Align prephenate dehydrogenase (NADP+) (EC 1.3.1.13) (characterized)
to candidate Ga0059261_2298 Ga0059261_2298 Prephenate dehydrogenase
Query= BRENDA::A8AAX2 (348 letters) >FitnessBrowser__Korea:Ga0059261_2298 Length = 249 Score = 90.9 bits (224), Expect = 3e-23 Identities = 78/246 (31%), Positives = 121/246 (49%), Gaps = 24/246 (9%) Query: 100 GIYGYGGMGEQLVKVFSRAGHRVVVTGRNLEKAEGLAKRFKVEWGEPKEVAKEVEWLILA 159 GI G+G G QL R VVVT + A V+ G + A + + ++LA Sbjct: 5 GIIGFGRFG-QLAARHLRDHFSVVVT--DTADVGEAAAAIGVKTGSLADAA-DCDVVMLA 60 Query: 160 VPPKAVPGLVKELAPLMRSGALLSDISSVKKTLVEEVLKVLPEYIEYISLHPLFGPEVEP 219 VP +A+ + +APL+R GAL+ D++SVK +L+ LPE ++ ++ HPLFGP+ Sbjct: 61 VPVQAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVATHPLFGPQSAR 120 Query: 220 ---LGETVVVVPVKSYDYWVRLVQNIFVSMGFEVITSTPEEHDRAMAVTQVLHHF---AL 273 G+ +VV V+ + V S+G V +T EEHDR MA Q L H AL Sbjct: 121 GGLEGQPLVVCAVRGERH--HKVAEFGRSLGLSVSITTAEEHDREMAYVQALTHLIGRAL 178 Query: 274 VSLDEAAKKLSKEYGVDYMRYATRSFKKTLETIQRLKELS-EVIDEIQEMNEYAAHAREE 332 V++ ++L T S++ LE +++ S E+ IQ +N YA + Sbjct: 179 VNIRIPDEELK-----------TNSYQHLLELCGLIRDDSKELFFAIQNLNPYAEEITRQ 227 Query: 333 FLKVAS 338 F+ A+ Sbjct: 228 FIAEAN 233 Lambda K H 0.317 0.135 0.382 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: 169 Number of extensions: 13 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: 348 Length of database: 249 Length adjustment: 26 Effective length of query: 322 Effective length of database: 223 Effective search space: 71806 Effective search space used: 71806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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