Align [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate WP_011373162.1 SUDEN_RS07995 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:Q976J5 (349 letters) >NCBI__GCF_000012965.1:WP_011373162.1 Length = 334 Score = 205 bits (522), Expect = 1e-57 Identities = 128/340 (37%), Positives = 194/340 (57%), Gaps = 16/340 (4%) Query: 2 IRVAVIGGSGYTGGELLRILAVHPKIEVTYVTSREYAGKPITLVHPNLRGFYNMNFSQFS 61 I V VIG SGYTG EL++IL HPK ++YV + E G ++ +HP+L+G + N + Sbjct: 4 IDVGVIGASGYTGLELIKILLKHPKFNLSYVANTE-GGATLSELHPSLKGAFECNVVKVD 62 Query: 62 FDKLGDKADAVFLGLPHKVSLEYVPKILEMGIQVIDLSADFRLKDPTLYKIWYGYEHPYP 121 D+L K + VFL +PH+ ++ YV ++E G++V+DLSAD+RL +Y+ +Y H Sbjct: 63 IDELAKKCELVFLAVPHQAAMAYVKPLIEKGLKVVDLSADYRL-SKDIYEEFY-CPHTDV 120 Query: 122 DLLKKAVYGLPELHYEELKNAKLIASPGCNATATILAGAPLVASSLLETYKLISDVKVGS 181 + L AVYGLPEL +++K AKL+A+PGC T+ IL P + + T +I D K G Sbjct: 121 ENLLHAVYGLPELFAQKIKKAKLVANPGCFPTSAILGLLPFMDKRVAHT-PIIVDSKTGV 179 Query: 182 SEGGAKPHEGSHHPERQNAIRPYEADGHRHAAEAEQELSLIAKRDVKVSLVPHAVSSVRG 241 S G K + +H + Y HRHA E Q+L + +V VPH V RG Sbjct: 180 SGAGKKLSDVTHFVNVNENLFAYNPLLHRHAPEIAQKLGVDFD---EVHFVPHLVPVTRG 236 Query: 242 ALASVHGWLSSDISEMDMWKKSIEFYKGRKFIRIIRSNIHPYPDPKFVIGSNFADIGFAI 301 L+S++ + D D + EFYK K +R+ ++ + D K V G+NF DI + Sbjct: 237 MLSSIYIQVEGD---FDAFSILSEFYKDAKHVRVSKNPV----DMKSVAGTNFCDI--YV 287 Query: 302 EKRMQRITMFSAIDNLMKGAAGQAVQAFNISRGFEEDEGL 341 +++ + + SAIDNLM+GA+ AV N+ GF+E+ G+ Sbjct: 288 KQKNNILFISSAIDNLMRGASSAAVVNANLMMGFDEELGI 327 Lambda K H 0.319 0.137 0.405 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: 338 Number of extensions: 23 Number of successful extensions: 6 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: 334 Length adjustment: 29 Effective length of query: 320 Effective length of database: 305 Effective search space: 97600 Effective search space used: 97600 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