective length of query: 392 Effective length of database: 427 Effective search space: 167384 Effective search space used: 167384 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 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