PROSITE logo
Black ribbon
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.
Amos Bairoch

PROSITE entry PS50035


View entry in original PROSITE format
View entry in raw text format (no links)
View entry auxiliary file in raw text format (no links)
PURL: https://purl.expasy.org/prosite/signature/PS50035

Direct ScanProsite submission
General information about the entry

Entry name [info] PLD
Accession [info] PS50035
Entry type [info] MATRIX
Date [info] 01-APR-2002 CREATED;
10-MAY-2017 DATA UPDATE;
29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info] PDOC50035
Associated ProRule [info] PRU00153

Name and characterization of the entry

Description [info] Phospholipase D phosphodiesterase active site profile.
Matrix / Profile [info] 
/GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=28;
/DISJOINT: DEFINITION=PROTECT; N1=3; N2=26;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-1.4560000; R2=0.0316000; TEXT='NScore';
/NORMALIZATION: MODE=-1; FUNCTION=LINEAR; R1=975.8386230; R2=0.5719298; PRIORITY=1; TEXT='Heuristic 5.0%';
/CUT_OFF: LEVEL=0; SCORE=316; H_SCORE=1157; N_SCORE=8.5; MODE=1; TEXT='!';
/CUT_OFF: LEVEL=-1; SCORE=252; H_SCORE=1120; N_SCORE=6.5; MODE=1; TEXT='?';
/DEFAULT: D=-20; I=-20; B1=-50; E1=-50; MM=1; MI=-105; MD=-105; IM=-105; DM=-105; M0=-10;

...
 
