Citrus Sinensis ID: 038519

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320----
MEKRKRSNSDILNSNSKGHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREAQCSEDCPLLKPSRLYKDSQRKTRSLANFLQADNSKEPDNIISSDFRERESESGEWKDKLVRRRQKSEDDSSTSVPEMLLKEDNSNTGGVPSITGKGLALRPAAASRTAVGADTQGCDDRISGVRKSSSTPSFEDQDASSPSPIWHGLPKPISRWKNKAALD
cccccccccccccccccccccccccccccEEEEEcccccHHHHHHHHHcccHHHHHHHHccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccc
cccccccccHcccccccccEEEcccccccEEEEEEcccccHHHEEEEEcEEHHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccHHHHHHHHHcccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccHHHHHccccccccccccHHHccccccccccccccccccccEccccccccccccccccccccccEEEcccccccccccccccccccccccccccHHHHHHHHcc
mekrkrsnsdilnsnskghfvyedlgrrgiiehqVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKtlqiplpgkhppspclsngyetrgqanhertpdhhvqhdLFDSfrslrlkskpqwkvspamnslqgyyglkptgqrppsegcemAVFRKReaqcsedcpllkpsrlykdsQRKTRSLANFLqadnskepdniissdfreresesgewKDKLVRRRQkseddsstsvpemllkednsntggvpsitgkglalrpaaasrtavgadtqgcddrisgvrkssstpsfedqdasspspiwhglpkpisrwknkaald
mekrkrsnsdilnsnskghfvYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREaqcsedcpllkpsrlykdsqRKTRSLAnflqadnskepdniissdfreresesgewkdklvrrrqkseddsstsvpemllkednsntggvpsITGKGLALRPAAAsrtavgadtqgcddrisgvrkssstpsfedqdasspspiwhglpkpisrwknkaald
MEKRKRSNSDILNSNSKGHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREAQCSEDCPLLKPSRLYKDSQRKTRSLANFLQADNSKEPDNIISSDFRERESESGEWKDKLVRRRQKSEDDSSTSVPEMLLKEDNSNTGGVPSITGKGLALRPAAASRTAVGADTQGCDDRISGVRKSSSTPSFEDQDASSPSPIWHGLPKPISRWKNKAALD
*****************GHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPL************************************************************YY*****************************************************************************************************************************************************************************************
*****************************IIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLP*********************************************************************************************************************************************************************************************************************************SPIWHGLPKPISRWKN*****
**********ILNSNSKGHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREAQCSEDCPLLKPSRLYKDSQRKTRSLANFLQADNSKEPDNIISS*******************************PEMLLKEDNSNTGGVPSITGK*******************GCDDRISG******************SPIWHGLPKPISRWKNKAALD
******************HFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHP*************************************L*****WKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKRE***********************************************************************************************************************RIS*******************SPIWHGLPKPISRWKNK****
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MEKRKRSNSDILNSNSKGHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREAQCSEDCPLLKPSRLYKDSQRKTRSLANFLQADNSKEPDNIISSDFRERESESGEWKDKLVRRRQKSEDDSSTSVPEMLLKEDNSNTGGVPSITGKGLALRPAAASRTAVGADTQGCDDRISGVRKSSSTPSFEDQDASSPSPIWHGLPKPISRWKNKAALD
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query324 2.2.26 [Sep-21-2011]
A0JNI1225 LysM and putative peptido yes no 0.145 0.208 0.489 6e-06
Q9D7V2215 LysM and putative peptido yes no 0.194 0.293 0.449 7e-06
Q9D0E3226 LysM and putative peptido yes no 0.145 0.207 0.489 1e-05
Q5HZA4227 LysM and putative peptido yes no 0.145 0.207 0.489 1e-05
Q6P606267 LysM and putative peptido yes no 0.169 0.205 0.381 1e-05
Q96S90227 LysM and putative peptido yes no 0.145 0.207 0.489 2e-05
Q9N012227 LysM and putative peptido N/A no 0.145 0.207 0.489 2e-05
Q8IV50215 LysM and putative peptido no no 0.175 0.265 0.45 2e-05
Q1JQA8215 LysM and putative peptido no no 0.175 0.265 0.45 2e-05
Q6DCC7289 LysM and putative peptido N/A no 0.169 0.190 0.381 2e-05
>sp|A0JNI1|LYSM1_BOVIN LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Bos taurus GN=LYSMD1 PE=2 SV=1 Back     alignment and function desciption
 Score = 52.0 bits (123), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 34/47 (72%)

