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_013451697.1 CALNI_RS07965 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A8AAF8 (356 letters) >NCBI__GCF_000183405.1:WP_013451697.1 Length = 333 Score = 228 bits (580), Expect = 2e-64 Identities = 130/346 (37%), Positives = 200/346 (57%), Gaps = 16/346 (4%) Query: 4 EVAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKFKRL 63 ++AI+GA+GYTG EL+++ HP + +K +TS A+K + +PHL+G+ +L Sbjct: 2 KIAIIGATGYTGFELIKIALRHPHIKLKYLTSDSSADKKISDIYPHLKGLCDMTLI---- 57 Query: 64 DDPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTWYGY 123 P+ + +V D+D VFL LPH S+ + V+DLSAD+R+ E Y++ Y Sbjct: 58 --PNDFNSIVSDIDAVFLCLPHGASMDAAKFFADHNKIVIDLSADFRISNREIYESTYKE 115 Query: 124 EHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRIVVD 183 H YPDLL++ VYG+PEL+GD IR +L+ANPGC TS IL + P +ID D I+ D Sbjct: 116 THKYPDLLKEFVYGIPELFGDDIRKTKLIANPGCYPTSIILPLYPLIKNELIDTDFIIAD 175 Query: 184 VKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTPHAV 243 K G S AG P H E +PY HRH E++ ++ + +++ V FTPH + Sbjct: 176 SKSGVSGAGKNPTEKTHFCEVNEDFKPYGIFNHRHNPEIDFILSG-SYKNLHVTFTPHLL 234 Query: 244 SMIRGSLASAYSWLTKDLAPLD-VQRIYAKYYAGKKFVKIVRGAPMPYPDVKNVYGSNYA 302 + RG L++ Y TK + L+ + + Y+ K FV+I P +KNV +N+ Sbjct: 235 PINRGILSTIY---TKSKSNLNLIIKCLRDTYSDKPFVRIYE---KDIPSIKNVAYTNFI 288 Query: 303 EVGFALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDEDEGL 348 ++G DK + + + +DNL+KGA+G AVQN+N++ G E +GL Sbjct: 289 DIGIYKDK--DNVIIVSTLDNLIKGASGQAVQNLNMLSGFKETDGL 332 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: 359 Number of extensions: 19 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: 333 Length adjustment: 29 Effective length of query: 327 Effective length of database: 304 Effective search space: 99408 Effective search space used: 99408 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