Align Prephenate dehydrogenase; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_004043624.1 C498_RS11765 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D4GXG3 (272 letters) >NCBI__GCF_000337315.1:WP_004043624.1 Length = 272 Score = 536 bits (1380), Expect = e-157 Identities = 272/272 (100%), Positives = 272/272 (100%) Query: 1 MDVLIVGAGAMGRWFGRTVDADLAFADADPESAVAAADALGGRAVPLDGDERFDVVCLAV 60 MDVLIVGAGAMGRWFGRTVDADLAFADADPESAVAAADALGGRAVPLDGDERFDVVCLAV Sbjct: 1 MDVLIVGAGAMGRWFGRTVDADLAFADADPESAVAAADALGGRAVPLDGDERFDVVCLAV 60 Query: 61 PMRLAADAVADNAHRADAAMCDVTGAMKPPVVAMRNHLPDRERLSLHPLFAPHNAPGNVA 120 PMRLAADAVADNAHRADAAMCDVTGAMKPPVVAMRNHLPDRERLSLHPLFAPHNAPGNVA Sbjct: 61 PMRLAADAVADNAHRADAAMCDVTGAMKPPVVAMRNHLPDRERLSLHPLFAPHNAPGNVA 120 Query: 121 AVADESGPKTDTLLADLDAAGNRVFETTPEEHDAAMETVQAAAHAAVLAFGVAADDVREE 180 AVADESGPKTDTLLADLDAAGNRVFETTPEEHDAAMETVQAAAHAAVLAFGVAADDVREE Sbjct: 121 AVADESGPKTDTLLADLDAAGNRVFETTPEEHDAAMETVQAAAHAAVLAFGVAADDVREE 180 Query: 181 FATPISAALDELVASVSGGTPRVYADIQSSFGGGADRVADAARALAAADDEAFDDLYRRV 240 FATPISAALDELVASVSGGTPRVYADIQSSFGGGADRVADAARALAAADDEAFDDLYRRV Sbjct: 181 FATPISAALDELVASVSGGTPRVYADIQSSFGGGADRVADAARALAAADDEAFDDLYRRV 240 Query: 241 SRGDSGVAAGADRVADDRSRDRDQTDKHDPVE 272 SRGDSGVAAGADRVADDRSRDRDQTDKHDPVE Sbjct: 241 SRGDSGVAAGADRVADDRSRDRDQTDKHDPVE 272 Lambda K H 0.317 0.131 0.379 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: 265 Number of extensions: 4 Number of successful extensions: 2 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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