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_005454511.1 SACCYDRAFT_RS05985 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase
Query= curated2:P09062 (423 letters) >NCBI__GCF_000244975.1:WP_005454511.1 Length = 607 Score = 231 bits (589), Expect = 5e-65 Identities = 156/465 (33%), Positives = 238/465 (51%), Gaps = 57/465 (12%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 + +P++GE + + + W +VGD + D+ + ++ TDK E+PSPV+G VL + Sbjct: 137 VTLPELGESVTEGTVTRWLKQVGDRVEVDEPLLEISTDKVDTEVPSPVAGTVLEITVGED 196 Query: 66 EVMAVGSELIRIEVEGSGNHVDV--PQAKPAEVPAAPVAAKPEPQKDVKPAAYQASAS-- 121 E + VG++L V GS + P A P P A PEPQ + +PA Q SA Sbjct: 197 ETVEVGAQLA---VVGSADAAPAQQPPAAPEPQPQQQAPAAPEPQPEPEPAPQQPSAPAP 253 Query: 122 --------------HEAAPIVP-------RQPGDKPLASPAVRKRALDAGIELRYVHGSG 160 EA P P R P +P VRK A + GI+L + GSG Sbjct: 254 QPQAQQPQAPAPAPQEAEPAKPAAAAPAERDGAGTPYVTPLVRKLAAEHGIDLSTLKGSG 313 Query: 161 PAGRILHED-LDAFMSKPQSAAGQT---------------PNGYARRTDSEQVPVIG--- 201 GRI +D L A +K + A T P+ A +D+E+ + G Sbjct: 314 VGGRIRKQDVLAAAEAKQKEVAAPTAQQPAPAAPSAQPARPSAPAPVSDAEKAALRGTVQ 373 Query: 202 ----LRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALRQQLNSKHGDSRG-KLTLLPFLV 256 +R+ A + +++ + A + V E+DVT + LRQ+ + G LT LPF Sbjct: 374 KANRIRQITAVKTKESLQVSAQLTQVHEVDVTKVAQLRQRAKGAFREREGVNLTFLPFFA 433 Query: 257 RALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQGDNGLMVPVLRHAEAGSLWANAG 316 +A V AL+ P +NA+Y++E + IT HGA+++G+A D GL+ V+ A SL A Sbjct: 434 KATVEALKQHPNVNASYNEETKEITYHGAINLGMAVDTDRGLLSVVIHDAGELSLAGLAH 493 Query: 317 EISRLANAARNNKASREELSGSTITLTSLGALGGIVSTPVVNTPEVAIVGVNRMVERPVV 376 I+ LA AR+NK + +EL+G T T+T+LG+ G + TP++ P+ I+GV +V RPVV Sbjct: 494 RIADLAARARSNKVTPDELTGGTFTITNLGSNGALFDTPIIVQPQSGILGVGAVVRRPVV 553 Query: 377 ---IDGQ--IVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGLLEQ 416 DG I VR M+ L ++DHR++DG DA F+ ++ LE+ Sbjct: 554 ATDADGNDTIAVRSMVYLPLTYDHRLIDGADAGRFLTTIKQRLEE 598 Score = 72.4 bits (176), Expect = 4e-17 Identities = 42/136 (30%), Positives = 69/136 (50%), Gaps = 11/136 (8%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 + +P++GE + + + W + GD + D+ + ++ TDK E+PSPV+G + + + Sbjct: 5 VTLPELGESVTEGTVTRWLKQEGDRVEVDEPLLEISTDKVDTEVPSPVAGTLSRIVARED 64 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 E + VG EL I+ +GSG AE AAP A +P++ P A QA A E Sbjct: 65 ETVEVGGELAVID-DGSGGGA-------AETAAAPEA---QPEQQAAPQAQQAEAQPEPQ 113 Query: 126 PIVPRQPGDKPLASPA 141 +Q P A+P+ Sbjct: 114 AAPAQQQAPAPAAAPS 129 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: 662 Number of extensions: 33 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: 607 Length adjustment: 34 Effective length of query: 389 Effective length of database: 573 Effective search space: 222897 Effective search space used: 222897 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: 52 (24.6 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