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 PS50960

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PURL: https://purl.expasy.org/prosite/signature/PS50960

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General information about the entry

Entry name [info]	HTH_PSQ
Accession [info]	PS50960
Entry type [info]	MATRIX
Date [info]	01-FEB-2004 CREATED; 01-OCT-2013 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC50960
Associated ProRule [info]	PRU00320

Name and characterization of the entry

Description [info]

Psq-type HTH domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=53;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=53;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=3.0544367; R2=0.0002543; TEXT='NScore';
/CUT_OFF: LEVEL=0; SCORE=44615; N_SCORE=14.4; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=13943; N_SCORE=6.6; MODE=1; TEXT='R?';
/DEFAULT: B1=*; E1=*; MM=*; II=*;

...

                A     C     D     E     F     G     H     I     K     L     M     N     P     Q     R     S     T     V     W     Y
/I:         B1=-8455; E0=*; BM=-44; BD=-5044;
/M: SY='M';  M=  316,-3779, -583, -470, -482, -946,-1979,-3827,  710, -603, 2002,  428, 1450,-1524,  916,  295, -499, -154,-3971,-3297; M0=-512;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='P';  M= -814,-3782,-2224,-1675,-4089,  983,-1996,-3826, 1282,-3793,-2879,  952, 1646,-1543, 1313,  669,-2296,  336,-3977,   -1; M0=-1041;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M= -214,-3781,-2200, 1233, -369,  258,  326,-1346, 2021,-3791,-2874,-1960,-3412,-1524, 1389,  -99,  688,-1040,-3972,-3298; M0=-926;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M=-2338,-3803,   34, -833,-4121,  342, 1213,-1045, 1308,-3818, 1127,  550,-3406,-1513, 2138,  168,  257,-1050, 1061,-3308; M0=-950;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M= -791,-3858,-2257,-1703,-4185, 1547,  327,-3928, 2242,-3870,-2950,  527,-3462,-1559, 1977, -742, -730,-3484,-4033,    0; M0=-1414;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=-1355,-3801,-2189,  181, -679,   21,  595,-1044, 1876,-1894,-2892,-1950, 1761, -444, 1741, -376, -548,-3421,-3987,-3307; M0=-845;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M=-2557,-2598,-3945,-3354,-2578,-3965,-2766, -435,  -27,  133,-1792,-3252, 1272,-2898, 2787, -247, -459, -510,-3031, 1881; M0=-1266;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=-3141,-4406,-3129,-2461,-4827,-4039,  533,-4469, 2317,-4358,-3509,  926,-4092,  -13, 1871,-3029, 1064, 1141, 1681,-3940; M0=-1955;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='Q';  M=  890,-3807, -440, -704, -420, -945,-1971, -928, -131,-3822,-2896, -121, -618, 1802, -330, 1559,  212,  281,-3991,-3309; M0=-671;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='W';  M=-2608,-2437,-4924, -982, -237,-4151,-3009,  245,-3890, 1770,-1633,-3786,-4201, -317, -600,-3235,-2548, -713, 3791, 2723; M0=-1727;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='T';  M= -972,-3844,   81, -391,-4162, -995,-2011,-3911,-1599,-1457,-2938,  538,-3441,-1554, -408, 1439, 2895,-3465,-4032,-3349; M0=-1309;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='L';  M=-2340,-3791,   33, 1287, -512,-3317, -240, -125, -737, 1723,-2882, -236, 1255, -143,  644,-1329,-2279,-3408,-3979,-3302; M0=-895;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='E';  M=  544,-3826, 1342, 2462,-4146,-3321,-1983,-3897,  715,-3842,-2915, 1008, -587,-1523, -950,-2231,  216,-3448,-4009, -120; M0=-1368;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='E';  M= -727,-3799, 1760, 2378, -418,-3314,-1973, -909, -318,-1553,  267,  348,-3407,  753,-2062,   52, -573,-3418,-3986,-3306; M0=-1010;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=-3540,-3460,-5391,-4469,  687,-4898,-3426,-2691, 2843, 1412, 2591,-4191,-4868,-3431, -642,-4043, -666,-2797,-3756,-3481; M0=-2343;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='M';  M=  844,-3328,  233,  317,-3470,-3471,-2160, 1425, -407,  572, 2185, -853,-3557,  376,-2316, -778, -578,  423,-3631,-3078; M0=-749;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='E';  M= 1122,  645,  240, 1953,-4139,-3317, -156,-3889, 1060,-3833,-2906, -104,-3410, 1591, 1359,-2224,-2283,-3439,-4000,-3317; M0=-1465;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='A';  M= 2937,-3890,-7059,-6734,-4551,-6759,-6754, 1294,-6673,-3347,  401,-6488,-6581,-6589,-6800,-6114,-4368, 1829,-6203,-5710; M0=-4137;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='I';  M=-1079,  809,-7032,-6670,-4362,-6785,-6517, 3027,-6581, 1846,-3108,-6446,-6543,-6420,-6658,-6112,-4363,  882,-5941,-5519; M0=-3871;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='E';  M=  437,-3810,   53, 1610, -487,-1082,  566,-3882,  600,-1100,-2899, -285,-3404, 1583, 1559, -411, -620,-3432,-3994,-3311; M0=-848;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='A';  M= 1993,  827,  463, -555,-3898,-3357,  531,-3601,-1637,  -76, -487,-2024,-3449,  636, 1643,  200,-2293,-1687,-3874, -108; M0=-976;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='V';  M=-2586,  911,-4931,-4295, -251,-4134,  379, 1799,-3890,  469,-1615,-3779,-4184, -412,-3690,-1065,-2527, 2527,-2869, 1374; M0=-1753;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M=-2338,-3810, 1375, 1649,-4130,-3312,  624,-3880,  268, -619,  334,-1947,-3405,  440, 1830,    2,  432,-3431, 1139,-3311; M0=-1136;
/I:         MM=-46; MI=-10161; MD=-5045; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='N';  M=  124,-3774,  287,  679,-4095,  186,-1933,-1010,  387,-3790,-2863, 1854,-3368,-1474, 1234, 1321,  -39,-3396,-3958,-3275; M0=-1011;
