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Entry: PS50050

General information about the entry

Entry name [info] TNFR_NGFR_2
Accession [info] PS50050
Entry type [info] MATRIX
Date [info] 01-NOV-1997 CREATED; 10-MAY-2017 DATA UPDATE; 27-SEP-2017 INFO UPDATE.
PROSITE Doc. [info] PDOC00561
Associated ProRule [info] PRU00206

Name and characterization of the entry

Description [info] TNFR/NGFR family cysteine-rich region domain profile.
Matrix / Profile [info]
/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=41;
/DISJOINT: DEFINITION=PROTECT; N1=5; N2=37;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-4.9359999; R2=0.0214000; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=575.5617065; R2=3.8765957; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=628; H_SCORE=3010; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=535; H_SCORE=2650; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: D=-20; I=-20; B1=*; E1=0; 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='P'; M= -4, -2,-25, -1,  3,-23,-13,-11,-19, -2,-21,-15, -1, 13, -2, -4,  3,  4,-17,-30,-19, -1;
/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='P'; M= -4, -7,-25, -5,  4,-24,-12, -3,-21,  1,-20,-11, -5,  5,  3,  0, -2, -7,-18,-24,-14,  2;
/M: SY='E'; M= -3,  0,-27,  4, 11,-23,-12, -7,-21, -2,-20,-15, -4, 11, -1, -9, -1, -6,-20,-27,-17,  4;
/M: SY='G'; M= -3,  3,-27,  1, -9,-28, 39,-11,-34, -9,-29,-19, 10,-17,-10,-10,  4,-12,-27,-26,-25, -9;
/I:         II=-7; MI=-8; IM=-8; 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='Y'; M=-11, -7,-23, -9,  1,  0,-21,  2,-12, -8, -7, -3, -6,-16, -1, -6, -4,  1,-12,-14,  4,  0;
/M: SY='Y'; M=-19,-22,-25,-26,-22, 44,-29,  7, -2,-17,  2,  0,-18,-29,-20,-13,-18,-10, -7, 16, 52,-22;
/M: SY='C'; M= -6, -8,  5,-12, -8,-14,-19,-11,-13,-12,-10, -8, -4,-18, -5,-10,  1,  3, -9,-27,-11, -7;
/M: SY='D'; M= -5, 10,-21, 11,  3,-21,-12, -1,-21, -3,-18,-15,  7,-11, -1, -4,  3, -1,-17,-29,-11,  0;
/M: SY='S'; M= -4, -3,-23, -3,  1,-18, -8, -4,-17, -4,-14,-10, -2,-12,  0, -5,  2,  0,-13,-24, -9, -1;
/I:         MD=-22;
/M: SY='W'; M= -2, -5,-20, -6, -3,-13, -6, -8,-15, -2,-15,-11, -3,-10, -3, -5, -1, -3,-13,  1, -6, -3; D=-4;
/I:         MD=-22;
/M: SY='N'; M=  0,  6,-14,  2, -1,-15,  1,  3,-15, -4,-17,-11, 13, -8, -2, -4,  7,  0,-14,-23,-11, -2; D=-4;
/I:         MD=-22;
/M: SY='H'; M= -3, -4,-13, -5,  0, -5, -9,  6, -8, -3, -6, -2, -2, -7,  3, -1, -2, -3, -8, -7,  2,  1; D=-4;
/I:         II=-4; MI=0; IM=0; 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='C'; M=  0,-10,  9,-12, -9, -4,-14, -9, -6,-12, -3, -4, -8,-15,-10,-10, -1,  1,  0,-19, -7, -9; D=-4;
/I:         DM=-22;
/M: SY='D'; M= -9,  5,-27,  7,  7,-23, -4, -5,-26,  2,-24,-16,  6, -5,  2,  2,  2, -5,-23,-27,-16,  3;
/M: SY='Q'; M= -5, -7,-24, -9,  1,-15,-19,  0,-10, -1,-10, -4, -4,-11,  2,  0, -3, -4,-10,-24, -7,  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;
