PROSITE entry PS50066

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General information about the entry

PURL [info]	https://purl.expasy.org/prosite/signature/PS50066
Entry name [info]	MADS_BOX_2
Accession [info]	PS50066
Entry type [info]	MATRIX
Date [info]	01-NOV-1997 CREATED; 26-FEB-2020 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC00302
Associated ProRule [info]	PRU00251

Name and characterization of the entry

Description [info]

MADS-box domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=61;
/DISJOINT: DEFINITION=PROTECT; N1=6; N2=56;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=0.4192000; R2=0.0140178; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=4160.3984375; R2=5.9630995; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=577; H_SCORE=7601; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=434; H_SCORE=6748; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: D=-20; I=-20; B1=-50; E1=-50; 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='M';  M=-10,-18,-21,-26,-16, -5,-21, -2, 13, -4, 12, 45,-17,-20,  1, -2,-17, -9,  7,-21, -2, -8;
/M: SY='G';  M=  6, -9,-25,-10,-14,-26, 44,-19,-30,-16,-24,-17, -2,-17,-16,-18,  3, -9,-21,-22,-26,-15;
/M: SY='R';  M=-20,-10,-30,-10,  0,-20,-20,  0,-30, 30,-20,-10,  0,-20, 10, 70,-10,-10,-20,-20,-10,  0;
/M: SY='G';  M= -5,-11,-29,-11,-14,-26, 36,-16,-32, -4,-25,-15, -2,-20,-12,  3, -4,-16,-21,-21,-23,-14;
/M: SY='K';  M=-11, -1,-30, -1, 10,-30,-20, -9,-30, 47,-29,-10,  0,-11, 12, 32,-10,-10,-20,-20,-10, 10;
/M: SY='I';  M= -8,-27,-26,-35,-26, -2,-36,-27, 40,-25, 16, 16,-20,-21,-16,-25,-16, -7, 28,-22, -3,-25;
/M: SY='E';  M=-10,  4,-31, 10, 40,-33,-20,  1,-26, 12,-21,-13, -1,  1, 30,  4, -1,-10,-29,-26,-17, 35;
/M: SY='I';  M=-10,-29,-27,-37,-27,  2,-36,-25, 41,-28, 25, 24,-22,-22,-18,-26,-22,-10, 25,-20,  0,-26;
/M: SY='K';  M=-10,  0,-28,  1, 15,-29,-18, -7,-29, 36,-27,-12,  1,-10, 13, 27, -4, -8,-21,-23,-12, 13;
/M: SY='R';  M=-18,-12,-29,-12, -3, -8,-22, -1,-23, 19,-17, -7, -5,-13,  2, 40,-12,-10,-17,-15, -1, -4;
/M: SY='I';  M=-10,-30,-29,-39,-29,  1,-39,-29, 47,-30, 23, 20,-21,-21,-20,-29,-21,-10, 28,-20,  0,-29;
/M: SY='E';  M=-11, 12,-29, 21, 48,-29,-19, -2,-29,  9,-19,-19,  1, -3, 15,  0, -1, -8,-27,-30,-18, 31;
/M: SY='N';  M=-13, 43,-23, 33,  5,-25, -3,  7,-25,  0,-30,-23, 49,-17,  0, -3,  7, -3,-30,-40,-20,  3;
/M: SY='K';  M= -2,  1,-23,  2,  5,-25,-14, -9,-21, 13,-22,-12,  2, -8,  6,  8,  4,  1,-15,-27,-14,  5;