Query: 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPL 77
          +EHQ++  DTLAG+A+KYGV +  I++ N L T+  +F  KTL IP+
Sbjct: 40 LEHQLAPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLHIPI 86

Bos taurus (taxid: 9913)
>sp|Q9D7V2|LYSM2_MOUSE LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Mus musculus GN=Lysmd2 PE=2 SV=2 Back     alignment and function description
>sp|Q9D0E3|LYSM1_MOUSE LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Mus musculus GN=Lysmd1 PE=1 SV=1 Back     alignment and function description
>sp|Q5HZA4|LYSM1_RAT LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Rattus norvegicus GN=Lysmd1 PE=2 SV=1 Back     alignment and function description
>sp|Q6P606|LYSM4_DANRE LysM and putative peptidoglycan-binding domain-containing protein 4 OS=Danio rerio GN=lysmd4 PE=2 SV=2 Back     alignment and function description
>sp|Q96S90|LYSM1_HUMAN LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Homo sapiens GN=LYSMD1 PE=1 SV=1 Back     alignment and function description
>sp|Q9N012|LYSM1_MACFA LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Macaca fascicularis GN=LYSMD1 PE=2 SV=1 Back     alignment and function description
>sp|Q8IV50|LYSM2_HUMAN LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Homo sapiens GN=LYSMD2 PE=1 SV=1 Back     alignment and function description
>sp|Q1JQA8|LYSM2_BOVIN LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Bos taurus GN=LYSMD2 PE=2 SV=1 Back     alignment and function description
>sp|Q6DCC7|LYSM4_XENLA LysM and putative peptidoglycan-binding domain-containing protein 4 OS=Xenopus laevis GN=lysmd4 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query324
225423753398 PREDICTED: uncharacterized protein LOC10 0.891 0.726 0.505 3e-71
224083910336 predicted protein [Populus trichocarpa] 0.888 0.857 0.481 5e-67
224096546411 predicted protein [Populus trichocarpa] 0.882 0.695 0.490 2e-65
356576791354 PREDICTED: uncharacterized protein LOC10 0.845 0.774 0.472 5e-64
225457497366 PREDICTED: uncharacterized protein LOC10 0.876 0.775 0.467 7e-63
449461683373 PREDICTED: uncharacterized protein LOC10 0.882 0.766 0.471 4e-61
297808309398 hypothetical protein ARALYDRAFT_489170 [ 0.876 0.713 0.452 4e-61
255559802398 conserved hypothetical protein [Ricinus 0.885 0.721 0.472 3e-60
224118088340 predicted protein [Populus trichocarpa] 0.895 0.852 0.441 5e-60
118487763359 unknown [Populus trichocarpa] 0.895 0.807 0.441 5e-60
>gi|225423753|ref|XP_002277134.1| PREDICTED: uncharacterized protein LOC100250730 [Vitis vinifera] gi|297737940|emb|CBI27141.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 170/336 (50%), Positives = 207/336 (61%), Gaps = 47/336 (13%)

Query: 31  IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNG 90
           IEHQVSK+DTLAGIAIKYGV+VADI+++NGL TDLQMFAL+TLQIPLPG+HPPSPCL N 
Sbjct: 68  IEHQVSKMDTLAGIAIKYGVEVADIKRMNGLVTDLQMFALRTLQIPLPGRHPPSPCLLNS 127

