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_0555 PP_0555 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha

Query= BRENDA::A0A222AKA3
         (368 letters)



>lcl|FitnessBrowser__Putida:PP_0555 PP_0555
           Acetoin:2,6-dichlorophenolindophenol oxidoreductase
           subunit alpha
          Length = 325

 Score =  126 bits (316), Expect = 9e-34
 Identities = 95/318 (29%), Positives = 144/318 (45%), Gaps = 10/318 (3%)

Query: 40  DRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSS-RGQEACQVGSALAVRPTDWLFPTY 98
           ++ L  Y  M   RAF  +       G +  +     G+EA   G    +R +D +  T+
Sbjct: 8   EQLLHAYEVMRTIRAFEERLHVEFATGEIPGFVHLYAGEEASAAGVMAHLRDSDCIASTH 67

Query: 99  RESVALLTRGIDPVQVLTLFRGDQH--CGYDPVTEHTAPQCTPL--ATQCLHA-----AG 149
           R     + +G+D   ++    G +   CG    + H A     +  A   + A     AG
Sbjct: 68  RGHGHCIAKGVDVYGMMAEIYGKKTGVCGGKGGSMHIADLEKGMLGANGIVGAGAPLVAG 127

Query: 150 LADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQ 209
            A AA++ G   V++A+ GDGA++EG   EA+N A++   P +F+ +NN YA +      
Sbjct: 128 AALAAKLKGRDDVSVAFFGDGASNEGAVFEAMNMASIMNLPCIFVAENNGYAEATASNWS 187

Query: 210 TAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTN 269
            A   +AD+AAG+GMPGV IDG D   VY A   A ERAR+G GP+LIE    R   H  
Sbjct: 188 VACDHIADRAAGFGMPGVTIDGFDFFAVYEAAGAAIERARSGQGPSLIEVKLSRYYGHFE 247

Query: 270 ADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSA 329
            D  T   P    ++  ++D + +       AG+L     D I A  +    +   R  +
Sbjct: 248 GDAQTYRAPDEVKNLRESRDCLMQFRNKTTRAGLLTAEQLDAIDARVEDLIEDAVRRAKS 307

Query: 330 PPTGDPMQMFRHVYHHLP 347
            P   P  +   VY   P
Sbjct: 308 DPKPQPADLLTDVYVAYP 325


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: 250
Number of extensions: 8
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: 325
Length adjustment: 29
Effective length of query: 339
Effective length of database: 296
Effective search space:   100344
Effective search space used:   100344
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