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 PS51351

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PURL: https://purl.expasy.org/prosite/signature/PS51351

Direct ScanProsite submission

General information about the entry

Entry name [info]	TFIIE_BETA_C
Accession [info]	PS51351
Entry type [info]	MATRIX
Date [info]	01-DEC-2007 CREATED; 10-MAY-2017 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51351
Associated ProRule [info]	PRU00682

Name and characterization of the entry

Description [info]

TFIIE beta central core DNA-binding domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=77;
/DISJOINT: DEFINITION=PROTECT; N1=6; N2=72;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-0.5422181; R2=0.0149058; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=5198.2871094; R2=2.4616542; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=607; H_SCORE=6693; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=473; H_SCORE=6363; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: M0=-5; D=-30; I=-30; B1=-500; E1=-500; MI=-50; MD=-50; IM=-50; DM=-50;

...

                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=-50; BD=-50;
/M: SY='A';  M= 12, -5,-28,  2,  0,-18, -8,-11,-14,  2,-14, -8, -9,  5,  9,  5,  6,  2, -7,-27,-16, -1;
/M: SY='T';  M=  8, -2,-18, -3, -7, -8,-14,-18,  8, -5,  1,  1, -1,-17,-10,-14,  4, 10, 10,-35, -9, -9;
/M: SY='N';  M=  3,  9,-19,  3,  1,-22, -7,  0,-12, -2,-14, -7, 18, -8,  7,-11,  8, 10,-16,-39,-20,  3;
/M: SY='G';  M= -3, -5,-33, -9, -8,-28, 32, -6,-16, -3,-21,-18, -3, 14, -4, -7, -1,-11,-29,-11,-23, -9;
/I:         I=-7; MD=-12;
/M: SY='I';  M=  6,-10,-15,-17,-13,  1,-11,-10, 18, -5, 10, 11, -3,-19, -9,-12, -5,  4, 15,-22, -5,-13; D=-7;
/I:         I=-7; MD=-12;
/M: SY='N';  M= -2, 15,-14, 15,  0, -5, -6,-11,-10,  5, -7, -4, 16, -9, -6, -5, -1, -3,-10,-23, -8, -4; D=-7;
/I:         I=-7; MI=0; MD=-12; IM=0; DM=-12;
/M: SY='I';  M=  0, -4,-12, -8,-10,  0,  1,-14, 10, -6,  5,  3, -3,-15,-13,-10, -6, -1,  5,-14,  0,-11; D=-7;
/I:         I=-7; DM=-12;
/M: SY='T';  M=  3, -6,-21, -3, -9, -9,-18,-16, -2, -5, -4, -8, -8,-14, -5, -1,  8, 10,  8,-24, -1, -9;
/M: SY='G';  M=  6,  5,-29, -3, -6,-20, 30,-20,-10,  1,-19, -9, 11,-10, -5,-10,  7, -4,-21,-19,-27, -7;
/M: SY='S';  M=  4, -2,-18, -4, -4,-14, -8,-14,-10,  1, -9, -2,  2, -8,  3,  1, 10,  9, -6,-28,-13, -3;
/M: SY='H';  M= -9, -2,-33, -3,  1,-24,-20, 49,-16, -5,-10,  3,  5,  7, -1,-13, -3, -2,-20,-41, -7,  0;
/M: SY='V';  M=  7, -3,-21, -4,-10, -5,-12,-16,  8, -6,  6,  7, -2,-19, -6, -9, -4,  4, 10,-31, -5,-10;
/M: SY='F';  M=  1,-11,-24,-18,-16, 22,-14,-15,  5, -6,  8,  0, -3,-25,-13,-12,  0,  0,  6,-20,  2,-17;
/M: SY='T';  M= 10, -4,-26, -7,-14,-13,-10,-18, -1, -7, -3, -4,  0, -8, -4,-19, 16, 28,  7,-34, -8,-11;
/M: SY='Q';  M=  6,-10,-25, -8,  5,-15,-18,-11,-10,  5,-11,  0,-10, -5, 32, 16, -5,  1, -9,-16, -3, 13;
/M: SY='I';  M= -1,-17,-14,-23,-17, 10,-21,-13, 26,-13, 22, 14,-12,-31,-13,-13,-15,  1, 19,-22, 10,-16;
/M: SY='M';  M=  5, -7,-24,-10, -5,-11,-17, 10,  0, -3,  3, 15, -5, -9, -4,-12, -1,  8,  1,-37, -5, -5;
/M: SY='Y';  M=-15,-15,-35,-15,-10,  7,-17,  4, -1, -3,  5,  4,-11,-14, -9, -7,-10, -9, -1,  1, 20,-11;
/M: SY='A';  M= 22, -8,-25,-13,-11,-11,-11,-20, 17, -8, -1,  6, -4,-18,  1,-12,  1, 10, 20,-39,-20, -9;
