GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Burkholderia phytofirmans PsJN

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate BPHYT_RS35280 BPHYT_RS35280 acetyltransferase

Query= BRENDA::Q8P8J7
         (203 letters)



>FitnessBrowser__BFirm:BPHYT_RS35280
          Length = 245

 Score = 69.7 bits (169), Expect = 4e-17
 Identities = 54/180 (30%), Positives = 83/180 (46%), Gaps = 4/180 (2%)

Query: 16  LRGQHVTLEPLRAA-HADGLRAAVADGALSRLW-YTSVPSAAQVDDYIAAALAAQADGTA 73
           L G++  +EP+    HA+ L  A       R W Y  V     +  Y      A A    
Sbjct: 30  LIGRYCRIEPVDVERHAEDLYDAYNSATDGRDWTYLGVGPFESLAAYREHLTRAAASADP 89

Query: 74  LPFVVRD-AAGEIAGSTRYYALDASVPKLSIGYTWYAPRVQRTGLNTEAKRLLLGHAFET 132
           L   V D A G+  G+     +D +   + +G+  Y+PR++RT + TEA  LL+   F+ 
Sbjct: 90  LHHAVIDLATGKAVGTLALMRIDRANGVIEVGHVTYSPRLKRTRIATEAMFLLMTQVFDK 149

Query: 133 LGCLSVVFETSWFNHTSRAAIARLGAKQDGVLRNHTRHADGTPRDTVVFSIINAEWAGVK 192
           LG     ++    N  SRAA  R G   +G+ R    + +   RDT  FSII++EW  ++
Sbjct: 150 LGYRRFEWKCDSLNAPSRAAALRYGFTFEGIFRQAIVYRERN-RDTAWFSIIDSEWPALR 208


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: 127
Number of extensions: 10
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: 245
Length adjustment: 22
Effective length of query: 181
Effective length of database: 223
Effective search space:    40363
Effective search space used:    40363
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: 46 (22.3 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