                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='Y';  M= -8, -8,-23, -8,-10, -4, -9, -9,-10, -9, -8, -6, -7,-17,-10, -9, -5, -3, -8,-16,  2,-11;
/M:         M= -8,  0,-24, -1, -5, -9, -9, -7,-14, -6, -9, -6,  0,-16, -6, -4, -5, -5,-13,-22, -7, -6;
/M:         M= -8,-10,-28,-11,-12, -9, -2,-10,-16, -6,-13, -9, -6,-16,-10, -2, -9,-11,-14, -6, -2,-12;
/M: SY='V';  M= -3,-19,-21,-22,-15, -3,-22,-17,  3, -7,  1,  1,-15,-20,-12, -3, -9, -2,  6,-14, -2,-15;
/M: SY='H';  M=-12, -1,-23, -8, -7, -7,-19,  9, -1,-11,  1,  6,  5,-22, -2, -8,-10, -8, -8,-24,  1, -6;
/M: SY='H';  M=-19,  5,-29,  3,  0,-20,-17, 89,-29, -9,-21, -3, 16,-20,  9,  0, -7,-17,-30,-31, 15,  0;
/M: SY='S';  M=  0,  2,-19, -1,  1,-18,-12, -3,-17, -4,-15,-10,  3,-12,  2, -2,  6,  5,-13,-28,-12,  1;
/M: SY='K';  M=-10,  0,-30,  0, 10,-30,-20,-10,-30, 49,-30,-10,  0,-10, 10, 32,-10,-10,-20,-20,-10, 10;
/M: SY='L';  M= -7,-23,-21,-28,-22, 10,-20,-18, 13,-23, 15,  9,-18,-24,-20,-19,-14, -4,  9,-15,  4,-22;
/M: SY='M';  M= -7,-26,-20,-31,-24, 15,-27,-15, 17,-21, 18, 19,-24,-26,-19,-18,-19, -8, 14, -8,  9,-21;
/M: SY='I';  M= -4,-28,-21,-32,-27, -1,-29,-27, 30,-24, 15, 13,-23,-24,-22,-23,-15, -5, 29,-19, -5,-26;
/M: SY='V';  M= -4,-25,-17,-29,-24,  7,-29,-25, 23,-22,  9,  8,-20,-23,-23,-21, -8,  1, 27,-22, -3,-25;
/M: SY='D';  M=-18, 45,-29, 64, 23,-39,-11,  0,-39,  1,-29,-29, 18, -9,  2, -9,  1, -9,-29,-39,-20, 13;
/M: SY='D';  M=-10, 23,-27, 28,  8,-31,  3, -1,-31, -1,-27,-21, 17,-14,  2, -4,  3, -8,-27,-33,-19,  4;
/M: SY='E';  M= -3,  0,-23,  1, 11,-20,-16, -6,-20,  8,-17,-11, -1,-11,  3,  5,  0, -1,-14,-25,-12,  6;
/I:         I=-6; MI=0; MD=-21; IM=0; DM=-21;
/M: SY='Y';  M= -7,-14,-19,-18,-13,  4,-22, -4,  5,-13,  3,  2,-12,-19, -9,-11, -8,  0,  3, -7, 11,-13; D=-4;
/I:         DM=-21;
/M: SY='A';  M= 15,-16,-12,-21,-17, -8,-12,-21,  3,-16, -2, -2,-13,-18,-16,-18,  4,  4, 12,-25,-12,-17;
/M: SY='Y';  M=-15,-21,-23,-25,-19, 21,-29,  6,  4,-20,  7,  4,-16,-26,-16,-15,-17,-10, -2, -2, 27,-19;
/M: SY='I';  M= -6,-27,-20,-31,-26,  2,-32,-25, 31,-24, 18, 13,-23,-25,-22,-22,-15, -3, 29,-22, -1,-26;
/M: SY='G';  M=  2, -8,-24,-10,-16,-25, 46,-18,-31,-17,-26,-16,  0,-17,-15,-17,  7, -6,-22,-24,-25,-16;
/M: SY='S';  M=  5, -3,-17, -6, -9,-21, 17,-15,-24,-12,-26,-17,  5,-12, -9,-12, 20, 10,-14,-31,-21, -9;
/M: SY='A';  M= 16,-12,-12,-19,-13, -7,-11,-13, -5,-13, -5, -4, -8,-17,-12,-15,  2, -1,  0,-22,-10,-13;
/M: SY='N';  M=-11, 40,-22, 29,  4,-24, -2,  7,-24,  0,-30,-22, 50,-18,  0, -2,  9, -1,-29,-40,-20,  2;
/M: SY='L';  M=-12,-30,-26,-34,-25, 17,-27,-19, 14,-25, 21, 13,-26,-27,-21,-20,-26,-13,  5, 12, 12,-22;
/M: SY='B';  M= -6, 14, -9, 14, -2,-20, -6, -8,-22, -9,-20,-16, 10,-17, -7,-12,  4, -1,-17,-31,-15, -5;
/M: SY='D';  M=-10, -1,-29,  2, -1,-16, -3, -9,-23, -5,-20,-13, -3, -2, -6,-10, -6, -9,-22,-13,-10, -4;
/M: SY='R';  M= -3, -1,-23, -1,  1,-22, -3,-10,-23,  5,-20,-14,  1,-13, -2, 10,  2, -1,-15,-26,-17, -2;
/M: SY='H';  M= -5, -4,-22, -6, -7, -8,-12, 13,-17, -5,-16,-10,  2,-19, -2,  1,  3, -1,-15,-15, 10, -7;
/I:         E1=0;
» more

Numerical results [info]

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


Total number of hits 417 in 231 different sequences
Number of true positive hits 415 in 229 different sequences
Number of 'unknown' hits 0
Number of false positive hits 2 in 2 different sequences
Number of false negative sequences 10
Number of 'partial' sequences 0
Precision (true positives / (true positives + false positives)) 99.52 %
Recall (true positives / (true positives + false negatives)) 97.65 %

Comments [info]

Taxonomic range [info] Eukaryotes, Prokaryotes (Bacteria), Eukaryotic viruses
Maximum number of repetitions [info] 2
Matrix type [info] protein_domain
Scaling database [info] reversed
Author [info] K_Hofmann
Feature key [info] DOMAIN
Feature description [info] PLD phosphodiesterase
Version [info] 5

