Alignments for a candidate for adh in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Pseudomonas fluorescens GW456-L13

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PfGW456L13_3880 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)

Query= BRENDA::A6T8Z5
         (462 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3880
          Length = 463

 Score =  638 bits (1645), Expect = 0.0
 Identities = 323/463 (69%), Positives = 368/463 (79%), Gaps = 1/463 (0%)

Query: 1   MMNLSA-THAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRR 59
           M N+S+ THA+S+NP TGE +   P+ S+  + AA+T AA G+R WR  P+  RA  L  
Sbjct: 1   MTNVSSLTHAISINPATGEQIGHYPFESDSALQAALTRAATGFRAWRGKPVEQRAQLLIN 60

Query: 60  IGAALRARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQ 119
           +G ALR   + +A MIT EMGKPIAQARGE+ K A LC WYAEHGPAML+ E TLVE  +
Sbjct: 61  LGQALRNNAQAMANMITQEMGKPIAQARGEIEKCAQLCQWYAEHGPAMLSPEPTLVEGGK 120

Query: 120 AVIEYRPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAA 179
           A IEYRPLG ILAVMPWNFP+WQV+RGAVP LLAGN+Y+LKHAPNVMGS  LL E F  A
Sbjct: 121 ARIEYRPLGPILAVMPWNFPIWQVLRGAVPTLLAGNTYVLKHAPNVMGSTYLLLEAFKQA 180

Query: 180 GLPDGVFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSD 239
             P+GVF  +N T DGVS+ I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSD
Sbjct: 181 DFPEGVFEVINVTPDGVSKAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSD 240

Query: 240 PFIVLNDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGD 299
           PFIVL+DADLDEAVKAAV GRYQN+GQVCAA+KR I+E GIA  FTRKFV+A   L +GD
Sbjct: 241 PFIVLDDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIAREFTRKFVEATQQLVVGD 300

Query: 300 PRDEQNYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGM 359
           P     Y+GPMARFDLRDEL QQV  TL EGATLL+G +K EG GNYY PTVLG+VT  M
Sbjct: 301 PLATTTYIGPMARFDLRDELDQQVRDTLKEGATLLMGGKKAEGPGNYYEPTVLGDVTDQM 360

Query: 360 TGFRQELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFL 419
           T F+QELFGPVA++ TARDA HAL LANDSEFGL+AT+YT +   AQ+ A ELE GGVF+
Sbjct: 361 TSFKQELFGPVASIITARDAAHALELANDSEFGLTATLYTRNVELAQQMASELETGGVFI 420

Query: 420 NGYCASDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462
           NGY ASD RV+FGGVKKSGFGRELSHFG+ EFCNAQTVW DRR
Sbjct: 421 NGYSASDPRVSFGGVKKSGFGRELSHFGVREFCNAQTVWLDRR 463


Lambda     K      H
   0.319    0.133    0.392 

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: 615
Number of extensions: 10
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: 462
Length of database: 463
Length adjustment: 33
Effective length of query: 429
Effective length of database: 430
Effective search space:   184470
Effective search space used:   184470
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: 51 (24.3 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, 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

GapMind for catabolism of small carbon sources