GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Pseudarthrobacter sulfonivorans Ar51

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_205630629.1 AU252_RS03450 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= BRENDA::A0A222AKA3
         (368 letters)



>NCBI__GCF_001484605.1:WP_205630629.1
          Length = 369

 Score =  246 bits (627), Expect = 9e-70
 Identities = 139/327 (42%), Positives = 192/327 (58%), Gaps = 2/327 (0%)

Query: 40  DRQLL-MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTY 98
           D QL  +Y  + V R  + +ATA  RQG L ++P   GQEA QVGS  A+R  D++F +Y
Sbjct: 32  DEQLCSLYEDLTVIRRIDVEATALQRQGELGLWPPLLGQEAAQVGSGRALRDDDFVFSSY 91

Query: 99  RESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTPLATQCLHAAGLADAARMAG 158
           RE+     RG+D   +  ++RG    G+DP + + A     +  Q LHA G A   +  G
Sbjct: 92  RENGVAYCRGVDLTDITRVWRGTASSGWDPYSVNMATPQIIIGAQTLHATGYAMGIQNDG 151

Query: 159 DPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADK 218
              VA+ Y GDGATSEGD +EA+ +AA  +APVVF   NN +AIS P+  Q+  + +AD+
Sbjct: 152 ADSVAVTYFGDGATSEGDVNEAMVFAASFQAPVVFFCSNNHWAISEPVRLQSHIQ-IADR 210

Query: 219 AAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRP 278
           A G+G+P +R+DGNDVL V  A   A +RAR G GPT IEAVTYR+  HT ADD TRYR 
Sbjct: 211 ATGFGIPSLRVDGNDVLAVMAATRVALDRARHGGGPTFIEAVTYRMGPHTTADDPTRYRD 270

Query: 279 AGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQM 338
           A E + WAA+DP+ R++  L   G+L       +   A++ A E+ +     P  +PM +
Sbjct: 271 ANELEDWAAKDPILRIKALLERKGLLTDQVQQHVHDKAESVAREIRSGCIGMPDPEPMDI 330

Query: 339 FRHVYHHLPPHLREQSERLAAELAADG 365
           F+HVY      L  Q +  A  LA+ G
Sbjct: 331 FKHVYSEPNSWLDRQQDHYARYLASFG 357


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: 316
Number of extensions: 10
Number of successful extensions: 2
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: 369
Length adjustment: 30
Effective length of query: 338
Effective length of database: 339
Effective search space:   114582
Effective search space used:   114582
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 Apr 09 2024. 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