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences		 229 sequences 

CLS1_BACAN  (Q81V75), CLS1_BACCR  (Q81I00), CLS1_BACSU  (P45860), 

CLS1_STAAC  (Q5HGA3), CLS1_STAAR  (Q6GH88), CLS1_STAEQ  (Q5HPM5), 
CLS1_STAES  (Q8CPD8), CLS2_BACAN  (Q81TR2), CLS2_BACCR  (Q81GK4), 
CLS2_STAAC  (Q5HEB2), CLS2_STAAR  (Q6GEY7), CLS2_STAEQ  (Q5HMD3), 
CLS2_STAES  (Q8CNK3), CLSA_BACSU  (P71040), CLSA_BUCA5  (B8D966), 
CLSA_BUCAI  (P57361), CLSA_BUCAP  (Q8K9P9), CLSA_BUCAT  (B8D7H0), 
CLSA_BUCBP  (Q89AL5), CLSA_CITK8  (A8AG50), CLSA_CROS8  (A7MNA4), 
CLSA_ECO24  (A7ZL20), CLSA_ECO27  (B7UQD9), CLSA_ECO45  (B7ML01), 
CLSA_ECO55  (B7LHJ4), CLSA_ECO57  (Q8XCC6), CLSA_ECO5E  (B5YYF4), 
CLSA_ECO7I  (B7NVL8), CLSA_ECO81  (B7MU36), CLSA_ECO8A  (B7LY04), 
CLSA_ECOBW  (C4ZTU1), CLSA_ECODH  (B1XAT9), CLSA_ECOHS  (A7ZZI5), 
CLSA_ECOK1  (A1AAH3), CLSA_ECOL5  (Q0TIC2), CLSA_ECOL6  (P0A6H9), 
CLSA_ECOLC  (B1ITK7), CLSA_ECOLI  (P0A6H8), CLSA_ECOLU  (B7N460), 
CLSA_ECOSE  (B6I9W2), CLSA_ECOSM  (B1LH51), CLSA_ECOUT  (Q1RCI7), 
CLSA_EDWI9  (C5BDA3), CLSA_ENT38  (A4WB84), CLSA_ERWT9  (B2VKV4), 
CLSA_ESCF3  (B7LS29), CLSA_KLEP3  (B5XQA9), CLSA_KLEP7  (A6TAJ7), 
CLSA_PECAS  (Q6D4S2), CLSA_PECCP  (C6DGY3), CLSA_PROMH  (B4EWI7), 
CLSA_PSEA8  (B7V5T6), CLSA_PSEAB  (Q02DW8), CLSA_PSEAE  (Q9HTH0), 
CLSA_PSEE4  (Q1I2L0), CLSA_PSEF5  (Q4K3D9), CLSA_PSEFS  (C3K1C4), 
CLSA_PSEP1  (A5WB80), CLSA_PSEPG  (B0KR91), CLSA_PSEPK  (Q88C19), 
CLSA_PSEPU  (P31048), CLSA_PSEPW  (B1JFN5), CLSA_PSESM  (Q87TY7), 
CLSA_PSEU2  (Q4ZL66), CLSA_SALA4  (B5F4L0), CLSA_SALAR  (A9MPD5), 
CLSA_SALCH  (Q57NS0), CLSA_SALDC  (B5FU52), CLSA_SALEP  (B5R3N1), 
CLSA_SALG2  (B5R6L2), CLSA_SALHS  (B4TJM2), CLSA_SALNS  (B4SUC9), 
CLSA_SALPA  (Q5PCS9), CLSA_SALPB  (A9MWP9), CLSA_SALPC  (C0Q393), 
CLSA_SALPK  (B5BIA8), CLSA_SALSV  (B4TX53), CLSA_SALTI  (P63799), 
CLSA_SALTY  (P63798), CLSA_SERP5  (A8GFA0), CLSA_SHIB3  (B2TZZ4), 
CLSA_SHIBS  (Q31ZU1), CLSA_SHIDS  (Q32GV1), CLSA_SHIFL  (Q83RM8), 
CLSA_SHISS  (Q3Z0W3), CLSA_SODGM  (Q2NT72), CLSA_WIGBR  (Q8D2I8), 
CLSA_YERE8  (A1JQ40), CLSA_YERP3  (A7FI50), CLSA_YERPA  (Q1C7R0), 
CLSA_YERPB  (B2K3U5), CLSA_YERPE  (Q8ZEI2), CLSA_YERPG  (A9R8K8), 
CLSA_YERPN  (Q1CJ46), CLSA_YERPP  (A4TJ85), CLSA_YERPS  (Q66AL9), 
CLSA_YERPY  (B1JKT9), CLSB_BACSU  (P45865), CLSB_ECO57  (P0AA85), 
CLSB_ECOL6  (Q8FJN9), CLSB_ECOLI  (P0AA84), CLSB_SALTI  (Q8Z883), 
CLSB_SALTY  (Q8ZQP4), CLSB_SHIFL  (P59715), CLSC_ECOLI  (P75919), 
CLS_ALKPO   (O66043), CLS_CLOP1   (Q0TQG9), CLS_CLOPE   (P0C2E2), 
CLS_CLOPS   (Q0ST20), CLS_GEOKA   (Q5L1S5), CLS_GEOSW   (C5D794), 
CLS_GEOTN   (A4IL76), CLS_HALH5   (Q9K8Z4), CLS_LISIN   (Q927Z0), 
