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 PS51027

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PURL: https://purl.expasy.org/prosite/signature/PS51027

Direct ScanProsite submission

General information about the entry

Entry name [info]	INTEGRASE_DBD
Accession [info]	PS51027
Entry type [info]	MATRIX
Date [info]	01-OCT-2004 CREATED; 10-MAY-2017 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51027
Associated ProRule [info]	PRU00506

Name and characterization of the entry

Description [info]

Integrase DNA binding domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=50;
/DISJOINT: DEFINITION=PROTECT; N1=6; N2=45;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=1.8148787; R2=0.0159785; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=2856.8085938; R2=1.9361702; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=419; H_SCORE=3668; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=294; H_SCORE=3426; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: M0=-9; D=-20; I=-20; 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='K';  M= -7, -7,-29, -7,  8,-15,-20, -4,-21, 11,-19,-10, -6,  3,  7,  6, -7,-10,-20,-19, -8,  7;
/M: SY='W';  M=-14,-25,-28,-28,-18, 13,-24,-15, -2,-14,  5,  9,-22,-17,-13, -9,-21,-11, -7, 17,  8,-15;
/M: SY='V';  M= -6,-27, 18,-32,-30,  4,-31,-27, 13,-24,  3,  2,-25,-31,-29,-23,-13, -5, 25,-27, -6,-30;
/M: SY='Y';  M=-16,-17,-29,-19,-14, 12,-26,  3, -6,  2, -4,  3,-17,-24, -7,  0,-19,-11,-11, 16, 38,-12;
/M: SY='W';  M=-18,-29,-35,-31,-26, 23,-27, -7, -2,-17, -5, -5,-28,-29,-18,-16,-27,-17,-11, 65, 48,-22;
/M: SY='R';  M=-14, -4,-30, -4,  6,-26,-20, -6,-30, 41,-26,-10,  0,-14, 10, 48,-10,-10,-20,-20,-10,  6;
/M: SY='D';  M=-13, 14,-26, 17,  3,-19,-19, -9, -7,-10, -6, -9,  7,-15, -6,-13, -6, -5,-10,-32,-12, -2;
/M: SY='P';  M= -9,-11,-29, -8, -1,-22,-11,-12,-16, -2,-18,-11, -7, 15, -3,  2, -6, -8,-16,-27,-19, -5;
/M: SY='R';  M= -9,-13,-26,-13, -8,-15, -5,-14,-16,  5, -3, -3, -9,-20, -6, 10,-12, -8,-12,-21,-11, -8;
/I:         I=-5; MD=-25;
/M: SY='D';  M=-12, 12,-22, 15,  6,-20,-15,  1,-20,  1,-13,-12,  7,-13,  3,  4, -1,  2,-16,-27,-10,  3; D=-5;
/I:         I=-5; MI=0; MD=-25; IM=0; DM=-25;
