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 PS51052

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PURL: https://purl.expasy.org/prosite/signature/PS51052

Direct ScanProsite submission

General information about the entry

Entry name [info]	CYCLOTIDE
Accession [info]	PS51052
Entry type [info]	MATRIX
Date [info]	01-DEC-2004 CREATED; 07-APR-2021 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51052
Associated ProRule [info]	PRU00395

Name and characterization of the entry

Description [info]

Cyclotides profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=29;
/DISJOINT: DEFINITION=PROTECT; N1=3; N2=27;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=2.1032069; R2=0.0062083; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=1428.9858398; R2=1.3886256; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=1031; H_SCORE=2861; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=709; H_SCORE=2414; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: M0=-11; 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='G';  M=  0,-10,-30,-10,-20,-30, 70,-20,-40,-20,-30,-20,  0,-20,-20,-20,  0,-20,-30,-20,-30,-20;
/M: SY='L';  M= -5,-16,-15,-21,-15,  1,-25,-20,  6,-21, 22,  6,-16,-21,-15,-15, -7, 18,  5,-25, -5,-15;
/M: SY='P';  M=-10,-20,-40,-10,  0,-30,-20,-20,-20,-10,-30,-20,-20, 90,-10,-20,-10,-10,-30,-30,-30,-10;
/I:         I=-6; MD=-32;
/M: SY='V';  M=  0,-16, -5,-16,-16,  0,-16,-16, 16,-11,  5,  5,-16,-16,-16,-11, -5,  0, 27,-16, -5,-16; D=-6;
/I:         I=-6; MI=-32; IM=-32; DM=-32;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='G';  M=  0,-10,-30,-10,-20,-30, 70,-20,-40,-20,-30,-20,  0,-20,-20,-20,  0,-20,-30,-20,-30,-20;
/M: SY='E';  M=-10, 10,-30, 20, 60,-30,-20,  0,-30, 10,-20,-20,  0,  0, 20,  0,  0,-10,-30,-30,-20, 40;
/M: SY='T';  M=  5,  0,-10, -5, -5,-15,-11,-15,-15,-10,-19,-15,  5,-10, -5,-10, 29, 36, -5,-35,-15, -5;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='V';  M=  0,-30,-10,-30,-30,  0,-30,-30, 30,-20, 10, 10,-30,-30,-30,-20,-10,  0, 50,-30,-10,-30;
/M: SY='W';  M= -9,-24,-39,-24,-25,-12, 29,-25,-31,-20,-25,-20,-18,-25,-20,-20,-18,-25,-30, 58, -2,-20;
/M: SY='G';  M= -5,-19,-30,-24,-25,-16, 19,-25,  1,-25, -7, -2, -9,-20,-20,-25, -9,-15, -2,-20,-16,-25;
/M: SY='P';  M= -5, -9,-24,-10, -5,-19,-20,-20,-15,-10,-19,-15, -9, 36,-10,-15,  6, 22,-14,-30,-19,-10;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='N';  M=-10,  8,-25, -8,-14,-11,-18, -8, 12,-14, -7, -2, 23,-20, -9,-14, -4, -5, -2,-31,-11,-14;
/M: SY='T';  M=  5,  0,-10, -5, -5,-15,-11,-15,-15,-10,-19,-15,  5,-10, -5,-10, 29, 36, -5,-35,-15, -5;
/M: SY='P';  M= -1,-11,-26, -5,  0,-25,-11,-15,-20,-10,-30,-20, -6, 44, -5,-15, 13,  4,-21,-35,-25, -5;
/I:         I=-6; MI=0; MD=-29; IM=0; DM=-29;
/M: SY='G';  M=  0,-10,-30,-10,-20,-30, 70,-20,-40,-20,-30,-20,  0,-20,-20,-20,  0,-20,-30,-20,-30,-20;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='T';  M=  5,  0,-10, -5, -5,-15,-11,-15,-15,-10,-19,-15,  5,-10, -5,-10, 29, 36, -5,-35,-15, -5;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='K';  M=  1,  0,-19,  0,  5,-25, -9,-10,-25, 18,-30,-15,  5,-10,  5,  8, 17,  6,-15,-31,-15,  5;
/M: SY='W';  M=-15, -3,-36,-12,-16, -4,-11,-12,-20,-11,-25,-20,  6,-25,-11,-11,-17,-16,-30, 63,  7,-11;
/M: SY='P';  M=-10,-11,-35, -5,  5,-30,-20,-15,-25, 18,-30,-15,-11, 44, -1,  3,-10,-10,-25,-25,-21, -1;
/M: SY='V';  M=  0,-30,-10,-30,-30,  0,-30,-30, 30,-20, 10, 10,-30,-30,-30,-20,-10,  0, 50,-30,-10,-30;
/M: SY='C';  M=-10,-20,120,-30,-30,-20,-30,-30,-30,-30,-20,-20,-20,-40,-30,-30,-10,-10,-10,-50,-30,-30;
/M: SY='Y';  M= -9, -9,-19,-15,-15,  8,-25, -2, -5,-10, -5, -5, -9,-19,-10,-10,  2, 22, -5, -2, 31,-15;
/M: SY='R';  M=-15, -5,-30, -5,  5,-25,-20, -5,-30, 39,-25,-10,  0,-15, 10, 52,-10,-10,-20,-20,-10,  5;
/M: SY='N';  M=-10, 40,-20, 20,  0,-20,  0, 10,-20,  0,-30,-20, 60,-20,  0,  0, 10,  0,-30,-40,-20,  0;
/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	207 in 201 different sequences
Number of true positive hits	207 in 201 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	21
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	90.79 %

