Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_014026304.1 PYRFU_RS03735 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q4JAQ3 (350 letters) >NCBI__GCF_000223395.1:WP_014026304.1 Length = 365 Score = 451 bits (1159), Expect = e-131 Identities = 217/350 (62%), Positives = 273/350 (78%), Gaps = 2/350 (0%) Query: 2 IRVAVIGGSGYTGGELLRLLAMHNKVEVTYITSREYAGKPISIIHPNLRGFYN-INFSQF 60 I V +IG SGYTGGELLRLLAMH EV TSREYAGKPI +H NLRGFY + FS Sbjct: 17 IPVCIIGASGYTGGELLRLLAMHPNAEVVIATSREYAGKPIGYVHFNLRGFYKGLRFSPL 76 Query: 61 SWDKIGEKAEAVFLALPHKVSVDYVPKLLEMGLQVVDLSADFRLKNPELYKLWYEFDHPY 120 + D+I +K EAVFLA+PH S++ VPKL E GL+++DLSADFRLKNPE YK WY +HPY Sbjct: 77 NIDEITDKCEAVFLAVPHGASLELVPKLYETGLKILDLSADFRLKNPEEYKRWYGREHPY 136 Query: 121 PDLLKKAVYGIPEIHYEELKGAKLIASPGCNSTATILAAAPLVYSNILDNYRLISDVKVG 180 PDLL+KAVYG+PE+H +E++ A+L+A PGCN+TA I AAAP+V ++D L+ DVKVG Sbjct: 137 PDLLEKAVYGLPELHRDEIRNARLVAVPGCNATAAIFAAAPVVKEKLVDLDHLVIDVKVG 196 Query: 181 SSEGGAKPSEGSHHPERQNAIRPYEAEGHRHAAEVEQELQYISKKEVKISLVPHAVSTIR 240 SSE G+KPS G HHPER+NAIRPY AEGHRH AEVEQEL ++ ++V+++ VPHAVS IR Sbjct: 197 SSEAGSKPSPGDHHPERENAIRPYSAEGHRHVAEVEQELGMLAGRDVRVAFVPHAVSAIR 256 Query: 241 GALASVHGWLISDDLNEIEFWKKIIEFYRGRKFVRVIRGNIHPYPDPKYVIGSNFVDIGF 300 GALA++H WL +D +E++ W+ Y FVR++R + YPDPKYVIG+NFVD+GF Sbjct: 257 GALATLHAWL-ADGADEMKVWRAYAAMYGKEPFVRIVRTGLLRYPDPKYVIGTNFVDVGF 315 Query: 301 AVEKRVGRITMFSAIDNLMKGAAGQAVQAFNVSRGFEEDEGLRIPPLRPA 350 AVEKR+GR+ F+AIDNL++GAAGQAVQ+FN+ GF+E GL PPL+PA Sbjct: 316 AVEKRIGRMAGFAAIDNLVRGAAGQAVQSFNIMMGFDETLGLLYPPLKPA 365 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: 463 Number of extensions: 20 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: 365 Length adjustment: 29 Effective length of query: 321 Effective length of database: 336 Effective search space: 107856 Effective search space used: 107856 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