Query: 91  YETRGQANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPS 150
            ET  Q N + TP   V  +LF++F+SLR+KS  Q  VSPAM++LQGYY LKP  QR   
Sbjct: 128 SET-PQRNSDWTPTDSVHRNLFETFQSLRVKSSSQRPVSPAMSTLQGYYRLKPEDQRNAP 186

Query: 151 EGCEMAVFRKREAQCSEDCPLLKPSRLYK---DSQRKTRSLANFLQADNSKEPDNIISSD 207
           +G EMAV+RK  A   ED P  K S +        RK RSLAN    +N +  D++   +
Sbjct: 187 KGFEMAVYRKESAHYLEDGPFSKQSSISNPLLSRVRKCRSLANGFMPENGEAADDMTILE 246

Query: 208 FRERESESGEWKDKLVRRRQKSEDDSSTSVPEMLLKEDNSN---TGGVPSITGKGLALRP 264
            +E +     W +KL+RRRQKSE D S S PEM LKEDN +    GG  +ITGKGLALR 
Sbjct: 247 AKEGDY---RWNEKLIRRRQKSETDFSCS-PEMPLKEDNRSGGGGGGFSAITGKGLALRT 302

Query: 265 AAASRTAVGADTQGCD------------DRISGVRKSSSTPSFEDQD------------- 299
            A +RTA  AD    +            D  +GVRKSSST + +DQD             
Sbjct: 303 KAVNRTATDADASLMNPIPVGLGDSIVTDSFAGVRKSSSTSNLQDQDSAIFPSIWPTSMW 362

Query: 300 -----------ASSPSPIWHGLPKPISRWKNKAALD 324
                      A+   PI+ GLPKPI+  KNKAALD
Sbjct: 363 NLKPDLQALSTAAITRPIFDGLPKPITGRKNKAALD 398

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224083910|ref|XP_002307170.1| predicted protein [Populus trichocarpa] gi|222856619|gb|EEE94166.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224096546|ref|XP_002310652.1| predicted protein [Populus trichocarpa] gi|222853555|gb|EEE91102.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356576791|ref|XP_003556513.1| PREDICTED: uncharacterized protein LOC100786352 [Glycine max] Back     alignment and taxonomy information
>gi|225457497|ref|XP_002267776.1| PREDICTED: uncharacterized protein LOC100266699 [Vitis vinifera] Back     alignment and taxonomy information
>gi|449461683|ref|XP_004148571.1| PREDICTED: uncharacterized protein LOC101221951 [Cucumis sativus] gi|449527189|ref|XP_004170595.1| PREDICTED: uncharacterized protein LOC101228443 [Cucumis sativus] Back     alignment and taxonomy information
>gi|297808309|ref|XP_002872038.1| hypothetical protein ARALYDRAFT_489170 [Arabidopsis lyrata subsp. lyrata] gi|297317875|gb|EFH48297.1| hypothetical protein ARALYDRAFT_489170 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|255559802|ref|XP_002520920.1| conserved hypothetical protein [Ricinus communis] gi|223539886|gb|EEF41465.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|224118088|ref|XP_002317729.1| predicted protein [Populus trichocarpa] gi|222858402|gb|EEE95949.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|118487763|gb|ABK95705.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query324
TAIR|locus:2181539409 AT5G08200 "AT5G08200" [Arabido 0.864 0.684 0.467 3.7e-64
TAIR|locus:2178272397 AT5G23130 "AT5G23130" [Arabido 0.864 0.705 0.470 2e-56
ZFIN|ZDB-GENE-040426-1895267 lysmd4 "LysM, putative peptido 0.333 0.404 0.325 1.4e-05
UNIPROTKB|E2RD13227 LYSMD1 "Uncharacterized protei 0.333 0.475 0.325 2.5e-05
UNIPROTKB|F1SSY1227 LYSMD1 "Uncharacterized protei 0.330 0.471 0.347 3.3e-05
UNIPROTKB|F1RYP8221 LYSMD2 "Uncharacterized protei 0.234 0.343 0.387 4e-05
RGD|1561865227 Lysmd1 "LysM, putative peptido 0.385 0.550 0.333 5.7e-05
UNIPROTKB|Q1JQA8215 LYSMD2 "LysM and putative pept 0.299 0.451 0.32 6.2e-05
UNIPROTKB|E1BT57195 LYSMD2 "Uncharacterized protei 0.206 0.343 0.4 6.9e-05
MGI|MGI:1917332215 Lysmd2 "LysM, putative peptido 0.256 0.386 0.370 8.2e-05
TAIR|locus:2181539 AT5G08200 "AT5G08200" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 609 (219.4 bits), Expect = 3.7e-64, Sum P(2) = 3.7e-64
 Identities = 151/323 (46%), Positives = 197/323 (60%)

