GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_4401
          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.

Links

Downloads

Related tools

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