Entry: PS51052

Forthcoming changes to the profile format
General information about the entry

Entry name [info] CYCLOTIDE
Accession [info] PS51052
Entry type [info] MATRIX
Date [info] DEC-2004 (CREATED); OCT-2013 (DATA UPDATE); SEP-2014 (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=30.83715; R2=12.41349; TEXT='HScore';
/CUT_OFF: LEVEL=0; SCORE=1031; N_SCORE=8.5; H_SCORE=6821; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=709; N_SCORE=6.5; H_SCORE=6821; 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 2014_10 which contains 546'790 sequence entries.


Total number of hits 113 in 108 different sequences
Number of true positive hits 113 in 108 different sequences
Number of 'unknown' hits
Number of false positive hits
Number of false negative sequences 10
Number of 'partial' sequences 0
Precision (true positives / (true positives + false positives)) 100.00 %
Recall (true positives / (true positives + false negatives)) 91.87 %

Comments [info]

Matrix type [info] protein_domain
Scaling database [info] reversed
Author [info] CJA_Sigrist
Taxonomic range [info] Eukaryotes
Maximum number of repetitions [info] 3
Version [info] 2

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences
108 sequences

CIRA_CHAPA  (P56871), CIRB_CHAPA  (P56879), CIRC_CHAPA  (P84641), 
CIRD_CHAPA  (P84642), CIRE_CHAPA  (P84643), CIRF_CHAPA  (P84644), 
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), 
CYCI_CLITE  (P86849), 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), CYH1_VIOHE  (P58433), CYH2_VIOHE  (P85233), 
CYH3_VIOHE  (P85232), CYH4_VIOHE  (P85234), CYLA_PSYLO  (P56872), 
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_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_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), 
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), CYVI_VIOBI  (B1NRQ9), 
CYVJ_VIOBI  (B1NRR0), CYVK_VIOBI  (B1NRR1), HYFLA_HYBFL (P84647), 
HYFLB_HYBFL (P84648), HYFLC_HYBFL (P84649), HYPAA_HYBPA (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)
» More

UniProtKB/Swiss-Prot
False negative sequences
10 sequences

CYCK_PETHY  (B3EWH6), CYCM_PETHY  (B3EWH7), CYO25_VIOOD (P85188), 
KAB12_OLDAF (P85130), KAB8_OLDAF  (P85175), KAB9_OLDAF  (P85127), 
PALIC_PALCO (P84645), TRIC_VIOAR  (P0C589), VHL1_VIOHE  (P84522), 
VIOLA_VIOOD (Q2HY54)
» More

PDB
[Detailed view]
28 PDB

1BH4; 1JJZ; 1K48; 1KAL; 1N1U; 1NB1; 1NBJ; 1ORX; 1PT4; 1VB8; 1ZNU; 2ERI; 2F2I; 2F2J; 2GJ0; 2JWM; 2K7G; 2KCG; 2KCH; 2KHB; 2KNM; 2KNN; 2KUK; 2KUX; 2LAM; 2M9O; 2MH1; 3E4H
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