Align prephenate dehydrogenase (NADP+) (EC 1.3.1.13) (characterized)
to candidate WP_011305946.1 MBAR_RS04985 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= BRENDA::A0A101IGG2 (310 letters) >NCBI__GCF_000195895.1:WP_011305946.1 Length = 505 Score = 323 bits (829), Expect = 4e-93 Identities = 157/292 (53%), Positives = 214/292 (73%), Gaps = 1/292 (0%) Query: 10 KNRMLIVGGTGGTGSWFAKYFKEHGFLVSIWGPSGKVEVAERLGVKFARDLMAEVAKSDV 69 K ++LI+GGTG G WF ++FK+ G+ V++WG GK E+A +LGV FA DL V +SD+ Sbjct: 19 KTKVLILGGTGEMGQWFTRFFKQKGYEVTVWGKGGKTEIASKLGVPFASDLEKAVPESDI 78 Query: 70 VLLSVPIKETAKVVEEVAPRMRPGSLLMDVTSLKAEPMKAMLRWAPDGVEVLGTHPMFGP 129 +++SVPI T + + E AP+M+ GSLLMD TS+K +P++AM ++AP VE+LGTHPMFGP Sbjct: 79 LIVSVPINVTEETIAEFAPKMKSGSLLMDFTSIKVKPVEAMKKFAPSDVEILGTHPMFGP 138 Query: 130 TIPTIRGQTVILVPAAGRCDEWLLPMEEIFQEDGARVEVLGAEEHDRIMAVVQALTHFAY 189 TIPTIRGQTVILVP GR ++W + E+F+E GA VE+ A EHDR+++VVQ LTHFAY Sbjct: 139 TIPTIRGQTVILVPVKGRSEKWFPVIRELFEEGGAHVEITTAAEHDRLVSVVQGLTHFAY 198 Query: 190 ISIGSTLRSLDFDIAHSRRLMSPVYEIMIDFVGRILAQSPELYSSIQ-ENPEAKRVREAY 248 I+IG+T+ LDFDI SR+ +SPVY IM+DFVGRIL Q+P LY+ IQ ENP V +A+ Sbjct: 199 ITIGTTIDRLDFDIKKSRKFVSPVYAIMLDFVGRILGQNPYLYALIQMENPGVLEVHDAF 258 Query: 249 IEECQRLSKLADTGNSEGFMEAMRSAADHFDEREVALARSDRLISLWIDHRE 300 I EC+ LS+L + E F++ M+SAA + + AL +SD+LI+ I E Sbjct: 259 IRECEELSRLVRAHDEESFVKKMKSAARKYGDTAHALRKSDKLINSRITEYE 310 Lambda K H 0.320 0.135 0.399 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: 415 Number of extensions: 14 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: 310 Length of database: 505 Length adjustment: 31 Effective length of query: 279 Effective length of database: 474 Effective search space: 132246 Effective search space used: 132246 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