Summary: PDDEXK-like family of unknown function
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PDDEXK-like family of unknown function Provide feedback
PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix . The family is not in general fused with any other domains, so its function cannot be predicted .
Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K; , BMC Struct Biol. 2007;7:40.: Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. PUBMED:17584917 EPMC:17584917
This tab holds annotation information from the InterPro database.
InterPro entry IPR006502
PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [PUBMED:17584917]. The family is not in general fused with any other domains, so its function cannot be predicted [PUBMED:22936940].
This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
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This example describes an architecture with one
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We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_4111 (release 7.5)|
|Author:||Waterfield DI, Finn RD|
|Number in seed:||102|
|Number in full:||801|
|Average length of the domain:||192.80 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||63.40 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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