/M: SY='N';  M= -9,  5,-28,  4,  6,-28,  0,  1,-28,  8,-27,-14, 10, -7,  7,  7, -1, -9,-27,-27,-17,  6;
/M: SY='E';  M= -7, -4,-22, -2,  7,-17,-19,-10,-13,  2, -7, -7, -5,-14,  2,  3, -1,  1, -9,-27,-12,  4;
/M: SY='W';  M=-18,-37,-48,-37,-29,  7,-12,-29,-22,-20,-21,-20,-37,-29,-20,-20,-37,-29,-30,135, 25,-20;
/M: SY='K';  M=-12, -3,-29, -1, 12,-21,-22,  0,-23, 29,-20, -8, -4,-13, 10, 16,-10,-10,-20,-16,  1, 10;
/I:         I=-6; MD=-32;
/M: SY='G';  M= -2, -3,-28, -2,-13,-29, 52,-16,-37,-12,-28,-19,  2,-17,-15,-14, -1,-17,-27,-20,-26,-14; D=-6;
/I:         I=-6; MI=-32; IM=-32; DM=-32;
/M: SY='P';  M=-10,-17,-37,-11, -2,-28,-15,-13,-17,-10,-25,-15,-16, 62, -4,-17, -9,-11,-26,-28,-24, -7;
/M: SY='D';  M= -7,  3,-27,  8, -4,-19, -5,-10,-20,-10,-14,-11, -4, -7, -6,-14, -5, -5,-18,-14, -9, -5;
/M: SY='P';  M=-12, -7,-31, -5,  6,-26,-20, -8,-20, 11,-22,-11, -4, 16,  6, 14, -7, -9,-20,-26,-17,  3;
/M: SY='V';  M=  0,-26,-16,-28,-24,  2,-27,-22, 22,-21, 14,  9,-24,-26,-22,-20,-12, -3, 28,-21, -1,-24;
/M: SY='L';  M=-10,-27,-10,-29,-18,  4,-31,-21, 18,-28, 36, 14,-26,-28,-19,-21,-25,-10,  9,-23, -4,-19;
/M: SY='W';  M=-10,-25,-31,-28,-22, -3,-19,-22,  3,-18, -6, -3,-21,-23,-12,-18,-17, -9, -2, 31,  7,-17;
/M: SY='W';  M=-11,-11,-35, -9,  1,-17,-13,-14,-27, 11,-23,-16,-12,-16, -1,  8,-16,-16,-24, 29, -1,  1;
/M: SY='G';  M=  8, -9,-25,-10,-16,-27, 52,-19,-33,-17,-27,-19,  0,-17,-16,-19,  6,-12,-23,-22,-27,-16;
/M: SY='R';  M=-10,  4,-27,  8, 12,-26,-16, -3,-29, 18,-22,-15,  3,-13, 10, 29, -2, -8,-21,-26,-14,  9;
/M: SY='G';  M= -1, -8,-30, -7,-13,-30, 62,-18,-39,-17,-29,-20,  0,-18,-17,-18,  0,-19,-30,-21,-29,-15;
/M: SY='A';  M= 21,-12,-17,-17,-10, -9, -5, -9,-13,-12,-13,-10, -9, -6,-10,-17,  5, -2, -8,-16, -5,-11;
/M: SY='V';  M= 19,-22,-14,-28,-22, -8,-19,-26, 17,-18,  3,  3,-20,-20,-20,-22, -3, -2, 26,-24,-12,-22;
/M: SY='C';  M= -2,-25, 34,-30,-27, -7,-28,-27,  5,-25,  6,  0,-25,-32,-26,-24,-13, -6, 17,-34,-16,-27;
/M: SY='V';  M= -4,-30,-16,-32,-28,  2,-32,-28, 31,-24, 20, 14,-28,-28,-26,-22,-16, -4, 38,-26, -6,-28;
/M: SY='K';  M= -8, -7,-25, -9, -1,  0,-19, -8,-18, 10,-17, -9, -3,-11, -3,  3, -4, -6,-15,-14,  2, -2;
/M: SY='D';  M=-12, 11,-28, 19,  7,-25,-17, -3,-20, -6,-21,-17,  3, 10, -4,-12, -2, -5,-18,-32,-15,  0;
