PROSITE entry PS51782

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General information about the entry

PURL [info]	https://purl.expasy.org/prosite/signature/PS51782
Entry name [info]	LYSM
Accession [info]	PS51782
Entry type [info]	MATRIX
Date [info]	01-NOV-2015 CREATED; 01-NOV-2015 DATA UPDATE; 29-MAY-2024 INFO UPDATE.
PROSITE Doc. [info]	PDOC51782
Associated ProRule [info]	PRU01118

Name and characterization of the entry

Description [info]

LysM domain profile.

Matrix / Profile [info]

/GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=45;
/DISJOINT: DEFINITION=PROTECT; N1=1; N2=45;
/NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=1.9349295; R2=0.0070080; TEXT='-LogE';
/CUT_OFF: LEVEL=0; SCORE=937; N_SCORE=8.5; MODE=1; TEXT='R';
/CUT_OFF: LEVEL=-1; SCORE=652; N_SCORE=6.5; MODE=1; TEXT='RR';
/DEFAULT: M0=-25; 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='M';  M=-41,-72,-24,-21,  5,-53, 14,  4, 30,  6, 35,-17,-36, 22,-16, 35,  7,  0,-73,-11;
/M: SY='W';  M=-16,-71,-33, 10, 22,-69,-19,  0, -2,-60,-59,-57,-24,-24,-26, 19, 62,-18, 72, 31;
/M: SY='Y';  M=-68,-16,-65,-40,-36,-77, 95,  6,-37,-54,-50,-61,-77,-57,-33,-64,-64,  8,-49,104;
/M: SY='T';  M=-57,-69,-20,-11,-65,-49,-20, 14, 23,-14,-54, 10,-10,-58,-21,-18, 72, 27,-83,-64;
/M: SY='V';  M=-10,-67,-82,-76,-19,-82,-82, 30,-74,  1,-41,-77,-78,-75,-76,-65,-31, 89,-82,-59;
/M: SY='Q';  M= -5,-12,-58, -5,-72,-20,-58,-63, 57,-67,-16,-37,-67, 62, 11, 11,  4, 13,-74, -5;
/M: SY='P';  M= 11,-74, -9,  8,-34,-25,-59,-70, 41,-47,-17, -3, 42, 25, -4, 34,  0,-50,-75,-10;
/M: SY='G';  M=-26,-76,  0,  1,-81, 88,-65,-54,-17,-51,-71,-11,-67,  5,-34,-33,-64,-78,-76,-74;
/M: SY='D';  M=-64,-80,105, 43,-83,-44,-53,-84,-52,-82,-79,-11,-65,-22,-60,-12,-57,-80,-93,-20;
/I:         I=-38; MI=0; MD=-97; IM=0; DM=-97;
/M: SY='T';  M=-49,-63,-55,-59,-44,-41,-62,-40,-57,-68,-63, 18,-62,-29,-63, 68, 87,-57,-83,-31;
/M: SY='C';  M=-39, 83,-83,-77,-15,-83,-72, 12,-77, 68, -1,-77,-83,-73,-76,-71,-38, 12,-75,-26;
/M: SY='W';  M=-29,-76, -8,-10, 12,-13,-60,-67,-59,-67,-15, 22,-70, 31,-63, 39, 20,-47,110, 42;
/M: SY='S';  M= 27,-69, -2,-13,-35, 12,-61,-11, -2,-28,-62,-30,-67,-12,  8, 60,  1,-39,-76,-12;
/M: SY='I';  M=-65,-75,-86,-82, 14,-88,-80, 91,-78, 31,  0,-78,-77,-75,-80,-74,-59, 11,-71,-52;
/M: SY='A';  M= 80,-12,-67,-61,-71,-22,-68,-60,-63,-14,-59,-60,-31,-59,-67, 41,-49, -6,-77,-69;
/M: SY='D';  M= 10,-74, 32, 16,-71,-32,-32,-24, 29,-11,-22, 24,-68, 22, 31, -2,-12,-20,-15,-40;
/M: SY='Q';  M=-24,-76,-14,  0,-76,-66, -7,-54, 57,-36,-16, 11,-66, 63, 40, 17, -2,-70,-77,-64;
/I:         I=-36; MI=0; MD=-90; IM=0; DM=-90;
/M: SY='Y';  M=-28, -7,-69,-68, 63,-73, 44,-19,-20,-36,-53,-15,-42, -8,-63, -4,-33,-60, 20, 95;