Query:    28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCL 87
             RG IEH++SK DTLAG+AIKYGV+VAD++K+N L TDLQMFALK+LQIPLPG+HPPSPCL
Sbjct:    75 RGYIEHRISKFDTLAGVAIKYGVEVADVKKMNNLVTDLQMFALKSLQIPLPGRHPPSPCL 134

Query:    88 SNGYETRGQ--ANHERTPDHHVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTG 145
             SNG    G+  + HE    +H + ++FDSF+SLRLKS  + KVSPAM SLQGYYGLKP  
Sbjct:   135 SNGSLNHGEGCSCHEPESPNHSEQEVFDSFQSLRLKSSEK-KVSPAMYSLQGYYGLKPAD 193

Query:   146 QRPPSEGC-EMAVFRKREAQC---SEDCPLLKP---SRLYKDSQRKTRSLANFLQADNSK 198
             +     GC EM  ++   +     + D   L+P   +    +  RK+RSL N L  + ++
Sbjct:   194 RTVSDGGCFEMGNYKTETSHHIFNNGDNGYLRPFPSTNTPLNHHRKSRSLVNALIEEVNQ 253

Query:   199 EPDNIISSDFRERESESGEWKDKLVRRRQKSEDDSSTSVPEMLLKEDN-SNTGGVPSITG 257
              PDN        +E  S    DK +RRRQKSE D S+  PE++LKE+N S+ GG  SI G
Sbjct:   254 SPDN------NTQEPTS----DKFMRRRQKSEADFSSRTPELVLKEENGSSNGGFLSIAG 303

Query:   258 KGLALRPAAASRTAVGADTQG--------------CDDRISGVRKSSSTPSFEDQDASSP 303
             KGLALR  A+SRT + A+++                 D  S VRKSSS  S +D D +S 
Sbjct:   304 KGLALRSKASSRTNLAAESENGNFNPVSMNLMDAPVSDSFSSVRKSSSASSLQDPDGNSN 363

Query:   304 S---PIWHGLPKPISRWKNKAAL 323
             +    +W     P S+W  K  L
Sbjct:   364 NGSLSLW-----PTSKWSLKPDL 381
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM
GO:0016998 "cell wall macromolecule catabolic process" evidence=ISS
TAIR|locus:2178272 AT5G23130 "AT5G23130" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-1895 lysmd4 "LysM, putative peptidoglycan-binding, domain containing 4" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|E2RD13 LYSMD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1SSY1 LYSMD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F1RYP8 LYSMD2 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|1561865 Lysmd1 "LysM, putative peptidoglycan-binding, domain containing 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q1JQA8 LYSMD2 "LysM and putative peptidoglycan-binding domain-containing protein 2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E1BT57 LYSMD2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:1917332 Lysmd2 "LysM, putative peptidoglycan-binding, domain containing 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00030204001
SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (398 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query324
cd0011845 cd00118, LysM, Lysine Motif is a small domain invo 3e-08
pfam0147643 pfam01476, LysM, LysM domain 2e-06
smart0025744 smart00257, LysM, Lysin motif 2e-06
COG1388124 COG1388, LytE, FOG: LysM repeat [Cell envelope bio 0.002
>gnl|CDD|212030 cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan Back     alignment and domain information 
 Score = 48.6 bits (117), Expect = 3e-08
 Identities = 15/45 (33%), Positives = 22/45 (48%)

