We are deeply saddened by the passing of Amos Bairoch (1957–2025), the creator of PROSITE. We wish to dedicate our latest paper, published shortly before his death, to him. He will always be a source of inspiration to us.
Our deepest condolences go out to his family and friends, and to all those who had the privilege of working with him. Rest in peace, Amos. Your work will live on long after you are gone.

PROSITE entry PS51913

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PURL: https://purl.expasy.org/prosite/signature/PS51913

Direct ScanProsite submission

General information about the entry

Entry name [info]	HTH_HARE
Accession [info]	PS51913
Entry type [info]	MATRIX
Date [info]	22-APR-2020 CREATED; 07-APR-2021 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51913
Associated ProRule [info]	PRU01261

Name and characterization of the entry

Description [info]

HARE-type HTH domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=70;
/DISJOINT: DEFINITION=PROTECT; N1=6; N2=65;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.1870663; R2=0.0071568; TEXT='-LogE';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=9651.2480469; R2=2.2973452; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=1162; H_SCORE=12321; N_SCORE=10.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=603; H_SCORE=11037; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: M0=-23; D=-150; I=-150; B1=-1000; E1=-1000; MI=-380; MD=-380; IM=-380; DM=-380;

...

                A    C    D    E    F    G    H    I    K    L    M    N    P    Q    R    S    T    V    W    Y
/I:         B1=0; BI=-380; BD=-380;
/M: SY='M';  M= -41, -53, -52, -24,  -8, -17, -58, -21,  31,  20,  87, -15, -19, -44,  12,  -6, -23, -28, -69,  21;
/M: SY='S';  M=  -2, -66, -29, -47, -52, -26, -22, -52, -32, -55, -64,   1, -11,  -9, -18,  70,  68, -60, -83, -66;
/M: SY='W';  M= -24, -73, -55, -19,  55, -76, -43,  -4, -31,  27,  64,  -1, -58, -25, -67, -56, -41,  -1,  76,  33;
/M: SY='I';  M=  -7, -72, -73, -37, -31, -46, -11,  46,  11,  38,  10, -34, -45, -62,   4, -38,  -3,  22, -74, -25;
/M: SY='D';  M= -28, -79,  79,  74, -30, -57, -54, -64, -26, -77, -49,  11, -50,   1, -40, -23, -45, -67, -42, -69;
/M: SY='A';  M=  51, -68, -75, -68, -15, -51, -34,  36, -31,  32,  20, -51, -49, -26, -54, -22, -15,   5,  25, -58;
/M: SY='A';  M=  84, -16, -51, -63, -54, -35, -71,  23, -65, -54, -56, -44, -68, -62, -69, -16, -18,   5, -77, -68;
/M: SY='Y';  M= -33, -78, -49,  35,  25, -76,  21,  21,  12, -29, -52, -28, -49,  -6, -34, -52, -35,  -9,   0,  84;
