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 Ac3H11_4092 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
Query= curated2:P09062 (423 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4092 Length = 546 Score = 215 bits (548), Expect = 2e-60 Identities = 148/429 (34%), Positives = 226/429 (52%), Gaps = 40/429 (9%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 +++PDIG+ V ++E VKVGD I +Q + V +DKA++EIPSP +G + L + G Sbjct: 114 VRVPDIGD-FKDVAVIEMLVKVGDTIKVEQSLFTVESDKASMEIPSPAAGVLKELKVKIG 172 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 + + +G +L+ I +EG+ A PA P A AA P P PA A+ + A Sbjct: 173 DTVNIG-DLVAI-LEGAA-----AAAAPAAAPVA--AAAPAPAPVAAPAVAAAAPAAATA 223 Query: 126 PIVPRQPGDK----PLASPAVRKRALDAGIELRYVHGSGPAGRILHEDLDAFMSKPQSAA 181 + QPG P ASP+VRK A + G+ + V G+GP GRI +D+ AF + + A Sbjct: 224 SVPAHQPGTPTAGLPHASPSVRKFARELGVPIDEVKGTGPKGRITQDDVAAFTKQVMAGA 283 Query: 182 GQTPNGYARRTDSEQVPVIGL----------------RRKIAQRMQDAKRRVAHFSYV-- 223 QT A+ S IGL RK R++ H ++V Sbjct: 284 VQTKAQAAKAPASGGGSGIGLDLLPWPKVDFTKFGPVERKDLSRIKKISGANLHRNWVVI 343 Query: 224 ------EEIDVTALEALRQQLNSKHGDSRGKLTLLPFLVRALVVALRDFPQINATYDDEA 277 ++ D+T LEA R Q N ++ S K+T+L F+++A V AL+ FP+ N++ D + Sbjct: 344 PHVTNHDDADITDLEAFRVQFNKENEKSGVKVTMLAFMIKAAVAALKKFPEFNSSLDGDQ 403 Query: 278 QIITRHGAVHVGIATQGDNGLMVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSG 337 ++ + H+G A NGL+VPV+R A+ + + E+ LA AR+ K +++G Sbjct: 404 LVLKNY--FHIGFAADTPNGLVVPVIRDADKKGIVQISQEMGDLAKKARDGKLGPADMTG 461 Query: 338 STITLTSLGALGGIVSTPVVNTPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRV 397 +++SLG +GG TP++N PEVAI+GV + P Q R M+ LS S+DHRV Sbjct: 462 GCFSISSLGGIGGRYFTPIINAPEVAIMGVCKSSIEPKWDGKQFAPRLMLPLSLSWDHRV 521 Query: 398 VDGMDAALF 406 +DG AA F Sbjct: 522 IDGAAAARF 530 Score = 59.3 bits (142), Expect = 3e-13 Identities = 46/127 (36%), Positives = 65/127 (51%), Gaps = 13/127 (10%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 I++PDIG+ +V ++E VKVGD + +Q + V +DKA++EIPS +G V L G Sbjct: 4 IQVPDIGD-FDEVGVIELLVKVGDTVKAEQSLITVESDKASMEIPSSHAGVVKELKIALG 62 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 + + GS + +E +G A PA P AP AA P P A A A A Sbjct: 63 DKVKQGSVIAVVESADAG-----AAAAPAAAP-APAAAAP------APVAAAAPAPAAAG 110 Query: 126 PIVPRQP 132 P+ R P Sbjct: 111 PVEVRVP 117 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: 508 Number of extensions: 19 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: 546 Length adjustment: 34 Effective length of query: 389 Effective length of database: 512 Effective search space: 199168 Effective search space used: 199168 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 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