Entry: PS51120

General information about the entry
Entry name LDLRB
Accession number PS51120
Entry type MATRIX
Date MAY-2005 (CREATED); MAY-2005 (DATA UPDATE); MAR-2013 (INFO UPDATE).
PROSITE Documentation PDOC51120
Associated ProRule PRU00461
Name and characterization of the entry
DescriptionLDL-receptor class B (LDLRB) repeat profile.
Matrix / Profile 
/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=43;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=43;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=1.7791114; R2=0.0232049; TEXT='-LogE';
/CUT_OFF: LEVEL=0; SCORE=381; N_SCORE=10.6; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=109; N_SCORE=4.3; MODE=1; TEXT='R?';
/DEFAULT: M0=-8; D=-100; I=-100; B1=-100; E1=-100; MI=-105; MD=-105; IM=-105; DM=-105;

                A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y   Z
/I:         B1=0; BI=-105; BD=-105;
/M: SY='D'; M= -9,  7,-28,  9,  3,-29,  8, -5,-31,  5,-27,-17,  9,-13,  4,  6,  0,-10,-26,-26,-18,  3;
/M: SY='R'; M=-13, -7,-24,-10, -3, -9,-21, -2,-13,  8, -9, -3, -2,-19,  1, 16, -8, -5,-12,-16,  2, -3;
/M: SY='I'; M= -8,-29,-22,-33,-25,  5,-32,-24, 31,-27, 29, 20,-25,-24,-20,-23,-22, -8, 22,-21, -2,-24;
/M: SY='Y'; M=-19,-23,-21,-26,-23, 38,-30,  5, -1,-17,  2, -1,-21,-30,-19,-14,-20,-11, -7, 23, 58,-23;
/M: SY='W'; M=-19,-36,-42,-38,-28, 21,-23,-24,-13,-20,-12,-13,-34,-30,-21,-18,-34,-24,-22,110, 32,-21;
/M: SY='T'; M=  8,-11,-10,-17,-14,-11,-16,-21,  1,-15, -5, -4, -8,-16,-13,-16,  9, 17,  8,-29,-13,-14;
/M: SY='D'; M=-17, 38,-27, 52, 17,-34,-11,  1,-34, -1,-27,-25, 17,-11,  1, -9,  1, -7,-26,-38,-18,  9;
/M: SY='A'; M=  1,-12,-24,-16,-11,-10,-12,-13, -9,-10,-11, -7, -9,-16, -6,-10, -3, -4, -8,  1, -3, -9;
/M: SY='N'; M= -5, -3,-24, -4, -4,-17, -1, -7,-19, -1,-17,-10,  1,-16, -4, -1,  0, -4,-15,-22,-11, -5;
/I:         I=-17; MD=-17;
/M: SY='T'; M= -6, -4,-21, -6, -1,-11,-17, -7,-11, -3, -5, -4, -3,-17,  0,  0, -2,  2,-10,-23, -7, -1; D=-17;
/I:         I=-17; MD=-17;
/M: SY='D'; M= -9,  8,-26, 10,  7,-25, -7,  2,-25,  4,-20,-12,  7,-10,  5,  4,  0, -8,-22,-28,-13,  5; D=-17;
/I:         I=-17; MI=0; MD=-17; IM=0; DM=-17;
/M: SY='R'; M= -5, -8,-18,-11, -7,-14,-14,-10,-12,  3,-11, -4, -5,-18, -4,  7, -2,  0, -6,-22, -8, -7;
/M: SY='I'; M= -8,-28,-27,-36,-27,  1,-34,-26, 39,-28, 20, 18,-21,-22,-20,-27,-19, -9, 25,-19,  0,-27;
/M: SY='E'; M= -8, -1,-23,  1, 13,-14,-14, -3,-20, -1,-15,-12, -1,-13,  3, -1,  0, -5,-18,-20, -7,  7;
/M: SY='R'; M= -6,-12,-14,-14, -9,-12,-19, -9,-10,  2,-12, -5, -7,-20, -5, 14, -2, -2, -2,-24, -8, -9;
/M: SY='A'; M= 13,-11, -4,-18,-14,-13,-13,-17, -2,-14, -7, -3, -8,-17,-12,-17,  3,  1,  4,-28,-15,-13;
/M: SY='N'; M= -9,  9,-23,  8,  2,-18,-11,  0,-23,  4,-20,-13, 10,-16,  0,  4,  0, -4,-20,-24, -9,  0;
/M: SY='L'; M=-10,-21,-24,-23,-15,  3,-26,-12,  8,-12, 13, 12,-19,-18,-11,-11,-18, -8,  2,-11,  6,-14;
