Align Putative [LysW]-L-2-aminoadipate 6-phosphate reductase; EC 1.2.1.103 (uncharacterized)
to candidate WP_019557049.1 F612_RS0107000 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:B9KZP8 (352 letters) >NCBI__GCF_000381085.1:WP_019557049.1 Length = 349 Score = 234 bits (596), Expect = 3e-66 Identities = 143/352 (40%), Positives = 201/352 (57%), Gaps = 11/352 (3%) Query: 3 VSVAILGGSGYTGGELLRLLLSHPEVEVKQVTSRSRAGKFVHTVHPNLRKRTALKFVPP- 61 V V I+GG+GYTG ELLR L +HP EV +TSRS G V ++PNLR L+F P Sbjct: 6 VQVGIVGGTGYTGVELLRSLANHPFAEVTMITSRSEQGVAVADMYPNLRGIYRLQFSVPD 65 Query: 62 -EALEPVDLLFACLPHGETAPIVDRLLELAPIVIDLSADFRLRDPAAYEQWYHWTHPRPD 120 E L+ DL+F PHG + L+E VIDL+ADFR+ D A +++WY Sbjct: 66 IEKLKNCDLVFFATPHGVATSMAFELIEAGVKVIDLAADFRIEDLAVWQKWYGIEPASEA 125 Query: 121 LLAQAVYGLPELHREEIRNARYIACPGCNSTTVILGLAPLFRAGLIDLDLPVTVECKVGS 180 L+A+AVYGLPE +RE+I++A+ IA PGC T+++LG+ PL +A L+ +D + + K G Sbjct: 126 LMAEAVYGLPEYYREKIKHAKVIANPGCYPTSILLGILPLLKADLVKVD-SIIADGKSGV 184 Query: 181 SGAGGEAGPASHHPERSGVIRPFKPGGHRHTAEVLQELT-VCGRTPSLGLSVTSVEAVRG 239 SGAG A A E S + + GHRH E+ ++++ + G+ L + VRG Sbjct: 185 SGAGKGASVAMLGAEMSESFKAYGVNGHRHLPEMQEKMSLLTGQEVGLTFVPHLLPMVRG 244 Query: 240 ILATAHLFPKQPLTDRDLWQVYRAAYGQEPFIRLVKEASGIHRYPEPKILAGSNYCDIGW 299 + +T + K T +L +Y AAY EPF+ ++ S PE +++ GSN C + Sbjct: 245 MESTIYATLKIDKTQAELQALYEAAYENEPFVDVMPAGS----LPETRMVKGSNMCRMA- 299 Query: 300 ELDELPGGRQRLVVMSAIDNLMKGAAGQAVQAMNIRLGFPETLGLEFPGLHP 351 P G +V+ S IDNL+KGAAGQA+Q MNI PET GL L P Sbjct: 300 --IYCPPGGNIVVITSVIDNLVKGAAGQAIQNMNIMFNLPETAGLNQVALLP 349 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: 338 Number of extensions: 15 Number of successful extensions: 5 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: 349 Length adjustment: 29 Effective length of query: 323 Effective length of database: 320 Effective search space: 103360 Effective search space used: 103360 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