/I:         I=-4; MD=-18;
/M: SY='Q';  M= -9,  0,-27,  1, 11,-27, -7, -2,-20,  4,-18, -9,  2,-12, 17,  9, -1, -9,-21,-23,-14, 13; D=-4;
/I:         I=-4; MD=-18;
/M: SY='E';  M= -5,  9,-19, 13, 14,-20, -1, -4,-20,  1,-15,-11,  4, -7,  2, -4,  0, -5,-17,-21,-14,  8; D=-4;
/I:         I=-4; MD=-18;
/M: SY='S';  M=  2,  3,-10,  1,  5,-12, -7, -1,-11,  0,-11, -8,  4, -6,  1, -2,  7,  5, -8,-17, -8,  3; D=-4;
/I:         I=-4; MI=0; MD=-18; IM=0; DM=-18;
/M: SY='E';  M= -9, 16,-27, 22, 23,-32, -6, -3,-30,  6,-25,-19,  9, -9, 11, -1,  3, -6,-26,-31,-18, 17;
/M: SY='K';  M= -3,  1,-25,  1,  2,-24, -2,-11,-24,  7,-21,-14,  3, -8, -2,  3,  0, -4,-19,-26,-17,  0;
/M: SY='P';  M= -6,-17,-29,-16,-12, -9,-24,-14,  0,-14, -8, -6,-17, 19,-13,-19,-10, -5, -6,-16,  1,-16;
/M: SY='V';  M= -7,-19,-23,-22,-13, -2,-25,-16,  4, -4,  4,  4,-14,-21, -9,  2,-12, -7,  5,-20, -4,-12;
/M: SY='W';  M= -9,-34,-34,-34,-26,  4,-23,-28, -1,-20, -4, -7,-33,-23,-21,-20,-27,-17, -3, 65, 10,-22;
/M: SY='I';  M= -7,-28,-21,-31,-24,  1,-34,-25, 33,-23, 16, 13,-24,-24,-22,-23,-16, -6, 31,-22, -1,-25;
/M: SY='P';  M= -7,-18,-38,-10,  0,-29,-19,-20,-20, -7,-29,-19,-18, 80, -9,-18, -9, -9,-28,-29,-28, -9;
/M: SY='R';  M=-12, -4,-28, -3,  5,-12,-17,  0,-21,  0,-16,-13, -3,-17,  1,  6, -5, -5,-20,  0,  1,  2;
/M: SY='R';  M=-17, -8,-29, -9,  1,-21,-20, -3,-29, 31,-21,-10,  0,-18,  9, 60, -8, -7,-19,-21,-10,  1;
/M: SY='H';  M=-15, -6,-26, -4, -5, -5,-23,  6,-12, -3,  3,  0, -7,-21, -6,  0,-16,-12,-11,-22,  1, -6;
/M: SY='V';  M=  6,-20,-10,-26,-20, -4,-23,-23, 13,-19, 11,  7,-19,-22,-18,-19, -7,  5, 18,-25, -9,-20;
/M: SY='K';  M=-13, -3,-30, -3,  7,-27,-20, -7,-30, 44,-27,-10,  0,-13, 10, 42,-10,-10,-20,-20,-10,  7;
/M: SY='F';  M= -9,-19,-26,-22,-13,  7,-20,-12, -6, -9, -4, -3,-12, -8,-12, -4,-12,-10, -7,-14, -1,-14;
/M: SY='I';  M= -2,-21,-23,-27,-22,  5,-28,-21, 22,-22, 10,  7,-17,-21,-19,-23,-13, -7, 16,-16,  3,-23;
/M: SY='P';  M= -4, -7,-29, -8, -1,-23,-18,-13,-12,  0,-20,-11, -3, 20, -2, -4, -3, -4,-16,-27,-18, -4;
/M: SY='D';  M=-10,  8, -8, 11, 11,-27,-17,-10,-27, -3,-25,-20,  2,  7, -2,-10,  0, -2,-23,-35,-22,  4;
/I:         E1=0; IE=-105; DE=-105;

