Align Prephenate dehydrogenase; PDH; EC 1.3.1.12 (uncharacterized)
to candidate WP_012282984.1 HM1_RS08660 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= curated2:P20692 (371 letters) >NCBI__GCF_000019165.1:WP_012282984.1 Length = 390 Score = 226 bits (577), Expect = 6e-64 Identities = 124/357 (34%), Positives = 194/357 (54%), Gaps = 6/357 (1%) Query: 8 ILLAGLGLIGGSIALAIKKNHPGKRIIGIDISDEQAVAALKLGVIDDRADSFISGVKEAA 67 +++ GLG+IGGS+A+A+ + +IG+D +E AL V EA Sbjct: 25 VVIIGLGVIGGSLAMALTQGQLVDEVIGVDRDEETRKLALATYAAHRVEADAAEAVAEAD 84 Query: 68 TVIIATPVEQTLVMLEELAHSGIEHELLITDVGSTKQKVVDYADQVLPSRYQFVGGHPMA 127 +++ATPV ++ + H ++ ++TDVGSTKQ V++ ++LP +FVGGHPMA Sbjct: 85 LIVLATPVCTYPAIIASIRHR-LKPGTIVTDVGSTKQWVLEQMGRLLPPGVRFVGGHPMA 143 Query: 128 GSHKSGVAAAKEFLFENAFYILTPGQKTDKQAVEQLKNLLKGTNAHFVEMSPEEHDGVTS 187 GS K G+ A +L ENA Y+LTP TD A++ L++L+K A + +S EEHD + + Sbjct: 144 GSEKQGIRGADRYLLENAVYVLTPDVDTDAAALQALEDLIKAAGARVLRISAEEHDSMVA 203 Query: 188 VISHFPHIVAASLVHQTHHSENLYPLVKRFAAGGFRDITRIASSSPAMWRDILLHNKDKI 247 ++SH PH++A +LV YP AAGGFRD TR+A+ P MW DI N++ + Sbjct: 204 LVSHLPHMMAVALVETLSEVAKEYPKAPMLAAGGFRDTTRVAAGDPQMWVDIACTNREPL 263 Query: 248 LDRFDEWIREIDKIRTYVEQEDA-----ENLFRYFKTAKDYRDGLPLRQKGAIPAFYDLY 302 L + +D++ ++ A E L A++ R +P + KG +P +++ Sbjct: 264 LHMIGCFRSALDRLEEQIDACGACGSKMEALRETLAHAREVRLSIPGKAKGILPGIHEIV 323 Query: 303 VDVPDHPGVISEITAILAAERISITNIRIIETREDINGILRISFQSDDDRKRAEQCI 359 + VPD PGVI I +L I+I +I I+ RE G +RI F D A + + Sbjct: 324 LTVPDEPGVIGTIARLLGDNGINIADIEILRVREGHGGTIRIGFYEAPDADGAVEVL 380 Lambda K H 0.319 0.136 0.388 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: 325 Number of extensions: 17 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: 371 Length of database: 390 Length adjustment: 30 Effective length of query: 341 Effective length of database: 360 Effective search space: 122760 Effective search space used: 122760 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 (21.8 bits) S2: 50 (23.9 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