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Entry: PS50302

General information about the entry

Entry name [info] PUM
Accession [info] PS50302
Entry type [info] MATRIX
Date [info] 01-JAN-2004 CREATED; 01-OCT-2013 DATA UPDATE; 20-DEC-2017 INFO UPDATE.
PROSITE Doc. [info] PDOC50302
Associated ProRule [info] PRU00317

Name and characterization of the entry

Description [info] Pumilio RNA-binding repeat profile.
Matrix / Profile [info]
/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=36;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=36;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.4344258; R2=0.0233314; TEXT='NScore';
/CUT_OFF: LEVEL=0; SCORE=218; N_SCORE=7.5; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=89; N_SCORE=4.5; MODE=1; TEXT='R?';
/DEFAULT: M0=-8; D=-30; I=-30; 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='E'; M= -2,  3,-23,  4, 15,-24,-12,  0,-23,  4,-19,-13,  3, -9,  8,  1,  3, -4,-19,-27,-13, 11;
/M: SY='L'; M= -9,-27,-21,-32,-24, 12,-30,-21, 23,-25, 25, 16,-23,-25,-21,-20,-19, -6, 17,-18,  2,-23;
/M: SY='M'; M= -5,-13,-20,-15, -8, -9,-20,-12, -2, -7,  0,  1,-11,-16, -7, -6, -8, -4, -1,-23, -7, -9;
/I:         I=-8; MI=0; MD=-29; IM=0; DM=-29;
/M: SY='D'; M= -6,  4,-26,  6,  3,-25,  3, -8,-26, -2,-24,-16,  5, -5, -2, -4,  2, -5,-22,-28,-18,  0;
/M: SY='H'; M=-10,  6,-22,  3,  2,-17,-13, 14,-20, -1,-18,-10, 10,-16,  3,  1, -1, -6,-20,-26, -3,  1;
/M: SY='L'; M= -6,-25,-12,-29,-22,  9,-28,-21, 15,-23, 17, 10,-22,-25,-20,-20,-16, -6, 13,-18,  1,-22;
/M: SY='V'; M= -5,-16,-19,-17,-12, -6,-22,-13,  4,-12,  2,  3,-14,-17,-11,-12,-10, -6,  6,-22, -3,-13;
/M: SY='E'; M= -7,  0,-24,  2, 10,-20,-17, -2,-19,  4,-17,-10,  0, -9,  6,  2,  0, -3,-16,-25,-10,  7;
/M: SY='L'; M= -9,-27,-19,-31,-23, 10,-30,-19, 21,-25, 30, 19,-25,-27,-19,-19,-22, -7, 14,-18,  2,-22;
/M: SY='A'; M= 12,-14,  4,-20,-16,-12,-12,-19, -4,-16, -7, -2,-11,-19,-13,-18,  4,  1,  3,-29,-15,-15;
/M: SY='T'; M= -7,-10,-14,-14, -8, -9,-20,-10, -6, -5, -5,  0, -6,-18, -5, -3, -4,  2, -3,-25, -7, -7;
/M: SY='D'; M=-14, 28,-25, 33, 10,-30, -9, 15,-30, -2,-26,-19, 20,-14,  4, -6,  3, -6,-27,-35,-12,  6;
/M: SY='K'; M= -8, -6,-27, -5,  5,-25,-19, -4,-19, 13,-19, -6, -4,  0, 12, 10, -5, -7,-18,-24,-12,  7;
/M: SY='Y'; M=-15,-10,-24,-14,-13, 19,-23, 11, -7,-14, -5, -4, -5,-24,-11,-10,-11, -8,-11, -2, 28,-13;
/M: SY='G'; M= 10,-10,-24,-11,-16,-27, 48,-19,-32,-17,-26,-18, -2,-18,-17,-19,  4,-12,-22,-21,-27,-16;