Query: 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQI 75
            + V   DTL  IA KYGV V ++   N L     ++  + L+I
Sbjct: 1  KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45

LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes. Length = 45
>gnl|CDD|144899 pfam01476, LysM, LysM domain Back     alignment and domain information
>gnl|CDD|197609 smart00257, LysM, Lysin motif Back     alignment and domain information
>gnl|CDD|224306 COG1388, LytE, FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 324
PRK06347592 autolysin; Reviewed 99.61
PRK10783456 mltD membrane-bound lytic murein transglycosylase 99.54
PRK06347592 autolysin; Reviewed 99.46
PF0147644 LysM: LysM domain; InterPro: IPR018392 This domain 99.36
PRK13914 481 invasion associated secreted endopeptidase; Provis 99.26
PRK14125103 cell division suppressor protein YneA; Provisional 99.17
TIGR0289944 spore_safA spore coat assembly protein SafA. in wh 99.09
cd0011846 LysM Lysin domain, found in a variety of enzymes i 99.07
PRK10871319 nlpD lipoprotein NlpD; Provisional 98.94
TIGR02907338 spore_VI_D stage VI sporulation protein D. SpoVID, 98.93
PRK10783456 mltD membrane-bound lytic murein transglycosylase 98.83
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 98.79
smart0025744 LysM Lysin motif. 98.77
PRK13914481 invasion associated secreted endopeptidase; Provis 98.61
PRK11198147 LysM domain/BON superfamily protein; Provisional 98.58
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 98.33
PF0422585 OapA: Opacity-associated protein A LysM-like domai 97.41
PRK10190310 L,D-transpeptidase; Provisional 97.29
PRK10260306 L,D-transpeptidase; Provisional 97.27
TIGR0350574 FimV_core FimV N-terminal domain. This region is f 97.24
COG1652269 XkdP Uncharacterized protein containing LysM domai 97.22
PF0147644 LysM: LysM domain; InterPro: IPR018392 This domain 96.85
COG3858 423 Predicted glycosyl hydrolase [General function pre 96.75
COG3858423 Predicted glycosyl hydrolase [General function pre 95.89
KOG2850186 consensus Predicted peptidoglycan-binding protein, 95.32
PRK11649439 putative peptidase; Provisional 95.29
TIGR0289944 spore_safA spore coat assembly protein SafA. in wh 95.25
PRK10871319 nlpD lipoprotein NlpD; Provisional 94.75
cd0011846 LysM Lysin domain, found in a variety of enzymes i 94.72
PRK14125103 cell division suppressor protein YneA; Provisional 93.73
TIGR02907338 spore_VI_D stage VI sporulation protein D. SpoVID, 93.48
PF0548960 Phage_tail_X: Phage Tail Protein X; InterPro: IPR0 92.81
smart0025744 LysM Lysin motif. 92.19
COG3061242 OapA Cell envelope opacity-associated protein A [C 90.74
COG0739277 NlpD Membrane proteins related to metalloendopepti 90.01
PRK11198147 LysM domain/BON superfamily protein; Provisional 87.24
COG3170 755 FimV Tfp pilus assembly protein FimV [Cell motilit 86.87
>PRK06347 autolysin; Reviewed Back     alignment and domain information 
Probab=99.61  E-value=1.6e-15  Score=157.05  Aligned_cols=113  Identities=19%  Similarity=0.224  Sum_probs=87.8

