PROSITE entry PS50258

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General information about the entry

Entry name [info]	LNR
Accession [info]	PS50258
Entry type [info]	MATRIX
Date [info]	01-JAN-2006 CREATED; 01-OCT-2013 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC50258
Associated ProRule [info]	PRU00525

Name and characterization of the entry

Description [info]

LNR (Lin-12/Notch) repeat profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=42;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=42;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.3577006; R2=0.0056736; TEXT='NScore';
/CUT_OFF: LEVEL=0; SCORE=1700; N_SCORE=12.0; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=1083; N_SCORE=8.5; MODE=1; TEXT='RR';
/DEFAULT: M0=-20; D=-80; I=-80; B1=-200; E1=-200; MI=-255; MD=-255; IM=-255; DM=-255;

...

                A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
/I:         B1=0; BI=-255; BD=-255;
/M: SY='C';  M=-41,146,-58,-45,-51,-56,-59,-58,-55,-49,-49,-28,-70,-62,-62,-43,-28,-46,-80,-61;
/M: SY='P';  M=-14,-53,-10, 28,-56,-35,-38,-28, 16,-45, -6, 40, 49, 11,-16, 17, 27,-36,-61,-49;
/M: SY='P';  M= 24,-55,-13, -5,-41,-44,-38,-13, 14,-13,-38,-15, 46, 29,-14, 16,-35,-28,  1, 39;
/M: SY='P';  M=  6,-13,  4,-15,-51, 16, 20,-16, -4,-14,-41,  1, 46,-10, 11, 22,-18,-23,-59,-27;
/I:         I=-14; MD=-45;
/M: SY='Y';  M=-14,-73,-71,-69,-36,-34,-60,  0,-32, -1,-49,-23,-76,-62,-26,-12,-36,-19,-62, 39; D=-14;
/I:         I=-14; MI=0; MD=-45; IM=0; DM=-45;
/M: SY='C';  M=-25, 65,-24, -1,-26, -9, 16,-50,  4,-47, -8, 12,-19, 40, 23,-12,-31,-40,-43, 60;
/M: SY='C';  M=-14,141,-58,-41,-29,-54,-58,-37,-54,-48,-47,-47, -4,-33,-60,-42,-40,-44,-75,-58;
/M: SY='W';  M= 22,-58,-16, 16,-31,-39, -1,-23,  4,-18, -1, 11,-18,  9, -6,-18,-26,-46,114, -8;
/M: SY='D';  M=-11,-56, 57, 29,-52,-13,-24,-52,  9,-28,  2, -2,-47, -1, 29,  7,-19,-35, 39,-20;
/M: SY='H';  M=-39,-57,-14,-31, 13,-53, 59,-39, 29, 15,-32,-28,-54,-10, 30, -9,-42,-18, 58, 43;
/M: SY='F';  M= 19,-51,-54,-49, 75,-33,-42,  9, -6, -9,-31,-47,-56,-27, -4, -1,-39,-14,-32, 40;
/I:         I=-24; MD=-77;
/M: SY='G';  M= 18,-52,-31,-41,-58, 61, 16,-59, 15,-58,-14, 37,-48,-17,  0,  6,-34,-54,-58,-50; D=-24;
/I:         I=-24; MI=-77; IM=-77; DM=-77;
/M: SY='N';  M=-45,-53, 85,-21,-62,-37,-27,-61,-31,-64,-56, 86,-49,-32,-40,-29,-31,-60,-79,-51;
/I:         I=-24; MD=-77;
/M: SY='G';  M=-30,-57,-28,-48,-60, 83,-16,-66, 14,-50,-52,-17,-48,-26,-34, -4,-24,-60,-55,-32; D=-24;
/I:         I=-24; MI=-77; IM=-77; DM=-77;
/M: SY='H';  M=-21,-55,-46,-24, 23,-54, 50, 22, -3,-28,-10, -6,-53, 35, 24,-18,-32, 25, -6, 27;
/M: SY='C';  M=-41,147,-61,-61,-51,-56,-61,-58,-57,-49,-49,-47,-72,-64,-63,-44,-41,-46,-81,-62;
/M: SY='D';  M=-46,-58,101, -3,-65,-41,  4,-64,-33,-63,-59, 48,-47,-32,-41,-23,-35,-62,-81,-49;
/M: SY='Q';  M=-12,-58,-13, 39,-52,-35,-36,-35, 28,-19,-27,-10, 47, 47,  3,  0,-24,-36,-54, -1;
/I:         I=-22; MI=0; MD=-71; IM=0; DM=-71;
/M: SY='E';  M= 24,-54, 15, 53,-22, 27, -5,-55,-29,-31,-21, -3,-44, 43,-30, -7,-38,-49,-57,-46;
/M: SY='C';  M=-41,147,-61,-61,-51,-56,-61,-58,-57,-49,-49,-47,-72,-64,-63,-44,-41,-46,-81,-62;
/M: SY='N';  M=-37,-48, 25,-33,-10,-33,-15,-54,-16,-59,-28,103,-52,-15,-36,  8,-27,-55,-69,-33;
/M: SY='N';  M=-30,-46,-27,-40,-10,-18,-33,-27,-35,-22,-41, 85,-49,-35,-41, 26, 42,-12,-63,-14;
/M: SY='H';  M= 33,-53,-14, 44,-29,-45, 44,-13,-15,-14,-27,-25, 35,-32,-40, -2,-27,-14,-54, 12;
/M: SY='E';  M= 40,-52, 10, 61,-60, 32,-40,-57, -9,-46,-49, -5,-29,-21,-39,-10,-37,-49,-58,-52;
/M: SY='C';  M=-40,146,-60,-61,-50,-29,-60,-58,-56,-49,-49,-46,-71,-63,-63,-43,-41,-46,-78,-38;
/M: SY='G';  M=-40,-54, 20,  2,-18, 41, -6,-40, -8, 36,-32, 30,-52, 15,-15,-31,-41,-43,-56,-42;
/M: SY='W';  M=-54,-62,-66,-59, 80,-58,-26,-38,-52,-32,-37,-41,-62,-54,-39,-54,-53,-45,129, 63;
/M: SY='D';  M=-47,-61,111,-11,-68,-44,-33,-66,-34,-64,-63,-15,-47,-34,-43,-35,-37,-63,-83,-50;
/M: SY='G';  M=-13,-54,-13,-49,-61, 86,-45,-65,-21,-63,-53, 33,-48,-42,-32,-19,-43,-49,-56,-55;
/M: SY='G';  M=-31,-54,-49,-54, 44, 68, -2,-43,-36, 12, 17,-15,-53,-47,-22,-31,-38,-44,-44, -5;
/M: SY='D';  M=-47,-61,107, 24,-67,-45,-33,-66,-33,-63,-62,-16,-45,-31,-42,-35,-37,-62,-80,-50;
/M: SY='C';  M=-41,147,-61,-61,-51,-56,-61,-58,-57,-49,-49,-47,-72,-64,-63,-44,-41,-46,-81,-62;
/I:         E1=0; IE=-255; DE=-255;
/M: SY='Q';  M=  6,-51,  1, 23,-54,-23,-21,-34,  4,-35,-18, -1,-30, 54,-14, 49,  4,-39,-57,-18;
/M: SY='N';  M=-20,-52, -9,  5,-26, 22,-39,-31, 16, 22,-36, 35, -1,  2,  2, 13, -7,-42,-57,-44;
/M: SY='N';  M=-19,-12, 24, 15,-54, 25, 24,-43, 17,-47,-35, 51,  0, -8,-36,  2,  0,-22,-62,-19;
/M: SY='S';  M=-28,-11,-25,  3,  6,-16, -4, -3, -9,  1, -1, -4,  4, 13,-17, 21, 20, 18, 10,-16;
/M: SY='P';  M=-12,-56,  1, 11, -1, 20,-12,-34,  8,-51, -8, 30, 47, 17, -1, -1,-16,-25,-55,-20;
/I:         I=-19; E1=0; MD=-61;
/M: SY='D';  M=  0, 15, 42, 16,-47,-34, 14,-42,-31,-54,-19,-11, 18, 19, -4,-16,  5,-12,-67,-14; D=-19;
/I:         I=-19; E1=0; MI=0; MD=-61; IM=0; DM=-61;
/M: SY='C';  M=-32, 88,-34,-16, -4,-29,-46,-24,  2,-20,-10,-13, 66,-11,  2,  1,-15,-34,-60,-48;
/I:         E1=0; IE=-255; DE=-255;
/M: SY='W';  M=-16,-32,-11,-11,-38,-33,-44,  1,  6, -6,-40, 44, 19,-29, -8, -5, -9,-36,109, -7;
/M: SY='P';  M= 25, 21,-26, -8,-17,-23,-42,-16, 23, -7,-26,-42, 38, -4,-16,-10,-22, -4, 19, 33;
/M: SY='N';  M=-17, 28, 20,  3,-44,  6,  2, -9, 16,-12,-40, 57,-27,-19, -9,-22,-30,-24,  6, 17;
/I:         E1=0; IE=-255; DE=-255;

