Align Putative [LysW]-L-2-aminoadipate 6-phosphate reductase; EC 1.2.1.103 (uncharacterized)
to candidate WP_086510219.1 BZY95_RS12275 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:B9KZP8 (352 letters) >NCBI__GCF_002151265.1:WP_086510219.1 Length = 344 Score = 249 bits (635), Expect = 1e-70 Identities = 153/355 (43%), Positives = 199/355 (56%), Gaps = 16/355 (4%) Query: 2 VVSVAILGGSGYTGGELLRLLLSHPEVEVKQVTSRSRAGKFVHTVHPNLR---KRTALKF 58 ++ V I+GG+GYTG ELLRLL H +VEV+ +TSRS AG V ++PNLR A Sbjct: 1 MIKVGIVGGTGYTGVELLRLLAQHSQVEVEAITSRSEAGVRVCDMYPNLRGHYDELAFSE 60 Query: 59 VPPEALEPVDLLFACLPHGETAPIVDRLLELAPIVIDLSADFRLRDPAAYEQWYHWTHPR 118 P+ L D +F PHG + LLE VIDLSADFRLRD + +WY H Sbjct: 61 PDPQRLGACDAVFFATPHGVAHALAGELLERGTRVIDLSADFRLRDAEVWAEWYGQPHGA 120 Query: 119 PDLLAQAVYGLPELHREEIRNARYIACPGCNSTTVILGLAPLFRAGLIDLDLPVTVECKV 178 P+LL +AVYGLPE+HRE IR AR IA PGC T V LGL PL AGLID D + +CK Sbjct: 121 PELLGEAVYGLPEMHRERIRQARLIAVPGCYPTAVQLGLLPLLEAGLIDAD-HLIADCKS 179 Query: 179 GSSGAGGEAGPASHHPERSGVIRPFKPGGHRHTAEVLQELTVCGRTPSLGLSVTS--VEA 236 G +GAG A S E S ++ + GHRH E+ Q L P +GL+ Sbjct: 180 GVTGAGRGAKVPSLLAEASESMKAYGASGHRHLPEISQGLRDAANGP-VGLTFVPHLTPM 238 Query: 237 VRGILATAHLFPKQPLTDRDLWQVYRAAYGQEPFIRLVKEASGIHRYPEPKILAGSNYCD 296 +RGI AT L+ + DL ++ + EPF+ ++ S +PE + + G+N C Sbjct: 239 IRGIHAT--LYGRLTGEPGDLQALFERRFADEPFVDVMPAGS----HPETRSVKGANVCR 292 Query: 297 IGWELDELPGGRQRLVVMSAIDNLMKGAAGQAVQAMNIRLGFPETLGLEFPGLHP 351 + PG +VV+S IDNL+KGA+GQAVQ +N+ GF E GL P L P Sbjct: 293 LA---VHRPGNGDTVVVLSVIDNLVKGASGQAVQNLNLMFGFDEHAGLAAPALMP 344 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: 395 Number of extensions: 18 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: 352 Length of database: 344 Length adjustment: 29 Effective length of query: 323 Effective length of database: 315 Effective search space: 101745 Effective search space used: 101745 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 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