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 PS51888

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PURL: https://purl.expasy.org/prosite/signature/PS51888

Direct ScanProsite submission

General information about the entry

Entry name [info]	CLIP
Accession [info]	PS51888
Entry type [info]	MATRIX
Date [info]	08-MAY-2019 CREATED; 08-MAY-2019 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51888
Associated ProRule [info]	PRU01236

Name and characterization of the entry

Description [info]

Clip domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=53;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=53;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=3.0961080; R2=0.0063122; TEXT='-LogE';
/CUT_OFF: LEVEL=0; SCORE=1094; N_SCORE=10.0; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=540; N_SCORE=6.5; MODE=1; TEXT='R?';
/DEFAULT: M0=-41; 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='P';  M= -11, -76,   2,  21,   7, -16, -59, -70,  -2, -20, -64, -57,  61, -52,  34,  40, -55, -68, -71,  10;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/M: SY='T';  M= -57, -72, -56, -54, -74,   9, -58, -18,   1, -70, -62,  33, -67,  40,  56,   0,  66, -63, -80, -65;
/I:         I=-33; MD=-84;
/M: SY='T';  M=  13, -67, -60, -63, -71, -67, -67, -58, -58, -66, -62,  33,   4, -62,   2, -45,  87,  15, -88, -69; D=-33;
/I:         I=-33; MD=-84;
/M: SY='P';  M= -14, -84, -66, -58, -84,   9, -66, -78, -54, -81, -70, -64,  95,   8,  43,  -2,   0, -76, -80, -77; D=-33;
/I:         I=-33; MI=0; MD=-84; IM=0; DM=-84;
/M: SY='N';  M= -62, -75,  76, -49,   3,  -4, -54, -80, -57, -81, -76,  77, -72, -56, -64,  33, -53, -79, -91, -68; D=-33;
/I:         I=-33; DM=-84;
/M: SY='G';  M= -57, -79,  26,  -7, -84,  71, -63, -84, -58, -81, -72,   2, -69,  51, -10, -51,  24, -79, -81, -74; D=-33;
/I:         I=-33; DM=-84;
/M: SY='E';  M= -59, -75,   4,  53, -70,  25, -59,  -6,  16,  -1,  26,   4, -65,  13,   5, -55,  22, -62, -78, -66;
/M: SY='Q';  M=  21, -74, -55,   1, -79,  -9, -58, -75,  35, -75, -65,  22,  36,  54,  19,  19,   5, -70, -78, -68;
/M: SY='G';  M=  34, -73, -64, -68, -81,  89, -69, -83,  15, -81, -71, -52, -67, -62, -66, -48, -63, -75, -74, -75;
/M: SY='Q';  M= -58, -71, -59, -57, -62, -69, -58,  20,  -9, -24, -54,  43, -69,  52,  20,   2,  52,  11, -75,  18;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/M: SY='I';  M= -61, -73, -74,  -4, -53, -83, -72,  59,  22,  31,  27, -71, -74, -62,   1, -68, -58,  44, -76, -59;
/M: SY='P';  M= -57, -74, -58, -59, -71, -17,  46, -62, -57, -18, -61,  47,  71, -57,  -4,  43,   3,   9, -84, -66;
/M: SY='I';  M=  -9, -71, -78, -75,   8, -77, -70,  59, -73,  30, -41, -72, -76, -69, -74,  18, -55,  38, -66,  38;
/M: SY='Y';  M= -60, -75, -53,  35, -58, -68,  51,  -3,  -1, -18, -58,  29, -69, -48,  35,  34,  -3, -63, -69,  53;
/M: SY='D';  M= -10, -74,  64,  42, -79, -62, -54, -74, -48, -76, -70,  32, -65,  18,  22,  44, -51, -21, -86, -68;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/M: SY='P';  M= -60, -79,  25,  24, -77,   8, -59, -74,  41, -19, -65, -53,  51,  30,  27,  -3,   1, -72, -78, -69;
/I:         I=-31; MI=0; MD=-79; IM=0; DM=-79;
/M: SY='Y';  M= -26, -73,   2, -65, -45, -70, -56,  34, -64, -14, -51,   9,  -1, -62, -67,  21,  37,  -3, -58,  81;
/M: SY='L';  M= -63, -72, -83, -76,  11, -84, -75,  48, -76,  56, -37, -79,  30, -74, -77, -72, -59,  42, -73, -55;
/M: SY='W';  M= -18, -76,   2,  33,  29, -77, -60, -53, -55,  47, -48, -68, -75, -56,  42, -66, -64, -57,  59,  34;
/M: SY='E';  M=   6, -77,  43,  61, -83,  26, -56, -81,   0, -77, -70,   6, -63,  55, -54,  -3, -58, -75, -80, -70;
/M: SY='Y';  M= -62, -73, -72, -67, -43, -78, -58,  14,  -4,  33,  19, -68, -76,  13,   0, -11,   5,  27, -59,  72;
/I:         I=-17; MD=-44;
/M: SY='L';  M= -67, -74, -85, -78, -47, -89, -74,  45, -74,  70, -35, -82, -83, -72,   1, -77, -63,  18, -76, -58; D=-17;