/M: SY='I';  M=  4,-17,-18,-26,-27,  3,-20,-23, 42,-19, 15,  6, -8,-30,-22,-21, -7, 10, 38,-32,  1,-26;
/M: SY='E';  M=  3, 15, -9, 25, 30,-33,-12, -9,-24, 12,-13,-10,  7, -2,  6,-10,  3, -9,-22,-28,-21, 22;
/M: SY='Y';  M=-25,-23,-38,-18,-15, 21,-23,  6, -7, -9, 15, -2,-25,-17,-11, -7,-13, -9,  0, 20, 44,-15;
/M: SY='L';  M= -2,-14,-11,-20,-14,  4,-16, -5, 24, -9, 26, 24, -9,-31,-17,-17,-13,  2, 12,-25,  8,-14;
/M: SY='K';  M= -1, -8,-24, -8, 12, -7,-16,-13,-18, 24,-13, 11, -5, -2, 12, 18, -5,-12,-17,-14, -6, 10;
/M: SY='K';  M=  6,  5,-22,  5, 11,-22, -5,-15,-16, 12,-15,  0,  5,  0,  9, -3,  5,  2,-16,-27,-17,  9;
/M: SY='R';  M= -3,-11,-27,-10,  2,-15,-17,  4,-15, 11,-14,  8, -8, -1, 17, 25, -5,-11,-13,-19, -6,  5;
/I:         I=-7; MI=0; MD=-11; IM=0; DM=-11;
/M: SY='D';  M=  1, 13,-26, 20, -6,-19, -1,-18,-18, -2,-11,-13,  8,-14,  0,  3, -2, -7,-12,-26,-13, -6;
/M: SY='W';  M= -9,-15,-15,-10, 15,-13,-11, -8,-21,  6,-13, -7,-19, -6, 11,  9, -8,-21,-19, 19,  0, 13;
/M: SY='P';  M= -7,-19,-26,-10, 10,-33,-10,  1,-24,  7,-24,-31,-28, 77,  0, -9, -9, -4,-31,-14,-15,  2;
/M: SY='L';  M= -3, -8,-13, -6, -9,  3,-19,-13, 12, -6, 18, 14,-13,-25,-14, -6,-13, -2, 10,-23, 12,-11;
/M: SY='T';  M=  8, -4,-21, -7, -9,-19,-13,-12, -6, -4, -8, -9, -2, 15, -2,-20, 16, 29, -3,-41,-14, -7;
/M: SY='F';  M= -5,-15,-23,-25,-24, 36,-20,-20, 14,-12, 16, -1, -6,-31,-19,-14, -9, -4, 15,-15, 13,-24;
/M: SY='D';  M=  0, 15,-16, 28, 15,-22,-14,-12,-22,  2, -7,-16,  2, -9,  6, -6,  1, -7,-18,-25, -9, 10;
/M: SY='E';  M= -3,  4, -5, 14, 37,-33,-15, -8,-28, 12,-13,-12, -7,  1, 19, -3, -4,-16,-28, -1,-12, 32;
/M: SY='I';  M= -2,-18,-16,-34,-26,  4,-12,-18, 53,-20, 24, 12, -4,-30,-20,-28,-12,  0, 34,-28, -3,-26;
/M: SY='Q';  M=  0, -7,-11, -8,  2, -6,-17, -7, -2, -1,  6, 11, -7,-17, 12,  6,-11, -4, -7,-21,  2,  6;
/M: SY='D';  M=  3, 22,-20, 35,  7,-29, -3,-15,-19,  0,-12,-19, 10,-12, -8,-12,  8, -2,-14,-33,-17,  0;
/I:         I=-7; MD=-12;
/M: SY='F';  M= -6, -9,-20, -9,  1,  9,-14,  1, -9,  3,  1, -1, -8, -6, -2, -3, -4, -8, -5, -3,  9, -1; D=-7;
/I:         I=-7; MI=0; MD=-12; IM=0; DM=-12;
/M: SY='Y';  M=-11,-16,-29,-15,-19, 13,-25, -5,  5,-14, 18,  1,-16,-19,-13,-15, -6, 10, 13,-11, 30,-17;
/I:         I=-9; MD=-15;
/M: SY='D';  M= -6,  2,-26, 11, -1,-16, -5,  9,-17,  0, -8, -5, -5, -4, -1,  5, -1,-10,-13,-13,  0, -3; D=-9;
/I:         I=-9; MI=-15; IM=-15; DM=-15;
/M: SY='I';  M= -7,-19,-15,-23,-17, 13,-18,-18, 20,-16, 16,  1,-19,-20,-15,-14,-15, -3, 15, -6, 14,-16;
/M: SY='G';  M=  3,  8,-26, 10, -1,-24, 16, -5,-16, -3,-17,-17,  5, -9,-10,-13, 15, -1,-20,-24,-21, -7;
/M: SY='L';  M= -6, -9, -5, -9, -3, -9,-18, -3, -3, -5,  3, -1,-10, -1, -6,-11, -7, -1, -8,-26, -5, -5;
/M: SY='P';  M= -3,  7,-27, 12,  5,-26,-11, 12,-22,  4,-19,-11,  5, 14,  1, -1,  1, -4,-23,-36,-15,  0;
/M: SY='Q';  M=  0, -3,-26, -2,  1,-13, -7,-12, -7,  3, -9, -6, -4, -2,  5, -1, -2, -1,-11,-19, -5,  0;
/M: SY='N';  M=  5,  9,-23,  8, -1,-18, -3,-16,-12,  4,-11, -1, 10, -9,  3, -3,  3,  3,-11,-32,-16, -1;
/M: SY='E';  M=  0,  0,-22,  8, 16,-23,-13, -6,-20,  7,-11,-12, -6, 10, 11, -3, -1, -4,-18,-19, -7, 12;
/M: SY='W';  M= -3,-15,-15,-17, -1,  3,-14,-17, -2, -3,  3, -1,-15,-18, -3, -8, -6, -6, -2,  5,  4, -2;
