PROSITE entry PS51375

View entry in original PROSITE format
View entry in raw text format (no links)
View entry auxiliary file in raw text format (no links)
PURL: https://purl.expasy.org/prosite/signature/PS51375

Direct ScanProsite submission

General information about the entry

Entry name [info]	PPR
Accession [info]	PS51375
Entry type [info]	MATRIX
Date [info]	01-APR-2008 CREATED; 01-OCT-2013 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51375
Associated ProRule [info]	PRU00708

Name and characterization of the entry

Description [info]

Pentatricopeptide (PPR) repeat profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=35;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=35;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=0.2521676; R2=0.0109613; TEXT='NScore';
/CUT_OFF: LEVEL=0; SCORE=753; N_SCORE=8.5; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=434; N_SCORE=5.0; MODE=1; TEXT='R?';
/DEFAULT: M0=-9; I0=-9; D=-200; I=-200; B1=-200; E1=-200; MI=-105; MD=-105; IM=-105; DM=-105;

...

                A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
/I:         B1=0; BI=-105; BD=-105;
/M: SY='D';  M=-17,-24, 64,  4,-53, -9, -8,-51, -7,-49,-41, 50,-17,-10,-14, 22, 13,-43,-63,-41;
/M: SY='P';  M=  8,-18,-13,  9,-16,-20,-12,  7, -6,  1, -2, -8, 16, -4, -5, 12, 11, 15,-41,-25;
/M: SY='V';  M= -1,-21, -8,  2, 16,-22,  6,  7, -3, -9, -4,-12,-16, -6, -3,  6,  2, 21,-12, 17;
/M: SY='T';  M= 13, -2,-24,-24,-19,-29, -9,  3,-26, -1,  7,-13,-17,-24,-32, 27, 53, 10,-50,-26;
/M: SY='Y';  M=-30, 23,-65,-54, 50,-58, 11,-16,-47, -2, -1,-45,-60,-38,-42,-33,-33,-18, 79, 86;
/M: SY='N';  M= -3, -8,  7,-10,-41, -2,  4,-27, -8,-31,-20, 65,-33,-11, -4, 23, 23,-19,-42,-33;
/M: SY='S';  M= 20,  7,-24,-18,-20,-22,-17, 11, -9, -1,  6, -8,-20,-13,-16, 26, 26, 10,-30,-22;
/M: SY='M';  M=-15,-33,-69,-53,  6,-64,-46, 30,-46, 49, 57,-58,-55,-37,-39,-39,-24, 27,-20,-19;
/M: SY='I';  M=-12,-24,-69,-55,  2,-62,-57, 52,-50, 37, 42,-59,-57,-45,-53,-29,-18, 32,-48,-25;
/M: SY='N';  M= -3,-12, 22, 10,-36, -8, 23,-37, 20,-32,-24, 26,-29, 13, 25, 21, -1,-28,-37,-13;
/M: SY='G';  M= 32, 23,-33,-22,-28, 39,-15,-13,-18,-11,  3,-15,-37,-22,-17, 16, -4, -6,-30,-20;
/M: SY='Y';  M=-25, 51,-65,-56, 42,-64,  9, -6,-48, 34, 10,-44,-62,-37,-47,-30,-31,-14,  8, 67;
/M: SY='C';  M= 22, 74,-44,-30, -7,  9,-34, -5,-26, -6, -7,-24,-42,-27,-26, 15, -2,  7,-30,-20;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='R';  M= -6,-40,  2, 15,-47,-20,  7,-38, 46,-33,-15, 11,-38, 26, 48,  4,-12,-28,-36,-31;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='N';  M= 16, 15, -6, 10,-20,-10, 13,-17,  6, -5,  1, 19,-37,  7,  1, 15,  0,-10,-35,-21;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='G';  M= -9,-30, -2, -5,-53, 68, -8,-65, 13,-55,-36, 14,-41, -6, 16, -3,-27,-56,-47,-50;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='R';  M=-20,-23, 26, 13,-17,-33,  9,-32, 27, -6, 15, 19,-35, 22, 37, -3,-20,-34,-18,-13;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='W';  M= -9,-23,-43,-32, 28,-34,  0, 14,-29, 20, 18,-33, 16,-25,-33,-15, -1, 19, 42, 19;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='D';  M= -5,-47, 45, 40,-43,-11,  5,-35, 15,-33,-26,  9,-16, 12, 11,  7, -8,-27,-38,-31;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='E';  M= -3,-41, 28, 48,-33,-14, -2,-29, 25,-16, -7, -4,-29, 14, 10,  0, -9,-26,-46,-27;
/I:         I=-61; MI=0; MD=-32; IM=0; DM=-32;
/M: SY='A';  M= 61,  0,-44,-29,-32, 15,-41,-10,-28,-19,  5,-36,-27,-29,-38, 12, -4, 12,-59,-42;
/M: SY='W';  M=-12,-11,-14, 16, 10,-43, -2,  9,  2, 20, 20,-20,-43, -4,  7,-16,-15,  7, 26,  6;
/M: SY='E';  M=  1,-26, 16, 34,-33,-14,  4,-37, 26,-28,-16,  4,-35, 27, 27, 10,-10,-26, -2,-21;
/M: SY='L';  M=-15,-10,-62,-48, 20,-61,-34, 31,-45, 40, 28,-53,-56,-36,-46,-32, -6, 36, -2, -2;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='F';  M=-30,-22,-62,-48, 62,-62, 22,  8,-35, 26, 13,-51,-58,-33,-21,-39,-30,  6, 40, 46;
/I:         I=-63; MI=0; MD=-33; IM=0; DM=-33;
/M: SY='E';  M= -7,-14, 27, 31,-34,-10, 12,-32, 23,-26,-14, 12,-34, 18, 26,  5,-10,-24,-32,-20;
/M: SY='E';  M=-12,-34, 16, 43,-28,-25,  4,-28, 22,-16, -3, -1,-39, 27, 26,  1,-10,-23,-13, -9;
/M: SY='M';  M= -7,-21,-66,-42, -1,-57,-40, 22,-36, 30, 95,-50,-55,-24,-37,-25,-18, 11,-13,-23;
/M: SY='K';  M=-12,-21,-15, 12,-21,-28, -6,  5, 26,  7, 10,-14, -7, 13, 24, -6,-10,  7,-27,-24;
/M: SY='E';  M=  1,-28, 16, 32,-33,-13, -3,-36, 29,-32,-19,  9,-30, 19, 31, 15, -5,-26,-39,-31;
/M: SY='R';  M= -2,-13,  3, 12, -9,-18, 11,-26, 24,-11,  5, 13,-29,  9, 25, 17, -5,-25, -8,-11;
/I:         E1=-50; MI=-40; IE=-105; DE=-105;
/M: SY='G';  M=-11,-39,  7, -5,-56, 71,-11,-66,  1,-62,-51, 20,-30,-12, -2,  0,-21,-55,-56,-50;
/M: SY='C';  M=-18, 37,-47,-34, 26,-42, -2, 29,-32, 20, 14,-32,-34,-27,-27,-20,-16, 26,  4, 13;
/M: SY='K';  M= -2,-12, -5, 18,-19,-21, -5, -9, 21,-12, -9, -6, 14, 11, 17,  7,  3,  5,-39,-17;
/M: SY='P';  M=  0,-23,-29,-22,-21,-35,-30,-10,-12,  1, -3,-27, 90,-19,-18, -3,-13, -5,-42,-36;
/I:         E1=0; IE=-105; DE=-105;

