Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_086510219.1 BZY95_RS12275 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q4JAQ3 (350 letters) >NCBI__GCF_002151265.1:WP_086510219.1 Length = 344 Score = 238 bits (606), Expect = 2e-67 Identities = 143/352 (40%), Positives = 206/352 (58%), Gaps = 11/352 (3%) Query: 1 MIRVAVIGGSGYTGGELLRLLAMHNKVEVTYITSREYAGKPISIIHPNLRGFYN-INFSQ 59 MI+V ++GG+GYTG ELLRLLA H++VEV ITSR AG + ++PNLRG Y+ + FS+ Sbjct: 1 MIKVGIVGGTGYTGVELLRLLAQHSQVEVEAITSRSEAGVRVCDMYPNLRGHYDELAFSE 60 Query: 60 FSWDKIGEKAEAVFLALPHKVSVDYVPKLLEMGLQVVDLSADFRLKNPELYKLWYEFDHP 119 ++G +AVF A PH V+ +LLE G +V+DLSADFRL++ E++ WY H Sbjct: 61 PDPQRLGA-CDAVFFATPHGVAHALAGELLERGTRVIDLSADFRLRDAEVWAEWYGQPHG 119 Query: 120 YPDLLKKAVYGIPEIHYEELKGAKLIASPGCNSTATILAAAPLVYSNILDNYRLISDVKV 179 P+LL +AVYG+PE+H E ++ A+LIA PGC TA L PL+ + ++D LI+D K Sbjct: 120 APELLGEAVYGLPEMHRERIRQARLIAVPGCYPTAVQLGLLPLLEAGLIDADHLIADCKS 179 Query: 180 GSSEGGAKPSEGSHHPERQNAIRPYEAEGHRHAAEVEQELQYISKKEVKISLVPHAVSTI 239 G + G S E +++ Y A GHRH E+ Q L+ + V ++ VPH I Sbjct: 180 GVTGAGRGAKVPSLLAEASESMKAYGASGHRHLPEISQGLRDAANGPVGLTFVPHLTPMI 239 Query: 240 RGALASVHGWLISD--DLNEIEFWKKIIEFYRGRKFVRVIRGNIHPYPDPKYVIGSNFVD 297 RG A+++G L + DL + F ++ + FV V+ H P+ + V G+N Sbjct: 240 RGIHATLYGRLTGEPGDLQAL-FERR----FADEPFVDVMPAGSH--PETRSVKGANVCR 292 Query: 298 IGFAVEKRVGRITMFSAIDNLMKGAAGQAVQAFNVSRGFEEDEGLRIPPLRP 349 + + + S IDNL+KGA+GQAVQ N+ GF+E GL P L P Sbjct: 293 LAVHRPGNGDTVVVLSVIDNLVKGASGQAVQNLNLMFGFDEHAGLAAPALMP 344 Lambda K H 0.319 0.138 0.411 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: 355 Number of extensions: 14 Number of successful extensions: 3 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: 350 Length of database: 344 Length adjustment: 29 Effective length of query: 321 Effective length of database: 315 Effective search space: 101115 Effective search space used: 101115 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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