Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate WP_028313700.1 G491_RS0104245 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A8AAF8 (356 letters) >NCBI__GCF_000429905.1:WP_028313700.1 Length = 350 Score = 240 bits (613), Expect = 4e-68 Identities = 138/343 (40%), Positives = 191/343 (55%), Gaps = 9/343 (2%) Query: 6 AIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKFKRLDD 65 A+VGA+GY G EL+R+L HP V +K VTSR+YA + + P +G+ P + Sbjct: 10 AVVGATGYAGAELVRILWDHPQVELKAVTSRQYAGQAIAQVFPAFQGVVPLVCEEFNAQS 69 Query: 66 PDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTWYGYEH 125 + +DVV FLALPHK+ + P+ ++VDLSAD+R Y+ Y H Sbjct: 70 IGERADVV------FLALPHKLPMAIAPQLEGTNTRIVDLSADFRFNDQAAYEAVY-QPH 122 Query: 126 PYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRIVVDVK 185 PDLL+K+VYGL ELY +I A ++ NPGC T S+L + P + +I IV+D K Sbjct: 123 TSPDLLKKSVYGLCELYRKEIAQAFIIGNPGCYPTCSLLPLAPFIQQGVISTRGIVIDAK 182 Query: 186 VGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTPHAVSM 245 G+S AG H+ E Y HRH E+E+++ GRDVK+ F PH V M Sbjct: 183 SGASGAGRGLSLTTHYCELTEGFSAYKVAAHRHCPEMEEILSREAGRDVKITFAPHLVPM 242 Query: 246 IRGSLASAYSWLTKDLAPLDVQRIYAKYYAGKKFVKIVRGAPMPYPDVKNVYGSNYAEVG 305 RG LA++YS L KDL I ++Y +FVKI + P +V G+NY + Sbjct: 243 SRGMLATSYSMLEKDLDTPAALEILREFYKDAEFVKICPDNAL--PRTSHVRGTNYVHIA 300 Query: 306 FALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDEDEGL 348 +D+ RL + + IDNL+KGAAG AVQNMN+M G+ E GL Sbjct: 301 ARVDEHANRLILVSVIDNLVKGAAGQAVQNMNIMFGLAEGAGL 343 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: 381 Number of extensions: 17 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: 356 Length of database: 350 Length adjustment: 29 Effective length of query: 327 Effective length of database: 321 Effective search space: 104967 Effective search space used: 104967 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