Entry: PS50302

Forthcoming changes to the profile format
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); JUL-2014 (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 2014_09 which contains 546'439 sequence entries.


Total number of hits 449 in 66 different sequences
Number of true positive hits 449 in 66 different sequences
Number of 'unknown' hits
Number of false positive hits
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)) 90.34 %

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
66 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), PUM20_ARATH (Q9XI17), PUM21_ARATH (Q9LXC5), 
PUM22_ARATH (Q9LNI2), PUM23_ARATH (Q9C552), PUM24_ARATH (Q9LRZ3), 
PUM2_ARATH  (Q9ZW06), PUM2_HUMAN  (Q8TB72), PUM2_MOUSE  (Q80U58), 
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]
37 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
» More

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