/M: SY='N'; M= -2,  7, 11, -2, -7,-19,-10, -7,-20, -9,-24,-17, 17,-20, -7, -9, 14,  6,-15,-39,-19, -7;
/M: SY='Y'; M=-16, -9,-21,-12, -9,  0,-22, 11,-15,  1,-11, -5, -3,-23, -4, 10,-12,-10,-15, -8, 17, -9;
/M: SY='V'; M=  0,-25,-12,-28,-24,  3,-27,-25, 20,-20, 10,  8,-24,-26,-24,-20,-10, -1, 30,-24, -5,-24;
/M: SY='I'; M= -4,-29,-17,-33,-26,  4,-31,-26, 29,-25, 21, 15,-26,-26,-23,-23,-18, -6, 28,-21, -3,-26;
/M: SY='Q'; M= -9,  0,-27,  0, 20,-32,-20,  4,-18,  7,-16, -3, -2,-10, 39,  5, -2, -9,-24,-22,-11, 29;
/M: SY='K'; M= -9, -4,-24, -5,  2,-21,-17,  0,-22, 19,-20, -8, -1,-14,  6, 16, -5, -6,-17,-19, -5,  3;
/M: SY='L'; M= -2,-22,  2,-28,-21, -1,-25,-20,  8,-20, 10,  7,-19,-25,-18,-19,-13, -6,  9,-24, -7,-20;
/M: SY='L'; M=-11,-29,-21,-33,-24, 13,-32,-21, 25,-27, 30, 17,-25,-27,-21,-22,-23, -9, 16,-16,  5,-23;
/M: SY='E'; M= -8,  9,-27, 13, 18,-26,-12, -3,-26,  7,-21,-15,  5, -8,  8,  2,  0, -5,-22,-27,-15, 13;
/M:         M= -7,-10,-18,-14,-10, -6,-19, -2, -5, -9, -5, -1, -7,-19, -7, -8, -5, -2, -4,-20,  0,-10;
/M: SY='A'; M=  3,-10, -7,-14,-12,-13, -4,-15,-12,-12, -9, -7, -7,-19,-11,-12, -1, -4, -6,-25,-14,-12;
/M: SY='S'; M= -4,  6,-20,  6,  1,-21,-10, -6,-21, -3,-21,-15,  5, -5, -2, -6,  7,  3,-16,-30,-15, -1;
/M: SY='E'; M= -5,  0,-24,  3,  6,-20,-12, -9,-19, -1,-17,-13, -3, -3, -1, -5, -1, -3,-15,-26,-13,  2;
/M: SY='E'; M= -3,  1,-24,  3,  8,-23,-12, -6,-20,  3,-19,-12,  0, -3,  1, -1,  1, -4,-16,-28,-15,  4;
/M: SY='E'; M= -8,  0,-23,  1,  9,-19,-17, -2,-15,  0,-13, -7, -1,-12,  9, -2, -3, -6,-14,-24, -8,  8;
/M: SY='R'; M= -8, -9,-24,-11, -2,-16,-21, -9,-10,  7,-10, -3, -6,-15,  3, 11, -7, -6, -8,-22, -8, -1;
/I:         I=-8; MI=0; MD=-29; IM=0; DM=-29;
/M: SY='E'; M= -7,  3,-24,  5,  8,-22,-15, -4,-19,  4,-16,-10,  1,-11,  6,  3, -2, -5,-16,-27,-12,  6;
/M: SY='R'; M= -6, -9,-22,-11, -3,-12,-19,-10, -8, -2, -6, -2, -7,-15, -1,  2, -6, -4, -7,-22, -8, -3;
/M: SY='I'; M= -9,-27,-21,-33,-24,  7,-32,-21, 27,-25, 24, 18,-23,-25,-19,-22,-20, -8, 19,-18,  2,-23;
/M: SY='I'; M= -7,-25,-20,-30,-24, 11,-29,-20, 20,-22, 16, 12,-21,-24,-20,-19,-15, -4, 18,-16,  4,-23;
/M: SY='D'; M= -6, 10,-22, 11, 11,-25,-10, -3,-24,  4,-22,-15,  9,-11,  6,  2,  4, -2,-20,-30,-15,  8;
/I:         E1=0; IE=-105; DE=-105;
» more

Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2017_12 which contains 556'388 sequence entries.


