GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PCBD in Pseudarthrobacter sulfonivorans Ar51

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 WP_058931872.1 AU252_RS17880 4a-hydroxytetrahydrobiopterin dehydratase

Query= curated2:A9WI69
         (93 letters)



>NCBI__GCF_001484605.1:WP_058931872.1
          Length = 108

 Score = 71.2 bits (173), Expect = 3e-18
 Identities = 37/86 (43%), Positives = 49/86 (56%), Gaps = 1/86 (1%)

Query: 4  LSEAEIAEQLAQRPDWSLENNEIVRTFRLANFPAAIAFVTHVAFLAEAAGHHPDIDIRYN 63
          L+   I   LA  PDW      +V  ++     AA+  +  V  +AE   HHPD+D RYN
Sbjct: 8  LTRERIEAVLAALPDWQYRLGGLVAVYKTPTAAAALELIAAVGRVAEEQNHHPDLDWRYN 67

Query: 64 RVRLALTTHDAGG-LTEKDFALAAAI 88
          RV L  T+HDAGG +TE+D A AAA+
Sbjct: 68 RVHLRYTSHDAGGEVTERDAAAAAAV 93


Lambda     K      H
   0.322    0.135    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: 48
Number of extensions: 3
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: 93
Length of database: 108
Length adjustment: 11
Effective length of query: 82
Effective length of database: 97
Effective search space:     7954
Effective search space used:     7954
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: 39 (21.0 bits)
S2: 39 (19.6 bits)

This GapMind analysis is from Apr 09 2024. 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 (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:

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