Entry: PS50050

General information about the entry
Entry name TNFR_NGFR_2
Accession number PS50050
Entry type MATRIX
Date NOV-1997 (CREATED); NOV-1997 (DATA UPDATE); MAR-2013 (INFO UPDATE).
PROSITE Documentation PDOC00561
Associated ProRule PRU00206
Name and characterization of the entry
DescriptionTNFR/NGFR family cysteine-rich region domain profile.
Matrix / Profile 
/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=41;
/DISJOINT: DEFINITION=PROTECT; N1=5; N2=37;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-4.936; R2=.0214; TEXT='-LogE';
/CUT_OFF: LEVEL=0; SCORE=627; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=534; 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;
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: 156 hits in 76 different sequences
  • Number of hits on proteins that are known to belong to the set under consideration: 155 hits in 75 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): 1 hits in 1 different sequences
  • Number of known missed hits: 19
  • 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)): 99.36 %
  • Recall (true hits / (true hits + false negatives)): 89.08 %
Comments
  • MATRIX_TYPE: protein_domain
  • Scaling database: UniProtKB/Swiss-Prot: reversed
  • Matrix author: K_Hofmann
  • Taxonomic range: Eukaryotes, Eukaryotic viruses
  • Maximum known number of repetitions of the pattern in a single protein: 4
  • FT_KEY: REPEAT
  • FT_DESC: TNFR-Cys
  • VERSION: 1
Cross-references
UniProtKB/Swiss-Prot True positive hits:
A53R_VACCW  (P24756), A53_VACCC   (P21071), ACCR1_ARATH (Q9S7D9), 
ACR4_ARATH  (Q9LX29), CD27_HUMAN  (P26842), CD27_MOUSE  (P41272), 
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), 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_CANFA  (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)
False negative hits (sequences which belong to the set under consideration, but which have not been picked up by the pattern or profile):
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)
False positive hits (sequences which do not belong to the set under consideration):
LAMA5_HUMAN (O15230)
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]		 1BZI; 1CDF; 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; 4E4D; 4FHQ; 4GIQ; 4J6G;

View entry in original PROSITE format
View entry in raw text format (no links)

If you would like to retrieve all the Swiss-Prot entries referenced in the DR lines of this entry (with the exception of false positive hits) , you can enter a file name. These entries will then be saved to a file under this name. (Please note that this temporary file will only be kept for 1 week.)

File name:

Format: Swiss-Prot Fasta

or