Comments [info]

Taxonomic range [info]	Eukaryotes
Maximum number of repetitions [info]	3
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	CJA_Sigrist
Version [info]	7

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

201 sequences

CIRA_CHACT  (C0HKH8), CIRA_CHAPA  (P56871), CIRB_CHAPA  (P56879),

CIRC_CHAPA  (P84641), CIRD_CHAPA  (P84642), CIRE_CHAPA  (P84643), 
CIRF_CHAPA  (P84644), CYC10_CLITE (C0HKG2), CYC11_CHACT (C0HKH6), 
CYC11_CLITE (C0HKG3), CYC12_CLITE (G1CWH8), CYC13_CHACT (I0B6G2), 
CYC13_CLITE (C0HJS0), CYC14_CLITE (C0HJS1), CYC15_CLITE (C0HJS2), 
CYC16_CLITE (C0HJS3), CYC17_CLITE (P86849), CYC18_CLITE (C0HJS5), 
CYC19_CLITE (C0HJS6), CYC1_CLITE  (G1CWH0), CYC20_CLITE (C0HJS7), 
CYC2_CHACT  (I0B6F2), CYC2_CLITE  (G1CWH1), CYC3_CHACT  (C0HKH3), 
CYC3_CLITE  (C0HKG1), CYC4_CLITE  (G1CWH3), CYC5_CHACT  (C0HKH2), 
CYC5_CLITE  (G1CWH4), CYC6_CHACT  (C0HKH1), CYC6_CLITE  (C0HKF9), 
CYC7_CHACT  (I0B6F4), CYC7_CLITE  (G1CWH5), CYC8_CHACT  (I0B6F5), 
CYC8_CLITE  (G1CWH6), CYC9_CHACT  (C0HKH0), CYC9_CLITE  (C0HKG0), 
CYCA_CLITE  (P86841), CYCA_PETHY  (B3EWH5), CYCB_CLITE  (P86842), 
CYCC_CLITE  (P86843), CYCD_CLITE  (P86844), CYCE_CLITE  (P86845), 
CYCF_CLITE  (P86846), CYCG_CLITE  (P86847), CYCH_CLITE  (P86848), 
CYCJ_CLITE  (P86850), CYCK_CLITE  (P86851), CYCL_CLITE  (P86852), 
CYCM_CLITE  (P86899), CYCN_CLITE  (P86900), CYCO_CLITE  (P86901), 
CYCP_CLITE  (P86902), CYCQ_CLITE  (P86904), CYCR_CLITE  (P86903), 
CYGPC_GLOPU (C0HL37), CYH1_VIOHE  (P58433), CYH2_VIOHE  (P85233), 
CYH3_VIOHE  (P85232), CYH4_VIOHE  (P85234), CYHEC_PIGEN (C0HLN7), 
CYHED_PIGEN (C0HLN8), CYHEE_PIGEN (C0HLN9), CYHEF_PIGEN (C0HLP0), 
CYHEG_PIGEN (C0HLP1), CYHEH_PIGEN (C0HLP2), CYHEI_PIGEN (C0HLP3), 
CYHEJ_PIGEN (C0HLP4), CYHEK_PIGEN (C0HLP5), CYHEL_PIGEN (C0HLP6), 
CYHEM_PIGEN (C0HLP7), CYLA_PSYLO  (P56872), CYLRA_LEOTR (C0HKI2), 
CYM45_MELRA (A9P3S1), CYMBA_MELOB (C0HKJ7), CYMBB_MELOB (C0HKJ8), 
CYMC1_MELCT (C0HK35), CYMC2_MELCT (C0HK36), CYMC3_MELCT (C0HK37), 
CYMC4_MELCT (C0HK38), CYMC5_MELCT (C0HK39), CYMC6_MELCT (C0HK40), 
CYMC7_MELCT (C0HK41), CYMEA_MELDN (C0HKI4), CYMEB_MELDN (C0HKI5), 
CYMEC_MELDN (C0HKI6), CYMEE_MELDN (C0HKI7), CYMEF_MELDN (C0HKI8), 
CYMEG_MELDN (C0HKI9), CYMEH_MELDN (C0HKJ0), CYMEI_MELDN (C0HKJ1), 
CYMEJ_MELDN (C0HKJ2), CYMEK_MELDN (C0HKJ3), CYMEL_MELDN (C0HKJ4), 
CYMEM_MELDN (C0HKJ5), CYMEN_MELDN (C0HKJ6), CYML1_MELLF (C0HK28), 