/M: SY='G';  M=-21,-15, -7, -9,-51, 78, 31,-84, 16,-81,-71, 35,-33,-35,-43,-34,-62,-79,-78,-70;
/M: SY='I';  M=-17, 10,-38,-23,-55,-18,-74, 55,-69,  6, -6,-43,-72,-68,-73, -5, 28, 48,-78,-16;
/M: SY='T';  M=-15,-69, 12,-20,-19,  1,-62,-68,  5,-29,-64,-13, 33,-21,-37, 49, 60,-63,-80,-66;
/M: SY='V';  M= -9,-68,-35,-44, -8,-53,-69, 14,-16, 16, 50,-33,-23,-65,-68, -3, 30, 51,-77,-21;
/M: SY='D';  M= 23, -1, 50,  4,-74,-18,-20,-71,-10,-32,  0, 35,-67, 33,-11, 27,  2,-67,-82,-30;
/I:         I=-36; MI=0; MD=-90; IM=0; DM=-90;
/M: SY='Q';  M=  9,-76, 56, 37,-78,-66,-26,-27, 26,-34,-64,  1,-65, 64,-18,-30, -9,-42,-81,-66;
/M: SY='I';  M=-68,-72,-85,-80, 60,-87,-74, 66,-78, 56,-35,-78,-80,-76,-78,-74,-33,-25,-63,-44;
/M: SY='K';  M= 14,-73,-67, -8,-57,-72,-63, 26, 34, 26, 27,-63,-71, 23,  4,-25, -2,-11, 22,  2;
/M: SY='K';  M=  7,-74, -5, 20, -9,-50,-56,-74, 49,-53,-64,  1,-66, 44, 43, 20,  1,-69,-75,-63;
/M: SY='W';  M= 23,-74,-53,-49,-28,-45,-72,-37,-48, 40,  6,-75,-76,-32,-30,-39,-29, 21,115, 17;
/M: SY='N';  M=-42,-67,-38,-58,-74,-52,-45,-33,-50,-77,-66,121,-73,-52,-58,-46,-47, -8,-95,-71;
/I:         I=-25; MI=0; MD=-63; IM=0; DM=-63;
/M: SY='N';  M=  8,-75,-11, -7,-79, 25, 31,-76, 28,-77,-66, 54, 40, 33,-19,-10,-24,-46,-81,-68;
/M: SY='L';  M=-62,-72,-21,-15, -6, 10,-70, 45,-45, 52, 23,-12,-76,-67,-72,-67,-28, 12,  1,-56;
/M: SY='N';  M=-18,-72, 25,-45,-33,-21,-23, 19, 35,-45,-14, 45,-14,-18,-13, 27, -7,  5,-79,-23;
/M: SY='N';  M=-18,-71, 34, -7,-35, -9,-24,-33, -4,-42,-66, 62, -9,-14, -5, 49,  7,-52,-84,-66;
/I:         I=-33; MI=0; MD=-84; IM=0; DM=-84;
/M: SY='C';  M=-16, 79, 14,-29,-22,-62,-79,-79,-55,-25,-19,-10, 59,-77,-83,-44, -5,-57,-96,-82; D=-33;
/I:         I=-33; DM=-84;
/M: SY='N';  M=-24,-72, 33,  5,-27,-18, 13,-55,-15,-50,-65, 62,-19, 27,-23, 39,  5,-52,-79, 11;
/M: SY='N';  M= -7,-32, 13,-16,-23,-27, 11,-61, 22,  1,-29, 66,-42,-12, -4,  8, -5,  1,-20,-63;
/M: SY='I';  M=-41,-72,-84,-78, -8,-85,-77, 72,-77, 54,-35,-78,-21,-73,-78,-43,-59, 26,-73,-55;
/M: SY='W';  M=-41,-77,-15, -2, 35,-45, 27,-26,  7,-27,-26,-11,-72, 48, -8,-16, -2,-17, 75, 56;
/M: SY='P';  M= 42,-71,-69,-63,-32,-65,-70, 32,-41,-10,-19,  1, 64,-21,-70, -3,-18, 21,-78,-66;
/M: SY='G';  M=-39,-75,-18,-44,-16, 91,-66,-83,-15,-39,-71, 16,-69,-63,-36,-34,-64,-79,-74,-71;
/M: SY='Q';  M=-16,-78, 30, -5,-27,-68,-51,-42,  7,-67, -5,-51,-67, 99, -7,-33, 15,-69,-69, 30;
/M: SY='K';  M= -2,-71,-39,  7,-66,-67,-61, -9, 40,-39,-58,-28,-11,  9, 13, 29, 38, 12,-75, 12;
/M: SY='L';  M=-45,-73,-82,-78,-20,-84,-67, 59,-76, 61,-35,-78,-80,-71,-75,-48,-60,  7,-63, 51;
/M: SY='C';  M=-35, 83,  4,-60,-60,-73,-65,-13, 36,-10,-56, -9,-75, 12,-29,-28,  0, 33, 41, 22;
/M: SY='I';  M=-30, 21,-83,-78,-24,-83,-81, 70,-75, 13,-14,-76,-34,-74,-78,-41,-31, 60,  3,-58;
/I:         E1=0; IE=-380; DE=-380;

