GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Pseudomonas fluorescens FW300-N2C3

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate AO356_24880 AO356_24880 ABC transporter substrate-binding protein

Query= BRENDA::A0A222AKA3
         (368 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24880
          Length = 325

 Score =  109 bits (272), Expect = 1e-28
 Identities = 69/199 (34%), Positives = 92/199 (46%)

Query: 149 GLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAK 208
           G A AAR+ G   VA+ + GDG ++EG   EA+N A+V   P +F+ +NN YA +     
Sbjct: 127 GAALAARLKGTDSVAVVFFGDGGSNEGAVFEAMNMASVWNLPCLFVAENNGYAEATASNW 186

Query: 209 QTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHT 268
             A   +AD+AAG+GMPGV +DG D   V+ A   A ERARAG GP+LIE    R   H 
Sbjct: 187 SVACDHIADRAAGFGMPGVTVDGFDFFAVHEAAGAAVERARAGEGPSLIEVKLTRYYGHF 246

Query: 269 NADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFS 328
             D  T   P         QD + +       AG+L     D I    D        +  
Sbjct: 247 EGDAQTYRAPDEVKHFRENQDCLMQFRERTTRAGLLTVEQLDQIDKEVDLLIENAVYKAK 306

Query: 329 APPTGDPMQMFRHVYHHLP 347
           + P      +   VY   P
Sbjct: 307 SDPKPSSADLLTDVYVSYP 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: 277
Number of extensions: 9
Number of successful extensions: 1
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 (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