Entry: PS50302

General information about the entry

Entry name [info] PUM
Accession [info] PS50302
Entry type [info] MATRIX
Date [info] JAN-2004 (CREATED); OCT-2013 (DATA UPDATE); MAY-2015 (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';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=675.32353; R2=15.04412; TEXT='HScore';
/CUT_OFF: LEVEL=0; SCORE=218; N_SCORE=7.5; H_SCORE=2974; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=89; N_SCORE=4.5; H_SCORE=2007; 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;
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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2015_07 which contains 548'872 sequence entries.


Total number of hits 466 in 68 different sequences
Number of true positive hits 466 in 68 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)) 90.66 %

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] 3

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences
68 sequences

FBF1_CAEEL  (Q9N5M6), FBF2_CAEEL  (Q09312), JSN1_YEAST  (P47135), 
K0020_HUMAN (Q15397), K0020_MOUSE (Q8BKS9), K0020_RAT   (Q562C7), 
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_PICPG  (C4R8S9), NOP9_PICST  (A3LXG0), 
NOP9_SCHJY  (B6K1Y8), NOP9_TRIVH  (D4D9R6), PEN_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 (O81465), 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), 
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_AJEDS  (C5JK19), 
NOP9_ASHGO  (Q75C70), NOP9_ASPCL  (A1CKL4), NOP9_ASPFC  (B0XXN5), 
NOP9_ASPFN  (B8N3R8), NOP9_ASPFU  (Q4WXY3), NOP9_ASPNC  (A2R3A7), 
NOP9_ASPOR  (Q2UKV0), 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_PENCW  (B6H3T4), 
NOP9_PENMQ  (B6Q5P5), NOP9_PHANO  (Q0U154), NOP9_PICGU  (A5DBF4), 
NOP9_PODAN  (B2AL40), NOP9_PYRTR  (B2W8X8), NOP9_PYRTT  (E3RP32), 
NOP9_SCHPO  (Q92347), NOP9_SORMK  (D1ZSG5), 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]
39 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
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