/M: SY='L';  M= -8,-16,-12,-20,-19, 26,-23, -9, 21,-18, 27, 10,-17,-31,-22,-17,-15, -2, 17,-20, 22,-19;
/I:         I=-7; MD=-12;
/M: SY='I';  M=  3,-12,-14,-15, -8,  3,-15,-12, 10, -6,  8,  6, -9,-19, -2, -3, -8, -2, 10,-18,  0, -6; D=-7;
/I:         I=-7; MI=0; MD=-12; IM=0; DM=-12;
/M: SY='E';  M= -2,  1, -9,  8, 27,-32,-15, -2,-26, 11,-17,-14, -3, 16, 20,  5, -4,-11,-27,-21,-18, 24;
/M: SY='I';  M= 10, -9,-18,-12, -9, -5, -9,-13, 12, -6,  5,  8, -6,-20, -6, -9,  3,  5, 10,-31,-11,-11;
/M: SY='L';  M= -8,-12, -4,-15, -9, 18,-20, -9, 17,-14, 32, 17,-16,-29,-17,-18,-17, -3,  9,-18, 21,-10;
/M: SY='K';  M=  0, -6,-27, -4, 11,-12,-12,-15,-18, 26,-19,  8, -6,  9,  6, 17,  0, -8,-16,-19, -9,  6;
/M: SY='N';  M=  2, 10,-18,  7,  5,-18, -4,-13,-16, 10,-17, -2, 17,-10,  4,  7,  1, -7,-17,-31,-21,  3;
/M: SY='N';  M= -5,  7,-20, -7,-10,-10, -7, 19,  3, -9, -1, 10, 25,-19,-10,-18, -6,  2,-11,-46,-13,-10;
/M: SY='P';  M= -2, 11,-21, 24, 13,-36,-10, -5,-27,  7,-18,-22,  0, 29,  2, -5, -3, -6,-25,-33,-19,  7;
/M: SY='R';  M= -4,-10,-22, -5,  8,-13,-16,-13,-26, 22,-19,  7,-11,  0, 20, 44, -5,-20,-16, -9, -6,  9;
/M: SY='I';  M=  1,-19,-18,-29,-27, 11,-20,-21, 42,-18, 19,  8,-10,-35,-24,-19,-12,  2, 36,-26,  5,-27;
/M: SY='Q';  M=  1, -7,-21, -3, 10,-19,-17,  3,-10,  6, -6,  3, -8, -7, 12,  5, -4, -8, -9,-19, -6, 10;
/M: SY='W';  M=-23,-31,-34,-32,-24, 45,-19,-23, -6,-10, 12,-11,-28,-31,-17, -5,-16,-19,  3, 49, 40,-24;
/I:         I=-5; MD=-8;
/M: SY='D';  M=  0, 22,-14, 25, -3,-18, -4,-11, -4, -3, -5, -8, 22,-14, -8,-12, -1, -1, -6,-33,-14, -6; D=-5;
/I:         I=-5; MD=-8;
/M: SY='P';  M=  5, -6,-18, -2,  8,-19, -5, -3,-13,  7,-14,-10, -9, 31,  2, -5,  2,  1,-14,-22,-17,  3; D=-5;
/I:         I=-5; MI=0; MD=-8; IM=0; DM=-8;
/M: SY='A';  M=  8, -4,-22, -2,  2,-16,-10,-18, -2,  4, -7,  1, -5, -9,  2, -2, -1, -1,  1,-25,-13,  1;
/M: SY='N';  M=  1, 14,-23, 15,  7,-22, -2, -4,-17,  7,-17, -6, 16, -7, -2, -7,  7, -2,-20,-34,-19,  1;
/M: SY='G';  M= -1,  8,-24,  3, -4,-25, 30,-18,-15, -1,-18,-13, 12,-11, -6, -5,  1,-13,-24,-14,-25, -5;
/M: SY='T';  M=  5, -3,-20, -9,-12,-10,-14,-20,  2, -3,  2,  6,  1, -6, -6,-19,  7, 25,  6,-36, -3, -8;
/M: SY='F';  M=-21,-27,-29,-38,-32, 76,-28,-22,  2,-12, 25,-12,-16,-36,-26,-10,-13,-15, 10, 10, 38,-32;
/M: SY='Q';  M=  9, -5,-16, -4,  9,-18,-14,-10,-11,  8, -7,  6, -5, -6, 11,  3,  3,  1, -8,-26,-14,  9;
/M: SY='Y';  M=-30,-29,-48,-26,-24, 47,-30,  8, -8,-11, 21,-10,-25,-23,-16, -5,-15,-15,  5, 23, 57,-24;
/M: SY='R';  M= -2,-12,-22,-11, -4, -6,-16,-15, -6, 12, -8, 10,-10,-11,  3, 25, -5,-11, -1,-16, -3, -4;
/M: SY='P';  M= -1,-14,-28, -7,  7,-31, -7,  3,-23,  7,-26,-31,-20, 72, -2,-10,  4,  6,-29,-32,-22, -2;
/M: SY='K';  M= -2, -7,-20, -8,  9,-10,-13,-13, -5, 15, -5,  8, -7, 10, -4, -6, -5, -3, -9,-23, -5,  3;
/M: SY='Y';  M=-24,-23,-42,-17,-16, 14,-27, 27,  0,-15, 19,  3,-25,-17,-12, -8,-16, -9,  5,  3, 45,-16;
/M: SY='D';  M= -1, 21,-26, 22, -2,-27,  3, -6,-17,  0,-16,-12, 21, -3, -9,-14,  3,  0,-20,-40,-21, -6;
/M: SY='I';  M=  2,-17,-19,-27,-27,  4,-12,-23, 43,-19, 16,  6, -9,-32,-23,-21,-11,  2, 34,-26,  0,-27;
/M: SY='R';  M= -6,-11,-22, -9, -7, -9,-19,  4,-14,  3,-10,  6, -7,-10,  9, 31, -7,-12, -7,-21, -2, -3;
/I:         E1=0; IE=-50; DE=-50;