CLS_LISMC   (C1KYS0), CLS_LISMF   (Q71WS5), CLS_LISMH   (B8DBK8), 
CLS_LISMO   (Q8Y4E3), CLS_LISW6   (A0ALI7), CLS_OCEIH   (Q8EM16), 
CLS_STAAM   (P63800), CLS_STAAN   (P63801), CLS_STAAS   (Q6G7M2), 
CLS_STAAW   (P63802), CLS_TRYB2   (Q584D1), DRMC_BACP9  (P0DW07), 
F13_FOWPN   (P36316), F13_MCV1(P26579), F13_MCV2(P25392), 
PG042_MONPV (A0A7H0DN15), PG042_VACCC (P20537), PG042_VACCW (P18377), 
PG057_MONPV (A0A7H0DN30), PG057_VACCA (O57179), PG057_VACCC (P20638), 
PG057_VACCI (P26653), PG057_VACCP (P29885), PG057_VACCW (P04021), 
PG057_VAR67 (P33815), PGPS1_BOVIN (Q2KJ28), PGPS1_CHICK (Q5ZHN9), 
PGPS1_CRIGR (Q9Z2Z7), PGPS1_DICDI (Q7KWX2), PGPS1_HUMAN (Q32NB8), 
PGPS1_MOUSE (Q8BHF7), PGPS1_PONAB (Q5R8K7), PGPS1_SACPS (P79001), 
PGPS1_YEAST (P25578), PLD1_CRIGR  (O08684), PLD1_HUMAN  (Q13393), 
PLD1_MOUSE  (Q9Z280), PLD1_RAT(P70496), PLD1_SCHPO  (Q09706), 
PLD2_BOVIN  (Q0V8L6), PLD2_HUMAN  (O14939), PLD2_MOUSE  (P97813), 
PLD2_RAT(P70498), PLD3_BOVIN  (Q2KJJ8), PLD3_HUMAN  (Q8IV08), 
PLD3_MACFA  (Q4R583), PLD3_MOUSE  (O35405), PLD3_PONAB  (Q5R4Y7), 
PLD3_RAT(Q5FVH2), PLD3_XENLA  (Q6PB03), PLD3_XENTR  (Q640B3), 
PLD4_HUMAN  (Q96BZ4), PLD4_MOUSE  (Q8BG07), PLD5_MOUSE  (Q3UNN8), 
PLD6_BOVIN  (E1BE10), PLD6_CANLF  (E2RD63), PLD6_CHLRE  (A8IW99), 
PLD6_HUMAN  (Q8N2A8), PLD6_MOUSE  (Q5SWZ9), PLD6_XENLA  (A1L1C2), 
PLD6_XENTR  (Q28DT3), PLDA1_ARATH (Q38882), PLDA1_BRAOC (O82549), 
PLDA1_CARPA (P86387), PLDA1_CYNCA (Q70EW5), PLDA1_MAIZE (Q43270), 
PLDA1_ORYSJ (Q43007), PLDA1_RICCO (Q41142), PLDA1_SPUBR (O04883), 
PLDA1_TOBAC (P93400), PLDA1_VIGUN (O04865), PLDA2_ARATH (Q9SSQ9), 
PLDA2_BRAOC (P55939), PLDA2_ORYSJ (P93844), PLDA3_ARATH (P58766), 
PLDA4_ARATH (Q9C888), PLDA_DICDI  (Q54UK0), PLDB1_ARATH (P93733), 
PLDB2_ARATH (O23078), PLDB_DICDI  (Q54WR4), PLDC_DICDI  (Q54Z25), 
PLDD1_ARATH (Q9C5Y0), PLDG1_ARATH (Q9T053), PLDG2_ARATH (Q9T051), 
PLDG3_ARATH (Q9T052), PLDL_CAEEL  (O17405), PLDY_DICDI  (Q54K50), 
PLDZ1_ARATH (Q9LRZ5), PLDZ2_ARATH (Q9M9W8), PLDZ_DICDI  (Q54SA1), 
PLD_PHYIN   (Q5BMR2), PLD_RICBR   (Q1RK58), PLD_RICCN   (Q92G53), 
PLD_RICFE   (Q4UJZ1), PLD_RICPR   (Q9ZCD8), PLD_RICTY   (Q68VT0), 
PLD_STRAT   (Q53728), PPK1_ECO57  (P0A7B2), PPK1_ECOL6  (Q8FF70), 
PPK1_ECOLI  (P0A7B1), PPK1_KLEPN  (Q07411), PPK1_SALTI  (Q8Z4R0), 
PPK1_SALTY  (O86090), PPK1_VIBCH  (Q9KU07), PPK1_VIBPA  (Q87S51), 
PPK1_VIBVU  (Q8DEW2), PPK1_VIBVY  (Q7MNJ0), PPK1_YERPE  (Q8ZCX2), 
PSS_ECOLI   (P23830), PSS_HAEIN   (P44704), SPO14_YEAST (P36126), 
Y190_HELPJ  (Q9ZMP2), Y190_HELPY  (P56117), Y988_STRMU  (P34001), 
YJHR_ECOLI  (P39369)
» more