/M: SY='T';  M= -5, -5,-18,-12, -9,-12,-21,-14, -4, -7, -6, -4, -1,-15, -3, -1,  6, 21, -1,-27, -9, -7;
/M: SY='N';  M= -8, 21,-21, 10,  1,-21, -6,  6,-22,  7,-28,-17, 35,-17,  2, 11, 10,  1,-24,-35,-16,  1;
/M: SY='R';  M=-20,-10,-30,-10,  0,-20,-20,  0,-30, 30,-20,-10,  0,-20, 10, 70,-10,-10,-20,-20,-10,  0;
/M: SY='Q';  M=-11, -2,-28, -3, 13,-31,-21, 15,-18,  5,-17,  0, -1,-13, 45,  6, -1, -7,-25,-19, -2, 28;
/M: SY='V';  M= -1,-22,-11,-24,-26, -2,-27,-26, 23,-18,  5,  6,-20,-28,-26,-18, -6,  3, 40,-31,-11,-26;
/M: SY='T';  M=  0,  0,-10,-10,-10,-10,-20,-20,-10,-10,-10,-10,  0,-10,-10,-10, 20, 50,  0,-30,-10,-10;
/M: SY='F';  M=-20,-28,-22,-36,-28, 70,-30,-12,  0,-26,  8,  0,-20,-30,-34,-18,-20,-10, -2, 14, 40,-28;
/M: SY='S';  M=  6, -3,  5, -7, -7,-18, -8,-15,-16,-13,-23,-16,  4,-15, -6,-14, 26, 17, -7,-38,-19, -7;
/M: SY='K';  M=-10,  0,-30,  0, 10,-30,-20,-10,-30, 50,-30,-10,  0,-10, 10, 30,-10,-10,-20,-20,-10, 10;
/M: SY='R';  M=-20,-10,-30,-10,  0,-20,-20,  0,-30, 30,-20,-10,  0,-20, 10, 70,-10,-10,-20,-20,-10,  0;
/M: SY='R';  M=-17, -7,-30, -7,  3,-23,-20, -3,-30, 36,-23,-10,  0,-17, 10, 57,-10,-10,-20,-20,-10,  3;
/M: SY='N';  M=  2, 13,-17,  1, -4,-13, -7,  4,-17, -5,-21,-14, 24,-16, -4, -6,  9,  4,-17,-30,-12, -4;
/M: SY='G';  M=  0,-10,-29,-10,-19,-30, 68,-20,-39,-20,-30,-20,  0,-20,-19,-20,  1,-19,-29,-21,-30,-19;
/M: SY='L';  M=-10,-30,-24,-34,-24,  6,-34,-24, 32,-30, 37, 20,-26,-26,-20,-24,-25,-10, 19,-20,  0,-24;
/M: SY='L';  M=-13,-28,-21,-34,-24, 26,-29,-17, 18,-25, 27, 23,-24,-27,-21,-19,-23,-10, 10,-12,  8,-22;
/M: SY='K';  M=-10,  0,-30,  0, 10,-30,-20,-10,-30, 50,-30,-10,  0,-10, 10, 30,-10,-10,-20,-20,-10, 10;
/M: SY='K';  M=-10,  0,-30,  0, 10,-30,-20,-10,-30, 50,-30,-10,  0,-10, 10, 30,-10,-10,-20,-20,-10, 10;
/M: SY='A';  M= 47,-10,-11,-20,-10,-20, -1,-19,-11, -8,-10,-10,-10,-10, -9,-16,  9,  0, -1,-20,-20,-10;
/M: SY='Y';  M=-16, -4,-28, -7, -6,  0,-19, 20,-16,  5,-15, -5,  1,-21,  1,  4,-11,-11,-19, -5, 26, -4;
/M: SY='E';  M=-10, 10,-30, 20, 60,-30,-20,  0,-30, 10,-20,-20,  0,  0, 20,  0,  0,-10,-30,-30,-20, 40;
/M: SY='L';  M=-10,-30,-22,-32,-22,  8,-32,-22, 25,-30, 45, 20,-28,-28,-20,-22,-28,-10, 14,-20,  0,-22;
/M: SY='S';  M= 13, -2,-10, -5, -4,-17, -5,-14,-15,-10,-22,-16,  4,-11, -4,-12, 31, 23, -5,-35,-18, -4;
/M: SY='V';  M= -2,-28,-13,-30,-28,  0,-30,-28, 28,-21, 14, 11,-27,-28,-27,-20,-11,  1, 41,-28, -8,-28;
/M: SY='L';  M=-10,-30,-20,-30,-20, 10,-30,-20, 20,-30, 50, 20,-30,-30,-20,-20,-30,-10, 10,-20,  0,-20;
