Entry: PS51027

General information about the entry
Entry name INTEGRASE_DBD
Accession number PS51027
Entry type MATRIX
Date OCT-2004 (CREATED); OCT-2004 (DATA UPDATE); MAR-2013 (INFO UPDATE).
PROSITE Documentation PDOC51027
Associated ProRule PRU00506
Name and characterization of the entry
DescriptionIntegrase DNA binding domain profile.
Matrix / Profile 
/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='-LogE';
/CUT_OFF: LEVEL=0; SCORE=419; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=294; 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;
Numerical results
  • UniProtKB/Swiss-Prot release number: 2013_05, total number of sequence entries in that release: 540052.
  • Total number of hits in UniProtKB/Swiss-Prot: 106 hits in 106 different sequences
  • Number of hits on proteins that are known to belong to the set under consideration: 106 hits in 106 different sequences
  • Number of hits on proteins that could potentially belong to the set under consideration: 0 hits in 0 different sequences
  • Number of false hits (on unrelated proteins): 0 hits in 0 different sequences
  • Number of known missed hits: 1
  • Number of partial sequences which belong to the set under consideration, but which are not hit by the pattern or profile because they are partial (fragment) sequences: 0
  • Precision (true hits / (true hits + false positives)): 100.00 %
  • Recall (true hits / (true hits + false negatives)): 99.07 %
Comments
  • MATRIX_TYPE: protein_domain
  • Scaling database: UniProtKB/Swiss-Prot: reversed
  • Matrix author: N_Hulo
  • Taxonomic range: Eukaryotes, Eukaryotic viruses
  • Maximum known number of repetitions of the pattern in a single protein: 1
  • FT_KEY: DNA_BIND
  • FT_DESC: Integrase-type
  • VERSION: 1
Cross-references
UniProtKB/Swiss-Prot True positive hits:
POK10_HUMAN (P10266), POK12_HUMAN (P63135), POK17_HUMAN (P63136), 
POK20_HUMAN (Q9UQG0), POK2_HUMAN  (Q9BXR3), POK3_HUMAN  (Q9WJR5), 
POK5_HUMAN  (P63132), POK6_HUMAN  (P63133), POL_ALV     (Q7SQ98), 
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_RSVSA   (Q04095), POL_RSVSB   (O92956), POL_SIVCZ   (P17283), 
POL_SIVEK   (Q1A249), POL_SIVG1   (Q02836), POL_SIVGB   (P22382), 
POL_SIVM1   (P05896), POL_SIVMB   (Q1A267), POL_SIVMK   (P05897), 
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)
False negative hits (sequences which belong to the set under consideration, but which have not been picked up by the pattern or profile):
POL1_CHICK  (P10399)
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]		 1C0M; 1C1A; 1C6V; 1EX4; 1IHV; 1IHW; 1QMC; 1WKN; 1ZA9; 2G3L;

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