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Numerical results [info]

Numerical results for UniProtKB/Swiss-Prot release 2025_02 which contains 573'230 sequence entries.

Total number of hits	390 in 236 different sequences
Number of true positive hits	390 in 236 different sequences
Number of 'unknown' hits	0
Number of false positive hits	0
Number of false negative sequences	7
Number of 'partial' sequences	0

Precision (true positives / (true positives + false positives))	100.00 %
Recall (true positives / (true positives + false negatives))	98.24 %

Comments [info]

Taxonomic range [info]	Bacteriophages, Eukaryotes, Prokaryotes (Bacteria)
Maximum number of repetitions [info]	6
Matrix type [info]	protein_domain
Scaling database [info]	reversed
Author [info]	CJA_Sigrist
Feature key [info]	DOMAIN
Feature description [info]	LysM
Version [info]	1

Cross-references [info]

UniProtKB/Swiss-Prot
True positive sequences

236 sequences

ACMA_LACLA  (Q9CIT4), ACMA_LACLC  (P0C2T5), ACMA_LACLM  (A2RHZ5),

ALYS_ENTFA  (P37710), AMIB_HAEIN  (P44493), CEBIP_ORYSJ (Q8H8C7), 
CERK1_ARATH (A8R7E6), CERK1_PHYPA (A9TXT1), CIH1_COLLN  (Q9P403), 
CPLR_DESHA  (Q8GFE2), CWLS_BACSU  (O31852), DIPM_CAUVN  (A0A0H3C9Q9), 
EAE_CITFR   (Q07591), EAE_ECO11   (O31000), EAE_ECO27   (P19809), 
EAE_ECO57   (P43261), EBPS_STAA3  (Q2FGW1), EBPS_STAA8  (Q2FYF1), 
EBPS_STAAB  (Q2YY76), EBPS_STAAC  (Q5HFU2), EBPS_STAAE  (A6QH29), 
EBPS_STAAM  (Q99U09), EBPS_STAAN  (Q7A5I6), EBPS_STAAR  (Q6GGT1), 
EBPS_STAAS  (Q6G983), EBPS_STAAU  (Q53630), EBPS_STAAW  (Q8NWM5), 
EBPS_STAEQ  (Q5HP65), EBPS_STAES  (Q8CP59), EBPS_STAHJ  (Q4L6I5), 
EBPS_STAS1  (Q49XT4), ENLYS_BPB03 (Q37896), ENLYS_BPPH2 (P11187), 
ENLYS_BPPZA (P07540), ENP1_LYSSH  (Q03415), ESTR_MYCTO  (P9WM38), 
ESTR_MYCTU  (P9WM39), EXSA_BACCE  (Q6B4J5), FB60_ARATH  (Q9FZ32), 
FIMV_PSEAB  (A0A0H2ZC68), FIMV_PSEAE  (Q9HZA6), KBP_ECOL6   (P0ADE7), 
KBP_ECOLI   (P0ADE6), KTXA_KLULA  (P09805), LDP_STAA8   (Q2G278), 
LPPB_HAEIN  (P44833), LPPB_HISSO  (P36685), LYK3_ARATH  (F4IB81), 
LYK4_ARATH  (O64825), LYK5_ARATH  (O22808), LYM1_ARATH  (Q93ZH0), 
LYM2_ARATH  (O23006), LYM3_ARATH  (Q6NPN4), LYP4_ORYSJ  (Q67UE8), 
LYP6_ORYSJ  (Q69T51), LYS10_PENEN (A0A0A2JAR6), LYS11_PENEN (A0A0A2J9B0), 
