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.
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:
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