Aligments for a candidate for adh in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Pseudomonas putida KT2440

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_3151 PP_3151 NAD+-dependent succinate semialdehyde dehydrogenase

Query= BRENDA::A6T8Z5
         (462 letters)



>FitnessBrowser__Putida:PP_3151
          Length = 461

 Score =  623 bits (1607), Expect = 0.0
 Identities = 310/457 (67%), Positives = 365/457 (79%), Gaps = 2/457 (0%)

Query: 5   SATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAAL 64
           S THA+S++P +GE + + P+ ++  ++AA+  A  GYRQWRQ  L  R++ L  +   L
Sbjct: 6   SLTHAISLDPYSGEQIGTYPFDTDAALEAALQRAKVGYRQWRQVSLGQRSEYLLALADTL 65

Query: 65  RARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEY 124
            A+ E  A MI+ E+GKPIAQARGEV+K   LC WYAEHGPAMLA E T VE  +A IEY
Sbjct: 66  EAKAEAFAHMISREIGKPIAQARGEVSKCVGLCRWYAEHGPAMLAAEPTQVE--KARIEY 123

Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184
           RPLG ILAVMPWNFPVWQV+RGAVP +LAGN+Y+LKHAPNVMGSA L+ E+F  AGLP+G
Sbjct: 124 RPLGPILAVMPWNFPVWQVLRGAVPAILAGNTYVLKHAPNVMGSAYLMAELFKDAGLPEG 183

Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244
           VF  +N T DGV++ IND RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFIVL
Sbjct: 184 VFEVLNVTPDGVTRAINDPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFIVL 243

Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304
            DADLD AV+AAV GRYQN+GQVCAA+KR I+EA I +AFT KFV+A   LK+G+P ++ 
Sbjct: 244 ADADLDAAVQAAVIGRYQNTGQVCAAAKRLIVEASIVDAFTHKFVEATRQLKVGNPLEDD 303

Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364
            Y+GPMAR+DLRDEL  QV ATL EGATLLLG  K+EG  N+YAPTV  NVT  MT F+Q
Sbjct: 304 TYIGPMARYDLRDELDGQVQATLAEGATLLLGGNKVEGVANFYAPTVFANVTPDMTAFKQ 363

Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424
           ELFGPVA + TARDADHA+ LANDSEFGL++T+YT D A A+R    L+ GGVF+NGYCA
Sbjct: 364 ELFGPVAAIITARDADHAVELANDSEFGLASTIYTADYALAERMTAALDTGGVFINGYCA 423

Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDR 461
           SD RVAFGGVKKSGFGRELSHFG+ EF NAQTVW DR
Sbjct: 424 SDPRVAFGGVKKSGFGRELSHFGVREFTNAQTVWLDR 460


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: 607
Number of extensions: 16
Number of successful extensions: 2
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: 461
Length adjustment: 33
Effective length of query: 429
Effective length of database: 428
Effective search space:   183612
Effective search space used:   183612
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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Steps (tab-delimited)
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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 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