GapMind for catabolism of small carbon sources

 

Aligments for a candidate for uxuL in Pseudomonas stutzeri RCH2

Align Gluconolactonase; EC 3.1.1.-; EC 3.1.1.17 (characterized, see rationale)
to candidate GFF363 Psest_0364 Gluconolactonase

Query= uniprot:Q88NN7
         (293 letters)



>lcl|FitnessBrowser__psRCH2:GFF363 Psest_0364 Gluconolactonase
          Length = 296

 Score =  437 bits (1123), Expect = e-127
 Identities = 212/291 (72%), Positives = 233/291 (80%), Gaps = 4/291 (1%)

Query: 4   ELIVDARNGTGESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIARSGQ 63
           ELIVD    TGESPVW   EQALYWVDIP R+L RW AADG+   WQGDEMLACIAR G 
Sbjct: 6   ELIVDLGCATGESPVWVAAEQALYWVDIPNRELLRWNAADGQISRWQGDEMLACIARHGD 65

Query: 64  GWVAGMESGIFQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLLDMQQ 123
           GWVAGMESG F LQ + DG LDS LL+ + H    MR NDGRCDR+GRFWAG+M LDM  
Sbjct: 66  GWVAGMESGFFSLQTRPDGRLDSHLLATIDHQLPAMRMNDGRCDREGRFWAGSMALDMAA 125

Query: 124 GAHVGALYRHDG---EGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYDT 180
           G  VGALYR D    +  L  Q DG IVPNGLAFSPDG+ MYLSDSHP+VQK+WAFDYD 
Sbjct: 126 GHPVGALYRLDSKSIDAPLVPQLDGFIVPNGLAFSPDGRTMYLSDSHPSVQKIWAFDYDI 185

Query: 181 DSGTPHGKHLFVDMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVPVK 240
           DSGTP  + LFVDM ++PGRPDGAA+D DGCYWICGNDAG IHRFTP+GRLDRSL+VPVK
Sbjct: 186 DSGTPSRRRLFVDMLDHPGRPDGAAVDADGCYWICGNDAGFIHRFTPDGRLDRSLAVPVK 245

Query: 241 KPAMCAFGGASLDILYVTSIRPTGIDLSDQPLAGGVFALDPGTKGLEEPAY 291
           KP+MCAFGGA LD L+VTSIRP G DLSDQPLAGGVFAL+PG  GLEEPA+
Sbjct: 246 KPSMCAFGGARLDTLFVTSIRPGG-DLSDQPLAGGVFALNPGVTGLEEPAF 295


Lambda     K      H
   0.320    0.139    0.455 

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: 546
Number of extensions: 32
Number of successful extensions: 3
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: 293
Length of database: 296
Length adjustment: 26
Effective length of query: 267
Effective length of database: 270
Effective search space:    72090
Effective search space used:    72090
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: 48 (23.1 bits)

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

Links

Downloads

Related tools

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:

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:

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:

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 preprint 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