Total number of hits 471 in 69 different sequences
Number of true positive hits 471 in 69 different sequences
Number of 'unknown' hits 0
Number of false positive hits 0
Number of false negative sequences 48
Number of 'partial' sequences 0
Precision (true positives / (true positives + false positives)) 100.00 %
Recall (true positives / (true positives + false negatives)) 90.75 %

Comments [info]

Matrix type [info] protein_domain
Scaling database [info] reversed
Author [info] P_Bucher, N_Hulo
Taxonomic range [info] Eukaryotes
Maximum number of repetitions [info] 9
Feature key [info] REPEAT
Feature description [info] Pumilio
Version [info] 4

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences
69 sequences

FBF1_CAEEL  (Q9N5M6    ), FBF2_CAEEL  (Q09312    ), JSN1_YEAST  (P47135    ), 
MCP2_SCHPO  (O74438    ), MPF1_SCHPO  (Q10238    ), MPT5_YEAST  (P39016    ), 
NOP9_ARTBC  (D4AMF9    ), NOP9_ARTGP  (E5QZZ6    ), NOP9_BOTFB  (A6S374    ), 
NOP9_CANAW  (C4YEN2    ), NOP9_CANDC  (B9W7H9    ), NOP9_CLAL4  (C4Y3N8    ), 
NOP9_DEBHA  (Q6BRH3    ), NOP9_KOMPG  (C4R8S9    ), NOP9_PICST  (A3LXG0    ), 
NOP9_SCHJY  (B6K1Y8    ), NOP9_TRIVH  (D4D9R6    ), PENG_DROME  (O61345    ), 
PUF12_CAEEL (Q09622    ), PUF2_YEAST  (Q12221    ), PUF3_SCHPO  (O94462    ), 
PUF3_YEAST  (Q07807    ), PUF4_YEAST  (P25339    ), PUF5_CAEEL  (Q20757    ), 
PUF6_CAEEL  (O01322    ), PUF6_SCHPO  (Q9UU76    ), PUF6_YEAST  (Q04373    ), 
PUF7_CAEEL  (O44169    ), PUM10_ARATH (Q9LP21    ), PUM11_ARATH (Q9LDW3    ), 
PUM12_ARATH (Q9LVC3    ), PUM13_ARATH (Q9FMH4    ), PUM14_ARATH (Q4PSD1    ), 
PUM15_ARATH (P0DN95    ), PUM16_ARATH (Q9FIE9    ), PUM17_ARATH (Q9C8B8    ), 
PUM18_ARATH (Q9LVG3    ), PUM19_ARATH (Q9LSS8    ), PUM1_ARATH  (Q9ZW07    ), 
PUM1_CHICK  (Q2VB19    ), PUM1_HUMAN  (Q14671    ), PUM1_MOUSE  (Q80U78    ), 
PUM1_PONAB  (Q5R5X3    ), PUM1_XENLA  (Q66KI6    ), PUM20_ARATH (Q9XI17    ), 
PUM21_ARATH (Q9LXC5    ), PUM22_ARATH (Q9LNI2    ), PUM23_ARATH (Q9C552    ), 
PUM24_ARATH (Q9LRZ3    ), PUM2_ARATH  (Q9ZW06    ), PUM2_HUMAN  (Q8TB72    ), 
PUM2_MOUSE  (Q80U58    ), PUM2_XENLA  (E3WDQ9    ), PUM3_ARATH  (Q9ZW02    ), 
PUM3_DANRE  (X1WGX5    ), PUM3_HUMAN  (Q15397    ), PUM3_MOUSE  (Q8BKS9    ), 
PUM3_RAT    (Q562C7    ), PUM4_ARATH  (Q9SS47    ), PUM5_ARATH  (Q9LJX4    ), 
PUM6_ARATH  (Q9C5E7    ), PUM7_ARATH  (Q9C9R6    ), PUM8_ARATH  (Q9LM20    ), 
PUM9_ARATH  (Q1PFN9    ), PUM_DROME   (P25822    ), YAD3_SCHPO  (Q09829    ), 
YDHE_SCHPO  (Q92359    ), YG58_SCHPO  (O60059    ), YN8E_SCHPO  (Q9P789    )
» more

