Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; Dihydrolipoamide branched-chain transacylase E2; EC 2.3.1.168 (characterized)
to candidate N515DRAFT_0354 N515DRAFT_0354 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)
Query= SwissProt::Q23571 (448 letters) >FitnessBrowser__Dyella79:N515DRAFT_0354 Length = 461 Score = 132 bits (333), Expect = 2e-35 Identities = 130/463 (28%), Positives = 179/463 (38%), Gaps = 86/463 (18%) Query: 33 FKLSDIGEGIAEVQVKEWYVKEGDTISQFDKVCEVQSDKAAVTISCRYDGIVKKLYHEVD 92 F L D+GEG+ + + EW+VKEGD I +C +++ KA V + Y G V+KLY Sbjct: 7 FHLPDLGEGLPDATIVEWHVKEGDYIKLDAPLCSMETAKAVVDVPSPYTGTVQKLYGAPG 66 Query: 93 GMARVGQALIDVEIEGNVEEPEQ---------PKKEAASSSPE----------------- 126 + G AL D + N ++ + PKK S +P+ Sbjct: 67 DIIETGAALADFAPDPNAKQRAEAEATGHHHGPKKSVGSPAPDNAAKVVASDEGGEVEAK 126 Query: 127 -----------APKSSAPKAPESAHSEGKVLATPAVRRIAIENKIKLAEVRGTGKDGRVL 175 A S E S G V A PAVR +A + K+ L VR TG DG V Sbjct: 127 GEREDEGTVVGAMVSGNTVHVEQVSSAGGVKAVPAVRALAKKLKVDLTRVRPTGADGVVT 186 Query: 176 KEDVLKF-------LGQVPADHTSGSTNIRTTHQAPQPSSKSYEPLKEDVAVPIR----- 223 +DV LG PA S + P+P + P+R Sbjct: 187 LQDVKTAAANGSAPLGAAPARAVPASAGRHLAPELPEPGAAPSRTAVSLAGKPVRTAPPS 246 Query: 224 -----------GYTRAMVKTMTEALKIPHFGYNDEINVDSLVKYRAELKEFAKERHIKLS 272 G R M + M EA H VD A+L + ++ I Sbjct: 247 VQASGQPEQLKGVRRNMARVMAEA----HANVVPTTLVDD-----ADLHGWIGKQDITAR 297 Query: 273 YMPFFIKAASLALLEYPSLNSTTDEKMENVIHKASHNICLAMDTPGGLVVPNIKNCEQRS 332 I+A A P+LN+ D K +I +A+DT GL VP ++N + Sbjct: 298 ----LIRAIVAACKAVPALNAWFDGKNLTRTLHPHVDIGIAVDTEDGLFVPALRNADVLD 353 Query: 333 IFEIAQELNRLLEAGKKQQIKREDLIDGTFSLSNIGNIGGTYASPVVFPPQVAIGAIGKI 392 + + RL + + I +L T SLSN G G YA+PVV PP VAI GK+ Sbjct: 354 GAGVRAAIKRLRAQVEDRSIPASELSGYTISLSNFGMFAGRYATPVVVPPTVAIIGAGKL 413 Query: 393 EKLPRFDKHDNVIPV------NIMKVSWCADHRVVDGATMARF 429 HD V + M +S DHR G ARF Sbjct: 414 -------CHDVVAVMGGIEVHRRMPISLTFDHRAATGGEAARF 449 Lambda K H 0.316 0.132 0.377 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: 439 Number of extensions: 23 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: 448 Length of database: 461 Length adjustment: 33 Effective length of query: 415 Effective length of database: 428 Effective search space: 177620 Effective search space used: 177620 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