CYML2_MELLF (C0HK29), CYML3_MELLF (C0HK30), CYML4_MELLF (C0HK31), 
CYML5_MELLF (C0HK32), CYML6_MELLF (C0HK33), CYML7_MELLF (C0HK34), 
CYMNA_MELAG (C0HKI3), CYMR1_MELRA (C0HL32), CYMR2_MELRA (C0HL33), 
CYMR3_MELRA (C0HL34), CYO10_VIOOD (P58442), CYO11_VIOOD (P58443), 
CYO12_VIOAR (P83835), CYO12_VIOOD (P83836), CYO13_VIOOD (Q5USN8), 
CYO14_VIOOD (P85177), CYO15_VIOOD (P85178), CYO16_VIOOD (P85179), 
CYO17_PSYBR (C0HL23), CYO17_VIOOD (P85180), CYO18_VIOOD (P85181), 
CYO19_VIOOD (P85182), CYO1_VIOOD  (P82230), CYO20_VIOOD (P85183), 
CYO21_VIOOD (P85184), CYO22_VIOOD (P85185), CYO23_VIOOD (P85186), 
CYO24_VIOOD (P85187), CYO2_PIGEN  (C0HLP8), CYO2_VIOBI  (P85526), 
CYO2_VIOOD  (P58434), CYO3_VIOOD  (P58435), CYO4_VIOOD  (P58436), 
CYO5_VIOOD  (P58437), CYO6_VIOOD  (P58438), CYO7_VIOOD  (P58439), 
CYO8_VIOOD  (P58440), CYO9_VIOBI  (B1NRR2), CYO9_VIOOD  (P58441), 
CYPLA_PALGU (C0HKJ9), CYPLA_PSYBR (C0HL24), CYPLA_PSYLE (C0HL27), 
CYPLB_PSYBR (C0HL25), CYPLB_PSYLE (C0HL28), CYPLC_PSYLE (C0HL29), 
CYPLD_PSYBR (C0HL26), CYPLD_PSYLE (C0HL30), CYPLE_PSYLE (C0HL31), 
CYVA_LEOCM  (P84637), CYVA_VIOBI  (P85239), CYVA_VIOCT  (P84635), 
CYVB_LEOCM  (P84638), CYVB_VIOBI  (P85240), CYVB_VIOCT  (P84636), 
CYVC_LEOCM  (P84639), CYVC_VIOBI  (P85241), CYVD_LEOCM  (P84640), 
CYVD_VIOBI  (P85242), CYVE_VIOBI  (B1NRQ8), CYVF_VIOBI  (P85244), 
CYVG_VIOBI  (P85245), CYVH_VIOBI  (P85246), CYVIA_VIODI (C0HKK0), 
CYVI_VIOBI  (B1NRQ9), CYVJ_VIOBI  (B1NRR0), CYVK_VIOBI  (B1NRR1), 
CYVNA_VIOIN (C0HKK1), CYVNB_VIOIN (C0HKK2), CYVUA_VIOPU (C0HKK3), 
CYVUB_VIOPU (C0HKK4), CYVUC_VIOPU (C0HKK5), HYFLA_HYBFL (P84647), 
HYFLB_HYBFL (P84648), HYFLC_HYBFL (P84649), HYPAA_POMPR (P58445), 
KAB10_OLDAF (P85128), KAB11_OLDAF (P85129), KAB13_OLDAF (P85131), 
KAB14_OLDAF (P85132), KAB15_OLDAF (P85133), KAB16_OLDAF (P85134), 
KAB17_OLDAF (P85135), KAB1_OLDAF  (P56254), KAB2_OLDAF  (P58454), 
KAB3_OLDAF  (P58455), KAB4_OLDAF  (P83938), KAB5_OLDAF  (P58456), 
KAB7_OLDAF  (P58457), KABS_OLDAF  (P58458), PABR1_PALRI (B3EWF1), 
VARA_VIOAR  (P58446), VARA_VIOBI  (P85525), VARA_VIOOD  (Q5USN7), 
VARB_VIOAR  (P58447), VARC_VIOAR  (P58448), VARD_VIOAR  (P58449), 
VARF_VIOAR  (P58451), VARG_VIOAR  (P58452), VARH_VIOAR  (P58453), 
VHL2_VIOHE  (P85231), VHR1_VIOHE  (P83937), VITA_VIOAR  (P83840), 
VITA_VIOBI  (B1NRR3), VODM_VIOOD  (P83839), VODN_VIOOD  (P83838)

