Align Prephenate dehydrogenase (characterized, see rationale)
to candidate YP_426060.1 Rru_A0972 prephenate dehydrogenase
Query= uniprot:A0A1L6J750 (249 letters) >NCBI__GCF_000013085.1:YP_426060.1 Length = 317 Score = 164 bits (414), Expect = 3e-45 Identities = 94/226 (41%), Positives = 131/226 (57%), Gaps = 6/226 (2%) Query: 5 GIIGFGRFGQLAARHLRDHFSVVVTDTADVGEAAA-AIGVKTGSLADAADCDVVMLAVPV 63 G+IG G FG HL F ++ D A G A A A+GV +LA+AA +V+ AVPV Sbjct: 38 GLIGLGAFGAFCVPHLSRFFHILGHDPARDGAARALALGVLPATLAEAAAASIVIPAVPV 97 Query: 64 QAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVATHPLFGPQSARGGL 123 +A AAIAP +RPGALV+DV S+K+ P + LP V +V THPLFGP S G+ Sbjct: 98 AVLAEVTAAIAPHLRPGALVVDVCSLKVEPMAVLERILPAGVIVVGTHPLFGPASGAKGI 157 Query: 124 EGQPLVVCAVRG----ERHHKVAEF-GRSLGLSVSITTAEEHDREMAYVQALTHLIGRAL 178 + + VC G + +VA F R LGL+V +A EHDR+MAYVQ LTHL+ R + Sbjct: 158 KDLRVAVCPGHGPAGAKAEDRVAAFLARRLGLAVHRVSAVEHDRQMAYVQGLTHLLARIV 217 Query: 179 VNIRIPDEELKTNSYQHLLELCGLIRDDSKELFFAIQNLNPYAEEI 224 + +P+ L T ++ HL+ + + DS+ LF I NP+ ++ Sbjct: 218 TKLDVPEMSLATGTFDHLMRMVHTVDRDSEALFRTITEANPFVGDL 263 Lambda K H 0.321 0.135 0.387 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: 188 Number of extensions: 11 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: 249 Length of database: 317 Length adjustment: 26 Effective length of query: 223 Effective length of database: 291 Effective search space: 64893 Effective search space used: 64893 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: 47 (22.7 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