Entry: PS50258

Forthcoming changes to the profile format
General information about the entry

Entry name [info] LNR
Accession [info] PS50258
Entry type [info] MATRIX
Date [info] JAN-2006 (CREATED); OCT-2013 (DATA UPDATE); MAR-2014 (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';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=3555.54134; R2=13.51166; TEXT='HScore';
/CUT_OFF: LEVEL=0; SCORE=1700; N_SCORE=12.0; H_SCORE=24134; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=1083; N_SCORE=8.5; H_SCORE=18189; 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 2014_04 which contains 544'996 sequence entries.


Total number of hits 61 in 21 different sequences
Number of true positive hits 61 in 21 different sequences
Number of 'unknown' hits
Number of false positive hits
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]

Matrix type [info] protein_domain
Scaling database [info] window20
Author [info] V_Lesaux
Taxonomic range [info] Eukaryotes
Maximum number of repetitions [info] 4
Feature key [info] REPEAT
Feature description [info] LNR
Version [info] 2

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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PDB
[Detailed view]
5 PDB

1PB5; 2OO4; 3ETO; 3I08; 3L95

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