GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:14859 b0727 dihydrolipoamide
           acetyltransferase (NCBI)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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