UniProtKB/Swiss-Prot
False negative sequences
48 sequences

MBD9_ARATH  (Q9SGH2    ), NOP9_AJEDR  (C5G8V2    ), NOP9_ASHGO  (Q75C70    ), 
NOP9_ASPCL  (A1CKL4    ), NOP9_ASPFC  (B0XXN5    ), NOP9_ASPFN  (B8N3R8    ), 
NOP9_ASPFU  (Q4WXY3    ), NOP9_ASPNC  (A2R3A7    ), NOP9_ASPOR  (Q2UKV0    ), 
NOP9_BLAGS  (C5JK19    ), NOP9_CANAL  (Q59QH0    ), NOP9_CANGA  (Q6FUX0    ), 
NOP9_CANTT  (C5MFB4    ), NOP9_COCP7  (C5P9D1    ), NOP9_COLGM  (E3QZF5    ), 
NOP9_COPC7  (A8P7F7    ), NOP9_EMENI  (Q5B3J5    ), NOP9_HUMAN  (Q86U38    ), 
NOP9_KLULA  (Q6CNC2    ), NOP9_LACTC  (C5DMC1    ), NOP9_LEPMJ  (E5A2Z3    ), 
NOP9_LODEL  (A5DWG1    ), NOP9_MOUSE  (Q8BMC4    ), NOP9_NECH7  (C7YQ16    ), 
NOP9_NEOFI  (A1D6V7    ), NOP9_NEUCR  (Q7S5H0    ), NOP9_PARBA  (C1H8W8    ), 
NOP9_PARBD  (C1FYU3    ), NOP9_PARBP  (C0S4C4    ), NOP9_PENRW  (B6H3T4    ), 
NOP9_PHANO  (Q0U154    ), NOP9_PICGU  (A5DBF4    ), NOP9_PODAN  (B2AL40    ), 
NOP9_PYRTR  (B2W8X8    ), NOP9_PYRTT  (E3RP32    ), NOP9_SCHPO  (Q92347    ), 
NOP9_SORMK  (D1ZSG5    ), NOP9_TALMQ  (B6Q5P5    ), NOP9_VANPO  (A7TH34    ), 
NOP9_YARLI  (Q6C9H2    ), NOP9_YEAS1  (B3LQ92    ), NOP9_YEAS2  (C7GV42    ), 
NOP9_YEAS7  (A6ZPV9    ), NOP9_YEAS8  (C8ZBK1    ), NOP9_YEAST  (P47077    ), 
NOP9_ZYGRC  (C5DQD7    ), PUM25_ARATH (Q9LK18    ), PUM26_ARATH (Q9FGE7    )
» more

PDB
[Detailed view]
52 PDB

1IB2; 1M8W; 1M8X; 1M8Y; 1M8Z; 2YJY; 3BSB; 3BSX; 3BWT; 3BX2; 3BX3; 3GVO; 3GVT; 3H3D; 3K49; 3K4E; 3K5Q; 3K5Y; 3K5Z; 3K61; 3K62; 3K64; 3Q0L; 3Q0M; 3Q0N; 3Q0O; 3Q0P; 3Q0Q; 3Q0R; 3Q0S; 3QG9; 3QGB; 3QGC; 3V6Y; 3V71; 3V74; 4DZS; 4WZR; 4WZW; 5BYM; 5BZ1; 5BZ5; 5BZU; 5BZV; 5KL1; 5KL8; 5KLA; 5WZG; 5WZH; 5WZI; 5WZJ; 5WZK
» more

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