UniProtKB/Swiss-Prot
False negative sequences		 10 sequences 

PGPS1_SCHPO (Q9HDW1), PLD5_HUMAN  (Q8N7P1), PLD6_DANRE  (A3KNW0), 

PPK1_PSEPK  (Q88CG4), PPK1_PSESM  (Q87UP6), PPK1_STAEQ  (Q5HLE0), 
PPK1_STAES  (Q8CR71), PPK1_STAHJ  (Q4L8X9), PPK1_STAS1  (Q4A040), 
ZUC_DROME   (Q9VKD7)
» more

UniProtKB/Swiss-Prot
False positive sequences		 2 sequences 

DYHA_CHLRE  (Q39610), TYDP1_CAEEL (Q9TXV7)


				
	

	

		PDB
[Detailed view]		
		
			40 PDB
			


			pdb_00001xdo; pdb_00001xdp; pdb_00002ze4; pdb_00002ze9; pdb_00003hsi; pdb_00004ggj; pdb_00004ggk; pdb_00006kz8; pdb_00006kz9; pdb_00006ohm; pdb_00006oho; pdb_00006ohp; 
			
				pdb_00006ohq; pdb_00006ohs; pdb_00006u8z; pdb_00007jrb; pdb_00007jrc; pdb_00007jru; pdb_00007jrv; pdb_00007jrw; pdb_00007js5; pdb_00007js7; pdb_00007svp; pdb_00008q1k; 
				pdb_00008q1x; pdb_00008s86; pdb_00008v05; pdb_00008v06; pdb_00008v07; pdb_00008v08; pdb_00008v5t; pdb_00008yr5; pdb_00008yr6; pdb_00009fhk; pdb_00009fhs; pdb_00009fiz; 
				pdb_00009fj0; pdb_00009fj1; pdb_00009fja; pdb_00009hah
			
			

			» more