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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	106 in 106 different sequences
Number of true positive hits	106 in 106 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	1
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	99.07 %

Comments [info]

Taxonomic range [info]	Eukaryotes, Eukaryotic viruses
Maximum number of repetitions [info]	1
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	N_Hulo
Feature key [info]	DNA_BIND
Feature description [info]	Integrase-type
Version [info]	5

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

106 sequences

PO113_HUMAN (P63132), POK10_HUMAN (P10266), POK11_HUMAN (Q9UQG0),

POK19_HUMAN (Q9WJR5), POK25_HUMAN (P63136), POK6_HUMAN  (Q9BXR3), 
POK7_HUMAN  (P63135), POK8_HUMAN  (P63133), POL_ALV (Q7SQ98), 
POL_ALVA(Q04095), POL_BIV29   (P19560), POL_BLVAU   (P25059), 
POL_BLVJ(P03361), POL_CAEVC   (P33459), POL_EIAV9   (P11204), 
POL_EIAVC   (P32542), POL_EIAVY   (P03371), POL_FIVPE   (P16088), 
POL_FIVSD   (P19028), POL_FIVT2   (P31822), POL_HTL1A   (P03362), 
POL_HTL1C   (P14078), POL_HTL1L   (P0C211), POL_HTL32   (Q0R5R2), 
POL_HTL3P   (Q4U0X6), POL_HTLV2   (P03363), POL_HV190   (O93215), 
POL_HV192   (O12158), POL_HV193   (O89290), POL_HV196   (Q9QBY3), 
POL_HV197   (Q9QBZ9), POL_HV19N   (O41798), POL_HV1A2   (P03369), 
POL_HV1AN   (Q77373), POL_HV1B1   (P03366), POL_HV1B5   (P04587), 
POL_HV1B9   (Q73368), POL_HV1BR   (P03367), POL_HV1EL   (P04589), 
POL_HV1ET   (Q75002), POL_HV1H2   (P04585), POL_HV1JR   (P20875), 
POL_HV1LW   (P0C6F2), POL_HV1M2   (Q9QBZ1), POL_HV1MA   (P04588), 
POL_HV1MN   (P05961), POL_HV1MP   (Q9QBZ5), POL_HV1MV   (Q79666), 
POL_HV1N5   (P12497), POL_HV1ND   (P18802), POL_HV1OY   (P20892), 
POL_HV1RH   (P05959), POL_HV1S2   (Q9WC54), POL_HV1S9   (Q9WC63), 
POL_HV1SE   (O89940), POL_HV1U4   (P24740), POL_HV1V9   (Q9Q720), 
POL_HV1VI   (Q9QSR3), POL_HV1Y2   (P35963), POL_HV1YB   (Q9IDV9), 
POL_HV1YF   (O91080), POL_HV1Z2   (P12499), POL_HV1Z6   (P04586), 
POL_HV2BE   (P18096), POL_HV2CA   (P24107), POL_HV2D1   (P17757), 
POL_HV2D2   (P15833), POL_HV2EH   (Q89928), POL_HV2G1   (P18042), 
POL_HV2KR   (Q74120), POL_HV2NZ   (P05962), POL_HV2RO   (P04584), 
POL_HV2SB   (P12451), POL_HV2ST   (P20876), POL_HV2UC   (Q76634), 
POL_IPHA(P04026), POL_IPMA(P11368), POL_IPMAI   (P12894), 
POL_JEMBR   (Q82851), POL_JSRV(P31623), POL_MMTVB   (P03365), 
POL_MMTVC   (P11283), POL_MPMV(P07572), POL_OMVVS   (P16901), 
POL_RSVP(P03354), POL_RSVSB   (O92956), POL_SIVCZ   (P17283), 
POL_SIVEK   (Q1A249), POL_SIVG1   (Q02836), POL_SIVGB   (P22382), 
POL_SIVM1   (P05896), POL_SIVM2   (P05897), POL_SIVMB   (Q1A267), 
POL_SIVS4   (P12502), POL_SIVSP   (P19505), POL_SIVTN   (Q8AII1), 
POL_SIVV1   (P27973), POL_SIVVG   (P27980), POL_SIVVT   (P05895), 
POL_SMRVH   (P03364), POL_SRV1(P04025), POL_SRV2(P51517), 
POL_VILV(P03370), POL_VILV1   (P23426), POL_VILV2   (P23427), 
POL_VILVK   (P35956)

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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

UniProtKB/Swiss-Prot
False negative sequences

1 sequence

POL1_CHICK  (P10399)

PDB
[Detailed view]

61 PDB

pdb_00001c0m; pdb_00001c1a; pdb_00001c6v; pdb_00001ex4; pdb_00001ihv; pdb_00001ihw; pdb_00001qmc; pdb_00003jca; pdb_00004fw1; pdb_00004fw2; pdb_00005d7u; pdb_00005ejk; pdb_00005llj; pdb_00005m0r; pdb_00005t3a; pdb_00005tc2; pdb_00005u1c; pdb_00006put; pdb_00006puw; pdb_00006puy; pdb_00006puz; pdb_00006t6e; pdb_00006t6i; pdb_00006t6j; pdb_00006u8q; pdb_00006v3k; pdb_00006vdk; pdb_00006voy; pdb_00007jn3; pdb_00007ku7; pdb_00007kui; pdb_00007sep; pdb_00007sjx; pdb_00007u32; pdb_00007usf; pdb_00007ut1; pdb_00007z1z; pdb_00007zpp; pdb_00008a1p; pdb_00008a1q; pdb_00008buv; pdb_00008cbr; pdb_00008cbs; pdb_00008cbt; pdb_00008cbu; pdb_00008cbv; pdb_00008e14; pdb_00008fn7; pdb_00008fnd; pdb_00008fng; pdb_00008fnh; pdb_00008fnj; pdb_00008fnl; pdb_00008fnm; pdb_00008fnn; pdb_00008fno; pdb_00008fnp; pdb_00008fnq; pdb_00008w09; pdb_00008w2r; pdb_00008w34
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