Aligments for a candidate for adh in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Pseudomonas simiae WCS417

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3655 PS417_18705 succinate dehydrogenase

Query= BRENDA::A6T8Z5
         (462 letters)



>lcl|FitnessBrowser__WCS417:GFF3655 PS417_18705 succinate
           dehydrogenase
          Length = 460

 Score =  635 bits (1637), Expect = 0.0
 Identities = 310/458 (67%), Positives = 371/458 (81%)

Query: 5   SATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAAL 64
           + THA+S+NP  GE V S P+ + +++DAA+  +   +R WR+ P++ RA+ L  + +AL
Sbjct: 3   ATTHALSINPANGETVGSYPYETAQQLDAALDRSTLAFRAWRRQPVSQRAELLLSLASAL 62

Query: 65  RARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEY 124
           R + E++AQMITLEMGKPIAQAR E+ K A L +WYA HGPAMLA E TLV+N  A IEY
Sbjct: 63  REQAEDMAQMITLEMGKPIAQARAEIEKCAQLSEWYAAHGPAMLAPEPTLVDNGSAQIEY 122

Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184
           RPLG I AVMPWNFPVWQV+RGAVP +LAGN+Y+LKHAPNVMGSA L+   F  AG  +G
Sbjct: 123 RPLGPIFAVMPWNFPVWQVLRGAVPTMLAGNTYVLKHAPNVMGSAYLIQRAFQKAGFAEG 182

Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244
           +F  VN TNDGVS+ I D RIAAVT+TGSVRAG AIG+QAGAALKKCVLELGGSDPFIVL
Sbjct: 183 LFEVVNVTNDGVSKAIADPRIAAVTLTGSVRAGIAIGSQAGAALKKCVLELGGSDPFIVL 242

Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304
           NDADLD AV+AA+ GR+QNSGQVCAA+KR I+E G+ EAFT KF++A  AL MGDP    
Sbjct: 243 NDADLDAAVQAALIGRFQNSGQVCAAAKRLIIEEGVVEAFTVKFLEASRALVMGDPTSAA 302

Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364
            Y+GPMARFDLRDELH QV ATL+EGATLLLG  K+ GAGNYY PTVL +VT  MT F+Q
Sbjct: 303 TYIGPMARFDLRDELHGQVQATLEEGATLLLGGHKVPGAGNYYEPTVLADVTDQMTSFKQ 362

Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424
           ELFGPVA++ TARDADHA+ALANDSEFGL+A+++TTD A+A+  A +LE GG+F+N +  
Sbjct: 363 ELFGPVASIITARDADHAVALANDSEFGLTASIFTTDSAKARDIANQLETGGIFINAFSV 422

Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462
           SD RVAFGGVKKSGFGRELSHFG+ EFCNAQTVW DR+
Sbjct: 423 SDPRVAFGGVKKSGFGRELSHFGVREFCNAQTVWLDRK 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: 574
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: 460
Length adjustment: 33
Effective length of query: 429
Effective length of database: 427
Effective search space:   183183
Effective search space used:   183183
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