Alignments for a candidate for pad-dh in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Pseudomonas putida KT2440

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate PP_3463 PP_3463 phenylacetaldehyde dehydrogenase

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



>FitnessBrowser__Putida:PP_3463
          Length = 497

 Score =  981 bits (2535), Expect = 0.0
 Identities = 486/497 (97%), Positives = 495/497 (99%)

Query: 1   MLCELPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDR 60
           ML ELPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAA+AEDVDR
Sbjct: 1   MLSELPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAAEAEDVDR 60

Query: 61  AVRAARQAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDV 120
           AVRAARQAFDDSPWSR+RPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQ+MDV
Sbjct: 61  AVRAARQAFDDSPWSRMRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQMMDV 120

Query: 121 QLAIDFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLAC 180
           QLAIDFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREA+GVVGAIVAWNFPLLLAC
Sbjct: 121 QLAIDFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAVGVVGAIVAWNFPLLLAC 180

Query: 181 WKLGPALATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHP 240
           WKLGPALATGCT+VLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHP
Sbjct: 181 WKLGPALATGCTVVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHP 240

Query: 241 GVDKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFN 300
           GVDKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFN
Sbjct: 241 GVDKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFN 300

Query: 301 QGQVCCAGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYI 360
           QGQVCCAGSRLYVHRKHFDNVVADIAGIAN MKLGNGLDPAVQMGPLISAKQQDRVTGYI
Sbjct: 301 QGQVCCAGSRLYVHRKHFDNVVADIAGIANAMKLGNGLDPAVQMGPLISAKQQDRVTGYI 360

Query: 361 ELGRELGATVACGGEGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIG 420
           ELGRELGAT+ACGGEGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDD+DEVIG
Sbjct: 361 ELGRELGATIACGGEGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDIDEVIG 420

Query: 421 MANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVG 480
           MANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGRE+G
Sbjct: 421 MANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMG 480

Query: 481 AAAIEHYTELKSVLIKL 497
           +AAIEHYTELKSVLIKL
Sbjct: 481 SAAIEHYTELKSVLIKL 497


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: 1036
Number of extensions: 29
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: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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.

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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