GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Dinoroseobacter shibae DFL-12

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 3608768 Dshi_2160 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase (RefSeq)

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Dino:3608768
          Length = 420

 Score =  224 bits (570), Expect = 5e-63
 Identities = 139/421 (33%), Positives = 224/421 (53%), Gaps = 19/421 (4%)

Query: 5   QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64
           ++ MP L  ++ EGT++KW+V  GD V+  D +AE+ TDK   E  +   G I +++   
Sbjct: 4   EILMPALSPTMEEGTLAKWMVKEGDSVSSGDLLAEIETDKATMEFEAVDDGIIGKILVAA 63

Query: 65  G-QTLQVGEMICKIETEGAN-PAEQKQEQPAASEAAENPVAKSAGAADQPNKKR----YS 118
           G   ++V  +I  +  EG    AE+  EQP    + +   A    A   P K       S
Sbjct: 64  GTDDVKVNTLIAILLEEGEELGAEKPAEQPPEPASVQQEAAPQETAKAPPPKTGDRVFAS 123

Query: 119 PAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASK 178
           P   RLA + G+DL ++ G+G  GRI + D+    +   V EQ        A AP++   
Sbjct: 124 PLARRLAKQKGLDLSEIRGSGPHGRIVKADVDAAEQPAAVPEQ--------AAAPQTRQP 175

Query: 179 PEPKEETSYPASAAGDK---EIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYR 235
             PK  +S  AS   D+   E+ + G+RK IA+ +  +K  IPH +     ++  ++ +R
Sbjct: 176 EGPKSASSV-ASIFADRPFTEVSLDGMRKTIAARLTEAKQTIPHFYLRRAANLDALLTFR 234

Query: 236 NSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATED 295
             +      + G  L+   F +KA A+AL+  P  N++WA D+I+Q +  ++++AVA E 
Sbjct: 235 TELNAQLAPS-GKKLSVNDFVIKACARALQSVPHANAVWAEDRILQMQRSDVAVAVAIEG 293

Query: 296 SLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGI 355
            LF PVIK+AD+K+I  +++++  LA + R+ KL   +  GGTF ++N G FG      +
Sbjct: 294 GLFTPVIKDADQKSISALSEEMKDLAARARERKLAPSEYVGGTFAISNLGMFGIENFDAV 353

Query: 356 INYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           IN P  AIL V + VK+P V  +G + V   +++ LS+DHRV+DG V    L  +   LE
Sbjct: 354 INPPHGAILAVGAGVKKPTVDADGAVTVATQMSMTLSVDHRVIDGSVGAALLAEIVSGLE 413

Query: 416 S 416
           +
Sbjct: 414 N 414


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: 398
Number of extensions: 16
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: 420
Length adjustment: 32
Effective length of query: 392
Effective length of database: 388
Effective search space:   152096
Effective search space used:   152096
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