/M: SY='C';  M= -8,-15, 90,-25,-25,-18,-28,-28,-25,-25,-18,-18,-15,-33,-25,-25, -3,  4, -8,-45,-25,-25;
/M: SY='D';  M=-14, 32,-30, 46, 12,-37,  7, -4,-38, -4,-29,-26, 13,-12,  0,-11,  0,-12,-30,-34,-22,  6;
/M: SY='A';  M= 34,-10, -1,-18,-11,-18, -6,-20,-10,-12,-12,-11, -9,-13,-11,-19, 12,  6,  1,-26,-19,-11;
/M: SY='E';  M=-11, 10,-29, 15, 37,-30,-18, -1,-29, 17,-23,-16,  4, -5, 19,  9, -1, -8,-27,-28,-16, 28;
/M: SY='V';  M= -3,-30,-16,-33,-30,  0,-33,-30, 36,-23, 13, 13,-27,-27,-27,-23,-13, -3, 44,-27, -7,-30;
/M: SY='A';  M= 20,-11, -8,-17,-11,-14, -4,-16, -8,-14, -6, -3, -8,-16, -9,-17,  8,  2, -2,-27,-16,-10;
/M: SY='L';  M= -7,-30,-18,-31,-24,  6,-31,-24, 26,-27, 37, 17,-29,-29,-23,-21,-24, -7, 23,-23, -3,-24;
/M: SY='I';  M= -9,-30,-24,-36,-27,  3,-36,-27, 39,-29, 27, 19,-24,-24,-21,-26,-21, -9, 27,-21, -1,-27;
/M: SY='I';  M= -6,-28,-21,-35,-28,  0,-33,-25, 37,-23, 17, 23,-24,-24,-20,-23,-17, -6, 34,-24, -4,-27;
/M: SY='F';  M=-11,-29,-19,-36,-27, 46,-29,-22, 11,-28, 17,  6,-22,-28,-32,-21,-19, -8, 10, -4, 14,-27;
/M: SY='S';  M= 13,  0,-12, -2, -3,-21,  5,-11,-21,-10,-28,-19,  9,-11, -3,-11, 33, 14,-11,-36,-21, -3;
/M: SY='S';  M= -2,  7,-20,  6, 11,-23, -7,  0,-23, -3,-27,-18, 13, -1,  3, -6, 17,  5,-21,-35,-18,  6;
/M: SY='T';  M= -2,  3,-17, -4, -3,-18,-11, -9,-19,  3,-20,-13,  9,-13,  0, 10, 13, 17,-12,-30,-14, -2;
/M: SY='G';  M= -4,  2,-28, -1,-13,-27, 45,-10,-34,-13,-28,-19, 12,-20,-13,-11,  1,-15,-29,-25,-25,-14;
/M: SY='K';  M=-11, -7,-27, -7,  2,-20,-22, -4,-20, 27,-13, -4, -5,-15,  4, 23,-12, -7,-14,-21, -7,  2;
/M: SY='L';  M= -8,-28,-18,-30,-23, 11,-29,-19, 20,-24, 32, 19,-28,-29,-21,-19,-22, -7, 18,-19,  2,-22;
/M: SY='Y';  M=-20,-16,-28,-18,-16, 22,-27, 37, -8,-14, -4,  1,-11,-27, -9, -9,-17,-13,-14,  6, 50,-16;
/M: SY='E';  M= -8, 12,-25, 17, 32,-27,-18,  0,-26,  3,-19,-17,  3, -5, 12, -3,  4,  4,-22,-30,-15, 22;
/M: SY='F';  M=-19,-26,-24,-31,-25, 55,-30, -3,  1,-22,  8,  1,-21,-30,-26,-16,-21,-10, -4, 17, 49,-25;
/M: SY='A';  M= 19, -8, -2,-14, -9,-16, -8,-15,-11,-13,-14,-11, -4,-14, -9,-16, 16, 11, -3,-30,-17, -9;
/M: SY='S';  M=  4,  3, -8, -3, -5,-17, -5,-12,-18,-10,-23,-17, 10,-12, -5,-10, 28, 26, -9,-36,-17, -5;
/M: SY='P';  M= -8, -7,-28, -4, -2,-22,-17,-12,-17, -5,-23,-15, -5, 31, -7, -8,  0,  1,-17,-29,-18, -7;
/M: SY='N';  M= -4, 10,-23, 11,  3,-27,  4, -8,-29,  7,-29,-19, 12,-12,  0,  0, 10,  0,-21,-31,-19,  2;
/I:         E1=0; IE=-105; DE=-105;

