Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_015818798.1 TERTU_RS06130 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000023025.1:WP_015818798.1 Length = 742 Score = 207 bits (527), Expect = 6e-58 Identities = 112/290 (38%), Positives = 162/290 (55%), Gaps = 3/290 (1%) Query: 2 FKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAV---ATDAAS 58 F KVVI G+GLIGGS A LR+ ++GV R ++ +A+E+G++D+ D Sbjct: 4 FNKVVIVGLGLIGGSLAAGLRKRAVCREVIGVARRPETCLKAQEMGVVDSAYCSLDDVLE 63 Query: 59 AVQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFI 118 ++ D+I +A P + ++ L IVTD S K V R G+ + Sbjct: 64 QLEAGDIIFIAVPTLTLREVFKALKGRLAEGVIVTDGASVKGSVERDVREIFGEFPPAVV 123 Query: 119 PAHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQE 178 HPIAG EK G EAA +ELY +V++T + END A V+ VA W A GA + + E Sbjct: 124 LGHPIAGSEKSGVEAAESELYVDHRVILTPVAENDPAAVKAVAKLWHAVGAEVLEMPVDE 183 Query: 179 HDAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLA 238 HD V SHLPHV+AF+LVD +A +F+YAA GFRDFTRIA+S MWRDI LA Sbjct: 184 HDMVLGCTSHLPHVIAFSLVDTLAHDSKNENIFRYAAGGFRDFTRIASSDAIMWRDIMLA 243 Query: 239 NRDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWAAAIE 288 N+ ++L +D + L +R +I+ D + ++ A+ AR ++ +E Sbjct: 244 NKASVLDAIDLFSDNLSRLRDIISREDAVEMTGVFTRAKSARDRFTNMLE 293 Lambda K H 0.320 0.132 0.376 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: 478 Number of extensions: 19 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: 295 Length of database: 742 Length adjustment: 33 Effective length of query: 262 Effective length of database: 709 Effective search space: 185758 Effective search space used: 185758 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 (21.9 bits) S2: 51 (24.3 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