Q ss_pred             ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCCCCCCCCCcccccccccccCC-CCcc
Q 038519           29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTP-DHHV  107 (324)
Q Consensus        29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~s~~~sngs~~r~~~~~~~ap-~~~~  107 (324)
                      ....|+|++|||||.||++|||++++|++||+|.. +.|++||.|.||............  ....       .+ ....
T Consensus       478 ~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~~s~~~t~~--~s~~-------~~~~~~~  547 (592)
T PRK06347        478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTTNNTNTAK--PSTN-------KPSNSTV  547 (592)
T ss_pred             cceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecCcccccccccC--CccC-------CccCccc
Confidence            35689999999999999999999999999999975 589999999999864322111000  0000       00 1123


Q ss_pred             cccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEE
Q 038519          108 QHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAV  157 (324)
Q Consensus       108 ~~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv  157 (324)
                      ..+.|++||+||.|++ +++|+  +..|..||+|.+   +.|++||.|.|
T Consensus       548 ~~Y~Vk~GDTL~sIA~-KygvS--v~~L~~~N~L~~---~~L~~GQ~L~I  591 (592)
T PRK06347        548 KTYTVKKGDSLWAISR-QYKTT--VDNIKAWNKLTS---NMIHVGQKLTI  591 (592)
T ss_pred             eeeecCCCCcHHHHHH-HhCCC--HHHHHHhcCCCc---ccCCCCCEEec
Confidence            4567799999999999 99999  999999999984   45999999976

>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Back     alignment and domain information
>PRK06347 autolysin; Reviewed Back     alignment and domain information
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation [] Back     alignment and domain information
>PRK13914 invasion associated secreted endopeptidase; Provisional Back     alignment and domain information
>PRK14125 cell division suppressor protein YneA; Provisional Back     alignment and domain information
>TIGR02899 spore_safA spore coat assembly protein SafA Back     alignment and domain information
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation Back     alignment and domain information
>PRK10871 nlpD lipoprotein NlpD; Provisional Back     alignment and domain information
>TIGR02907 spore_VI_D stage VI sporulation protein D Back     alignment and domain information
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Back     alignment and domain information
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>smart00257 LysM Lysin motif Back     alignment and domain information
>PRK13914 invasion associated secreted endopeptidase; Provisional Back     alignment and domain information
>PRK11198 LysM domain/BON superfamily protein; Provisional Back     alignment and domain information
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein Back     alignment and domain information
>PRK10190 L,D-transpeptidase; Provisional Back     alignment and domain information
>PRK10260 L,D-transpeptidase; Provisional Back     alignment and domain information
>TIGR03505 FimV_core FimV N-terminal domain Back     alignment and domain information
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown] Back     alignment and domain information
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation [] Back     alignment and domain information
>COG3858 Predicted glycosyl hydrolase [General function prediction only] Back     alignment and domain information
>COG3858 Predicted glycosyl hydrolase [General function prediction only] Back     alignment and domain information
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only] Back     alignment and domain information
>PRK11649 putative peptidase; Provisional Back     alignment and domain information
>TIGR02899 spore_safA spore coat assembly protein SafA Back     alignment and domain information
>PRK10871 nlpD lipoprotein NlpD; Provisional Back     alignment and domain information
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation Back     alignment and domain information
>PRK14125 cell division suppressor protein YneA; Provisional Back     alignment and domain information
>TIGR02907 spore_VI_D stage VI sporulation protein D Back     alignment and domain information
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX Back     alignment and domain information
>smart00257 LysM Lysin motif Back     alignment and domain information
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PRK11198 LysM domain/BON superfamily protein; Provisional Back     alignment and domain information
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query324
2djp_A77 The Solution Structure Of The Lysm Domain Of Human 3e-06
>pdb|2DJP|A Chain A, The Solution Structure Of The Lysm Domain Of Human Hypothetical Protein Sb145 Length = 77 Back     alignment and structure 
Iteration: 1

 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 33/47 (70%)
Query: 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPL 77
          +EHQ+   DTLAG+A+KYGV +  I++ N L T+  +F  KTL IP+
Sbjct: 16 LEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPI 62

