Alignments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2E3

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate AO353_19510 AO353_19510 aldehyde dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_19510
          Length = 496

 Score =  818 bits (2113), Expect = 0.0
 Identities = 403/491 (82%), Positives = 444/491 (90%)

Query: 7   ILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAAR 66
           +LPA  AF++R  +M IGA+W +AA G+T+   NPATGEVL  VP A  +DVDRAV AAR
Sbjct: 6   LLPAVSAFIQRAPRMLIGAEWVEAADGQTMPLHNPATGEVLCVVPKATPDDVDRAVLAAR 65

Query: 67  QAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDF 126
            AFDDS W+R RPRERQNLLW+LADLMERDA  LA+LECLNNGKSAAVAQVMDVQL+IDF
Sbjct: 66  NAFDDSAWTRTRPRERQNLLWKLADLMERDAELLAQLECLNNGKSAAVAQVMDVQLSIDF 125

Query: 127 LRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPA 186
           LRYMAGWATKIEGS+VE S+PLMP+DQFH F+RREA+GVVGAIVAWNFPLLLACWKLGPA
Sbjct: 126 LRYMAGWATKIEGSSVEVSLPLMPDDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPA 185

Query: 187 LATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLT 246
           LATGCT+VLKPADETPL+ LKLAELV EAGYP+GVFNVVTGTG++AG+AL+ +P VDKLT
Sbjct: 186 LATGCTVVLKPADETPLTALKLAELVLEAGYPSGVFNVVTGTGISAGSALTHNPLVDKLT 245

Query: 247 FTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCC 306
           FTGST VGK IGK AMD+MTRVTLELGGKSPTIVM DA+L  AAAGAA+AIFFNQGQVCC
Sbjct: 246 FTGSTAVGKQIGKIAMDSMTRVTLELGGKSPTIVMADADLGSAAAGAASAIFFNQGQVCC 305

Query: 307 AGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGREL 366
           AGSRLYV RKHFDNVVADIAGIAN MKLGNGLDP+V MGPLISA+QQ+RV  YIE+GRE 
Sbjct: 306 AGSRLYVQRKHFDNVVADIAGIANAMKLGNGLDPSVDMGPLISARQQERVYNYIEMGRES 365

Query: 367 GATVACGGEGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNP 426
           GAT+ CGGE FGPG+FVKPTVIVDVDQ+H LVQEEIFGPVLVA+PFDD  + + MAND+P
Sbjct: 366 GATIVCGGEQFGPGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSP 425

Query: 427 YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEH 486
           YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGRE+G AAIEH
Sbjct: 426 YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEH 485

Query: 487 YTELKSVLIKL 497
           YTELKSVLIKL
Sbjct: 486 YTELKSVLIKL 496


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: 926
Number of extensions: 34
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: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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