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_012969354.1 ALVIN_RS00525 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A8AAF8 (356 letters) >NCBI__GCF_000025485.1:WP_012969354.1 Length = 340 Score = 243 bits (621), Expect = 4e-69 Identities = 152/353 (43%), Positives = 202/353 (57%), Gaps = 26/353 (7%) Query: 5 VAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKFKRLD 64 V IVG +GYTG ELLR+LA HP V+TSR + PV PHLRG RLD Sbjct: 4 VGIVGGTGYTGAELLRLLARHPQAAPAVITSRSESGLPVAEMFPHLRG---------RLD 54 Query: 65 ----DPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTW 120 +PD + + + DLVF A P+ ++ VP+ LE G +V+DL+AD+RLK ++ W Sbjct: 55 LCFSEPD--TGALAECDLVFFATPNGTAMQSVPELLERGTRVIDLAADFRLKDPALWERW 112 Query: 121 YGYEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRI 180 YG H PDLL + VYGLPE+ D IR A+L+ANPGC T+ L LP R +D + Sbjct: 113 YGMPHQCPDLLAETVYGLPEVNRDAIRRARLIANPGCYPTAVTLGFLPLLERRAVDPSWL 172 Query: 181 VVDVKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTP 240 + D K G S AG K E + + Y GHRH+ E+ Q ++ + G +V + F P Sbjct: 173 IADAKSGVSGAGRKAETSLLMAEVGESFKAYSVSGHRHLPEITQNLQTFAGIEVGLTFVP 232 Query: 241 HAVSMIRGSLASAYSWLTKDLAPLDVQRIYAKYYAGKKFVK-IVRGAPMPYPDVKNVYGS 299 H V MIRG A+ Y+ LT D LD+ +Y YA + FV +V G+ PD ++V GS Sbjct: 233 HLVPMIRGIEATLYARLTDD--GLDLAALYQSRYADEPFVDFMVSGS----PDTRSVRGS 286 Query: 300 NYAEVGFALDKRVGRLAMF-AAIDNLMKGAAGTAVQNMNLMLGMDEDEGLKNL 351 N + A R G + + + IDNL+KGAAG AVQNMNLM G DE GL+ L Sbjct: 287 NDCRIAVA---RQGDIVIVQSVIDNLVKGAAGQAVQNMNLMFGFDETLGLEAL 336 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: 383 Number of extensions: 21 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: 340 Length adjustment: 29 Effective length of query: 327 Effective length of database: 311 Effective search space: 101697 Effective search space used: 101697 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 Jul 25 2024. The underlying query database was built on Jul 25 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