/I:         I=-17; MD=-44;
/M: SY='K';  M= -62, -75, -59, -52, -73, -71, -59, -60,  64, -24,  20,  40, -70,  50,   2, -56,  19,  16, -81, -66; D=-17;
/I:         I=-17; MD=-44;
/M: SY='T';  M= -63, -77,   8,  -3, -81, -72,  30, -73,  -8, -76, -70,  24, -72,  38, -63,  17,  62, -17, -94, -71; D=-17;
/I:         I=-17; MD=-44;
/M: SY='P';  M= -16, -91,  -3,  14, -97,  13, -77, -94, -72, -94, -86, -68,  33,  23, -78,  31, -12, -88, -97, -88; D=-17;
/I:         I=-17; MD=-44;
/M: SY='N';  M= -86,-102,   0, -12, -91,   8, -78, -95, -78, -31, -87,  30,  24,   9, -22, -79, -83, -97, -96,  10; D=-17;
/I:         I=-17; MI=0; MD=-44; IM=0; DM=-44;
/M: SY='T';  M= -20, -88,  25, -73, -95, -81, -82, -90, -75, -93, -87, -67,   5, -76, -15,  33,  52, -83,-106, -88; D=-17;
/I:         I=-17; DM=-44;
/M: SY='P';  M= -17, -97,  -9,  16, -95,   7,  66, -94, -72, -92, -81, -70,  70,  -7, -78, -71, -76, -92, -97, -80; D=-17;
/I:         I=-17; DM=-44;
/M: SY='E';  M=  19, -78,   4,  55, -78, -67, -59, -79, -55, -78, -71,   9, -69,  48, -61,  33,  -9, -74, -80,  14; D=-17;
/I:         I=-17; DM=-44;
/M: SY='D';  M= -21, -82,  72, -56, -74,  38, -64,  -5, -66, -21, -69,   7, -76,   7, -72, -61, -65, -18, -84,  13; D=-17;
/I:         I=-17; DM=-44;
/M: SY='T';  M=   5, -76, -69, -21, -65, -77, -68,  28, -57, -19, -58,  10, -75, -62,  46, -58,  50,  -7, -79,  15; D=-17;
/I:         I=-17; DM=-44;
/M: SY='R';  M= -66, -76,  -7, -66,  26, -75, -66, -10, -19,  15, -58,  32, -78, -63,  36,  19,  24, -13, -80, -60; D=-17;
/I:         I=-17; DM=-44;
/M: SY='F';  M= -73, -79,  22, -71,  68, -81,  23, -58, -74,  18, -55, -69, -84, -72, -73,  -7,  -1, -62, -56,  67; D=-17;
/I:         I=-17; DM=-44;
/M: SY='L';  M= -67, -71, -83, -78, -47, -87, -73,  19, -78,  76, -35, -79, -82, -73, -77, -71,  26,  -4, -77, -58; D=-17;
/I:         I=-17; DM=-44;
/M: SY='R';  M= -59, -77,   5,  -3, -78, -66, -53, -80,   5, -76, -66,  10, -69,  38,  86,  43, -55, -74, -79, -64;
/I:         I=-42; MI=0; MD=-106; IM=0; DM=-106;
/M: SY='A';  M=  42, -71, -13,  -1, -73,  27, -65,  -3,  17, -66, -61,   7,  14,   5,  -8, -51,   2,  15, -79, -69;
/M: SY='S';  M=  -9, -68,   6, -58, -67, -58, -61, -59, -60,  16, -59,  30,  35, -55, -65,  77, -45,  -5, -82, -66;
/M: SY='Q';  M= -58, -75, -60,  19, -66, -72,  28,  22,  -2,   6, -50, -58, -69,  82, -54,  19, -56,  28, -77, -60;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/M: SY='G';  M= -52, -75, -59,  17, -78,  80, -65, -79, -11, -24, -68, -52, -67,  11,   3,   2,   2, -75, -75, -72;
/I:         I=-17; MD=-42;
/M: SY='Y';  M= -66, -77,  27,  -5,  48, -14,  31, -63, -66,   2, -58, -61, -76, -64, -69,  14,  13, -65,  61,  61; D=-17;
/I:         I=-17; MD=-42;
/M: SY='R';  M= -73, -89,  -3,  33,   0,  27, -71, -85, -19, -24, -76,  12, -81, -63,  38, -68, -13, -83, -88, -75; D=-17;
/I:         I=-17; MI=0; MD=-42; IM=0; DM=-42;
/M: SY='N';  M=  11, -74,   1, -60, -80,  31, -58, -77,  -3, -23, -70,  82, -74,  17, -62,  -4, -57, -75, -87, -74; D=-17;
/I:         I=-17; DM=-42;
/M: SY='W';  M= -63, -82, -62,  -6, -78,  51, -65, -10, -53, -80, -72,  47,   8, -58,  52, -20, -65, -77,  54, -71; D=-17;
/I:         I=-17; MI=0; MD=-42; IM=0; DM=-42;
/M: SY='Q';  M= -57, -74, -56,   0, -63,  11, -55,  -4, -10, -63, -58,  46, -70,  66,  -2,  -3,   2,  24, -71,  37;
/M: SY='P';  M= -17, -82, -63,  22, -66, -72, -64,  -9, -58,   0, -57, -69,  94,  11,  -2, -62, -59,   6, -73,  18;
/M: SY='I';  M= -26, -74,  23, -61, -54, -76,  26,  46,  19,  34, -44, -62, -73,   8, -61,  -8, -57,  20, -73,  15;
/M: SY='V';  M= -58, -70, -85, -80,  31, -86, -82,  61, -77,  -7, -40, -78, -78, -78, -78, -70, -55,  78, -75, -53;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/M: SY='C';  M=-109, 159,-129,-129,-119,-124,-129,-126,-124,-116,-117,-115,-139,-132,-131,-111,-109,-113,-149,-130;
/I:         E1=0; IE=-380; DE=-380;

