GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Escherichia coli BW25113

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 14859 b0727 dihydrolipoamide acetyltransferase (NCBI)

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Keio:14859
          Length = 405

 Score =  253 bits (645), Expect = 1e-71
 Identities = 145/416 (34%), Positives = 229/416 (55%), Gaps = 21/416 (5%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           M+   + +P L ESV + T++ W   PGD V + + + E+ TDKV  EVP+S  G +  +
Sbjct: 1   MSSVDILVPDLPESVADATVATWHKKPGDAVVRDEVLVEIETDKVVLEVPASADGILDAV 60

Query: 61  VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120
           + +EG T+   +++ ++  EG +    K+    + E A  P  +   + ++ N    SPA
Sbjct: 61  LEDEGTTVTSRQILGRLR-EGNSAG--KETSAKSEEKASTPAQRQQASLEEQNNDALSPA 117

Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180
           + RL  EH +D   + GTG GGR+TR+D++                K  A AP   S P 
Sbjct: 118 IRRLLAEHNLDASAIKGTGVGGRLTREDVE----------------KHLAKAPAKESAPA 161

Query: 181 PKEETSYPASAA-GDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIK 239
                + PA AA  +K +P+T +RK +A  +  +K       T  EV++  ++  R    
Sbjct: 162 AAAPAAQPALAARSEKRVPMTRLRKRVAERLLEAKNSTAMLTTFNEVNMKPIMDLRKQYG 221

Query: 240 DSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFV 299
           ++F+K  G  L F +F+VKAV +ALK +P++N+   GD ++     ++S+AV+T   L  
Sbjct: 222 EAFEKRHGIRLGFMSFYVKAVVEALKRYPEVNASIDGDDVVYHNYFDVSMAVSTPRGLVT 281

Query: 300 PVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYP 359
           PV+++ D   +  I K I  LA K RDGKLT +D+ GG FT+ N G FGS+ S  IIN P
Sbjct: 282 PVLRDVDTLGMADIEKKIKELAVKGRDGKLTVEDLTGGNFTITNGGVFGSLMSTPIINPP 341

Query: 360 QAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           Q+AIL + +I  RP+ + NG + +  M+ L LS DHR++DG     FL  +K++LE
Sbjct: 342 QSAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLE 396


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: 381
Number of extensions: 22
Number of successful extensions: 4
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: 405
Length adjustment: 31
Effective length of query: 393
Effective length of database: 374
Effective search space:   146982
Effective search space used:   146982
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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