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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2024_04 which contains 571'864 sequence entries.

Total number of hits	60 in 21 different sequences
Number of true positive hits	60 in 21 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	0
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	100.00 %

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	3
Matrix type [info]	protein_domain
Scaling database [info]	window20
Author [info]	V_Lesaux
Feature key [info]	REPEAT
Feature description [info]	LNR
Version [info]	3

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

21 sequences

GLP1_CAEEL  (P13508), GNPTA_DANRE (Q5RGJ8), GNPTA_HUMAN (Q3T906),

GNPTA_MOUSE (Q69ZN6), LIN12_CAEEL (P14585), NOTC1_CRIGR (G3I6Z6), 
NOTC1_DANRE (P46530), NOTC1_HUMAN (P46531), NOTC1_MOUSE (Q01705), 
NOTC1_RAT   (Q07008), NOTC1_XENLA (P21783), NOTC1_XENTR (A2RUV0), 
NOTC2_HUMAN (Q04721), NOTC2_MOUSE (O35516), NOTC2_RAT   (Q9QW30), 
NOTC3_HUMAN (Q9UM47), NOTC3_MOUSE (Q61982), NOTC3_RAT   (Q9R172), 
NOTC4_HUMAN (Q99466), NOTC4_MOUSE (P31695), NOTCH_DROME (P07207)

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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

PDB
[Detailed view]

12 PDB

1PB5; 2OO4; 3ETO; 3I08; 3L95; 4ZLP; 5CZV; 5CZX; 6XSW; 7ABV; 7S05; 7S06