Alignments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N1B4

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= metacyc::MONOMER-15732
         (497 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171
          Length = 477

 Score =  810 bits (2093), Expect = 0.0
 Identities = 401/477 (84%), Positives = 434/477 (90%)

Query: 21  MRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPR 80
           M IG DW +A  G+T+   NPATGEVL  VP A  EDVDRAV AARQAFDDS W+R RPR
Sbjct: 1   MLIGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPR 60

Query: 81  ERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGS 140
           ERQNLLW+LADLM+RDA  LA+LECLNNGKSAAVAQVMDVQL+IDFLRYMAGWATKIEGS
Sbjct: 61  ERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGS 120

Query: 141 TVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADE 200
           +VE SMPLMPNDQFH F+RREA+GVVGAIVAWNFPLLLACWKLGPALATGCT+VLKPADE
Sbjct: 121 SVEVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADE 180

Query: 201 TPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGKA 260
           TPL+ LKLAELV EAGYPAGVFNVVTGTG+ AG+AL+ +P VDKLTFTGST VGK IGK 
Sbjct: 181 TPLTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKI 240

Query: 261 AMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDN 320
           AM++MTRVTLELGGKSPTIVM DA+L+ AAAGAA+AIFFNQGQVCCAGSRLYV RKHFDN
Sbjct: 241 AMESMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDN 300

Query: 321 VVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEGFGPG 380
           VVADIA IAN MKLGNGLDP+V+MGPLISA+QQ+RV GYIE GRE GAT+ACGGE FGPG
Sbjct: 301 VVADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESGATIACGGEQFGPG 360

Query: 381 YFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSNDLAA 440
           YFVKPTVIVDVDQ+H LVQEEIFGPVLVA+PFDD  + + MAND+PYGLGASIWSNDLAA
Sbjct: 361 YFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDLAA 420

Query: 441 VHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLIKL 497
           VHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGRE+G AAIEHYTELKSVLIKL
Sbjct: 421 VHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIKL 477


Lambda     K      H
   0.320    0.137    0.413 

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: 892
Number of extensions: 27
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: 497
Length of database: 477
Length adjustment: 34
Effective length of query: 463
Effective length of database: 443
Effective search space:   205109
Effective search space used:   205109
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources