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 GFF2174 Psest_2217 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes
Query= SwissProt::O06159 (393 letters) >FitnessBrowser__psRCH2:GFF2174 Length = 382 Score = 164 bits (415), Expect = 4e-45 Identities = 121/386 (31%), Positives = 183/386 (47%), Gaps = 17/386 (4%) Query: 10 FPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGAEG 69 F +P LG + E T+ W V G+ +E + + V+TAKA V++ ++G ++EL G Sbjct: 4 FKLPSLGADMDEGTLLQWKVKPGERIERGEVIAVVDTAKAAVDVECWHSGEVLELLVEPG 63 Query: 70 DVLKVGAELVRIDTGPTAVAQPNGEGAVPTLVGYGAD----TAIETSRRTSRPLAAPVVR 125 + VG L R+ A + P V A+ TA+ TSR +PV R Sbjct: 64 SKIPVGTPLARLLEPGEAREAALAQSPAPVPVAVAAEQPPVTAVAPPADTSRARISPVAR 123 Query: 126 KLAKELAVDLAALQRGSGAGGVITRADVLAAARGGVGAGPDVRPVHGVHARMAEKMTLSH 185 + A EL +D A L GSG G +T DV AAA A + + +A M+ S Sbjct: 124 RRAAELGIDPATLS-GSGPHGSVTLQDVEAAAAKAAPADRNA----AMRQAIAAAMSRSK 178 Query: 186 KEIPTAKASVEVICAELLRLRDRF-VSAAPE--ITPFALTLRLLVIALKHNVILNSTWVD 242 +EIP S V R + PE + L L+ + +AL+ LN W D Sbjct: 179 REIPHYYLSETVAFGAAARWLQAYNAERIPEERLLVSVLLLKAVALALRDYPQLNGYWRD 238 Query: 243 SGEGPQVHVHRGVHLGFGAATERG-LLVPVVTDAQDKNTRELASRVAELITGAREGTLTP 301 P G+HLG + +G L+ P + D + +L + +L+ AR G+L Sbjct: 239 GAFQPG----EGIHLGTAISLRQGGLIAPALHDVAGQPLPQLMQALGDLVQRARAGSLRS 294 Query: 302 AELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCV 361 +EL +T TV+ G GVD VI P+ A++G+G I RP V G + P++ L+ Sbjct: 295 SELSDATLTVTQLGEQGVDSVFGVIYPPQVALVGVGRIVERPWVEAGALCVMPSVVLSLA 354 Query: 362 FDHRVVDGAQVAQFMCELRDLIESPE 387 DHR DG A+F+ E+R L+++PE Sbjct: 355 ADHRASDGHYGARFLAEVRRLLQNPE 380 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: 369 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: 393 Length of database: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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