PROSITE entry PS50068

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General information about the entry

Entry name [info]	LDLRA_2
Accession [info]	PS50068
Entry type [info]	MATRIX
Date [info]	01-NOV-1997 CREATED; 26-FEB-2020 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC00929
Associated ProRule [info]	PRU00124

Name and characterization of the entry

Description [info]

LDL-receptor class A (LDLRA) domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=37;
/DISJOINT: DEFINITION=PROTECT; N1=4; N2=35;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-1.4750000; R2=0.0125000; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=1183.4930420; R2=3.1229405; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=798; H_SCORE=3676; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=638; H_SCORE=3176; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: D=-20; I=-20; B1=-30; E1=-30; MI=-105; MD=-105; IM=-105; DM=-105; MM=1; M0=-1;

...

                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='T';  M= -4, -2,-21, -4,  1,-17,-13, -9,-15, -2,-14, -9, -1, -9,  0, -2,  3,  5,-11,-27,-13,  0;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='S';  M= -4, -1,-25,  0,  2,-22, -8, -6,-20, -2,-20,-13,  0,  1,  1, -4,  3, -2,-17,-28,-16,  0;
/I:         II=-7; MI=-7; IM=-7; MD=-15; DM=-15; I=0,0,-15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
/M: SY='P';  M= -1, -5,-21, -3,  3,-22,-10,-12,-18, -4,-19,-13, -5, 11, -2, -8,  1, -3,-16,-27,-18, -1; D=-3;
/I:         DM=-17;
/M: SY='N';  M= -7,  8,-23,  8,  1,-21,  0, -3,-24, -5,-20,-15,  9,-14, -3, -5,  4, -1,-19,-28,-13, -2;
/I:         DM=-17;
/M: SY='E';  M= -9,  0,-27,  3, 19,-22,-15,  3,-22,  4,-17, -9, -1,-10, 16,  2, -2, -8,-22,-21, -9, 17;
/M: SY='F';  M=-17,-27,-22,-34,-26, 58,-29,-12,  0,-24,  7,  1,-18,-28,-31,-16,-18,-10,  0,  7, 27,-26;
/M: SY='Q';  M= -6, -3,-25, -4,  6,-24,-17,  0,-19,  9,-17, -6, -2,-10, 15, 13, -1, -3,-17,-24,-10,  9;
/M: SY='C';  M=-10,-20,119,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-48,-30,-30;
/M: SY='S';  M= -2, -1,-24, -1,  0,-22, -3, -7,-22,  0,-20,-13,  0, -6, -2, -1,  2, -4,-17,-26,-15, -2;
/M: SY='N';  M= -5, 18,-20, 14,  1,-22, -2, -1,-22, -4,-24,-17, 22,-15, -2, -6, 10,  1,-20,-33,-17, -1;
/I:         II=-4; MI=-5; IM=-5; MD=-15; DM=-15; I=0,0,-20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
/M: SY='G';  M= -5, -4,-26, -5, -8,-23, 25, -8,-28, -8,-22,-14,  2,-16, -8, -7,  0,-11,-23,-23,-18, -9; D=-2;
/I:         DM=-15;
/M: SY='R';  M= -8, -5,-24, -6,  4,-19,-18, -2,-16,  8,-14, -6, -2,-14,  8, 13, -1, -2,-13,-24, -8,  5;
/M: SY='C';  M=-10,-20,118,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-29,-10,-10,-10,-49,-29,-30;
