Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate WP_089299389.1 CHB84_RS00130 2-oxo acid dehydrogenase subunit E2
Query= curated2:P37942 (424 letters) >NCBI__GCF_900188115.1:WP_089299389.1 Length = 485 Score = 196 bits (497), Expect = 2e-54 Identities = 151/476 (31%), Positives = 213/476 (44%), Gaps = 67/476 (14%) Query: 3 IEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVG 62 ++ +P GE +TE I W VAPGD+V+ I E+ T K E+P + G +TEL+ Sbjct: 4 LKSFPLPDAGEGLTEAEIINWHVAPGDEVDVNQIIVEIETAKAAVELPCPWAGVVTELLA 63 Query: 63 EEGQTLQVGEMICKIETE--GANPAEQKQEQPAA--------SEAAENPVAKSAGAADQ- 111 E GQT++VG I I+ + GA P+ +Q A S AA + SAG+ Sbjct: 64 EPGQTVEVGTPILTIDVDPNGAAPSPGEQAPAGAAAEPTSTGSTAASTNGSSSAGSGGSG 123 Query: 112 ------------PNK----KRY---------------------------------SPAVL 122 P+K KR P V Sbjct: 124 GDESVATLVGYGPSKPSEVKRRRRTDSPGALNDAVSPSSGGNASFSSTTEYVPLAKPPVR 183 Query: 123 RLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE-- 180 +LA E G+DL VTG G GG ITR+D+ R V P A P + + P Sbjct: 184 KLAKELGVDLRTVTGHGTGGVITREDVHRAA-AAPVNGTTPATAPAAGDEPTAEAGPAAG 242 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P ++ S A + +P+ VRKA A M S PH + VDVT M+ R+ +K+ Sbjct: 243 PAAGSAVAPSDAREHRVPIRSVRKATAQAMVSSAFTAPHVTEFLTVDVTPMMELRDRLKN 302 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMW--AGDKIIQKKDINISIAVATEDSLF 298 G LT AF KA+ A K P+ N+ W ++I+ K I++ +A AT+ L Sbjct: 303 Q-PAYSGVRLTPLAFAAKAMCMAAKRTPEANASWDEENEEIVYKDYIHLGVAAATQRGLI 361 Query: 299 VPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINY 358 VP +++AD + +A I L R G DM GT T+ N G FG IIN Sbjct: 362 VPKVRDADAMNLAELAAAIDDLTDAARAGTTPPADMVNGTITITNVGVFGVDTGTPIINP 421 Query: 359 PQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQIL 414 ++AIL +I P V+D G + R + L LS DHR++DG +FL V +L Sbjct: 422 GESAILAFGAIRDTPWVVD-GQVVPRRVCQLALSFDHRLVDGQQGSQFLADVGALL 476 Lambda K H 0.312 0.129 0.359 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: 471 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 424 Length of database: 485 Length adjustment: 33 Effective length of query: 391 Effective length of database: 452 Effective search space: 176732 Effective search space used: 176732 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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