» more

Post-processing [info]

COMPETES_SEQ_WITH

PS50005

Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2025_03 which contains 573'661 sequence entries.

Total number of hits	5'780 in 512 different sequences
Number of true positive hits	5'779 in 511 different sequences
Number of 'unknown' hits	0
Number of false positive hits	1
Number of false negative sequences	22
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	99.98 %
Recall (true positives / (true positives + false negatives))	99.62 %

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	27
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	N_Hulo
Feature key [info]	REPEAT
Feature description [info]	PPR
Version [info]	4

Cross-references [info]

UniProtKB/Swiss-Prot True positive sequences	511 sequences AEP3_CANGA (Q6FKT1), AEP3_KLULA (Q6CIF3), ATP4_MAIZE (B4F8Z1), » more Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits: [Clustal format, color, condensed view] [Clustal format, color] [Clustal format, plain text] [Fasta format] Retrieve the sequence logo from the alignment
UniProtKB/Swiss-Prot False negative sequences	22 sequences AEP3_EREGS (Q750L0), AEP3_YEAST (Q12089), ATP18_TRYBB (P0DPG4), » more
UniProtKB/Swiss-Prot False positive sequences	1 sequence ATPB1_PSYIN (A1SS55)
PDB [Detailed view]	87 PDB 3J9M; 3JD5; 4G23; 4G24; 4G25; 4G26; 4LEU; 4M57; 4M59; 4OE1; 5DIZ; 5FT9; » more