GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCalpha in Pseudomonas putida KT2440

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate PP_4401 PP_4401 branched-chain alpha-keto acid dehydrogenase complex, alpha subunit

Query= BRENDA::A0A222AKA3
         (368 letters)



>lcl|FitnessBrowser__Putida:PP_4401 PP_4401 branched-chain
           alpha-keto acid dehydrogenase complex, alpha subunit
          Length = 410

 Score =  192 bits (488), Expect = 1e-53
 Identities = 128/350 (36%), Positives = 180/350 (51%), Gaps = 26/350 (7%)

Query: 29  AAAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAV 88
           A  P A  + P       RAM+  R F+ +     RQ +++ Y  S G+EA   G ALA+
Sbjct: 64  AQGPWAEDIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALAL 123

Query: 89  RPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTP--------- 139
             TD  FPTYR+   L+ R +  V+++     ++    DP+     P             
Sbjct: 124 NRTDMCFPTYRQQSILMARDVSLVEMICQLLSNER---DPLKGRQLPIMYSVREAGFFTI 180

Query: 140 ---LATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQ 196
              LATQ + A G A A+ + GD  +A A+IGDGAT+E DFH AL +A V RAPV+  V 
Sbjct: 181 SGNLATQFVQAVGWAMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVV 240

Query: 197 NNQYAISVPLAKQTA-ARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPT 255
           NNQ+AIS   A     + T A +  G G+  +R+DGND + VY A   AAERAR G GP+
Sbjct: 241 NNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPS 300

Query: 256 LIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAA 315
           LIE VTYR   H+ +DD ++YRPA +   +   DP+ RL++ L+  G    +  +  A  
Sbjct: 301 LIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIG--HWSEEEHQAVT 358

Query: 316 ADAFAGELSARFSAPPTG--------DPMQMFRHVYHHLPPHLREQSERL 357
           A+  A  ++A+  A   G            MF  VY  +P HLR Q + L
Sbjct: 359 AELEAAVIAAQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLRRQRQEL 408


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: 355
Number of extensions: 15
Number of successful extensions: 4
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: 410
Length adjustment: 30
Effective length of query: 338
Effective length of database: 380
Effective search space:   128440
Effective search space used:   128440
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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