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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	7 in 7 different sequences
Number of true positive hits	7 in 7 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]	CJA_Sigrist
Feature key [info]	DNA_BIND
Feature description [info]	TFIIE beta
Version [info]	5

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

7 sequences

T2EB_BOVIN  (Q2KJF9), T2EB_DICDI  (Q54KJ8), T2EB_HUMAN  (P29084),

T2EB_MOUSE  (Q9D902), T2EB_SCHPO  (P79011), T2EB_XENLA  (P29540), 
T2EB_YEAST  (P36145)

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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]

69 PDB

pdb_00001d8j; pdb_00001d8k; pdb_00005fmf; pdb_00005fyw; pdb_00005fz5; pdb_00005iy6; pdb_00005iy7; pdb_00005iy8; pdb_00005iy9; pdb_00005iya; pdb_00005iyb; pdb_00005iyc; pdb_00005iyd; pdb_00005oqj; pdb_00005oqm; pdb_00005sva; pdb_00006gyl; pdb_00006gym; pdb_00006o9l; pdb_00007eg9; pdb_00007ega; pdb_00007egb; pdb_00007egc; pdb_00007ena; pdb_00007enc; pdb_00007lbm; pdb_00007ml0; pdb_00007ml1; pdb_00007ml2; pdb_00007ml4; pdb_00007nvr; pdb_00007nvs; pdb_00007nvt; pdb_00007nvu; pdb_00007nvy; pdb_00007nvz; pdb_00007nw0; pdb_00007o4i; pdb_00007o4j; pdb_00007o4k; pdb_00007o4l; pdb_00007o72; pdb_00007o73; pdb_00007o75; pdb_00007zs9; pdb_00007zsa; pdb_00007zsb; pdb_00008bvw; pdb_00008byq; pdb_00008cen; pdb_00008ceo; pdb_00008gxq; pdb_00008gxs; pdb_00008s51; pdb_00008s52; pdb_00008s55; pdb_00008s5n; pdb_00008umh; pdb_00008umi; pdb_00008uoq; pdb_00008uot; pdb_00008wak; pdb_00008wal; pdb_00008wan; pdb_00008wao; pdb_00008wap; pdb_00008waq; pdb_00008war; pdb_00008was
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