Alignments for a candidate for xad in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Pseudomonas simiae WCS417

Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate GFF5251 PS417_26890 dihydroxy-acid dehydratase

Query= SwissProt::P77596
         (655 letters)



>FitnessBrowser__WCS417:GFF5251
          Length = 613

 Score =  195 bits (495), Expect = 6e-54
 Identities = 159/517 (30%), Positives = 236/517 (45%), Gaps = 49/517 (9%)

Query: 88  GHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLI 147
           GH  +    Q  A+EI R GG+          DG + G  GM  SLP R   A     ++
Sbjct: 49  GHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMV 108

Query: 148 RSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGA-----TLPPTVGEDAGKVQ 202
            +     A++ ++ CDK  P  ++A   ++ +P I V GG      T   + G D     
Sbjct: 109 NA-HCADAIVCISNCDKITPGMLMAALRLN-IPVIFVSGGPMEAGKTKLASHGLDLVDAM 166

Query: 203 TIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPSG 262
            I A  +  +  + E     C  C    G C  + TA +   + EALGLALP +    + 
Sbjct: 167 VIAADSSASDEKVAEYERSACPTC----GSCSGMFTANSMNCLVEALGLALPGNGSTLAT 222

Query: 263 QAVWLEIARQSARAVSELDSR-------GITTRDILSDKAIENAMVIHAAFGGSTNLLLH 315
            +   ++  Q+ R + EL  R        +  R+I + KA ENAM +  A GGSTN +LH
Sbjct: 223 HSDREQLFLQAGRTIVELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILH 282

Query: 316 IPAIAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLHLRDL 375
           + A A  A     D+    R++R VP+L  V PN   YH       AGG+  ++  L   
Sbjct: 283 LLAAAQEAEIEF-DLRDIDRLSRHVPQLCKVAPNIQKYH-MEDVHRAGGIFSILGSLARG 340

Query: 376 GLLHLDAMTVTGQTVGENLEWWQASE------------------RRARFRQCLR--EQDG 415
           GLLH D  TV  +++ E +  W  ++                   +  F Q  R    D 
Sbjct: 341 GLLHTDLPTVHSKSIAEGIAKWDITQTDDEAVHTFFKAGPAGIPTQTAFSQSTRWDTLDD 400

Query: 416 VEPDDVILPPEKAKAKGLTSTVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRV 475
              +  I   E A +K     V +  GNIA +G V+K   +D S      ++   G  ++
Sbjct: 401 DRENGCIRSVEHAYSKEGGLAVLY--GNIALDGCVVKTAGVDES------IHVFEGNAKI 452

Query: 476 FVSEAQAIKAIKREEIVQGDIMVVIGGGP-SGTGMEETYQLTSALKHISWGKTVSLITDA 534
           F S+  A++ I  +E+  GDI+++   GP  G GM+E    TS LK    GK  +L+TD 
Sbjct: 453 FESQDSAVRGILADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDG 512

Query: 535 RFSGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAV 571
           RFSG ++G   GH SPEA AGG IG ++D D + I +
Sbjct: 513 RFSGGTSGLSIGHASPEAAAGGAIGLVQDGDKVLIDI 549


Lambda     K      H
   0.319    0.136    0.411 

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: 933
Number of extensions: 39
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 655
Length of database: 613
Length adjustment: 38
Effective length of query: 617
Effective length of database: 575
Effective search space:   354775
Effective search space used:   354775
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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