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_111392718.1 CLV31_RS09795 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P09062 (423 letters) >NCBI__GCF_003253485.1:WP_111392718.1 Length = 505 Score = 213 bits (543), Expect = 8e-60 Identities = 140/427 (32%), Positives = 223/427 (52%), Gaps = 47/427 (11%) Query: 8 MPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPGEV 67 +P +GE I +V L W K GD + D+++A+V +DKAT E+P+ +G +L + G+V Sbjct: 108 VPTVGESITEVTLANWIKKDGDFVTLDEIIAEVDSDKATFELPAEATG-ILRHVAKEGDV 166 Query: 68 MAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAAPI 127 + +G + +IEV + AK PA P A+ ++ AS+S+ A Sbjct: 167 LEIGGLICKIEV------TEEAPAKTESAPAEPTAS----------SSSSASSSYAAGH- 209 Query: 128 VPRQPGDKPLASPAVRKRALDAGIELRYVHGSGPAGRILHED-LDAFMSKPQSAAGQ--- 183 ASPA K + GI V GSG GRI ED L A S P AA + Sbjct: 210 ----------ASPAASKILAEKGISPESVSGSGKDGRITKEDALSAKKSAPAPAAEKPAP 259 Query: 184 ------TPNGYARRTDSEQVPVIGLRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALR-- 235 +P + + + LR+ +++R+ K A + E+++ + LR Sbjct: 260 KVQESASPAAAPGSRNVRREKMSSLRKTVSRRLVAVKNETAMLTTFNEVNMKPIMDLRAK 319 Query: 236 --QQLNSKHGDSRGKLTLLPFLVRALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQ 293 Q KHG G + F +A+ VAL+++P +NA D I + + IA Sbjct: 320 FKDQFKEKHGVGLG---FMSFFTKAVCVALQEWPAVNAMIDGNE--IVYNDFCDISIAVS 374 Query: 294 GDNGLMVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSGSTITLTSLGALGGIVS 353 GL+VPV+R+AEA S E+ RLA AR+NK S EE++G T T+T+ G G ++S Sbjct: 375 APKGLVVPVIRNAEAMSFDQIEKEVVRLAGKARDNKLSIEEMTGGTFTITNGGVFGSMMS 434 Query: 354 TPVVNTPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGL 413 TP++N P+ AI+G++ +VERP+ ++G++ + MM ++ S+DHR++DG ++ F+ V+ L Sbjct: 435 TPIINAPQSAILGMHNIVERPMAVNGEVKILPMMYVALSYDHRIIDGRESVSFLVRVKQL 494 Query: 414 LEQPACL 420 LE P L Sbjct: 495 LEDPTRL 501 Score = 60.8 bits (146), Expect = 9e-14 Identities = 34/108 (31%), Positives = 62/108 (57%), Gaps = 3/108 (2%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 +++P +GE I++V + +WF K GD + D+V+ ++ +DKAT E P+ +G +L + Q G Sbjct: 5 MRVPTVGESISEVTVGQWFKKDGDQVQLDEVLCELESDKATFEFPAEAAG-ILRIKAQEG 63 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKP 113 + + +G + IE E ++KP PAA +A E ++ + P Sbjct: 64 DTVEIGGLICVIE-EADAASKPATESKP-PAPAAKASASGEVKEMIVP 109 Lambda K H 0.316 0.133 0.376 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: 457 Number of extensions: 13 Number of successful extensions: 6 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: 423 Length of database: 505 Length adjustment: 33 Effective length of query: 390 Effective length of database: 472 Effective search space: 184080 Effective search space used: 184080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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