/M: SY='I';  M= -8,-29,-25,-36,-28,  2,-36,-27, 40,-27, 20, 17,-22,-23,-21,-26,-19, -8, 29,-20,  0,-28;
/M: SY='P';  M= -3, -4,-28, -1,  2,-24,-13, -9,-19, -5,-23,-15, -4, 27, -3,-10,  2, -3,-21,-29,-19, -3; D=-4;
/I:         II=-7; MI=-15; IM=-15; MD=-15; DM=-15; I=0,0,-20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
/M: SY='R';  M= -5, -8,-24,-10, -2,-15,-14, -9,-11, -1, -9, -3, -5,-11, -1,  1, -5, -6,-10,-21,-10, -3;
/M: SY='S';  M= -3,  0,-21,  0,  2,-17, -9, -3,-18, -3,-16,-11,  2,-14,  0, -2,  6,  0,-14,-25,-10,  1;
/M: SY='W';  M=-11,-17,-30,-19,-10,  0,-20,-12,-13, -3, -8, -7,-15,-22, -5, -2,-17,-13,-15, 25,  8, -7;
/M: SY='V';  M= -8,-19,-22,-21,-14, -6,-24,-14,  2, -4,  2,  3,-16,-22, -9,  3,-13, -6,  7,-16, -5,-12;
/M: SY='C';  M=-10,-20,115,-29,-29,-20,-30,-29,-29,-29,-20,-19,-20,-39,-28,-29,-10,-10,-10,-49,-29,-29;
/M: SY='D';  M=-17, 46,-27, 56, 14,-34, -8,  2,-34,  0,-29,-27, 29,-13,  0, -8,  2, -7,-29,-40,-20,  7;
/M: SY='G';  M= -3, -5,-28, -6,-13,-25, 42,-11,-33,-13,-25,-16,  3,-19,-12,-11, -1,-15,-26,-22,-22,-13;
/M: SY='D';  M= -8,  1,-24,  3,  2,-15,-18, -3,-12, -2,-12, -8, -2,-16, -1, -4, -4, -5, -8,-25, -6,  0;
/I:         II=-7; MI=-15; IM=-15; MD=-15; DM=-15; I=0,0,-15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
/M: SY='B';  M= -7,  8,-23,  7,  1,-18,-14, -6,-17, -3,-18,-13,  8, -5, -3, -5, -1, -4,-15,-27,-13, -2;
/M: SY='D';  M=-18, 44,-29, 59, 18,-37, -9,  2,-37,  0,-28,-27, 21,-11,  1, -8,  0, -9,-29,-39,-19, 10;
/M: SY='C';  M=-10,-20,119,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-48,-30,-30;
/M: SY='G';  M= -3, -6,-26, -4, -1,-22,  3, -9,-21, -5,-18,-12, -4, -2, -4, -6,  0, -7,-18,-25,-16, -4;
/M: SY='D';  M=-16, 39,-28, 52, 13,-33, -6,  0,-35, -2,-28,-26, 20,-11, -1, -9,  1, -8,-28,-36,-17,  6;
/M: SY='G';  M= -3, -4,-26, -6,-11,-24, 33,-10,-30,-11,-24,-15,  4,-18,-10,-11,  0,-13,-25,-19,-19,-11;
/M: SY='S';  M=  5,  2,-15,  2,  5,-20, -4, -8,-20, -7,-24,-16,  7,-11,  1, -9, 25, 11,-13,-35,-17,  3;
/M: SY='D';  M=-18, 42,-29, 60, 18,-36,-10,  0,-37, -1,-27,-27, 16,-11, -1,-10, -1, -9,-27,-36,-18,  8;
/M: SY='E';  M=-10, 11,-29, 20, 53,-29,-18, -1,-29,  8,-20,-20,  1, -2, 17, -1,  1, -9,-28,-30,-19, 35;
/I:         II=-7; MI=-15; IM=-15; MD=-15; DM=-15; I=0,0,-15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
/M: SY='E';  M= -1, -3,-22, -3,  6,-19,-16, -6,-14,  2,-11, -7, -3,-11,  3,  0, -2, -4,-12,-25,-11,  4; D=-3;
/I:         DM=-13;
/M: SY='N';  M= -8,  8,-23,  6, -1,-20, -2, -2,-19, -5,-17,-12, 10,-15, -2, -5,  0, -6,-18,-28,-12, -3;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='S';  M= -1, -3,-22, -3,  0,-21, -4, -9,-19, -5,-19,-13, -1, -2, -4, -6,  4, -1,-14,-28,-18, -3;
/I:         E1=0; IE=-105; DE=-105;

