Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate Ac3H11_2575 Cyclohexadienyl dehydrogenase (EC 1.3.1.12)(EC 1.3.1.43)
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2575 Length = 290 Score = 250 bits (638), Expect = 3e-71 Identities = 126/283 (44%), Positives = 176/283 (62%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60 MF+++ + G GL+GGSFALA+++AG +VG +S + +RAR+LG+ID A A AV Sbjct: 1 MFEQLGLIGCGLMGGSFALAMKKAGLVKRVVGYSKSPSTTDRARQLGVIDVEAPSALLAV 60 Query: 61 QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120 GAD++LVA PVA T L +I + PQ ++ D GSTK+DVV AA+ +L D++ F+PA Sbjct: 61 AGADIVLVAVPVAATEATLKAIKHLVTPQMLIMDVGSTKADVVHAAQRSLRDQVGSFVPA 120 Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180 HPI GRE G E A A+LY G++V++T ++ W A G + +SP+ HD Sbjct: 121 HPITGREVSGVEHAEADLYSGRQVILTPTERTLTVHLQNAEKIWNALGCRVTSMSPESHD 180 Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240 A FA+VSHLPHVLAFA+++ I + H A GFRDFTRIAAS P++WRDI LANR Sbjct: 181 AAFAAVSHLPHVLAFAMMNSITGQAHGDDFLSLAGPGFRDFTRIAASDPKVWRDIMLANR 240 Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283 + LL + + L NI + G+ +E + A R W Sbjct: 241 EELLAQSKLFQQALHNIEQAMEKGNAQALEDMLTLASETRAHW 283 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: 252 Number of extensions: 8 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: 290 Length adjustment: 26 Effective length of query: 269 Effective length of database: 264 Effective search space: 71016 Effective search space used: 71016 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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