/I:         MD=-15;
/M: SY='R'; M= -4, -7,-16, -8, -3, -8,-16, -2, -6, -1, -4, -2, -5,-14, -2,  3, -5, -2, -3,-17, -3, -4; D=-6;
/I:         I=-6; MI=-20; MD=-20; IM=-20; DM=-20;
/M: SY='P'; M= -4, -6,-21, -4,  1,-17,-12, -7,-12, -3,-14, -9, -4, 14,  1, -1,  0, -3,-14,-21,-14, -1; D=-6;
/I:         DM=-15;
/M: SY='C'; M=-12,-19, 78,-26,-25,-17,-28,-14,-27,-25,-18,-16,-18,-36,-22,-24,-13,-13,-14,-28,-17,-24;
/M: SY='T'; M= -4, -4,-19, -7, -4,-15,-15, -9,-16,  2,-16, -9,  0,-13,  0,  8,  9, 14, -9,-26, -9, -3;
/I:         II=-6; MI=-8; IM=-8; 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='R'; M= -8, -6,-25, -8, -3,-16,-18, -2,-11,  0,-12, -5, -2, -6,  0,  1, -4, -3,-11,-24, -8, -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='E'; M= -7,  3,-27,  5,  9,-24,-10, -6,-22,  0,-21,-15,  3,  5,  2, -4,  1, -3,-21,-29,-18,  4;
/I:         MD=-15;
/M: SY='P'; M= -6, -7,-28, -5, -1,-21,-11,-10,-16, -5,-17,-11, -5, 19, -6, -9, -4, -6,-17,-27,-18, -5; D=-4;
/I:         MD=-15;
/M: SY='G'; M= -3,  0,-26, -1, -7,-24, 31,-11,-29,-10,-24,-16,  5,-17,-10,-11,  1,-11,-23,-23,-21, -9; D=-4;
/I:         MD=-15;
/M: SY='Q'; M= -9, -5,-22, -6,  0, -7,-12,  0,-13, -8, -6, -2, -4,-16,  1, -7, -4, -2,-13,-20, -2,  0; D=-4;
/I:         II=-7; MI=0; IM=0; 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:         M= -6, -9,-20, -9, -3, -8, -7, -7,-10, -4,-10, -6, -7,-16, -6,  0, -4, -6, -5,-17, -4, -5; D=-4;
/I:         DM=-15;
/M: SY='V'; M= -4,-18,-11,-18, -8, -8,-23,-19,  5,-13,  3,  3,-18,-18,-14,-14, -9, -4, 11,-27,-11,-11;
/M: SY='V'; M= -2,-12,-20,-15, -8,-11,-21,-14,  0, -3, -2,  2,-10,-18, -5, -5, -5,  1,  4,-24, -8, -7;
/M: SY='Q'; M= -2, -4,-23, -7,  3,-20,-15, -5,-16,  7,-16, -6, -1,-13, 10,  7,  2, -3,-13,-24,-11,  6;
/M: SY='P'; M= -8, -2,-28,  1,  2,-20,-14, -9,-16, -5,-16,-12, -3, 12, -5, -9, -4, -6,-17,-28,-16, -3;
/M: SY='C'; M= -4,-16, 73,-23,-23,-22,-10,-22,-29,-24,-21,-18,-14,-32,-24,-24, -6,-11,-13,-41,-27,-24;
/M: SY='T'; M= -1,  0,-17, -4, -5,-17,-12,-15,-14, -7,-15,-12,  2, -6, -6, -9, 12, 23, -8,-30,-14, -6;
/M: SY='R'; M=  1, -3,-24, -3,  2,-22, -7, -9,-20,  1,-18,-12, -2, -6,  0,  3,  2, -3,-15,-24,-16,  0;
/I:         MD=-20;
/M: SY='T'; M= -5,  4,-19,  1,  1,-17,-14, -8,-15, -1,-17,-11,  6, -9,  0, -4,  7, 12,-12,-26,-11,  1; D=-6;
/I:         II=-7; MI=-8; IM=-8; 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='S'; M= -2,  0,-21, -2,  1,-23, -4, -5,-22,  1,-21,-12,  4,-13,  7,  5,  9,  5,-17,-28,-14,  3;
/M: SY='D'; M=-12, 34,-26, 37, 11,-30, -8,  3,-29,  1,-28,-23, 26, -8,  1, -5,  4, -5,-27,-37,-19,  6;
/M: SY='T'; M=  7, -7,-13,-14,-11,-12,-17,-19, -7, -8, -9, -8, -5,-11,-11, -7, 11, 25,  4,-28,-13,-12;
/M: SY='V'; M= -6,-16,-20,-16,-10,-11,-27,-15, 10, -9,  1,  3,-16,-18,-10,-11, -9, -3, 16,-27, -9,-11;
/M: SY='C'; M= -9,-19,115,-29,-29,-20,-29,-29,-29,-29,-20,-20,-18,-39,-29,-29, -9,-10,-10,-49,-30,-29;
/I:         E1=0; IE=-105; DE=-105;
» more

Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2017_09 which contains 555'594 sequence entries.


Total number of hits 159 in 79 different sequences
Number of true positive hits 158 in 78 different sequences
Number of 'unknown' hits 0
Number of false positive hits 1
Number of false negative sequences 19
Number of 'partial' sequences 0
Precision (true positives / (true positives + false positives)) 99.37 %
Recall (true positives / (true positives + false negatives)) 89.27 %

Comments [info]

Matrix type [info] protein_domain
Scaling database [info] reversed
Author [info] K_Hofmann
Taxonomic range [info] Eukaryotes, Eukaryotic viruses
Maximum number of repetitions [info] 4
Feature key [info] REPEAT
Feature description [info] TNFR-Cys
Version [info] 5

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences
78 sequences

A53R_VACCW  (P24756    ), A53_VACCC   (P21071    ), ACCR1_ARATH (Q9S7D9    ), 
ACR4L_ARATH (Q9LX29    ), CD27_HUMAN  (P26842    ), CD27_MOUSE  (P41272    ), 
CKI4_ORYSJ  (Q75J39    ), CRI4_MAIZE  (O24585    ), CRMB_CAMPM  (P68636    ), 
CRMB_CAMPS  (P68637    ), CRMB_CWPXG  (O73559    ), CRMB_VAR67  (P34015    ), 
TNF6B_HUMAN (O95407    ), TNR11_HUMAN (Q9Y6Q6    ), TNR11_MOUSE (O35305    ), 
TNR14_HUMAN (Q92956    ), TNR16_CHICK (P18519    ), TNR16_HUMAN (P08138    ), 
TNR16_MOUSE (Q9Z0W1    ), TNR16_RAT   (P07174    ), TNR19_HUMAN (Q9NS68    ), 
TNR19_MOUSE (Q9JLL3    ), TNR1A_BOVIN (O19131    ), TNR1A_HUMAN (P19438    ), 
TNR1A_MOUSE (P25118    ), TNR1A_PIG   (P50555    ), TNR1A_RAT   (P22934    ), 
TNR1B_HUMAN (P20333    ), TNR1B_MOUSE (P25119    ), TNR1B_RAT   (Q80WY6    ), 
TNR21_HUMAN (O75509    ), TNR21_MOUSE (Q9EPU5    ), TNR21_RAT   (D3ZF92    ), 
TNR22_MOUSE (Q9ER62    ), TNR23_MOUSE (Q9ER63    ), TNR25_HUMAN (Q93038    ), 
TNR26_MOUSE (P83626    ), TNR27_HUMAN (Q9HAV5    ), TNR27_MOUSE (Q8BX35    ), 
TNR3_HUMAN  (P36941    ), TNR3_MOUSE  (P50284    ), TNR4_HUMAN  (P43489    ), 
