Align [amino group carrier protein]-6-phospho-L-2-aminoadipate reductase (EC 1.2.1.103); [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_011950947.1 SWIT_RS00480 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::O50146 (344 letters) >NCBI__GCF_000016765.1:WP_011950947.1 Length = 313 Score = 68.6 bits (166), Expect = 2e-16 Identities = 80/289 (27%), Positives = 115/289 (39%), Gaps = 37/289 (12%) Query: 63 EKLEPADILVLALPHGVFAREFDRYSALAPILIDLSADFRLKDPELYRRYYGEHPRPDLL 122 E L AD +VL LP + A +ID S R Sbjct: 46 EALNAADAVVLCLPDDAAREAVALIANPAVRVIDASTAHRTAAD---------------- 89 Query: 123 GCFVYAVPEL---YREALKGADWIAGAGCNATATLLGLYPLLKAGVLKP-TPIFVTLLIS 178 + Y EL REAL GA I+ GC T L + PL++AG+L TP+ V + Sbjct: 90 --WAYGFAELDPGQREALAGATRISNPGCYPTGFLALVRPLVRAGLLPADTPLSVNAVSG 147 Query: 179 TSAAGAEASPASHHPERAGS----IRVYK-PTGHRHTAEVVENLP-GRPEVHLTAIATDR 232 S G P + R Y GH+H E+ + P + L ++A Sbjct: 148 YSGGGKSMIAMFEDPASPDATDTAFRAYALGLGHKHVPEMQKRAGLAHPPIFLPSVART- 206 Query: 233 VRGILMTAQCFVQDGWSERDVWQAYRE----AYAGEPFIRLVKQKKGVHRYPDPRFVQGT 288 RG+L+ + R A RE AY G +R+ + V GT Sbjct: 207 YRGMLVEVPLHLHL-LPGRPTGAAIRELLAAAYEGSRIVRVATDDRPVLTIEQ---AAGT 262 Query: 289 NYADIGFELEEDTGRLVVMTAIDNLVKGTAGHALQALNVRMGWPETLGL 337 + ++ +E G+ ++ A+DNL KG AG A+Q LN+ +G ET GL Sbjct: 263 DRLELFVHADEKAGQARLIAALDNLGKGAAGAAVQNLNIALGLDETEGL 311 Lambda K H 0.321 0.140 0.431 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: 290 Number of extensions: 16 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: 344 Length of database: 313 Length adjustment: 28 Effective length of query: 316 Effective length of database: 285 Effective search space: 90060 Effective search space used: 90060 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