PROSITE entry PS50302

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PURL: https://purl.expasy.org/prosite/signature/PS50302

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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; 29-MAY-2024 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;

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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2025_03 which contains 573'661 sequence entries.

Total number of hits	480 in 70 different sequences
Number of true positive hits	480 in 70 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	47
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	91.08 %

Comments [info]

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

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

70 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_CANAL  (Q59QH0), 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)

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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

UniProtKB/Swiss-Prot
False negative sequences

47 sequences

MBD9_ARATH  (Q9SGH2), NOP9_AJEDR  (C5G8V2), NOP9_ASPCL  (A1CKL4),

NOP9_ASPFC  (B0XXN5), NOP9_ASPFN  (B8N3R8), NOP9_ASPFU  (Q4WXY3), 
NOP9_ASPNC  (A2R3A7), NOP9_ASPOR  (Q2UKV0), NOP9_BLAGS  (C5JK19), 
NOP9_CANGA  (Q6FUX0), NOP9_CANTT  (C5MFB4), NOP9_COCP7  (C5P9D1), 
NOP9_COLGM  (E3QZF5), NOP9_COPC7  (A8P7F7), NOP9_EMENI  (Q5B3J5), 
NOP9_EREGS  (Q75C70), NOP9_FUSV7  (C7YQ16), NOP9_HUMAN  (Q86U38), 
NOP9_KLULA  (Q6CNC2), NOP9_LACTC  (C5DMC1), NOP9_LEPMJ  (E5A2Z3), 
NOP9_LODEL  (A5DWG1), NOP9_MOUSE  (Q8BMC4), 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)

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PDB
[Detailed view]

67 PDB

1IB2; 1M8W; 1M8X; 1M8Y; 1M8Z; 2YJY; 3BSB; 3BSX; 3BWT; 3BX2; 3BX3; 3GVO;
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