/M: SY='E';  M=  -1, -43,  24,  55, -56, -61,  18,  -2,  27, -23,   0, -14, -65,  24,  12, -34,  -6, -20, -79, -47;
/M: SY='V';  M= -14, -70, -81, -77,   2, -82, -76,  58, -61,  12, -22, -75, -77, -73, -75, -35, -39,  68, -72,  16;
/M: SY='L';  M= -22, -69, -82, -45, -19, -83, -68,   6, -76,  84,  24, -81, -81, -69, -74, -74, -62, -33, -71, -53;
/M: SY='K';  M=  -4, -75, -25,  45, -75, -53, -27, -35,  54, -38, -63, -16, -65,  28,  38,  13,  -6, -39, -77, -48;
/M: SY='E';  M=   3, -76,  29,  66, -54, -56,  -9, -40,  17, -46, -65,  20, -63,  39,   9, -13, -21, -44, -80, -67;
/M: SY='K';  M=  26, -27, -34,  31, -26, -49,   5, -25,  34, -52, -62,  28, -32,  10,  -4,  23,  -2, -16, -76, -12;
/M: SY='G';  M= -41, -76,   7,  -7,  -8,  54,  -2, -65,  49, -77, -68,  25, -17,  13,   7,  -8, -27, -75, -76, -65;
/I:         I=-31; MI=0; MD=-79; IM=0; DM=-79;
/M: SY='K';  M= -45, -34, -25,  45, -43, -10, -10, -75,  48, -73, -26,  14, -34,  37,  38, -29,  18, -42, -78, -46; D=-31;
/I:         I=-31; DM=-79;
/M: SY='P';  M=   7, -82, -49, -18, -43,  -8, -67, -72, -27, -70, -68, -27, 107, -32, -69,   8, -29, -55, -17, -53;
/M: SY='M';  M= -19, -69, -62, -72,  18, -78, -63,   6, -47,  50,  96, -72, -76, -17, -69, -45,  -9,   0, -69,  -9;
/M: SY='H';  M= -38, -71,   1, -10, -69, -54,  91, -72, -17, -58, -62,  29,  -4, -51, -19,  41,  50, -51, -85,   0;
/M: SY='F';  M=   5,   5, -76, -73,  72, -66,   7,  14, -71, -10, -49, -71,   8, -71, -71, -23, -33,  11, -51,  69;
/M: SY='K';  M= -12, -75, -13,  14, -48, -30,  -5, -48,  45, -37, -43,  39, -36,  26,  32,  11, -23, -47, -71,  32;
/M: SY='E';  M= -10, -78,  56,  79, -81, -56, -55, -77,   0, -75, -41, -16, -61,  33, -43, -26, -11, -34, -23, -69;
/M: SY='I';  M= -65, -74, -85, -81, -25, -88, -78,  87, -78,  44,  28, -78, -77, -73, -79, -74, -59,   5, -73, -55;
/M: SY='W';  M=  10, -33, -79, -72,  20, -58, -41,  19, -37,  21,  20, -72, -75, -53, -62, -37,  25,  10, 112,   3;
/M: SY='E';  M=  -4, -76,  48,  55, -79, -34,   6, -78,  32, -63, -68,  29, -64,  37,  -7,  -5, -28, -60, -82, -42;
/M: SY='E';  M=  -4, -51, -32,  45, -66, -72,  13,   8,  34, -16, -10, -27, -67,  32,  34, -34, -38,   1, -74,   6;
/M: SY='I';  M=  35, -45, -78, -74, -46, -20, -77,  66, -72,  -9,  19, -70, -73, -69, -75, -29, -17,  44,  -1, -60;
/M: SY='Q';  M=  13,  15, -63,   9, -26, -53, -41,  13,  20,  12, -19, -12, -70,  47, -44,  -3,  -5,  16,   6, -35;
/M: SY='E';  M=  10, -75,  29,  55, -79, -41, -56, -55,  45, -60, -49,  -6, -45,  27,  20,   0, -16, -52, -79, -68;
/M: SY='K';  M= -14, -45,  -7,  15, -13, -27,  -6,  -9,  30,  21,   8,  15, -70,  11,  25,  -4, -27, -17, -75, -28;
