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_057509081.1 ABB28_RS13310 2-oxo acid dehydrogenase subunit E2
Query= SwissProt::O06159 (393 letters) >NCBI__GCF_001431535.1:WP_057509081.1 Length = 464 Score = 147 bits (371), Expect = 6e-40 Identities = 130/457 (28%), Positives = 195/457 (42%), Gaps = 86/457 (18%) Query: 8 RSFPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGA 67 ++F +PDLGEGL + T+ W V GD + +++ L S+ETAKA VE+PSP +G+I++L GA Sbjct: 5 KNFNLPDLGEGLPDATIVEWFVKEGDTIRLDEPLVSMETAKAVVEVPSPVSGKILKLSGA 64 Query: 68 EGDVLKVGAELVRIDTGPTAVAQPNGE-----------GAVP------------------ 98 GD++ GA L + P + +G+ A P Sbjct: 65 AGDIIPTGAVLASFELDPNLPQRADGQDTGHSHGHAAPAAAPSTGQPAPAQADAVVASDE 124 Query: 99 --------------TLVG-YGADTAI--ETSRRTSRPLAAPVVRKLAKELAVDLAALQRG 141 T+VG + A+ E + A P VR +A++L VDL+ + R Sbjct: 125 GGEIKDGGERDDAGTVVGAMQSSNAVHAEQAVAVGGVKAVPAVRAMARKLGVDLSRV-RA 183 Query: 142 SGAGGVITRADVLAAARGG---VGAGP------DVRPVHGVHARMAEK----MTLSHKEI 188 SG G +T ADV AA G VGA P PV E M+ + K + Sbjct: 184 SGTEGAVTMADVKQAAADGSAKVGAAPAAAAAAQSAPVSAPAPARVESQRAPMSAAGKPM 243 Query: 189 PT------AKASVEVICAELLRLRDRFVSAAPEITPFALT------------------LR 224 T AK E + + A ++ P L +R Sbjct: 244 RTQPPGVVAKGQPEQLKGVRRNMARVMADAHSKVVPTTLNDDADLHAWLPGNDVTARLVR 303 Query: 225 LLVIALKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELA 284 +V+A + +N+ W D GE +H V +G TE GL VP + +A + R + Sbjct: 304 AIVVACQKVPAMNA-WFD-GEALTRTLHAHVDVGIAVDTEEGLFVPALRNADMLDARGIR 361 Query: 285 SRVAELITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPV 344 V L ++ +EL G T ++SNFG PV+ P AI+G G + + Sbjct: 362 EGVNRLREQVEARSIAASELSGYTISLSNFGMFAGRYATPVVVPPCVAIVGAGRARHQMT 421 Query: 345 VVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRD 381 V G V A + L+ FDHRV G + A+F+ + D Sbjct: 422 PVMGGVEAHKVIPLSVTFDHRVATGGEAARFLRAMMD 458 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: 494 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 393 Length of database: 464 Length adjustment: 32 Effective length of query: 361 Effective length of database: 432 Effective search space: 155952 Effective search space used: 155952 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: 51 (24.3 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