Align [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate 17997 b3958 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI)
Query= curated2:Q976J5 (349 letters) >FitnessBrowser__Keio:17997 Length = 334 Score = 179 bits (454), Expect = 9e-50 Identities = 118/346 (34%), Positives = 176/346 (50%), Gaps = 18/346 (5%) Query: 1 MIRVAVIGGSGYTGGELLRILAVHPKIEVTYVT---SREYAGKPITLVHPNLRGFYNMNF 57 M+ ++G SGY G EL+ + HP + +T +T AGK I+ +HP L+G ++ Sbjct: 1 MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60 Query: 58 SQFS-FDKLGDKADAVFLGLPHKVSLEYVPKILEMGIQVIDLSADFRLKDPTLYKIWYGY 116 S + D VFL H+VS + P+ LE G V DLS FR+ D T Y+ +YG+ Sbjct: 61 QPMSDISEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGF 120 Query: 117 EHPYPDLLKKAVYGLPELHYEELKNAKLIASPGCNATATILAGAPLVASSLLETYKL-IS 175 H YP+LL++A YGL E +LK A LIA PGC TA LA PL+ + LL+ + + Sbjct: 121 THQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVI 180 Query: 176 DVKVGSSEGGAKPHEGSHHPERQNAIRPYEADGHRHAAEAEQELSLIAKRDVKVSLVPHA 235 + G S G K + E +++PY HRH E L V PH Sbjct: 181 NATSGVSGAGRKAAISNSFCE--VSLQPYGVFTHRHQPEIATHLG------ADVIFTPHL 232 Query: 236 VSSVRGALASVHGWLSSDISEMDMWKKSIEFYKGRKFIRIIRSNIHPYPDPKFVIGSNFA 295 + RG L ++ L S +++ + + + Y + +R+ + P K V+G F Sbjct: 233 GNFPRGILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGV---PALKNVVGLPFC 289 Query: 296 DIGFAIEKRMQRITMFSAIDNLMKGAAGQAVQAFNISRGFEEDEGL 341 DIGFA++ + + + + DNL+KGAA QAVQ NI G+ E + L Sbjct: 290 DIGFAVQG--EHLIIVATEDNLLKGAAAQAVQCANIRFGYAETQSL 333 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: 296 Number of extensions: 13 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: 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 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