/M: SY='G';  M= -23, -74, -10, -22, -41,  59, -22, -40,  32,   0,  16,  30, -69, -12,  -7, -15, -51, -44, -75, -25;
/M: SY='L';  M= -42, -34, -21, -13,   1,  27,  -3, -27,  -8,  48,   7,   7, -23,  15, -49, -36, -47, -31,  -7,  16;
/M: SY='W';  M= -20, -74,  24, -36,  16, -65,  -8,  12,   7,   9,  -8, -40, -73,  -9,  19, -14,  -1,  14,  57,  30;
/M: SY='S';  M= -32, -21,  34,  16, -36, -49, -26, -37,  27, -43, -65,  16,  14,  14, -10,  41,  33, -42, -82, -66;
/I:         I=-19; MD=-49;
/M: SY='W';  M= -72, -60, -17, -26, -25, -62,  -8, -46,  -3, -39, -45, -37, -24, -27, -23,   9,  -5, -40,  33, -83; D=-19;
/I:         I=-19; MI=0; MD=-49; IM=0; DM=-49;
/M: SY='G';  M= -47,-103, -61, -99, -45,  52, -35,-104, -77, -78, -97, -31, -67, -93, -71, -12, -58, -51,-102, -31; D=-19;
/I:         I=-19; DM=-49;
/M: SY='K';  M=  -3, -75,   3,  24, -23, -47, -10, -40,  63, -27, -24,  -3,  -1,  20, -11,   1,  -4, -33,   9, -36;
/M: SY='T';  M= -13, -69,  30,  36, -74, -24, -10, -55,  -3, -70, -24,  29, -63,  -2, -33,  14,  69, -41, -85, -67;
/M: SY='P';  M= -29, -18,  21,  22, -57, -59, -62, -34, -25, -57, -66, -19,  89,  36, -15,  -2, -11, -29, -25, -32;
/M: SY='W';  M=   4,  -8,   0,  34, -30, -38,  -8,   4,   5,   5, -20, -26, -22,  -4,  10,  -9, -20,  11,  59, -43;
/M: SY='A';  M=  43, -70,   1,  18, -76, -50, -16, -45,  27, -54, -19,  24,  -4,  24,   3,  10,  16, -43, -80, -67;
/M: SY='T';  M=  -7,  14,   8,   7, -69, -53, -22, -14, -15, -31, -17,  -2, -65,  22, -12,  32,  66, -19, -82, -37;
/M: SY='L';  M=   5, -71, -55, -44, -24, -74, -65,   8,   5,  39,  36, -14, -14,  -9,  15, -23, -40,  30,   7, -19;
/M: SY='I';  M=  15, -32, -52, -23, -50,   1, -40,  39, -14,  -2,  18,  33, -71,  16,   3,   2, -25, -13, -22,  11;
/I:         I=-42; MD=-106;
/M: SY='A';  M=  63, -69, -65, -34, -75,  12, -41, -29, -63, -52, -65, -15, -56,  -2, -34,  35,  11, -27, -36, -46; D=-42;
/I:         I=-42; MD=-106;
/M: SY='Q';  M=  -3, -81, -20,  13, -36, -44, -14, -37,  -8, -34,  20, -11, -74,  55,  40,   2,  -8, -33, -81, -29; D=-42;
/I:         I=-42; MI=-106; IM=-106; DM=-106;
/M: SY='L';  M= -51, -71, -84, -78,  53, -85, -18,  48, -77,  62,  -8, -79, -81, -74, -58, -74, -62,   6, -65, -27;
/M: SY='Y';  M= -11, -42, -48, -56,   3, -35,  40, -36, -51, -20, -53,  -3, -76, -37, -46,  19, -20, -46,   2, 106;
/M: SY='T';  M=  -2, -42, -37, -14, -67, -35, -24, -37, -22, -23,  13,  -3, -66,   2,  30,   8,  73,   9, -82, -64;
/M: SY='D';  M= -30, -45,  82,  37, -54, -45,   7, -45, -35, -23, -34,  13, -66,  20,  -2,  -2, -18, -62, -86, -34;