/I:         MM=-2; MI=-10118; MD=-11160; IM=-894; II=-1115; DM=-383; DD=-2100;
/M: SY='G';  M=-2354,-3822, -814,  660,-4141, 2824,  327,-3890,  805,-1618,-2913,  300,-3419,-1527,-2077, -783, -597,-1126,-4007,-3325; M0=-1252;
/I:         MM=-243; MI=-10161; MD=-2700; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=-2142,-3616, -437, 1473,-3937, 1341,-1774,-3688, 1964,-3632,-2705,  414,  289,  326,  557, -526, -888,-3238,-3799,-3116; M0=-1132;
/I:         MM=-547; MI=-9921; MD=-1668; IM=-894; II=-1115; DM=-134; DD=-3496;
/M: SY='M';  M=-2248,-2076,-4563,  224, -200,-3797,-2669, 1242, -580, 1163, 3674,-3433,-3844,-3161,-3345,-2882, -125,  442,-2537,-2197; M0=-1462;
/I:         MM=-3; MI=-9715; MD=-10757; IM=-894; II=-1115; DM=-84; DD=-4140;
/M: SY='S';  M=-2339,-3805, -396, -384,-4124, -206,-1973,-3872,  254,-3820,  197,-1950, -724,-1514,  240, 2651, 1037,-1125,-3990,-3309; M0=-1223;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=  -91,-2447,-4630,-4013,  702,-4087,-2943, -372, 1484,  401,  647,-3635, -250, 1071,  178,-3159,  158, 1307,-2900,  789; M0=-1015;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='S';  M=  876,  756,-2188,-1639,-4122,-1082,  712,-3871, 1355,-1548,  266, 1080,-1090,  838,  819, 1393, -746,-3425,-3989,-3308; M0=-897;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='Q';  M= -203,-3811,  240, 1002,-4133,-1310, 1347,-3883, 1901,-3827,-2901,-1947,-3405, 1947,  685,  722, -504,-3433,-3995,-3312; M0=-1267;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='A';  M= 2551,-3921,-7103,-6771,-4497,-6898,-6826, 1932,-6720,   45,-3208,-6570,-6646,-6618,-6850,-6259,-4412, 1823,-6196,-5729; M0=-3940;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='A';  M= 2713, 1859,-6151,-6197,-5921,  514,-5418,-5645,-5895,-5925, 1352,-4741,-4822, -338,-5705, 1716,-3576,-4686,-6207,-6053; M0=-3424;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M=  489,-3812, -513,-1638,-4133,-1763,-1972,-3884, 1530,-3828,-2901,  583,-3406, 1101, 2740, -273,-1121,-1073,-3995,-3313; M0=-1316;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='E';  M=  387,-3633,  248, 1637,-1154,-3362,-2030,  963,  752, -108, 1314, -372,-3453,-1599, 1297,-2276, -749,-3214,-3864, -755; M0=-792;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='F';  M=-5919,-5209,-6955,-7045, 3573,-6680,  640, -699,-6589,  670,-4395,-5514,-6575,-5563, -243,-5882,-5809,-5009,-2531, 2914; M0=-3954;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='G';  M=-3680,-5361,  391, -537,-5614, 3058,  501,-5439, -601,-5348,-4523, 1717,-4412, -176,-3676, -929,-3678,-4956,-5526,-4689; M0=-2502;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='I';  M=-4470, 2775,-7166,-6853,-4574,-7034,-7098, 2898,-6834,  399,-3256,-6688,-6741,-6774,-7008,-6424,-4460, 2297,-6384,-5890; M0=-4318;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='P';  M= -916,  705, -418,-1734,-3912, -241,-2032,-3616, -415,-1495,-2767, -229, 3171,-1598,-2138,  990, -626,-3243, 1062,-3247; M0=-1143;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='H';  M= -877,-3785,-2197,  141, -417,-1191, 1497, -972, 1063,-3797,  286, -211,  131,  709, 1318,  374, -486, -905,  978, 1409; M0=-553;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='S';  M=-2417,-3896, -569, -530,-4216,  360,-2042,-3969,-1634,-3912,-2988,  500,  243,  -36,  697, 2606,  583,-3518,-4079,-3392; M0=-1364;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='T';  M=-3294,-3930,-5183,-5494,-6488,-4128,-5389,-6351,-5546,-6549,-5627,-4606,-4916, 1881,-5475, -103, 3726,-5095,-6633,-6477; M0=-4117;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='L';  M=-1262,-4298,-7318,-6836,  616,-6991,-6133, 1725,-6654, 2626,-2315,-6665,-6524,-5973,-6439,-6279,-4722,  976,-5167,-5116; M0=-3771;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='W';  M= -202,-3667,-2266,  284,-3925,-3352,-2018,-1306,  175,-1447,-2772, -181,-3444,   51, 1676,  992,-2291, -321, 2647, 2392; M0=-940;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M=-2340,-3782, 1505,-1651, -392, 1000,-1979,-3831, -234, -615,  348, -306,-3412,  624, 1748, -158,  610,-3397,-3973,  927; M0=-825;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='W';  M=-2615,-2606,-4164, -892, -277,-4046, 1452, 2566, 1005,-2461,-1803,-3391,-4102,-3036, 1305,-3094,-2553, -613, 2631, 1512; M0=-1580;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='C';  M=  344, 2433,-4924,-4288, -126,-4132,-3003,-1903,  -49, 1410, 1448,-3776,-4182,-3509, -765,-3216,-2525, 1981,-2870,  994; M0=-1576;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M= -129,-3825,  249,-1651,-4147,-3325,  327,-3897, 2500,-3840,-2914, 1159,-3418, 1604, 1525, -880,-2292,-3448,-4005, -181; M0=-1506;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='R';  M= -900,-3817,  688,  746,-4138,  530, 1341,-3889, 1364,-3833,-2906, 1648,-3409,  -85, 1941, -829,-2283,-3439,-4000,-3317; M0=-1288;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=-1144,-3925,-2425, 1055,-4249,-3501,-2115,-3966, 2392, -216,-3022,-2146,-3585, -350, 2099,-2426,  252,  -82,-4086,-3454; M0=-1359;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='G';  M=  242,-3810,  -42, 1170,-4132, 1256, 1099,-3882,  961,-2233,-2900,  843,  182,  426,-2057,-1326,  172,-3432,-3994,  862; M0=-849;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='K';  M=    5,-3792, -489,  203,-4105,  368,-1975, 1289, 1754, -564,  258, -236,-3409, 1498,-2065, -817, -548,-3410,-3981,  -59; M0=-722;
/I:         MM=-2; MI=-10161; MD=-11203; IM=-894; II=-1115; DM=-701; DD=-1378;
/M: SY='I';  M= -842,  932,-1034,  -50,  573,-4044,-2885, 1802, -837,  979, 1519,-3506, -646,-3197,  169, -964,  161,  338,-2933,-2576; M0=-711;
/I:         B0=*; E1=-1000;