LYS12_PENEN (A0A0A2JP37), LYS13_PENEN (A0A0A2KDU4), LYS14_PENEN (A0A0A2J621), 
LYS15_PENEN (A0A0A2KPB9), LYS16_PENEN (A0A0A2K2W7), LYS17_PENEN (A0A0A2JFC6), 
LYS18_PENEN (A0A0A2JVV3), LYS19_PENEN (A0A0A2JQ23), LYSM1_ARTBC (D4ALG0), 
LYSM1_BOVIN (A0JNI1), LYSM1_COLHI (H1VSQ9), LYSM1_GIBM7 (W7LFX0), 
LYSM1_HUMAN (Q96S90), LYSM1_MACFA (Q9N012), LYSM1_MOUSE (Q9D0E3), 
LYSM1_PENEN (A0A0A2ILW0), LYSM1_POCC1 (A0A4Q7JJ79), LYSM1_PYRO7 (G4N906), 
LYSM1_RAT   (Q5HZA4), LYSM1_TRIRC (F2ST24), LYSM1_XENLA (Q5PQ30), 
LYSM1_ZYMT9 (A0A1X7S147), LYSM1_ZYMTI (F9XHX3), LYSM2_ARTBC (D4B4P8), 
LYSM2_BEAB2 (J4URT3), LYSM2_BOVIN (Q1JQA8), LYSM2_COLHI (H1UVH3), 
LYSM2_DANRE (Q6DEF4), LYSM2_HUMAN (Q8IV50), LYSM2_MOUSE (Q9D7V2), 
LYSM2_PENEN (A0A0A2JVC2), LYSM2_POCC1 (A0A4Q7K4T8), LYSM2_PYRO7 (G4N891), 
LYSM2_TRIRC (F2SIK4), LYSM2_VERDV (G2X4U8), LYSM2_XENLA (Q3KPL3), 
LYSM2_XENTR (Q3B7I8), LYSM3_ARTBC (D4AZ68), LYSM3_CHICK (Q5ZKK0), 
LYSM3_DANRE (Q6IQA2), LYSM3_HUMAN (Q7Z3D4), LYSM3_MOUSE (Q99LE3), 
LYSM3_PENEN (A0A0A2JY92), LYSM3_POCC1 (A0A4Q7K9F4), LYSM3_RAT   (Q5M836), 
LYSM3_XENTR (Q28DG6), LYSM3_ZYMT9 (A0A1X7S690), LYSM3_ZYMTI (F9XMT4), 
LYSM4_ARTBC (D4B4Q2), LYSM4_BEAB2 (J5JHE8), LYSM4_DANRE (Q6P606), 
LYSM4_HUMAN (Q5XG99), LYSM4_MOUSE (Q8CC84), LYSM4_PENEN (A0A0A2JB06), 
LYSM4_POCC1 (A0A4Q7JG83), LYSM4_PONAB (Q5REP3), LYSM4_VERDV (G2WSX9), 
LYSM4_XENLA (Q6DCC7), LYSM5_ARTBC (D4AVW3), LYSM5_BEAB2 (J5J7Y8), 
LYSM5_PENEN (A0A0A2IBU9), LYSM5_VERDV (G2X444), LYSM6_ARTBC (D4AY86), 
LYSM6_BEAB2 (J5JFB6), LYSM6_PENEN (A0A0A2JT36), LYSM6_VERDV (G2XA95), 
LYSM7_BEAB2 (J4VU52), LYSM7_PENEN (A0A0A2IRW3), LYSM8_BEAB2 (J4KL74), 
LYSM8_PENEN (A0A0A2KE57), LYSM9_PENEN (A0A0A2JH00), LYSMA_ASPFU (Q4WER9), 
LYSMB_ASPFU (Q4WRR0), LYSMX_ZYMT9 (A0A1X7S1V5), LYSMX_ZYMTI (P9WEM2), 
LYSM_PASFU  (B3VBK9), LYTE_BACSU  (P54421), LYTF_BACSU  (O07532), 
LYTN_STAA8  (Q9ZNI1), LYTN_STAAC  (Q5HGI5), LYTN_STAAM  (Q99UM3), 
LYTN_STAAN  (Q7A5Y8), LYTN_STAAR  (Q6GHI8), LYTN_STAAS  (Q6G9W6), 
LYTN_STAAW  (Q7A123), MEPM_ECOL6  (P0AFT0), MEPM_ECOLI  (P0AFS9), 
MEPM_SHIFL  (P0AFT1), MLTD_ECOL6  (P0AEZ8), MLTD_ECOLI  (P0AEZ7), 
MUR2_ENTHA  (P39046), NCOA7_CHICK (Q5ZMS4), NCOA7_HUMAN (Q8NI08), 
NCOA7_MOUSE (Q6DFV7), NLPD_BUCAI  (P57493), NLPD_ECOLI  (P0ADA3), 
NLPD_PSEAE  (P45682), NLPD_SALDU  (P39700), NLPD_SALTI  (Q56131), 
