GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Cupriavidus basilensis 4G11

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate RR42_RS33045 RR42_RS33045 pyruvate dehydrogenase

Query= BRENDA::A0A222AKA3
         (368 letters)



>FitnessBrowser__Cup4G11:RR42_RS33045
          Length = 355

 Score =  239 bits (610), Expect = 8e-68
 Identities = 135/327 (41%), Positives = 184/327 (56%), Gaps = 1/327 (0%)

Query: 27  PAAAAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSAL 86
           P  A PA A + P+  L +YRAMV+ R F+ +A A  R G++  + S+ GQEA  VG A 
Sbjct: 21  PTQALPAFA-LDPEALLPLYRAMVLTRQFDLKAIALQRTGQIGTFASALGQEAVGVGVAS 79

Query: 87  AVRPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTPLATQCLH 146
           A+R  D L P+YR+  A   RG+   + L  + GD+         H    C P+  Q  H
Sbjct: 80  AMRAQDVLVPSYRDHAAQFQRGVSMTESLLYWGGDERGNAFAAAPHDFANCVPIGNQVCH 139

Query: 147 AAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPL 206
           AAG+A A ++  +P   +  +GDG TS+GDF+E +N A    AP+V +V NNQ+AIS+P 
Sbjct: 140 AAGIAYAMKLRREPRATVCLLGDGGTSKGDFYEGMNMAGAWHAPLVLVVNNNQWAISMPR 199

Query: 207 AKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDA 266
           ++QTAARTLA KA   G+PG+++DGNDV+ V +   DA ERAR G G TLIEA+TYR+  
Sbjct: 200 SQQTAARTLAQKAIAAGIPGLQVDGNDVVAVRQVTLDALERARGGGGATLIEAITYRLGD 259

Query: 267 HTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSAR 326
           HT ADD +RYR + +       +PV RL   LL  G  D    D +A    A        
Sbjct: 260 HTTADDASRYRDSEQVRQHWLLEPVARLRNYLLRLGAWDAPREDALAKDCAAQVAAAVQA 319

Query: 327 FSAPPTGDPMQMFRHVYHHLPPHLREQ 353
           + A P  +   MF  +Y  LP  L  Q
Sbjct: 320 YLATPLPETAAMFDCLYASLPKALAGQ 346


Lambda     K      H
   0.319    0.132    0.395 

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: 281
Number of extensions: 13
Number of successful extensions: 1
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: 368
Length of database: 355
Length adjustment: 29
Effective length of query: 339
Effective length of database: 326
Effective search space:   110514
Effective search space used:   110514
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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