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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2025_02 which contains 573'230 sequence entries.

Total number of hits	211 in 211 different sequences
Number of true positive hits	211 in 211 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	0
Number of 'partial' sequences	0

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

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	1
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	K_Hofmann
Feature key [info]	DOMAIN
Feature description [info]	MADS-box
Version [info]	6

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

211 sequences

1AP1_BRAOT  (Q96355), 2AP1_BRAOT  (Q96356), 3AP1_BRAOL  (Q39371),

AG103_ARATH (Q9LSB2), AG104_ARATH (Q9LM46), AG11C_VITVI (F6I457), 
AG11S_VITVI (A0A217EJJ0), AGL11_ARATH (Q38836), AGL12_ARATH (Q38841), 
AGL13_ARATH (Q38837), AGL14_ARATH (Q38838), AGL15_ARATH (Q38847), 
AGL15_BRANA (Q39295), AGL16_ARATH (A2RVQ5), AGL17_ARATH (Q38840), 
AGL18_ARATH (Q9M2K8), AGL19_ARATH (O82743), AGL1_ARATH  (P29381), 
AGL21_ARATH (Q9SZJ6), AGL23_ARATH (O80807), AGL24_ARATH (O82794), 
AGL27_ARATH (Q9AT76), AGL28_ARATH (Q9LMM8), AGL29_ARATH (O64703), 
AGL30_ARATH (Q1PFA4), AGL31_ARATH (Q9FPN7), AGL36_ARATH (Q7XJK6), 
AGL3_ARATH  (P29383), AGL42_ARATH (Q9FIS1), AGL49_ARATH (Q9ZUI9), 
AGL53_ARATH (Q7X9N2), AGL5_ARATH  (P29385), AGL61_ARATH (Q4PSU4), 
AGL62_ARATH (Q9FKK2), AGL63_ARATH (Q9SA07), AGL65_ARATH (Q7X9I0), 
AGL66_ARATH (Q1PFC2), AGL6_ARATH  (P29386), AGL6_SOLLC  (A0A3Q7EKL1), 
AGL70_ARATH (Q9LSR7), AGL71_ARATH (Q9LT93), AGL72_ARATH (Q9FLH5), 
AGL75_ARATH (Q9FLL0), AGL80_ARATH (Q9FJK3), AGL81_ARATH (Q9FIX0), 
AGL82_ARATH (Q9FIM0), AGL86_ARATH (Q9C6V3), AGL8_ARATH  (Q38876), 
AGL8_SINAL  (Q41274), AGL8_SOLCO  (O22328), AGL8_SOLLC  (Q40170), 
AGL8_SOLTU  (Q42429), AGL90_ARATH (Q7XJK5), AGL92_ARATH (Q9C6V4), 
AGL93_ARATH (Q7X9H9), AGL97_ARATH (Q9C633), AGL9_ARADE  (Q38694), 
AGL9_PETHY  (Q03489), AGL9_SINAL  (O04067), AGL9_SOLLC  (Q42464), 
AG_ARATH(P17839), AG_BRANA(Q01540), AG_PANGI(Q40872), 
AG_PETHY(Q40885), AG_SOLLC(Q40168), AG_TOBAC(Q43585), 
ANR1_ARATH  (Q9SI38), AP1A_BRAOA  (B4YPW6), AP1A_BRAOB  (Q8GTF5), 
AP1C_BRAOA  (B4YPV4), AP1C_BRAOB  (Q8GTF4), AP1_ARALL   (D7KWY6), 
AP1_ARATH   (P35631), AP1_BRARP   (P0DI14), AP1_CITSI   (A2IB53), 
AP1_SINAL   (Q41276), AP1_VITVI   (Q6E6S7), AP32_ASAEU  (Q9LLA7), 
AP3_ARATH   (P35632), AP3_VITVI   (E0CPH4), ARGR1_YEAST (P07249), 
CALA_BRAOB  (Q6R4R9), CALB_BRAOB  (Q6R4R8), CALC_BRAOB  (Q6R4R7), 
CALD_BRAOB  (Q6R4R6), CAL_ARALL   (D7KQR8), CAL_ARATH   (Q39081), 
CAL_BRAOT   (Q39375), CAL_BRARC   (Q6R4S6), CAL_BRARP   (Q9SBK9), 
CAL_BRARR   (Q6R4S3), CMB1_DIACA  (Q39685), CMB2_DIACA  (Q42498), 
DEF21_ANTMA (Q8RVL4), DEFA_ANTMA  (P23706), EJ2_SOLLC   (Q7Y040), 
FBP1_PETHY  (Q03488), FBP24_PETHY (Q9ATE5), FLC_ARATH   (Q9S7Q7), 