/M: SY='D'; M=-13, 30,-26, 36, 10,-28, -8,  2,-30, -1,-25,-21, 19,-12,  0, -6,  2, -5,-25,-33,-16,  5;
/M: SY='G'; M= -1, -5,-27, -5,-13,-28, 49,-17,-35,-15,-28,-19,  2,-17,-15,-16,  3,-13,-26,-23,-27,-14;
/I:         I=-18; MI=0; MD=-18; IM=0; DM=-18;
/M: SY='S'; M= -1, -1,-17, -3,  0,-16, -9, -6,-14, -4,-13, -9,  1,-12,  0, -3,  8,  8, -9,-26,-12,  0; D=-18;
/I:         I=-18; DM=-18;
/M: SY='N'; M= -8,  8,-24,  7,  3,-20, -4,  5,-23, -2,-21,-14, 11,-13,  1, -2,  3, -3,-21,-27,-11,  1;
/M: SY='R'; M=-11, -6,-20, -8, -2,-16,-18, -3,-19,  6,-15, -9,  0,-15,  1, 22, -5, -6,-14,-22, -9, -3;
/M: SY='R'; M= -7, -6,-24, -6,  4,-19,-19, -7,-14,  7,-13, -6, -4,-12,  4, 10, -3, -2, -9,-25,-11,  2;
/M: SY='V'; M= -4,-13,-18,-17,-13, -9,-24,-18,  7,-11, -2,  2,-12,-16,-11,-11, -2,  9, 12,-26, -8,-13;
/M: SY='L'; M= -7,-25,-20,-28,-22,  2,-29,-21, 23,-22, 24, 14,-22,-26,-19,-18,-18, -7, 20,-23, -4,-22;
/M: SY='I'; M= -4,-25,-19,-29,-23,  4,-28,-21, 20,-22, 16, 10,-22,-24,-20,-19,-15, -6, 19,-18, -1,-23;
/M: SY='N'; M= -3,  3,-20,  0,  1,-18,-12, -4,-17,  0,-17,-10,  5,-15,  3,  0,  5,  1,-14,-26,-10,  2;
/M: SY='N'; M= -5,  4,-22,  3,  3,-21, -6, -3,-20, -2,-20,-13,  8,-12,  2, -3,  7,  1,-16,-29,-14,  2;
/I:         I=-21; MD=-22;
/M: SY='N'; M= -6,  4,-21,  4, -1,-20,  1, -2,-21, -3,-18,-11,  6,-11, -1, -4,  3, -3,-18,-24,-12, -2; D=-21;
/I:         I=-21; MI=0; MD=-22; IM=0; DM=-22;
/M: SY='L'; M= -7,-17,-21,-19,-14, -2,-23,-16, 10,-18, 14,  7,-14,-20,-14,-15,-13, -5,  8,-24, -6,-15;
/M:         M= -5, -3,-24, -2, -1,-18, -7, -4,-16, -5,-14, -8, -2,-11, -2, -5, -2, -5,-13,-24,-10, -3;
/M: SY='H'; M= -9, -8,-25,-11, -6,-11,-15,  3,-12, -6,-10, -4, -3,-17,  0, -2, -6, -5,-13,-11, -1, -4;
/M: SY='P'; M= -5,-18,-30,-13, -6,-21,-20,-20, -8,-12,-17,-11,-17, 47,-12,-18, -7, -5,-12,-29,-22,-12;
/M: SY='H'; M=-10, -1,-23, -3,  1, -6,-17,  6,-16, -3,-13, -7,  2,-17, -2,  2, -4, -6,-14,-21,  0, -2;
/M: SY='G'; M=  7, -3,-21, -4, -9,-25, 21,-14,-25,-13,-22,-16,  0, -9,-10,-16,  5, -7,-18,-26,-23,-10;
/M: SY='L'; M=-10,-28,-23,-33,-24,  9,-32,-22, 28,-26, 29, 20,-24,-25,-19,-21,-23, -9, 18,-18,  2,-23;
/M: SY='A'; M= 21, -9,-12,-15,-11,-16, -8,-19, -7,-10,-10, -8, -9,-14,-11,-15,  7,  6,  3,-24,-16,-11;
/M: SY='V'; M= -6,-27,-18,-30,-25,  7,-30,-23, 24,-23, 17, 12,-24,-27,-23,-21,-16, -4, 26,-20,  1,-25;
/M: SY='D'; M=-16, 21,-25, 30,  4,-16,-16,  5,-25, -6,-19,-17,  7,-16, -6,-10, -4, -8,-19,-26, -3, -1;
/M: SY='W'; M=-11,-16,-34,-14, -6,-10,-17, -1,-14,-12,-14,-10,-14, -1, -7,-13,-15,-14,-19, 14,  4, -8;
/M:         M= -7,-10,-22,-11, -8, -7,-20,-11, -3,-10, -3, -2, -9,-14, -9,-11, -8, -5, -3,-20, -3, -9;
/M: SY='S'; M= -3, -1,-22, -3,  0,-16, -5, -2,-19, -3,-17,-11,  2,-15, -1, -3,  4, -1,-16,-21, -8, -1;
/I:         E1=0; IE=-105; DE=-105;
Numerical results
  • UniProtKB/Swiss-Prot release number: 2013_05, total number of sequence entries in that release: 540052.
