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 Echvi_0772 Echvi_0772 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component)
Query= curated2:P37942 (424 letters) >FitnessBrowser__Cola:Echvi_0772 Length = 524 Score = 263 bits (672), Expect = 9e-75 Identities = 159/419 (37%), Positives = 237/419 (56%), Gaps = 25/419 (5%) Query: 3 IEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVG 62 +++M +P +GES+TE T++ WL GD V + IAEV +DK E+P+ G I + V Sbjct: 116 VKEMVVPTVGESITEVTLASWLKEDGDFVEMDEIIAEVDSDKATFELPAEAQG-ILKRVA 174 Query: 63 EEGQTLQVGEMICKIET-EGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRY---- 117 EEG TL++G +ICKIE EG + P A + A+ +S +A Y Sbjct: 175 EEGDTLEIGGLICKIEVVEG--------DAPEADDTADTSKEESTSSASSSGSGSYAEGH 226 Query: 118 -SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSA 176 SPA ++ E GID +V GTG GR+T++D ++ Q+Q P K AA S+ Sbjct: 227 ASPAAAKILAEKGIDAKEVKGTGKDGRVTKEDAEK------AQKQAP---KPAASKSSSS 277 Query: 177 SKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRN 236 + E E A K ++ +RK I+ + +K E T EV++ ++ R Sbjct: 278 AAKETAPEAPKVAGERNMKREKMSSLRKTISKRLVAAKNETAMLTTFNEVNMKPIMDLRK 337 Query: 237 SIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296 K+ FK+ NL F +FF KAV AL+E+P +N+ G++II ++SIAV+ Sbjct: 338 QYKEMFKEKHNVNLGFMSFFTKAVCVALQEWPAVNAQIDGNEIIYHDFCDVSIAVSAPKG 397 Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356 L VPVI+NA+ + + K++ LA K RDGKLT ++M GGTFT+ N G FGS+ S II Sbjct: 398 LVVPVIRNAESLSFDQVEKEVVRLATKARDGKLTIEEMTGGTFTITNGGIFGSMMSTPII 457 Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 N PQ+AIL + +IV+RP+ + NG + + M+ + LS DHR++DG FL R+KQ+LE Sbjct: 458 NQPQSAILGMHNIVERPMAV-NGEVKILPMMYIALSYDHRIIDGRESVSFLVRLKQLLE 515 Score = 64.7 bits (156), Expect = 6e-15 Identities = 40/122 (32%), Positives = 67/122 (54%), Gaps = 6/122 (4%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P +GES+TE TI +W G+ V + I E+ +DK E+ + G +T + E Sbjct: 4 EIKVPAVGESITEVTIGQWFKNSGEYVEMDEVICELESDKATFELTAEADGILT-VKAEA 62 Query: 65 GQTLQVGEMICKIET----EGANPA-EQKQEQPAASEAAENPVAKSAGAADQPNKKRYSP 119 G TL++G +IC+I+T + A PA E+K+E PA S+ ++ + S K+ P Sbjct: 63 GDTLEIGAVICEIDTKASADDAAPAKEEKKEAPADSKESKGSSSDSKSGKTGEVKEMVVP 122 Query: 120 AV 121 V Sbjct: 123 TV 124 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: 518 Number of extensions: 27 Number of successful extensions: 7 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: 524 Length adjustment: 33 Effective length of query: 391 Effective length of database: 491 Effective search space: 191981 Effective search space used: 191981 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