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_050655910.1 C1M55_RS30490 2-oxo acid dehydrogenase subunit E2
Query= SwissProt::O06159 (393 letters) >NCBI__GCF_002893965.1:WP_050655910.1 Length = 407 Score = 273 bits (697), Expect = 8e-78 Identities = 168/398 (42%), Positives = 225/398 (56%), Gaps = 24/398 (6%) Query: 10 FPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGAEG 69 F +PDLGEGL E + W V VGD V I+Q + VETAKA V++P P+AG ++EL G +G Sbjct: 6 FMLPDLGEGLAEADIAEWHVKVGDVVTIDQIVVEVETAKAAVDVPIPFAGTVIELHGKDG 65 Query: 70 DVLKVGAELVRIDTGPT--AVAQPNGE--------GAVPTLVGYGADTAIETSRRTSRP- 118 D LKVG L+ + G + AV N E G+ L+GYG RR + P Sbjct: 66 DTLKVGTPLITVSGGESVDAVVSANHERYREEERAGSGNVLIGYGTSEDAPLRRRRAAPS 125 Query: 119 --LAAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAARGGVG-----AGPDVRPVH 171 + +P+VRKLA + ++DL + GSGAGGVITRADV A + G A P+ Sbjct: 126 VRVISPIVRKLASDNSIDLTTIS-GSGAGGVITRADVEAGSNTGTELETSHAADQRIPIK 184 Query: 172 GVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPE---ITPFALTLRLLVI 228 G+ +A+K++ S +EIP A V+V ELL R + P+ I+ AL RL + Sbjct: 185 GLRKVVADKLSTSRREIPDATTWVDVDATELLAARAEINKSLPDSDKISLMALLARLTIA 244 Query: 229 ALKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVA 288 AL LNS+ VD+ G V H HLG A T +GL+VPV+ +A +T ELA + Sbjct: 245 ALAQYPELNSS-VDTARGEIVR-HARTHLGIAAQTPKGLMVPVIRNADALSTVELAQALR 302 Query: 289 ELITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGG 348 AR+G L PA L G TFT++N+G GVD P+INHPEAAILG+G I +P VV G Sbjct: 303 VTTDLARDGKLEPARLTGGTFTLNNYGVFGVDGSTPIINHPEAAILGIGRIIDKPWVVNG 362 Query: 349 EVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESP 386 E+ R ++ FDHRV DG + F+ D IE+P Sbjct: 363 ELTVRKVTQISLSFDHRVCDGGEAGGFLRLFGDYIENP 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: 419 Number of extensions: 20 Number of successful extensions: 5 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: 407 Length adjustment: 31 Effective length of query: 362 Effective length of database: 376 Effective search space: 136112 Effective search space used: 136112 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