GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCalpha in Burkholderia phytofirmans PsJN

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate BPHYT_RS29360 BPHYT_RS29360 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha

Query= BRENDA::A0A222AKA3
         (368 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS29360 BPHYT_RS29360
           acetoin:2,6-dichlorophenolindophenol oxidoreductase
           subunit alpha
          Length = 327

 Score =  112 bits (281), Expect = 1e-29
 Identities = 85/282 (30%), Positives = 130/282 (46%), Gaps = 11/282 (3%)

Query: 76  GQEACQVGSALAVRPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQH--CGYDPVTEHT 133
           G+EA  VG+ L +   D++  T+R     + +G+D   ++    G +   C     + H 
Sbjct: 47  GEEASAVGTMLHLNDADYVATTHRGHGHCIAKGVDVRGMMAEIYGRKTGVCHGKGGSMHI 106

Query: 134 APQCTPL--ATQCLHA-----AGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAV 186
           A     +  A   + A      G A AA+      V + + GDGA+++G   E+LN A+V
Sbjct: 107 ADLSKGMLGANGIVGAGGPLICGAALAAKYKKSGGVGVCFFGDGASNQGVIFESLNLASV 166

Query: 187 RRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAE 246
            R P +F+ +NN YA +       A   +AD+A+G+GMPGV +DG D   V+ A+ +A E
Sbjct: 167 WRLPAIFVAENNGYAEATSSTWSVATDNIADRASGFGMPGVIVDGFDFFAVHEALGEAIE 226

Query: 247 RARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEAD-VWAAQDPVDRLERDLLAAGVLD 305
           RAR G GPTL+E    R   H   D  T YR  GE   +   +D + R E  ++ A +L 
Sbjct: 227 RARQGGGPTLVEVKFSRYFGHFEGDAQT-YRAPGEVQKLRDEKDCLKRFEERVVRAEMLS 285

Query: 306 RAAADGIAAAADAFAGELSARFSAPPTGDPMQMFRHVYHHLP 347
                G+ A   +          A P      +   VY   P
Sbjct: 286 VDQLRGVDAEVKSLIDSAVTEAKAAPLPTAEDLLSDVYVSYP 327


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: 246
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 368
Length of database: 327
Length adjustment: 29
Effective length of query: 339
Effective length of database: 298
Effective search space:   101022
Effective search space used:   101022
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 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