GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Acidovorax sp. GW101-3H11

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 Ac3H11_2466 Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex (EC 2.3.1.61)

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2466
          Length = 422

 Score =  228 bits (582), Expect = 2e-64
 Identities = 143/419 (34%), Positives = 222/419 (52%), Gaps = 10/419 (2%)

Query: 1   MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60
           MAI ++ +PQL ESV E T+  W    G+ V   + + E+ TDKV  EVP+   G ++E+
Sbjct: 1   MAIVEVKVPQLSESVAEATMLTWKKKAGEAVTVDEILIEIETDKVVLEVPAPSAGVLSEI 60

Query: 61  VGEEGQTLQVGEMICKIETEG-ANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSP 119
           +  +G T+   ++I KI+TEG A  A       A + AA  P A  A A          P
Sbjct: 61  IQGDGATVVAEQLIAKIDTEGKAGAAAAAPAAAAPAPAAAAPAAAPAAAGGSKGDVAM-P 119

Query: 120 AVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGG-VQEQNPEELKTAAP--APKSA 176
           A  +L  ++ + +  V G+G  GR+T+ D+   +  G       P  + T  P  A    
Sbjct: 120 AAAKLLADNNLSVSAVAGSGKDGRVTKGDVLAAVAGGAKAAVAAPSVIPTGVPSKALPQV 179

Query: 177 SKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRN 236
           + P  KE+ S       ++ +P++ +R  +A  + +S++      T  EV++  ++  R 
Sbjct: 180 AAPAGKEDLS----GRPEQRVPMSRLRARVAERLLQSQSTNAILTTFNEVNMAPVMDLRK 235

Query: 237 SIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296
             +DSF K  G  L F +FFVKA   ALK++P +N+   G+ I+     +I IAV +   
Sbjct: 236 KFQDSFTKEHGAKLGFMSFFVKAAVHALKKYPVLNASVDGNDIVYHGYFDIGIAVGSPRG 295

Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356
           L VP+++NAD+ +   I K I    KK  +GKL  ++M GGTF+++N G+FGS+ S  II
Sbjct: 296 LVVPILRNADQMSFADIEKKIAEFGKKAAEGKLGIEEMTGGTFSISNGGTFGSMMSTPII 355

Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415
           N PQ+AIL V +   R +V +NG + VR M  L +S DHR++DG      L  +K  LE
Sbjct: 356 NPPQSAILGVHATKDRAMV-ENGQVVVRPMNYLAMSYDHRIIDGREAVLGLVAMKDALE 413


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: 411
Number of extensions: 21
Number of successful extensions: 3
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: 422
Length adjustment: 32
Effective length of query: 392
Effective length of database: 390
Effective search space:   152880
Effective search space used:   152880
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