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_086510768.1 BZY95_RS15330 dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_002151265.1:WP_086510768.1 Length = 514 Score = 249 bits (636), Expect = 1e-70 Identities = 148/414 (35%), Positives = 231/414 (55%), Gaps = 24/414 (5%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ P ES+ EGT++ W G+ V + D +A++ TDKV EV + G + E+ EE Sbjct: 113 EVKAPTFPESIQEGTVATWHKKVGEAVKRDDVLADIETDKVVLEVVAPADGALAEIKVEE 172 Query: 65 GQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQP-NKKRYSPAVLR 123 G + E + I TEGA A+ + A+ A + G+ D+ K +PA + Sbjct: 173 GSQV-ASEAVLAIFTEGAGGADTTADTTPAASADD-------GSGDERIGDKILAPAARK 224 Query: 124 LAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPA--PKSASKPEP 181 + EH +D+ ++ GTG GGRI ++D+QR ++ G + K+AAPA PK A+ P Sbjct: 225 MVAEHDLDVSKIEGTGKGGRILKEDVQRAVQAGTAK-------KSAAPAAAPKQAATAAP 277 Query: 182 KEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDS 241 E P +K +P++ +R+ IA + +++ T EVD+ ++ R KD+ Sbjct: 278 AFEGERP-----EKRVPMSRLRQTIAKRLVQAQQTAAMLTTYNEVDMGAVMDLRAQYKDT 332 Query: 242 FKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVPV 301 F+K L F FFVKA ++ALK FP +N+ G I+ +I +AV+T+ L VPV Sbjct: 333 FQKAHDVKLGFMGFFVKAASEALKRFPDVNASIDGTDIVYHGYQDIGVAVSTDRGLVVPV 392 Query: 302 IKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQA 361 +++ D I + K I K+ RDGKL ++MQGGTFT+ N G FGS+ S I+N PQ Sbjct: 393 LRDTDSMKIADVEKGIVDFGKRARDGKLGIEEMQGGTFTITNGGIFGSLMSTPILNPPQT 452 Query: 362 AILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 AIL + I +RP+ + NG + +R M+ L LS DHR++DG +FL +K++LE Sbjct: 453 AILGMHKIQERPMAV-NGKVEIRPMMYLALSYDHRMIDGKDAVQFLVTIKELLE 505 Score = 71.6 bits (174), Expect = 5e-17 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 10/183 (5%) Query: 9 PQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQTL 68 P ESV EG+++ W PGD V + + I E+ TDKV EV + GT++E++ EEG T+ Sbjct: 8 PTFPESVAEGSVAAWHKKPGDSVERDELIVEIETDKVVLEVVAPEAGTLSEVLVEEGDTV 67 Query: 69 QVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVLRLAGEH 128 Q +++ KI AE+K E+ A ++AA AK+A AA + + +P E Sbjct: 68 QSEQVLGKIGAGSTKGAEKKSEK-ADAKAAPQSEAKAAPAAGGKSHEVKAPTFPESIQEG 126 Query: 129 GIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPKEETSYP 188 + G + R D+ IET V L+ APA + ++ + +E + Sbjct: 127 TV---ATWHKKVGEAVKRDDVLADIETDKV------VLEVVAPADGALAEIKVEEGSQVA 177 Query: 189 ASA 191 + A Sbjct: 178 SEA 180 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: 521 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 424 Length of database: 514 Length adjustment: 33 Effective length of query: 391 Effective length of database: 481 Effective search space: 188071 Effective search space used: 188071 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