Align Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex; Branched-chain alpha-ketoacid dehydrogenase complex component E2; BCKADH E2; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 (characterized)
to candidate AO353_15585 AO353_15585 branched-chain alpha-keto acid dehydrogenase subunit E2
Query= SwissProt::O06159 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15585 Length = 369 Score = 202 bits (513), Expect = 2e-56 Identities = 138/395 (34%), Positives = 203/395 (51%), Gaps = 39/395 (9%) Query: 7 IRSFPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGG 66 ++ F +PDLGEGLQE + W V VGD V+ +Q L SVETAKA V+IP+PY G + + G Sbjct: 1 MKYFKLPDLGEGLQEAEIVEWHVKVGDTVKADQLLVSVETAKALVDIPAPYDGVVAKTFG 60 Query: 67 AEGDVLKVGAELV----RIDTGPTAVAQPNGEGAVPT---LVGYGADTAIETSRRTSRPL 119 EGD+L VG L+ D G T V + G G+ VG A ++R P Sbjct: 61 GEGDILHVGEPLLGYEGEADAG-TVVGRLEGGGSHQDDQFFVG-----AAPSTREHMSPR 114 Query: 120 AAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAAR------GGVGAGPDVRPVHGV 173 A P VR+LA++L V+L L GSG G+ITR+DV +A++ GG + GV Sbjct: 115 ATPAVRQLARQLGVELTGLS-GSGPDGLITRSDVESASQTERDKFGG-------EKLRGV 166 Query: 174 HARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPEITPFALTLRLLVIALKHN 233 MA+ MT SH E+ + R RD + A + + A Sbjct: 167 RRSMAQNMTRSHAEVVPVTIYADADLHRWGRARDPLIRLA----------KAMAAACAVE 216 Query: 234 VILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAELITG 293 +LNS + G+ + H ++LG T GL VPV+ D ++++ +L + L Sbjct: 217 PMLNSGF--DGKSLSIKHHDALNLGIAVDTPDGLFVPVLRDVGNRSSDDLKEGITRLRAD 274 Query: 294 AREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVAR 353 + ++ E+ G+T T+SNFG + PV+ P+ AIL GAI+ PV + G+VV Sbjct: 275 VQARSIPAKEMMGATLTLSNFGTMFGRYANPVVVPPQVAILAAGAIRDEPVAMAGKVVVH 334 Query: 354 PTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPET 388 P + L+ FDHRVV G + A+F L + +E P++ Sbjct: 335 PILPLSLTFDHRVVTGGEAARFFKVLVEALEQPDS 369 Lambda K H 0.317 0.135 0.388 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: 428 Number of extensions: 26 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: 393 Length of database: 369 Length adjustment: 30 Effective length of query: 363 Effective length of database: 339 Effective search space: 123057 Effective search space used: 123057 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 (21.7 bits) S2: 50 (23.9 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