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 Pf1N1B4_1018 Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
Query= SwissProt::O06159 (393 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1018 Length = 369 Score = 192 bits (487), Expect = 2e-53 Identities = 138/398 (34%), Positives = 191/398 (47%), Gaps = 47/398 (11%) Query: 7 IRSFPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGG 66 ++ F +PDLGEGLQE + W V VGD V +Q L SVETAKA V+IP+PY G + + G Sbjct: 1 MKYFKLPDLGEGLQEAEIVRWHVKVGDTVTADQLLVSVETAKALVDIPAPYDGVVAKTFG 60 Query: 67 AEGDVLKVGAELVRIDTGPTAVAQPNGEGAVPTLVGYGADT-----------AIETSRRT 115 EGD+L VG L+ + GE T+VG D A ++R Sbjct: 61 GEGDILHVGEPLLGYE----------GEADAGTVVGRLEDGGTNQEDAFFIGAAPSTREH 110 Query: 116 SRPLAAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAAR------GGVGAGPDVRP 169 A P VR+LA++L V+L+ L GSG G ITR+DV AA+ GG Sbjct: 111 LANRATPAVRQLARQLGVELSGLT-GSGQDGQITRSDVENAAQTERERFGG-------EK 162 Query: 170 VHGVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPEITPFALTLRLLVIA 229 + GV MA M SH E+ + + R+ + A + + A Sbjct: 163 LRGVRRSMALNMARSHAEVVPVTIFGDADLHRWGQAREPLIRLA----------KAMAAA 212 Query: 230 LKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAE 289 +LNS + G+ + H + LG T GL VPV+ D + +L V Sbjct: 213 CAVEPVLNSAF--DGKTQALKQHERLDLGIAVDTPDGLFVPVLRDVGQRTAADLKEGVMR 270 Query: 290 LITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGE 349 L + ++ P E+ G+T T+SNFG L PV+ P+ AIL GAI+ PV V G Sbjct: 271 LRADVQARSIPPQEMMGATLTLSNFGTLFGRYANPVVVPPQVAILAAGAIREEPVAVEGA 330 Query: 350 VVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPE 387 VV P + L+ FDHRVV G + A+F L + +E PE Sbjct: 331 VVVHPILPLSLTFDHRVVTGGEAARFFKALVEALEQPE 368 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: 434 Number of extensions: 22 Number of successful extensions: 3 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