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_007691426.1 C447_RS04725 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::O50146 (344 letters) >NCBI__GCF_000336675.1:WP_007691426.1 Length = 345 Score = 324 bits (830), Expect = 2e-93 Identities = 169/342 (49%), Positives = 219/342 (64%), Gaps = 4/342 (1%) Query: 4 KTLSIVGASGYAGGEFLRLALSHPYLEVKQVTSRRFAGEPVHFVHPNLRGRTNLKFIPPE 63 KT S+VGASG+ GGE LRL SHP E++ TSR + + + VHPNLRG +F P Sbjct: 3 KTASVVGASGFTGGELLRLIDSHPEFELEAATSREYTNKTLGSVHPNLRG-IEQRFSDPT 61 Query: 64 KLEPADILVLALPHGVFAREFDRYSALAPILIDLSADFRLKDPELYRRYYGEHPRPDLLG 123 +L D+L A PHGV + D + +A ++DLSADFRL + Y +Y H RP+LL Sbjct: 62 ELASVDVLFAATPHGVSMEQIDAFREVADTVVDLSADFRLDSEDQYEEWYDGHSRPELLD 121 Query: 124 CFVYAVPELYREALKGADWIAGAGCNATATLLGLYPLLKAGVLK-PTPIFVTLLISTSAA 182 VYA+PE +R+ L GA IA GCNATAT+LGL PL AG+L+ I V + + +S Sbjct: 122 ESVYALPERHRDELPGASLIAAGGCNATATVLGLGPLFDAGILEGDEQIVVDVKVGSSEG 181 Query: 183 GAEASPASHHPERAGSIRVYKPTGHRHTAEVVENLPGRPEVHLTAIATDRVRGILMTAQC 242 GA AS HPER+G +R Y PTGHRH AE+V+ V TA A D VRG T Sbjct: 182 GAGGGDASSHPERSGVVRPYAPTGHRHEAEIVQEFGC--SVAFTAHAVDMVRGASATCHV 239 Query: 243 FVQDGWSERDVWQAYREAYAGEPFIRLVKQKKGVHRYPDPRFVQGTNYADIGFELEEDTG 302 F + S D+W A+RE+Y EPF+RLV GV+RYP+P+ V GTN+A++GFEL+ Sbjct: 240 FPDEPVSTGDLWSAFRESYDDEPFVRLVAGGSGVYRYPEPKAVAGTNHAEVGFELDPSNK 299 Query: 303 RLVVMTAIDNLVKGTAGHALQALNVRMGWPETLGLDFPGLHP 344 R+VV +AIDN++KG+AG A+QA NV G+ ET GLDF GLHP Sbjct: 300 RIVVFSAIDNMMKGSAGQAIQAANVAFGYDETAGLDFQGLHP 341 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: 416 Number of extensions: 20 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: 344 Length of database: 345 Length adjustment: 29 Effective length of query: 315 Effective length of database: 316 Effective search space: 99540 Effective search space used: 99540 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 Apr 09 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