TNR4_MOUSE  (P47741    ), TNR4_RAT    (P15725    ), TNR5_BOVIN  (Q28203    ), 
TNR5_CALJA  (Q3LRP1    ), TNR5_CANLF  (Q7YRL5    ), TNR5_HORSE  (Q3ZTK5    ), 
TNR5_HUMAN  (P25942    ), TNR5_MOUSE  (P27512    ), TNR5_PIG    (Q8SQ34    ), 
TNR6_BOVIN  (P51867    ), TNR6_CERAT  (Q9BDN4    ), TNR6_HUMAN  (P25445    ), 
TNR6_MACFA  (Q9TSN4    ), TNR6_MACMU  (Q9BDP2    ), TNR6_MACNE  (Q9BDN0    ), 
TNR6_MOUSE  (P25446    ), TNR6_PIG    (O77736    ), TNR6_RAT    (Q63199    ), 
TNR8_HUMAN  (P28908    ), TNR8_MOUSE  (Q60846    ), TNR8_RAT    (P97525    ), 
TNR9_HUMAN  (Q07011    ), TR10A_HUMAN (O00220    ), TR10B_HUMAN (O14763    ), 
TR10B_MOUSE (Q9QZM4    ), TR10C_HUMAN (O14798    ), TR10D_HUMAN (Q9UBN6    ), 
TR11B_BOVIN (A5D7R1    ), TR11B_HUMAN (O00300    ), TR11B_MOUSE (O08712    ), 
TR11B_RAT   (O08727    ), UL144_HCMVM (F5HAM0    ), UL144_HCMVO (Q68396    ), 
VT2_MYXVL   (P29825    ), VT2_RFVKA   (P25943    ), WGN_DROME   (Q9VWS4    )
» more

UniProtKB/Swiss-Prot
False negative sequences
19 sequences

ACCR2_ARATH (O80963    ), C22L_VACCC  (P21106    ), EDAR_HUMAN  (Q9UNE0    ), 
EDAR_MOUSE  (Q9R187    ), EDAR_ORYLA  (Q90VY2    ), TNR12_HUMAN (Q9NP84    ), 
TNR12_MOUSE (Q9CR75    ), TNR17_HUMAN (Q02223    ), TNR17_MOUSE (O88472    ), 
TNR18_HUMAN (Q9Y5U5    ), TNR18_MOUSE (O35714    ), TNR9_MOUSE  (P20334    ), 
TR13B_HUMAN (O14836    ), TR13B_MOUSE (Q9ET35    ), TR13C_HUMAN (Q96RJ3    ), 
TR13C_MOUSE (Q9D8D0    ), TR19L_HUMAN (Q969Z4    ), TR19L_MACFA (Q9N092    ), 
TR19L_MOUSE (Q8BX43    )
» more

UniProtKB/Swiss-Prot
False positive sequences
1 sequence

LAMA5_HUMAN (O15230    )

		
PDB
[Detailed view]
52 PDB

1D0G; 1D4V; 1DU3; 1EXT; 1FT4; 1JMA; 1NCF; 1SG1; 1TNR; 1ZA3; 2AW2; 2H9G; 2HEV; 2HEY; 3ALQ; 3BUK; 3IJ2; 3K51; 3ME2; 3ME4; 3MHD; 3MI8; 3QBQ; 3QD6; 3QO4; 3THM; 3TJE; 3U3P; 3U3Q; 3U3S; 3U3T; 3U3V; 3URF; 3X3F; 4E4D; 4FHQ; 4GIQ; 4I9X; 4J6G; 4KGG; 4KGQ; 4MSV; 4MXW; 4N90; 4OD2; 4RSU; 4YN0; 5BNQ; 5DMI; 5DMJ; 5IHL; 5L36
» more

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