/M: SY='M';  M= -27,  -9, -79, -63, -29, -79, -71,  61, -50,  45,  61, -42, -54, -68, -73,  -1, -14,   1, -75, -56;
/I:         I=-23; MI=0; MD=-58; IM=0; DM=-58;
/M: SY='N';  M= -35, -73, -26, -64, -74,  34, -37, -32, -14, -30,  -8,  72, -30, -26, -12,   5,  24, -12, -23, -70; D=-23;
/I:         I=-23; DM=-58;
/M: SY='E';  M= -13, -76,  11,  25, -67, -16, -13,   2,  -4,  20,  14, -24,  12,  24,  -8, -41,  -4,   0, -81, -65; D=-23;
/I:         I=-23; DM=-58;
/M: SY='D';  M= -20, -40,  92,  13, -65, -26,  -5, -82,  -1, -68, -56,   9, -31, -15, -35,  13, -34, -78, -93, -70; D=-23;
/I:         I=-23; DM=-58;
/M: SY='S';  M=  -1, -44, -13, -59, -58,  43, -36, -63,  -3, -76, -49,  13,  15, -17, -11,  61,  11, -45, -80, -70; D=-23;
/I:         I=-23; DM=-58;
/M: SY='R';  M= -23, -54, -28, -20, -69, -74, -58,  -2,   7,  -7, -34, -27,  13, -16,  88, -23, -10, -33, -22, -44;
/M: SY='F';  M= -73, -71, -87, -81, 117, -70, -68, -36, -77, -17, -28, -76, -85, -37, -75, -73, -66, -13, -43,  -9;
/M: SY='V';  M=   0, -26, -53, -18,   4, -65, -48,  45, -11,  -2,  14, -69, -74, -37, -14, -44,  -8,  52, -21,  26;
/M: SY='R';  M= -25,  15, -63, -55,   3, -71,  13, -34,  49, -13, -26, -22, -18,   1,  59,  10, -18, -36, -69,  25;
/M: SY='V';  M=  -9,   2, -71, -39, -21, -65, -46,  22, -52,  25,   4, -14, -57, -31, -47, -31,  44,  52, -78, -15;
/I:         I=-31; MD=-79;
/M: SY='G';  M=  15, -74,  -3,   6, -65,  70, -10, -50, -18, -79, -71, -10, -25,  -8, -37,  24, -33, -74, -78, -72; D=-31;
/I:         I=-31; MI=0; MD=-79; IM=0; DM=-79;
/M: SY='P';  M= -32, -79,  45,  31, -54, -44, -25, -77,  13, -61, -41,  24,  69, -13,  26,   2, -22, -75, -82, -70;
/M: SY='G';  M=  -5, -73,  10, -42, -60,  69, -20, -61, -32, -69, -69,  60, -68,  -1, -32,  -5,  -5, -51, -79, -38;
/M: SY='T';  M= -60, -41, -62,   4, -25, -48,   0, -10,  27,  10,  12, -21, -70,  16,  38, -23,  40,   4,  -7,   8;
/M: SY='W';  M= -60, -84, -89, -79,  73, -77, -70, -40, -72, -46,  -7, -83, -82, -51, -72, -75, -74, -51, 144,  67;
/M: SY='G';  M=  39,  -3,   0, -29,   5,  58, -67, -30, -20, -61, -25, -43, -69, -18, -26,   1,  -5, -65,  43, -25;
/M: SY='L';  M= -50, -26, -83, -76, -42, -84, -41,   9, -77,  85, -30, -81, -82, -70, -75, -45, -40, -12, -72, -38;
/M: SY='R';  M= -24, -43, -27, -50, -51, -69, -56, -52,  62, -56, -43,   3, -69, -16,  77,   8,   0, -35, -75, -28;
/M: SY='E';  M=  15, -72,  22,  56, -76, -12, -32, -33,  13, -61, -66,   1, -39, -17, -11,  39,  -5, -22, -81, -69;
/M: SY='W';  M= -42, -47, -11, -11,   4, -29, -67, -25, -14,  -8,  -5,  17, -20,   0,  21,  -4, -32, -68, 130,   3;
/I:         E1=0; IE=-380; DE=-380;