  • Total number of hits in UniProtKB/Swiss-Prot: 683 hits in 62 different sequences
  • Number of hits on proteins that are known to belong to the set under consideration: 683 hits in 62 different sequences
  • Number of hits on proteins that could potentially belong to the set under consideration: 0 hits in 0 different sequences
  • Number of false hits (on unrelated proteins): 0 hits in 0 different sequences
  • Number of known missed hits: 5
  • Number of partial sequences which belong to the set under consideration, but which are not hit by the pattern or profile because they are partial (fragment) sequences: 0
  • Precision (true hits / (true hits + false positives)): 100.00 %
  • Recall (true hits / (true hits + false negatives)): 99.27 %
Comments
  • MATRIX_TYPE: protein_domain
  • Scaling database: UniProtKB/Swiss-Prot: reversed
  • Matrix author: N_Hulo
  • Taxonomic range: Eukaryotes
  • Maximum known number of repetitions of the pattern in a single protein: 37
  • FT_KEY: REPEAT
  • FT_DESC: LDL-receptor class B
  • VERSION: 1
Cross-references
UniProtKB/Swiss-Prot True positive hits:
CUE_DROAN   (B3M8G0), CUE_DROER   (B3NBB6), CUE_DROGR   (B4IXJ2), 
CUE_DROME   (Q95RU0), CUE_DROMO   (B4L8V5), CUE_DROPE   (B4H1F5), 
CUE_DROPS   (Q29FE9), CUE_DROSE   (B4HVU2), CUE_DROSI   (B4QMF4), 
CUE_DROVI   (B4LCX4), CUE_DROWI   (B4MLE8), CUE_DROYA   (B4PD96), 
EGF_CANFA   (Q9BEA0), EGF_FELCA   (Q95ND4), EGF_HUMAN   (P01133), 
EGF_MOUSE   (P01132), EGF_PIG     (Q00968), EGF_RAT     (P07522), 
LDLR1_XENLA (Q99087), LDLR2_XENLA (Q99088), LDLR_CRIGR  (P35950), 
LDLR_HUMAN  (P01130), LDLR_MOUSE  (P35951), LDLR_PIG    (Q28832), 
LDLR_RABIT  (P20063), LDLR_RAT    (P35952), LRP1B_HUMAN (Q9NZR2), 
LRP1B_MOUSE (Q9JI18), LRP1_CHICK  (P98157), LRP1_HUMAN  (Q07954), 
LRP1_MOUSE  (Q91ZX7), LRP2_HUMAN  (P98164), LRP2_MOUSE  (A2ARV4), 
LRP2_RAT    (P98158), LRP4_HUMAN  (O75096), LRP4_MOUSE  (Q8VI56), 
LRP4_RAT    (Q9QYP1), LRP5L_HUMAN (A4QPB2), LRP5_HUMAN  (O75197), 
LRP5_MOUSE  (Q91VN0), LRP6_HUMAN  (O75581), LRP6_MOUSE  (O88572), 
LRP8_CHICK  (Q98931), LRP8_HUMAN  (Q14114), LRP8_MOUSE  (Q924X6), 
LRP_CAEEL   (Q04833), NID1_HUMAN  (P14543), NID1_MOUSE  (P10493), 
NID2_HUMAN  (Q14112), NID2_MOUSE  (O88322), NID2_RAT    (B5DFC9), 
SORL_CHICK  (Q98930), SORL_HUMAN  (Q92673), SORL_MOUSE  (O88307), 
SORL_RABIT  (Q95209), VGR_SOLIN   (Q6X0I2), VLDLR_CHICK (P98165), 
VLDLR_HUMAN (P98155), VLDLR_MOUSE (P98156), VLDLR_RABIT (P35953), 
VLDLR_RAT   (P98166), YL_DROME    (P98163)
False negative hits (sequences which belong to the set under consideration, but which have not been picked up by the pattern or profile):
7LESS_DROME (P13368), 7LESS_DROVI (P20806), CUE_AEDAE   (Q16YE7), 
CUE_ANOGA   (Q7QIQ6), CUE_CULQU   (B0WH58)
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]		 1IJQ; 1LPX; 1LRX; 1N7D; 1NDX; 1NPE; 3M0C; 3P5B; 3P5C; 3S2K; 3S8V; 3S8Z; 3S94; 3SOB; 3SOQ; 3SOV; 3V64; 3V65; 4A0P; 4DG6;

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