GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Acidovorax sp. GW101-3H11

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Ac3H11_3931 GCN5-related N-acetyltransferase

Query= BRENDA::Q8P8J7
         (203 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3931
          Length = 196

 Score =  152 bits (385), Expect = 3e-42
 Identities = 85/186 (45%), Positives = 113/186 (60%), Gaps = 2/186 (1%)

Query: 15  TLRGQHVTLEPLRAAHADGLRAAVADGALSRLWYTSVPSAAQVDDYIAAALAAQADGTAL 74
           TLR + V LEPL  +H +GLR A ADG L +L  TSVP       YI  ALA + D  A 
Sbjct: 8   TLRDRGVRLEPLALSHEEGLRLAAADGELWKLRVTSVPEPQDTRAYIETALATR-DRFAF 66

Query: 75  PFVVRDAAGEIAGSTRYYALDASVPKLSIGYTWYAPRVQRTGLNTEAKRLLLGHAFETLG 134
             VV +A   + GST Y+ +  +  ++ IGYTWY   VQR+ +NT  K L++GHAF+TLG
Sbjct: 67  A-VVDEATNAVLGSTSYHDILPAARRVEIGYTWYRQSVQRSHVNTTCKLLMMGHAFDTLG 125

Query: 135 CLSVVFETSWFNHTSRAAIARLGAKQDGVLRNHTRHADGTPRDTVVFSIINAEWAGVKRH 194
           C  V + T  +N  S+ AI RLGAK+DGV+R H    DGT RDTV++S+   EW   +  
Sbjct: 126 CHVVGWRTDNYNFASQKAIERLGAKKDGVIRGHALRRDGTIRDTVMYSMRTGEWPEARAQ 185

Query: 195 LQFRLD 200
           L + L+
Sbjct: 186 LLYLLE 191


Lambda     K      H
   0.321    0.131    0.398 

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: 125
Number of extensions: 5
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: 196
Length adjustment: 21
Effective length of query: 182
Effective length of database: 175
Effective search space:    31850
Effective search space used:    31850
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 (21.9 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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