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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2025_04 which contains 573'661 sequence entries.

Total number of hits	98 in 98 different sequences
Number of true positive hits	98 in 98 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, Prokaryotes (Bacteria)
Maximum number of repetitions [info]	1
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	CJA_Sigrist
Feature key [info]	DOMAIN
Feature description [info]	HTH HARE-type
Version [info]	2

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

98 sequences

ASXL1_HUMAN (Q8IXJ9), ASXL1_MOUSE (P59598), ASXL2_CHICK (Q5ZM88),

ASXL2_HUMAN (Q76L83), ASXL2_MOUSE (Q8BZ32), ASXL3_HUMAN (Q9C0F0), 
ASXL3_MOUSE (Q8C4A5), RLT1_ARATH  (F4HY56), RLT2_ARATH  (Q9FFH1), 
RPOE_BACAH  (A0RLC4), RPOE_BACAN  (Q81JW0), RPOE_BACC1  (Q72XA8), 
RPOE_BACC2  (B7IQZ2), RPOE_BACC4  (B7HFN7), RPOE_BACC7  (B7HY99), 
RPOE_BACCQ  (B9IRX2), RPOE_BACCR  (Q814T1), RPOE_BACCZ  (Q630Q9), 
RPOE_BACHK  (Q6HAU4), RPOE_BACLD  (Q65DT6), RPOE_BACP2  (A8FIE6), 
RPOE_BACSU  (P12464), RPOE_BACVZ  (A7Z9T5), RPOE_HALH5  (Q9K6D6), 
RPOE_LACAC  (Q5FME7), RPOE_LACDA  (Q1GBQ3), RPOE_LACDB  (Q04C52), 
RPOE_LACJO  (Q74LG3), RPOE_LACLA  (Q9CHT4), RPOE_LACLM  (A2RIW1), 
RPOE_LACLS  (Q030Z9), RPOE_LACPL  (Q88Z77), RPOE_LEUCK  (B1MXM6), 
RPOE_LEUMM  (Q03YU3), RPOE_LIGS1  (Q1WV31), RPOE_LIMF3  (B2GA55), 
RPOE_LIMRD  (A5VI25), RPOE_LIMRJ  (B2G5K4), RPOE_LISIN  (Q927T3), 
RPOE_LISMF  (Q71WL9), RPOE_LISMO  (Q8Y494), RPOE_LISW6  (A0ALP6), 
RPOE_MACCJ  (B9E8H2), RPOE_MYCGE  (P47268), RPOE_MYCPN  (P75090), 
RPOE_OCEIH  (Q8EM52), RPOE_OENOB  (Q04D45), RPOE_PEDPA  (Q03DX9), 
RPOE_SHOC1  (Q5WB42), RPOE_STAA1  (A7X4Y0), RPOE_STAA2  (A6U3L3), 
RPOE_STAA3  (Q2FF00), RPOE_STAA8  (Q2FWD0), RPOE_STAA9  (A5IUS3), 
RPOE_STAAB  (Q2YUM5), RPOE_STAAC  (Q5HE72), RPOE_STAAE  (A6QIX2), 
RPOE_STAAM  (P66714), RPOE_STAAN  (P66715), RPOE_STAAR  (Q6GEU7), 
RPOE_STAAS  (Q6G7I2), RPOE_STAAT  (A8YY93), RPOE_STAAW  (P66716), 
RPOE_STACT  (B9DMC7), RPOE_STAEQ  (Q5HM94), RPOE_STAES  (Q8CRM5), 
RPOE_STAS1  (Q49Z74), RPOE_STRA1  (Q3K3S3), RPOE_STRA3  (Q8E7P9), 
RPOE_STRA5  (Q8E291), RPOE_STRE4  (C0M8K7), RPOE_STRGC  (A8AVB9), 
RPOE_STRMU  (Q8DWG2), RPOE_STRP1  (P66719), RPOE_STRP2  (Q04LZ9), 
RPOE_STRP3  (P0DF34), RPOE_STRP4  (B5E1U3), RPOE_STRP6  (Q5XA09), 
RPOE_STRP7  (C1C5L8), RPOE_STRP8  (Q8NZF7), RPOE_STRPG  (A2RCL2), 
RPOE_STRPI  (B1IA31), RPOE_STRPJ  (B8ZLX1), RPOE_STRPN  (P66717), 
RPOE_STRPQ  (P0DF35), RPOE_STRPS  (B2IM97), RPOE_STRR6  (P66718), 
RPOE_STRS2  (A4VZE7), RPOE_STRS7  (C0MFQ8), RPOE_STRSY  (A4VT63), 
RPOE_STRT1  (Q5M1S8), RPOE_STRT2  (Q5M6C1), RPOE_STRTD  (Q03MQ8), 
RPOE_STRU0  (B9DTJ7), RPOE_STRZJ  (C1CCN9), RPOE_STRZP  (C1CIY6), 
RPOE_STRZT  (C1CQ00), RPOE_UREPA  (Q9PPP2)

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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]

13 PDB

pdb_00002krc; pdb_00002m4k; pdb_00004nc7; pdb_00004nc8; pdb_00006zca; pdb_00006zfb; pdb_00007f75; pdb_00008h1t; pdb_00008svf; pdb_00008x6g; pdb_00008xa6; pdb_00008xa7; pdb_00008xa8
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