GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PCBD in Dechlorosoma suillum PS

Align Putative pterin-4-alpha-carbinolamine dehydratase; PHS; EC 4.2.1.96; 4-alpha-hydroxy-tetrahydropterin dehydratase; Pterin carbinolamine dehydratase; PCD (uncharacterized)
to candidate Dsui_3224 Dsui_3224 pterin-4a-carbinolamine dehydratase

Query= curated2:Q47IX1
         (112 letters)



>lcl|FitnessBrowser__PS:Dsui_3224 Dsui_3224 pterin-4a-carbinolamine
           dehydratase
          Length = 111

 Score =  104 bits (260), Expect = 3e-28
 Identities = 49/104 (47%), Positives = 66/104 (63%)

Query: 6   NLADRQCTPCEGGIAPLENSVAAVMLDTLPGWTLDGQRLDKTYVFRNHYEAMAFVNAIAW 65
           +LA   C    G    L+++  A++L  LPGW+ +   + KT+ F  +  AM F N +AW
Sbjct: 5   DLARDTCRHLSGPQHRLDDATVAMLLPLLPGWSREDGHIAKTFHFTGYEAAMLFANGVAW 64

Query: 66  VSHRENHHPELIVGYKDVRVRYWTHAIGGLSENDFICAAKLEKL 109
           ++ R+NHHPEL V Y  VRV Y TH +GGLS NDFICAAK+E L
Sbjct: 65  LAQRQNHHPELQVNYNTVRVTYGTHDVGGLSRNDFICAAKIEAL 108


Lambda     K      H
   0.322    0.136    0.438 

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: 48
Number of extensions: 1
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: 112
Length of database: 111
Length adjustment: 12
Effective length of query: 100
Effective length of database: 99
Effective search space:     9900
Effective search space used:     9900
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: 40 (21.5 bits)
S2: 40 (20.0 bits)

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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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