GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Trichormus variabilis ATCC 29413

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate WP_011320317.1 AVA_RS18285 aspartate-semialdehyde dehydrogenase

Query= curated2:A0L482
         (349 letters)



>NCBI__GCF_000204075.1:WP_011320317.1
          Length = 347

 Score = 68.6 bits (166), Expect = 2e-16
 Identities = 61/190 (32%), Positives = 87/190 (45%), Gaps = 29/190 (15%)

Query: 1   MGRTLRVAILGATGYTGGELIRLL--HRHPGAELSFVSSERFAGQSIAKVYTHLQAVGHL 58
           M +T RVAILGATG  G EL+ LL     P AEL  ++SER  G+S       L   G  
Sbjct: 1   MSKTYRVAILGATGAVGTELLELLESRNFPVAELKLLASERSVGRS-------LPFKGEN 53

Query: 59  ICQPMDAKKACEAADFIFCALPHVTSMEVVPELLQRGAKVVDLSADFRLKSAETYAHWYG 118
           I     + +A E  D +  +    TS       +++GA V+D S+ FR+           
Sbjct: 54  IIVEAVSDRALENVDIVLASAGGSTSKAWASVAVEKGAVVIDNSSAFRMNP--------D 105

Query: 119 TQHLAPELLPQAAYGLPELFRESIKGANLVANPGCYPTSVQLPLFPLLQEGMIDPALVIA 178
              + PE+ PQAA           KG  ++ANP C    + L ++PL Q   +    ++A
Sbjct: 106 VPLIVPEVNPQAA--------ADHKG--IIANPNCTTILMTLAVWPLHQVRPVQ--RIVA 153

Query: 179 DSKSGVSGAG 188
            +    SGAG
Sbjct: 154 ATYQSASGAG 163


Lambda     K      H
   0.320    0.135    0.406 

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: 268
Number of extensions: 18
Number of successful extensions: 4
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: 349
Length of database: 347
Length adjustment: 29
Effective length of query: 320
Effective length of database: 318
Effective search space:   101760
Effective search space used:   101760
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 (21.8 bits)
S2: 49 (23.5 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