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 PP_4188 PP_4188 2-oxoglutarate dehydrogenase dihydrolipoyltranssuccinylase subunit
Query= curated2:P37942 (424 letters) >FitnessBrowser__Putida:PP_4188 Length = 407 Score = 258 bits (659), Expect = 2e-73 Identities = 159/419 (37%), Positives = 238/419 (56%), Gaps = 25/419 (5%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAIE + P ESV +GT++ W PG+ V + + I ++ TDKV EV ++ G + ++ Sbjct: 1 MAIE-IKAPTFPESVADGTVATWHKKPGEAVKRDELIVDIETDKVVLEVLATADGVLGDI 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 V EG T+ E++ I GA A PAA+ AA A + D P +PA Sbjct: 60 VKGEGDTVLSDELLGSIVEGGAAAAPAAAAAPAAAPAA----AAADAGEDDPIA---APA 112 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 +LA E+GIDL V GTG GGR+T++D+ + K +APA A+KP Sbjct: 113 ARKLAEENGIDLATVAGTGKGGRVTKEDVVAAVAK-----------KKSAPAAAPAAKPA 161 Query: 181 PKEETSYPASAAGD---KEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237 AAGD K +P+T +R IA + +++ + T EVD+T ++A R+ Sbjct: 162 AAAAAPVVV-AAGDRTEKRVPMTRLRAKIAERLVEAQSNMAMLTTFNEVDMTEVMALRSK 220 Query: 238 IKDSFKKTE-GFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296 KD F+KT G L F +FFVKA +ALK FP +N+ G+ I+ ++ +AV+++ Sbjct: 221 YKDLFEKTHNGVRLGFMSFFVKAATEALKRFPAVNASIDGNDIVYHGFADVGVAVSSDRG 280 Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356 L VPV++NA+ ++ I I KK RDGKL+ ++M GGTFT+ N G+FGS+ S I+ Sbjct: 281 LVVPVLRNAESMSLAEIENGIATFGKKARDGKLSIEEMTGGTFTITNGGTFGSMMSTPIV 340 Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 N PQAAIL + +I++RP+ + NG + +R M+ L LS DHR++DG FL +K +LE Sbjct: 341 NPPQAAILGMHNIIQRPMAI-NGQVVIRPMMYLALSYDHRLIDGKEAVTFLVTIKNLLE 398 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: 433 Number of extensions: 27 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: 424 Length of database: 407 Length adjustment: 31 Effective length of query: 393 Effective length of database: 376 Effective search space: 147768 Effective search space used: 147768 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: 50 (23.9 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