FULL_VITVI  (D7SMN6), GGM13_GNEGN (Q9XGJ4), GLOB_ANTMA  (Q03378), 
GLOB_TOBAC  (Q03416), J2_SOLLC(K4DEK0), JOIN_SOLLC  (Q9FUY6), 
M17_MAIZE   (Q8VWM8), MAD13_ORYSJ (Q2QW53), MAD14_ORYSI (P0C5B1), 
MAD14_ORYSJ (Q10CQ1), MAD15_ORYSJ (Q6Q9I2), MAD16_ORYSJ (Q944S9), 
MAD17_ORYSJ (Q7XUN2), MAD18_ORYSI (A2YNI2), MAD18_ORYSJ (Q0D4T4), 
MAD20_ORYSJ (Q2QQA3), MAD21_ORYSJ (Q8RU31), MAD22_ORYSJ (Q9XJ66), 
MAD23_ORYSJ (Q6VAM4), MAD25_ORYSJ (Q84NC5), MAD26_ORYSI (A2YQK9), 
MAD26_ORYSJ (Q0J8G8), MAD27_ORYSJ (Q6EP49), MAD29_ORYSJ (Q6H711), 
MAD30_ORYSJ (Q655V4), MAD31_ORYSJ (Q84NC2), MAD32_ORYSJ (Q8S151), 
MAD33_ORYSJ (Q2QW55), MAD34_ORYSJ (Q6Q9H6), MAD47_ORYSJ (Q5K4R0), 
MAD50_ORYSJ (Q9XJ60), MAD51_ORYSJ (Q9XJ61), MAD55_ORYSJ (Q69TG5), 
MAD56_ORYSI (A2Z9Q7), MAD56_ORYSJ (P0C5B2), MAD57_ORYSJ (Q6Z6W2), 
MAD58_ORYSJ (Q2V0P1), MADS1_ORYSI (A2XDY1), MADS1_ORYSJ (Q10PZ9), 
MADS1_PETHY (Q07472), MADS1_VITVI (Q93XH4), MADS2_ORYSJ (Q40702), 
MADS2_PETHY (Q07474), MADS2_VITVI (Q8LLR2), MADS3_ORYSJ (Q40704), 
MADS3_VITVI (Q8LLR1), MADS4_ORYSJ (Q40703), MADS4_SOLLC (K4BND8), 
MADS4_VITVI (Q8LLR0), MADS5_ORYSI (A2Y9P0), MADS5_ORYSJ (Q0DEB8), 
MADS6_ORYSJ (Q6EU39), MADS7_ORYSI (P0C5B0), MADS7_ORYSJ (Q0J466), 
MADS8_ORYSJ (Q9SAR1), MADS9_VITVI (Q0HA25), MAF5_ARATH  (Q683D7), 
MBX1_SCHPO  (O42954), MCM1_CANAL  (Q5AFP3), MCM1_YEAST  (P11746), 
MEF2A_BOVIN (A2VDZ3), MEF2A_CHICK (Q9W6U8), MEF2A_HUMAN (Q02078), 
MEF2A_MOUSE (Q60929), MEF2A_PIG   (A2ICN5), MEF2A_PONAB (Q5REW7), 
MEF2A_RAT   (Q2MJT0), MEF2A_XENLA (Q03414), MEF2B_HUMAN (Q02080), 
MEF2B_MOUSE (O55087), MEF2C_BOVIN (Q2KIA0), MEF2C_HUMAN (Q06413), 
MEF2C_MOUSE (Q8CFN5), MEF2C_PIG   (A4UTP7), MEF2C_PONAB (Q5R444), 
MEF2C_RAT   (A0A096MJY4), MEF2D_HUMAN (Q14814), MEF2D_MOUSE (Q63943), 
MEF2D_RAT   (O89038), MEF2D_XENLA (Q03413), MEF2_CAEEL  (Q9U325), 
MEF2_DROME  (P40791), MIG1_PYRO7  (G4MWZ7), MIG1_PYROR  (A9YDN6), 
MTF1_PEA(O65874), PHE1_ARATH  (O80805), PHE2_ARATH  (Q7XJK8), 
PIST_ARATH  (P48007), PMAP1_SCHPO (P78926), PVG4_SCHPO  (Q9HGP0), 
RLM1_YEAST  (Q12224), RLMA_ASPFC  (B0XYE0), RLMA_ASPFU  (Q4WX78), 
SEP1_ARATH  (P29382), SEP2_ARATH  (P29384), SEP3_ARATH  (O22456), 
SMP1_YEAST  (P38128), SOC1_ARATH  (O64645), SRFA_DICDI  (Q54TY7), 
SRFB_DICDI  (Q54RY6), SRFC_DICDI  (Q55F37), SRFD_DICDI  (Q54QY7), 
SRF_CAEEL   (Q18955), SRF_CHICK   (Q90718), SRF_DROME   (Q24535), 
SRF_HUMAN   (P11831), SRF_MOUSE   (Q9JM73), SRF_XENLA   (P23790), 
SVP_ARATH   (Q9FVC1), TM6_VITVI   (Q003J2), TT16_ARATH  (Q8RYD9), 
VRN1_BRADI  (I1GN76)

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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

PDB
[Detailed view]

21 PDB

1C7U; 1EGW; 1HBX; 1K6O; 1MNM; 1N6J; 1SRS; 1TQE; 3KOV; 3MU6; 3P57; 5F28; 6BYY; 6BZ1; 6C9L; 6WC2; 6WC5; 7NB0; 7X1N; 7XUZ; 8C84
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