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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	962 in 170 different sequences
Number of true positive hits	962 in 170 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	11
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	98.87 %

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	36
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	K_Hofmann
Feature key [info]	DOMAIN
Feature description [info]	LDL-receptor class A
Version [info]	7

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

170 sequences

AEGP_HUMAN  (Q6UXC1), AEGP_MOUSE  (A2AJA7), AEGP_RAT(Q63191),

CD320_BOVIN (A6QNY1), CD320_HUMAN (Q9NPF0), CD320_MOUSE (Q9Z1P5), 
CD320_RAT   (Q5HZW5), CDA1_BOMMO  (H9J9M0), CFAI_HUMAN  (P05156), 
CFAI_MOUSE  (Q61129), CFAI_PONAB  (Q5R5A4), CFAI_RAT(Q9WUW3), 
CO6_BOVIN   (Q29RU4), CO6_HUMAN   (P13671), CO6_PANTR   (P61134), 
CO6_PONPY   (P61135), CO6_RAT (Q811M5), CO7_BOVIN   (Q29RQ1), 
CO7_HUMAN   (P10643), CO7_PIG (Q9TUQ3), CO7_PONAB   (Q5RAD0), 
CO8A_HUMAN  (P07357), CO8A_MOUSE  (Q8K182), CO8A_RABIT  (P98136), 
CO8B_HUMAN  (P07358), CO8B_MOUSE  (Q8BH35), CO8B_ONCMY  (Q90X85), 
CO8B_PAROL  (Q9PVW7), CO8B_RABIT  (P98137), CO8B_RAT(P55314), 
CO9_BOVIN   (Q3MHN2), CO9_HORSE   (P48770), CO9_HUMAN   (P02748), 
CO9_MOUSE   (P06683), CO9_ONCMY   (P06682), CO9_RABIT   (P48747), 
CO9_RAT (Q62930), CO9_TAKRU   (P79755), CORIN_HUMAN (Q9Y5Q5), 
CORIN_MOUSE (Q9Z319), CORIN_RAT   (Q80YN4), CPROH_CONVC (A0A0F7YYX3), 
CTX_SEPES   (B2DCR8), EGG1_CAEBR  (A8X765), EGG1_CAEEL  (Q09967), 
EGG1_CAERE  (E3LYX0), EGG2_CAEEL  (Q21629), ENTK_BOVIN  (P98072), 
ENTK_HUMAN  (P98073), ENTK_MOUSE  (P97435), ENTK_PIG(P98074), 
GLBL_LAMSP  (P16222), GLBL_TYLHE  (P18207), GLBM_TYLHE  (P18208), 
GR101_LYMST (P46023), IDD_HUMAN   (P98153), IDD_MOUSE   (P98154), 
LDLR1_XENLA (Q99087), LDLR2_XENLA (Q99088), LDLR_BOVIN  (P01131), 
LDLR_CRIGR  (P35950), LDLR_HUMAN  (P01130), LDLR_MOUSE  (P35951), 
LDLR_PIG(Q28832), LDLR_RABIT  (P20063), LDLR_RAT(P35952), 
LRAD1_HUMAN (Q5T700), LRAD2_HUMAN (Q5SZI1), LRAD3_HUMAN (Q86YD5), 
LRAD3_MOUSE (A2AR95), LRAD3_XENTR (A4IHY6), LRAD4_HUMAN (O15165), 
LRAD4_MOUSE (Q8BWJ4), LRP10_HUMAN (Q7Z4F1), LRP10_MOUSE (Q7TQH7), 
LRP11_HUMAN (Q86VZ4), LRP11_MOUSE (Q8CB67), LRP12_HUMAN (Q9Y561), 
LRP12_MACFA (Q9BE74), LRP12_MOUSE (Q8BUJ9), LRP12_PONAB (Q5R662), 
LRP1B_HUMAN (Q9NZR2), LRP1B_MOUSE (Q9JI18), LRP1_CHICK  (P98157), 
LRP1_HUMAN  (Q07954), LRP1_MOUSE  (Q91ZX7), LRP1_RAT(G3V928), 
LRP2_HUMAN  (P98164), LRP2_MOUSE  (A2ARV4), LRP2_PIG(C0HL13), 
LRP2_RAT(P98158), LRP3_HUMAN  (O75074), LRP3_RAT(O88204), 
LRP4_HUMAN  (O75096), LRP4_MOUSE  (Q8VI56), LRP4_RAT(Q9QYP1), 
LRP5_HUMAN  (O75197), LRP5_MOUSE  (Q91VN0), LRP6_HUMAN  (O75581), 
LRP6_MOUSE  (O88572), LRP8_CHICK  (Q98931), LRP8_HUMAN  (Q14114), 
LRP8_MOUSE  (Q924X6), LRP_CAEEL   (Q04833), LTK_DANRE   (F1QVU0), 
MALR1_HUMAN (Q5VYJ5), MALR1_MOUSE (A2AJX4), MFRP_HUMAN  (Q9BY79), 
MFRP_MOUSE  (Q8K480), MIG13_CAEEL (G5EF33), MLRP1_ACRMI (B3EWZ5), 
MLRP2_ACRMI (B3EWZ6), MODSP_DROME (Q9VER6), MUA3_CAEEL  (P34576), 
NETO1_HUMAN (Q8TDF5), NETO1_MOUSE (Q8R4I7), NETO2_HUMAN (Q8NC67), 
NETO2_MOUSE (Q8BNJ6), NETO2_RAT   (C6K2K4), NUDEL_DROME (P98159), 
PGBM_HUMAN  (P98160), PGBM_MOUSE  (Q05793), PROH4_APIME (P85831), 
PROH4_CAMFO (E2AX35), RSVR_COTJA  (P98162), RXFP1_HUMAN (Q9HBX9), 
RXFP1_MOUSE (Q6R6I7), RXFP1_PONAB (Q5R5V8), RXFP1_RAT   (Q6R6I6), 
RXFP2_CANLF (Q5XM32), RXFP2_HUMAN (Q8WXD0), RXFP2_MOUSE (Q91ZZ5), 
SCD2_CAEEL  (O76411), SORL_CHICK  (Q98930), SORL_HUMAN  (Q92673), 
SORL_MOUSE  (O88307), SORL_RABIT  (Q95209), SORL_RAT(P0DSP1), 
SPIT1_HUMAN (O43278), SPIT1_MOUSE (Q9R097), SSPO_BOVIN  (P98167), 
SSPO_CHICK  (Q2PC93), SSPO_HUMAN  (A2VEC9), SSPO_MOUSE  (Q8CG65), 
SSPO_RAT(Q700K0), ST14_BOVIN  (Q0IIH7), ST14_HUMAN  (Q9Y5Y6), 
ST14_MOUSE  (P56677), SVH1_CAEEL  (Q17800), TMPS2_HUMAN (O15393), 
TMPS2_MOUSE (Q9JIQ8), TMPS3_HUMAN (P57727), TMPS3_MOUSE (Q8K1T0), 
TMPS6_HUMAN (Q8IU80), TMPS6_MOUSE (Q9DBI0), TMPS7_HUMAN (Q7RTY8), 
TMPS7_MOUSE (Q8BIK6), TMPS7_RAT   (P86091), TMPS9_HUMAN (Q7Z410), 
TMPS9_MOUSE (P69525), TMPS9_RAT   (P69526), UNC52_CAEEL (Q06561), 
VGR_SOLIN   (Q6X0I2), VLDLR_CHICK (P98165), VLDLR_HUMAN (P98155), 
VLDLR_MOUSE (P98156), VLDLR_RABIT (P35953), VLDLR_RAT   (P98166), 
YL54_CAEEL  (P34434), YL_DROME(P98163)

