Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate PP_1770 PP_1770 3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__Putida:PP_1770 Length = 746 Score = 236 bits (602), Expect = 1e-66 Identities = 125/281 (44%), Positives = 173/281 (61%) Query: 4 KVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAVQGA 63 ++V+ G+GLIGGSFA LR +G +VGV S ++A LG++D D A+A GA Sbjct: 15 RLVVVGLGLIGGSFAKGLRESGLCREVVGVDLDAPSRKQAVALGVVDRCEEDLAAACVGA 74 Query: 64 DLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPAHPI 123 D+I +A P+ +LA +A AI+TD GS K +VV AR G R+ +F+P HPI Sbjct: 75 DVIQLAVPILAMEKVLARLALLDLGDAIITDVGSAKGNVVREARAVFGARLPRFVPGHPI 134 Query: 124 AGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHDAVF 183 AG E+ G EA+ A L+ KV++T L E D A + +V WRA A + +S + HD V Sbjct: 135 AGSEQSGVEASNATLFRRHKVILTPLAETDPAALVLVDRLWRALDADVEHMSVERHDEVL 194 Query: 184 ASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANRDAL 243 A+ SHLPH+LAF LVD +A + +F+YAA GFRDFTRIA S P MW DI LANRDA+ Sbjct: 195 AATSHLPHLLAFGLVDSLAKRNENLEIFRYAAGGFRDFTRIAGSDPTMWHDIFLANRDAV 254 Query: 244 LTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284 L +D + L +R IA GDG + ++ A+ AR+ ++ Sbjct: 255 LRTLDTFRSDLDALRDAIAEGDGHQLLGVFTRARVAREHFS 295 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: 538 Number of extensions: 22 Number of successful extensions: 1 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: 746 Length adjustment: 33 Effective length of query: 262 Effective length of database: 713 Effective search space: 186806 Effective search space used: 186806 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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