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Post-processing [info]

PROMOTED_BY

PS50240

Numerical results [info]

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

Total number of hits	24 in 23 different sequences
Number of true positive hits	24 in 23 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	4
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	85.71 %

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	2
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	CJA_Sigrist
Feature key [info]	DOMAIN
Feature description [info]	Clip
Version [info]	1

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

23 sequences

CFB_TACTR   (Q27081), CLB10_ANOGA (Q7QBP4), CLB14_ANOGA (Q9NAS8),

CLB15_ANOGA (Q9NAS9), CLB4_ANOGA  (Q7PEV7), CLB9_ANOGA  (F5HKX0), 
CLC9_ANOGA  (A0A1S4GMJ4), EAST_DROME  (P13582), GRASS_DROME (Q9VB68), 
HAYAN_DROME (A8JUP7), HP8_BOMMO   (Q2VG86), MP1_DROME   (A0A126GUP6), 
PCE_TACTR   (P21902), PPAE1_SPOLT (Q49QW1), PPAE_BOMMO  (Q9XXV0), 
PPAF1_HOLDI (O97366), PPAF2_HOLDI (Q9GRW0), PPAF3_HOLDI (Q8I6K0), 
PSH_DROME   (Q9VWU1), SER7_DROME  (Q9V3Z2), SNAK_DROME  (P05049), 
SPE_DROME   (Q9VCJ8), VSP_BOMIG   (B5U2W0)

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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

4 sequences

CLA28_ANOGA (A0A1S4H5M5), CLA30_ANOGA (A0A1S4HE51), CLA8_ANOGA  (A0A1S4H5S2),

CLB8_ANOGA  (Q8MZM7)

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PDB
[Detailed view]

2 PDB

pdb_00002b9l; pdb_00002xxl