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 SMc01032 SMc01032 dihydrolipoamide S-acetyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__Smeli:SMc01032 Length = 447 Score = 206 bits (524), Expect = 1e-57 Identities = 130/441 (29%), Positives = 221/441 (50%), Gaps = 34/441 (7%) Query: 6 MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65 +TMP L ++ EG ++KWLV GDKV D IAE+ TDK EV + GT+ ++V G Sbjct: 5 ITMPALSPTMEEGNLAKWLVKEGDKVKSGDVIAEIETDKATMEVEAVDEGTVAKIVVPAG 64 Query: 66 -QTLQVGEMICKIETEG---------------ANPAEQKQEQ----------PAASEAAE 99 + ++V +I + EG A PA + +E PAA+ A + Sbjct: 65 TEGVKVNALIAVLAAEGEDVATAAKGGNGAAGAVPAPKPKETAETAPAAAPAPAAAPAPQ 124 Query: 100 NPVAKSAGAADQPNKKRYS-PAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGV 158 S AD K+ +S P RLA E GIDL + G+G GR+ +KD++ + G Sbjct: 125 AAAPASPAPADGEGKRIFSSPLARRLAKEAGIDLSAIAGSGPHGRVVKKDVETAVSGGAA 184 Query: 159 QEQNPEELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIP 218 + P AAPAP + +K ++ + +P G+RK IA + SK IP Sbjct: 185 K---PAGAPAAAPAPATLAKGMSEDAVLKLFEPGSYELVPHDGMRKTIAKRLVESKQTIP 241 Query: 219 HAWTMMEVDVTNMVAYRNSIKDSFKKTEG---FNLTFFAFFVKAVAQALKEFPQMNSMWA 275 H + ++ ++ ++A R + + + +G + L+ +KA+A AL++ P N W Sbjct: 242 HFYVSVDCELDALMALRAQLNAAAPEKDGKPVYKLSVNDMVIKALALALRDVPDANVSWT 301 Query: 276 GDKIIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQ 335 +++ K ++ +AV+ L P+++ A+ K++ I+ ++ L K+ ++ KL ++ Q Sbjct: 302 DQNMVKHKHADVGVAVSIPGGLITPIVRQAELKSLSAISNEMKDLGKRAKERKLKPEEYQ 361 Query: 336 GGTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDH 395 GGT V+N G G ++N P A IL V + R VV + M+ + +++ + LS DH Sbjct: 362 GGTTAVSNMGMMGVKDFAAVVNPPHATILAVGAGEDRVVVRNKEMV-IANVMTVTLSTDH 420 Query: 396 RVLDGLVCGRFLGRVKQILES 416 R +DG + L K+ +E+ Sbjct: 421 RCVDGALGAELLAAFKRYIEN 441 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: 448 Number of extensions: 34 Number of successful extensions: 7 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: 424 Length of database: 447 Length adjustment: 32 Effective length of query: 392 Effective length of database: 415 Effective search space: 162680 Effective search space used: 162680 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 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