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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

UniProtKB/Swiss-Prot
False negative sequences

11 sequences

ALK_HUMAN   (Q9UM73), ALK_MOUSE   (P97793), GLU2B_BOVIN (Q28034),

GLU2B_HUMAN (P14314), GLU2B_MOUSE (O08795), PKD1_HUMAN  (P98161), 
PKD1_MOUSE  (O08852), TMPS4_HUMAN (Q9NRS4), TMPS4_MOUSE (Q8VCA5), 
TMPSD_HUMAN (Q9BYE2), TMPSD_MOUSE (Q5U405)

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PDB
[Detailed view]

102 PDB

1AJJ; 1CR8; 1D2J; 1D2L; 1F5Y; 1F8Z; 1J8E; 1JRF; 1K7B; 1LDL; 1LDR; 1N7D; 1V9U; 1XFE; 2FCW; 2FYJ; 2FYL; 2I1P; 2JM4; 2KNX; 2KNY; 2KRI; 2LGP; 2M0P; 2M7P; 2M96; 2XRC; 3A7Q; 3DPR; 3M0C; 3OJY; 3P5C; 3T5O; 4A5W; 4E0S; 4ZRP; 4ZRQ; 5B4X; 5B4Y; 5F0E; 5FMW; 5H7V; 5H9O; 5HJO; 5HJR; 5IED; 5IEE; 5IEF; 5IEG; 5O32; 5OY9; 5OYL; 6BYV; 6CXO; 6DLW; 6H03; 6H04; 7F56; 7F57; 7F59; 7F5A; 7F5B; 7FFF; 7FFL; 7FFN; 7JTY; 7K9N; 7K9O; 7K9Q; 7K9T; 7KAD; 7KB6; 7KB8; 7KBJ; 7KBR; 7KRY; 7L9E; 7MEQ; 7N1H; 7NYC; 7NYD; 7QBD; 7QBE; 7QBF; 7QBG; 7TMW; 7WQX; 8B0F; 8B0G; 8B0H; 8D43; 8DE6; 8EM4; 8EM7; 8EMR; 8IHP; 8JHZ; 8JI0; 8S9P; 8UFB; 8UFC; 8VGT
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