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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	39 in 37 different sequences
Number of true positive hits	39 in 37 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]	2
Matrix type [info]	protein_domain
Scaling database [info]	window20
Author [info]	PS_Langendijk_Genevaux
Feature key [info]	DOMAIN
Feature description [info]	HTH psq-type
Version [info]	4

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

37 sequences

BAB1_DROME  (Q9W0K7), BAB2_DROME  (Q9W0K4), CENP1_HUMAN (B2RD01),

CENPB_CRIGR (P48988), CENPB_HUMAN (P07199), CENPB_MOUSE (P27790), 
DANR_DROME  (Q9VBW9), DANR_DROPS  (Q29CW0), DAN_AEDAE   (Q16IB4), 
DAN_CULQU   (B0X560), DAN_DROME   (Q9VBW6), DAN_DROPS   (Q29CW2), 
JERKL_HUMAN (Q9Y4A0), JERKL_MOUSE (B2RRL2), JERKY_HUMAN (O75564), 
JERKY_MOUSE (Q60976), LCORL_CHICK (Q5ZJK5), LCORL_HUMAN (Q8N3X6), 
LCORL_MOUSE (Q3U285), LCOR_HUMAN  (Q96JN0), LCOR_MOUSE  (Q6ZPI3), 
LOV_DROME   (P14083), MBLK1_APIME (Q95YM8), MBR1_CAEEL  (G5EGQ5), 
TIGD1_HUMAN (Q96MW7), TIGD2_HUMAN (Q4W5G0), TIGD2_MOUSE (Q0VBL1), 
TIGD3_HUMAN (Q6B0B8), TIGD3_MOUSE (Q7TM95), TIGD4_HUMAN (Q8IY51), 
TIGD4_MOUSE (Q8BUZ3), TIGD5_BOVIN (G3MY25), TIGD5_HUMAN (Q53EQ6), 
TIGD5_MOUSE (Q499M4), TIGD5_RAT   (B1WC39), TIGD6_HUMAN (Q17RP2), 
TIGD7_HUMAN (Q6NT04)

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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]

4 PDB

pdb_00001bw6; pdb_00001hlv; pdb_00002cob; pdb_00002elh