GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Thiohalospira halophila DSM 15071 HL 3

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_093428507.1 BM272_RS09265 phosphoribosyl-AMP cyclohydrolase

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>NCBI__GCF_900112605.1:WP_093428507.1
          Length = 133

 Score = 80.1 bits (196), Expect = 2e-20
 Identities = 41/90 (45%), Positives = 52/90 (57%), Gaps = 1/90 (1%)

Query: 17  GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76
           GL+PVI Q   SG VLM  + + EAL +T   G+  ++SR++ +LW KGE SGN   V  
Sbjct: 15  GLVPVIAQDRDSGRVLMFAWADREALRRTAAEGRAVYYSRSRGKLWPKGEESGNVQEVHD 74

Query: 77  IAPDCDND-TLLVLANPIGPTCHKGTSSCF 105
           I  DCD D  LL +    G  CH G  SCF
Sbjct: 75  IRLDCDGDVVLLSITQHGGAACHTGRESCF 104


Lambda     K      H
   0.317    0.132    0.384 

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: 80
Number of extensions: 6
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: 203
Length of database: 133
Length adjustment: 18
Effective length of query: 185
Effective length of database: 115
Effective search space:    21275
Effective search space used:    21275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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