We are deeply saddened by the passing of Amos Bairoch (1957–2025), the creator of PROSITE. We wish to dedicate our latest paper, published shortly before his death, to him. He will always be a source of inspiration to us.
Our deepest condolences go out to his family and friends, and to all those who had the privilege of working with him. Rest in peace, Amos. Your work will live on long after you are gone.

PROSITE entry PS50258

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PURL: https://purl.expasy.org/prosite/signature/PS50258

Direct ScanProsite submission

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 2025_04 which contains 573'661 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]

13 PDB

pdb_00001pb5; pdb_00002oo4; pdb_00003eto; pdb_00003i08; pdb_00003l95; pdb_00004zlp; pdb_00005czv; pdb_00005czx; pdb_00006xsw; pdb_00007abv; pdb_00007s05; pdb_00007s06; pdb_00009bgf
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