GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCalpha in Pseudomonas fluorescens FW300-N1B4

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate Pf1N1B4_1020 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)

Query= BRENDA::A0A222AKA3
         (368 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1020 Branched-chain
           alpha-keto acid dehydrogenase, E1 component, alpha
           subunit (EC 1.2.4.4)
          Length = 332

 Score =  230 bits (586), Expect = 5e-65
 Identities = 130/320 (40%), Positives = 171/320 (53%), Gaps = 2/320 (0%)

Query: 45  MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTYRESVAL 104
           +YR MV+ R F+++A A  R GR+  Y  + GQEA  V     +   D L P YR++   
Sbjct: 4   LYRQMVLTRLFDQKAVALQRTGRIGTYAPTLGQEAIGVAVGSLMHAEDVLIPYYRDTAVQ 63

Query: 105 LTRGIDPVQVLTLFRGDQHCG--YDPVTEHTAPQCTPLATQCLHAAGLADAARMAGDPIV 162
           L RG+   ++L  + GD+      DP      P C P+ATQ LHA G+A A ++ G+  V
Sbjct: 64  LMRGVRMEEILLYWGGDERGSDFADPAVAQDFPICVPIATQALHACGVASAFKIRGEHRV 123

Query: 163 ALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGY 222
           A+   GDG TS+GDF EALN A   + PVVF+V NNQ+AISVP   Q  A TLA KA G 
Sbjct: 124 AVTTCGDGGTSKGDFLEALNVAGAWQLPVVFMVNNNQWAISVPRRIQCGAPTLAQKAIGA 183

Query: 223 GMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEA 282
           G  G ++DGND+L VY  V  A ER R G GP L+E ++YR+  HT ADD TRYR A E 
Sbjct: 184 GFHGEQVDGNDMLAVYDRVQAALERTRHGKGPVLLECLSYRLGDHTTADDATRYRSADEV 243

Query: 283 DVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQMFRHV 342
                ++P+ RL+R +   GV D      + +            F A     P  +  HV
Sbjct: 244 KQAWLEEPIKRLQRFMAGQGVWDEGREQALISECQGLVQRAVDNFEAAGLQAPESVMDHV 303

Query: 343 YHHLPPHLREQSERLAAELA 362
           Y   P  L EQ E     +A
Sbjct: 304 YAQWPQALAEQREDFLERVA 323


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: 279
Number of extensions: 9
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: 332
Length adjustment: 29
Effective length of query: 339
Effective length of database: 303
Effective search space:   102717
Effective search space used:   102717
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 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