Align arogenate dehydrogenase (NADP+) (EC 1.3.1.78) (characterized)
to candidate WP_041456419.1 AVA_RS22330 prephenate/arogenate dehydrogenase
Query= BRENDA::P73906 (279 letters) >NCBI__GCF_000204075.1:WP_041456419.1 Length = 281 Score = 325 bits (833), Expect = 7e-94 Identities = 158/279 (56%), Positives = 201/279 (72%) Query: 1 MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKI 60 M+IG++GLGLIG SL DLR +GH+++GVSR+QSTCE AV VDEA D+SLL A++ Sbjct: 1 MQIGILGLGLIGGSLGYDLRSQGHHVLGVSRKQSTCETAVSLGSVDEASVDISLLTAAEV 60 Query: 61 IFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQ 120 +F+CTPI LI+P +E+LI HL + +VTDV SVK I E S LW F+GGHPMAGT Sbjct: 61 VFICTPIGLIVPQVEQLINHLPQSTVVTDVGSVKAPIVEAISPLWENFVGGHPMAGTTDS 120 Query: 121 GIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHL 180 GI+ A+ NLF + PYVLTP T +A + ++ LG KIY C P HD+AV+WISHL Sbjct: 121 GIESAQRNLFAHRPYVLTPEPTTPKGAIALVEEIVRSLGAKIYYCQPEQHDRAVSWISHL 180 Query: 181 PVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKS 240 PVMVS++LI AC E D ++L+LAQNLASSGFRDTSRVGGGNPELG MMA YN++ALL S Sbjct: 181 PVMVSSSLIAACISETDPEVLQLAQNLASSGFRDTSRVGGGNPELGVMMAQYNRQALLGS 240 Query: 241 LQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYVE 279 L YR++LD++I L+ + W L L T R +V+ Sbjct: 241 LHQYRRNLDEVIALVEQENWSALETKLHTTQQARPNFVD 279 Lambda K H 0.318 0.135 0.396 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: 268 Number of extensions: 7 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: 279 Length of database: 281 Length adjustment: 26 Effective length of query: 253 Effective length of database: 255 Effective search space: 64515 Effective search space used: 64515 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 (21.7 bits) S2: 47 (22.7 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