Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate N515DRAFT_3769 N515DRAFT_3769 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A8AAF8 (356 letters) >FitnessBrowser__Dyella79:N515DRAFT_3769 Length = 319 Score = 141 bits (355), Expect = 3e-38 Identities = 109/343 (31%), Positives = 166/343 (48%), Gaps = 42/343 (12%) Query: 5 VAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKFKRLD 64 + IVGA G+TG EL+R++A HP + + V+SRE + V H+ G Y L++ LD Sbjct: 8 IGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVA---EHVDG-YAGELRYANLD 63 Query: 65 DPDQLSDVVGDVDLVFLALPHKVSLHYVPK--ALEVGYKVVDLSADYRLKRVEDYKTWYG 122 + D+V LALP+ + YV A + ++DLSADYR + WY Sbjct: 64 PAAVAAQ---GADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFN-----ERWY- 114 Query: 123 YEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRIVV 182 YGLPEL K RG + ++NPGC AT+ L++ P + ++ + Sbjct: 115 -------------YGLPELTRGKWRGERRISNPGCYATAIQLSIAP--LKDVLAAPPVSF 159 Query: 183 DVKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTPHA 242 V G S AG P + + PY GH H E + + + V F PH Sbjct: 160 GVS-GYSGAGTTPSDKNNPEKLRDNLMPYSLTGHTHEQEASRHL------GLPVEFMPHV 212 Query: 243 VSMIRGSLASAYSWLTKDLAPLDVQRIYAKYYAGKKFVKIVRGAPMPYPDVKNVYGSNYA 302 RG + +L + + ++ + + Y G+K VK+V AP V + ++A Sbjct: 213 APHFRGLTVTTNLYLVRPMKREEILQRFRHAYDGEKLVKVVDEAPW----VSQIAHRHHA 268 Query: 303 EVG-FALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDE 344 EVG FA+ R+ + A +DNL+KGAA A+QN+N +G+DE Sbjct: 269 EVGGFAVSVDGKRVVIVATLDNLLKGAATQAIQNINRAIGVDE 311 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: 377 Number of extensions: 25 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: 319 Length adjustment: 28 Effective length of query: 328 Effective length of database: 291 Effective search space: 95448 Effective search space used: 95448 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