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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

21 sequences

CYC10_CHACT (C0HKH7), CYC12_CHACT (C0HKH5), CYC21_CLITE (C0HJS8),

CYCK_PETHY  (B3EWH6), CYCM_PETHY  (B3EWH7), CYGPA_GLOPU (C0HL35), 
CYGPB_GLOPU (C0HL36), CYO25_VIOOD (P85188), CYPBA_PSYBR (C0HL20), 
CYPBB_PSYBR (C0HL21), CYPBC_PSYBR (C0HL22), CYV1_VIOOD  (C0HL14), 
CYV2_VIOOD  (C0HL15), CYV3_VIOOD  (C0HL16), KAB12_OLDAF (P85130), 
KAB8_OLDAF  (P85175), KAB9_OLDAF  (P85127), PALIC_PALCO (P84645), 
TRIC_VIOAR  (P0C589), VHL1_VIOHE  (P84522), VIOLA_VIOOD (Q2HY54)

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PDB
[Detailed view]

51 PDB

pdb_00001bh4; pdb_00001df6; pdb_00001jjz; pdb_00001k48; pdb_00001kal; pdb_00001n1u; pdb_00001nb1; pdb_00001nbj; pdb_00001orx; pdb_00001pt4; pdb_00001vb8; pdb_00001yp8; pdb_00001za8; pdb_00001znu; pdb_00002b38; pdb_00002eri; pdb_00002f2i; pdb_00002f2j; pdb_00002fqa; pdb_00002gj0; pdb_00002jue; pdb_00002jwm; pdb_00002k7g; pdb_00002kcg; pdb_00002kch; pdb_00002khb; pdb_00002knm; pdb_00002knn; pdb_00002kuk; pdb_00002kux; pdb_00002kvx; pdb_00002lam; pdb_00002m9o; pdb_00002mh1; pdb_00002mn1; pdb_00002mw0; pdb_00003e4h; pdb_00004ttm; pdb_00004ttn; pdb_00004tto; pdb_00007lhc; pdb_00007rfa; pdb_00007rih; pdb_00007rii; pdb_00007rij; pdb_00007rmq; pdb_00007rmr; pdb_00007rms; pdb_00007rn3; pdb_00007s55; pdb_00008tyi
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