PROSITE entry 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; 27-MAR-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;» more |
Numerical results [info]
| 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]
| 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 |
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)» more
|
| 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)» more |
| PDB [Detailed view] |
66 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; 5SVD; 5WTX; 5WTY; 5WZG; 5WZH; 5WZI; 5WZJ; 5WZK; 5YKH; 5YKI; 6NOC; 6NOF; 6NOH; 6NY5; 6PUN; 6WPI; 7RZZ; 7S02; 8SJ7 » more |