Align prephenate dehydrogenase (NADP+) (EC 1.3.1.13) (characterized)
to candidate WP_013645633.1 METBO_RS10195 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= BRENDA::A8AAX2 (348 letters) >NCBI__GCF_000191585.1:WP_013645633.1 Length = 435 Score = 122 bits (306), Expect = 2e-32 Identities = 75/242 (30%), Positives = 126/242 (52%), Gaps = 3/242 (1%) Query: 101 IYGYGGMGEQLVKVFSRAGHRVVVTGRNLEKAEGLAKRFKVEWGEPKEVAKEV-EWLILA 159 I G G+G + K + G V++TGRN+ E ++K+ + +A E + +I++ Sbjct: 7 IGGTRGLGRWIAKFLAEKGFDVLITGRNVTDGELVSKKIGTGYTNNNSLAAETSDVVIIS 66 Query: 160 VPPKAVPGLVKELAPLMRSGALLSDISSVKKTLVEEVLKVLPEYIEYISLHPLFGPEVEP 219 VP A P ++KELAPLM+ G+LL D++SVK+ + + E +E + HP+FGP + Sbjct: 67 VPIHATPNIIKELAPLMKPGSLLMDVTSVKEESSHLMEQYAAEGVEVVPSHPMFGPRIRS 126 Query: 220 LGETVVVVPVKSYDYWVRLVQNIFVSMGFEVITSTPEEHDRAMAVTQVLHHFALVSLDEA 279 L VVV+ W V +I +TPE HDR M++ Q L HFA VS+ Sbjct: 127 LDGQVVVLTPSVDGSWYTKVYKFLEHENTRIIVTTPEIHDRMMSIVQGLTHFAYVSIAAT 186 Query: 280 AKKLSKEYGVDYMRYATRSFKKTLETIQRLKELSE-VIDEIQEMNEYAAHAREEFLKVAS 338 +L + + ++A+ + L+TI R+ + ++ IQ N+Y A E F + + Sbjct: 187 IDRLDIDI-KESRKFASPIYNLMLDTIARITAQNPYLVYSIQTSNKYIKDAHETFNETFN 245 Query: 339 QM 340 ++ Sbjct: 246 EL 247 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: 280 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 348 Length of database: 435 Length adjustment: 30 Effective length of query: 318 Effective length of database: 405 Effective search space: 128790 Effective search space used: 128790 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: 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