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 WP_011781239.1 MVAN_RS20470 2-oxo acid dehydrogenase subunit E2
Query= SwissProt::O06159 (393 letters) >NCBI__GCF_000015305.1:WP_011781239.1 Length = 400 Score = 450 bits (1158), Expect = e-131 Identities = 246/404 (60%), Positives = 290/404 (71%), Gaps = 22/404 (5%) Query: 6 SIRSFPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELG 65 ++R F VPDLGEGL+E TVT W VA+GD V +NQTLC+VET KAEVEIPSP+AGRI ELG Sbjct: 3 TVREFLVPDLGEGLEEATVTAWQVAIGDVVTLNQTLCTVETNKAEVEIPSPFAGRIAELG 62 Query: 66 GAEGDVLKVGAELVRIDTGPTAV------AQPNGEGAV---------PTLVGYGADTAIE 110 GA G L VG+ LVRID G +G+ A P LVGYGAD ++ Sbjct: 63 GAAGQTLPVGSVLVRIDLGNDTENDRAGDTDSDGDSATDAEKDAPRRPVLVGYGADHTMD 122 Query: 111 TSRRTSRPLAAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAARGGVGAGPDVRPV 170 SRR +R A P VRKLA +L VDL+ + GSG G++TR DVLA GG V Sbjct: 123 GSRRRAR--AKPRVRKLAADLDVDLSRID-GSGPDGIVTRDDVLAVTDGGTSQDS---VV 176 Query: 171 HGVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPE-ITPFALTLRLLVIA 229 GV MA +M+LS EIP A ASVEV +ELLRLRDR +A + +TPF L LRLLV+A Sbjct: 177 SGVRLAMARRMSLSRSEIPDAHASVEVDGSELLRLRDRLAAAGADGVTPFVLVLRLLVVA 236 Query: 230 LKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAE 289 L+ + +LN+TWVD+ +GP+VHVH VHLG G A RGLLVPVVTDAQ+++TR LA VA Sbjct: 237 LRRHPVLNATWVDTVDGPRVHVHPAVHLGVGVAAPRGLLVPVVTDAQERSTRRLADEVAR 296 Query: 290 LITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGE 349 L+ AR GTL P EL+GSTFTVSN+GALG+DDGVPVINHPEAAI+G+G++KPR VVVGG Sbjct: 297 LVAAARAGTLKPGELQGSTFTVSNYGALGLDDGVPVINHPEAAIVGVGSLKPRAVVVGGA 356 Query: 350 VVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPETALLDL 393 VVARPTM LTC FDHRV DGAQVA F+ ELR LIE PE ALLDL Sbjct: 357 VVARPTMRLTCAFDHRVADGAQVAAFLAELRSLIELPELALLDL 400 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: 522 Number of extensions: 20 Number of successful extensions: 6 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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 24 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