Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate 3608357 Dshi_1759 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
Query= curated2:A8AAF8 (356 letters) >FitnessBrowser__Dino:3608357 Length = 341 Score = 235 bits (599), Expect = 1e-66 Identities = 147/356 (41%), Positives = 201/356 (56%), Gaps = 18/356 (5%) Query: 3 YEVAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGI-YPASLKFK 61 Y +AI+GASGYTG EL+R++A HP + + +++ A + + PHLR + PA +K Sbjct: 2 YNIAILGASGYTGAELVRLIATHPRMRITALSADRKAGQTMGAVFPHLRHLDLPALVK-- 59 Query: 62 RLDDPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTWY 121 +DD D G VDLVF ALPH S + AL K+VDLSAD+RL+ E Y WY Sbjct: 60 -IDDID-----FGGVDLVFCALPHATSQSVIA-ALPKSVKIVDLSADFRLRDPEAYAKWY 112 Query: 122 GYEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRIV 181 G H DL +AVYGL E Y ++IR A+LVA GCNA + A+ P A +IDLD I+ Sbjct: 113 GGPHAALDLQAEAVYGLTEFYREQIRDARLVAGTGCNAATGQYALRPLIAAGVIDLDEII 172 Query: 182 VDVKVGSSEAGAKPYRGGHHPEREGTARPYDAEG-HRHVAELEQVIRDYTGRDVKVGFTP 240 +D+K G S AG H E A Y G HRH+ E +Q GR++KV FTP Sbjct: 173 IDLKTGVSGAGRSLKENLLHAELSEGAHAYAVGGMHRHLGEFDQEFSALAGREIKVQFTP 232 Query: 241 HAVSMIRGSLASAYSWLTKDLAPLDVQRIYAKYYAGKKFVKIVRGAPMPYPDVKNVYGSN 300 H + RG LA+ Y K A ++ A Y + FV ++ +P ++V GSN Sbjct: 233 HLLPANRGILATVY---VKGEA-TEIYDALADAYEDEPFVVMLPEG--EHPSTRHVRGSN 286 Query: 301 YAEVGFALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDEDEGLKNLVPVRP 356 + +G D+ GR + AA+DNL KG++G A+QN NLML ++E GL + PV P Sbjct: 287 FVHIGVVRDRIPGRAVVIAALDNLTKGSSGQALQNANLMLDIEETTGLM-MTPVFP 341 Lambda K H 0.319 0.138 0.410 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: 376 Number of extensions: 21 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: 356 Length of database: 341 Length adjustment: 29 Effective length of query: 327 Effective length of database: 312 Effective search space: 102024 Effective search space used: 102024 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