NLPD_SALTY  (P40827), NLPD_SHIFL  (P0ADA4), OXR1_BOVIN  (A5PKL1), 
OXR1_HUMAN  (Q8N573), OXR1_MOUSE  (Q4KMM3), OXR1_RAT(Q4V8B0), 
OXR1_XENLA  (B4F6Q9), OXR1_XENTR  (A8KBE0), P60_LISGR   (Q01835), 
P60_LISIN   (Q01836), P60_LISIV   (Q01837), P60_LISMO   (P21171), 
P60_LISSE   (Q01838), P60_LISWE   (Q01839), PGDA_ARTBC  (D4B5F9), 
RPF_MICLU   (O86308), SAFA_BACSU  (O32062), SLE1_STAA3  (Q2FJH7), 
SLE1_STAA8  (Q2G0U9), SLE1_STAAB  (Q2YVT4), SLE1_STAAC  (Q5HIL2), 
SLE1_STAAN  (Q7A7E0), SLE1_STAAR  (Q6GJK9), SLE1_STAAS  (Q6GC24), 
SLE1_STAAU  (P0C1U7), SLE1_STAAW  (Q7A1T4), SLE1_STAEQ  (Q5HRU2), 
SLE1_STAES  (Q8CMN2), SLE1_STAHJ  (Q4L3C1), SLE1_STAS1  (Q49UX4), 
SLEL_BACAN  (P0DPJ9), SLEL_BACCE  (Q9K3E4), SLEL_BACSU  (P37531), 
SP6D_BACSU  (P37963), SPA_STAA8   (P02976), SPA_STAAE   (A0A0H3K686), 
SPA_STAAM   (P0A015), SPA_STAAN   (P99134), SPA_STAAU   (P38507), 
SSAAL_STAA8 (Q2G0D4), TAGH_ENTFA  (Q831L8), TAGH_LACLA  (Q9CH26), 
XKDP_BACSU  (P54335), XLYA_BACSU  (P39800), XLYB_BACSU  (O34391), 
Y310_BUCAP  (Q8K9M4), Y367_STRMU  (Q8DVU8), Y593_CHLPN  (Q9Z7W1), 
Y880_LISMO  (Q8Y8L7), Y888_DEIRA  (Q9RVY3), Y9443_DICDI (Q54HI1), 
YCFS_ECOLI  (P75954), YDHD_BACSU  (O05495), YEEJ_ECO57  (Q8X8V7), 
YEEJ_ECOLI  (P76347), YEEJ_ECOLU  (B7NC15), YGER_ECOLI  (Q46798), 
YKUD_BACLD  (Q65K99), YKUD_BACSU  (O34816), YKUD_SHOC1  (Q5WC42), 
YKVP_BACSU  (O31681), YKZQ_BACSU  (C0H403), YNEA_BACLD  (Q65J41), 
YNEA_BACP2  (A8FDP8), YNEA_BACSU  (Q45056), YNEA_BACVZ  (A7Z553), 
YNEA_GEOKA  (Q5L0C2), YNEA_GEOTN  (A4IMK2), YNEA_LISIN  (Q92C50), 
YNEA_LISMC  (C1L2L0), YNEA_LISMF  (Q720B8), YNEA_LISMH  (B8DG24), 
YNEA_LISMO  (Q8Y7H6), YNEA_LISW6  (A0AIA4), YNEA_PRIM3  (Q5ZNC8), 
YNHG_ECOLI  (P76193), YOCH_BACSU  (O34669), YPBE_BACSU  (P50731), 
YQBP_BACSU  (P45932), YQFZ_BACSU  (P54483)

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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

7 sequences

CERK1_ORYSJ (A0A0P0XII1), LYK3_MEDTR  (Q6UD73), NFP_MEDTR   (Q0GXS4),

RLK10_ORYSJ (D7UPN3), SHYA_VIBCH  (Q9KN86), SHYB_VIBCH  (Q9KUL5), 
SHYC_VIBCH  (Q9KU93)

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PDB
[Detailed view]

27 PDB

1E0G; 1Y7M; 2DJP; 2GU1; 2MKX; 2MPW; 2MTZ; 3ZQD; 4A1I; 4A1J; 4A1K; 4A52;
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