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query324
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 6e-16
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 1e-08
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 1e-05
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 5e-05
>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 77 Back     alignment and structure
 Score = 70.6 bits (173), Expect = 6e-16
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPS 84
          +EHQ+   DTLAG+A+KYGV +  I++ N L T+  +F  KTL IP+  +    
Sbjct: 16 LEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPILTEPRDL 69
>1e0g_A Membrane-bound lytic murein transglycosylase D; cell WALL, hydrolase, glycosidase, lipoprotein, outer membrane, multigene family; NMR {Escherichia coli} SCOP: d.7.1.1 Length = 48 Back     alignment and structure
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Length = 167 Back     alignment and structure
>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A* Length = 212 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query324
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.65
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.52
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 99.46
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 99.43
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 99.39
2gu1_A361 Zinc peptidase; alpha/beta, beta barrel, structura 99.22
4a1k_A165 Putative L, D-transpeptidase YKUD; transferase, pe 98.49
2gu1_A361 Zinc peptidase; alpha/beta, beta barrel, structura 97.66
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 97.19
3slu_A371 M23 peptidase domain protein; outer membrane, hydr 96.95
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 96.73
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 96.69
>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A* Back     alignment and structure
Probab=99.65  E-value=8.6e-17  Score=145.72  Aligned_cols=113  Identities=12%  Similarity=0.081  Sum_probs=91.1

Q ss_pred             CCcceEEEEecCCCcHHHHHHHhCCCH--------HHHHHHc-CCCCCCCCCCCCEEEeCCCCCCCCCCCCCCCcccccc
Q 038519           26 GRRGIIEHQVSKLDTLAGIAIKYGVDV--------ADIRKLN-GLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQ   96 (324)
Q Consensus        26 ~~~~~~~h~Vq~GDTL~~IA~KYgVsV--------~eI~~~N-~L~~~~~L~~GQ~L~IP~~~~~~~s~~~sngs~~r~~   96 (324)
                      +...+..|+|++|||||.||++||+++        ++|+++| +|.+++.|++||.|+||......     . +.  .  
T Consensus         5 C~~a~~~Y~V~~GDTL~~IA~~~~vsv~~~~~~~~~~I~~~Np~l~~~~~l~~Gq~L~IP~~~~~~-----~-~~--~--   74 (212)
T 4eby_A            5 CPLALASYYLENGTTLSVINQNLNSSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVPFPCECQ-----P-GD--F--   74 (212)
T ss_dssp             CSCEEEEEECCTTCCHHHHHHHTCCSSSCCCSSCCHHHHTTCTTCSCTTSCCTTCEEEEEECCEEE-----T-TT--E--
T ss_pred             CccceEEEEeCCCCCHHHHHHHHCCCchhccccCHHHHHHhccCCCCcCccCCCCEEEEecccccc-----C-Cc--c--
Confidence            334788999999999999999999999        9999999 89767899999999999753211     0 00  0  


Q ss_pred             cccccCCCCcccccccccccccccCC-CCCcc--cChhHHHHhhhhCCCCCCCCCCCCCceeEEEecC
Q 038519           97 ANHERTPDHHVQHDLFDSFRSLRLKS-KPQWK--VSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKR  161 (324)
Q Consensus        97 ~~~~~ap~~~~~~~vv~sgdSl~~~s-~~~~~--vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv~~k~  161 (324)
                             ......++|+.||+||.++ . ++.  ++  +..|+.||++.|   +.+.+|++|.|....
T Consensus        75 -------~~~~~~Y~V~~GDTL~~IA~~-~y~~lvt--~~~L~~~N~~~~---~~l~~Gq~L~IP~~~  129 (212)
T 4eby_A           75 -------LGHNFSYSVRQEDTYERVAIS-NYANLTT--MESLQARNPFPA---TNIPLSATLNVLVNC  129 (212)
T ss_dssp             -------EEEEEEEECCTTCCHHHHHHT-TTTTSSC--HHHHHHHCCSCT---TCCCTTCEEEEEEEC
T ss_pred             -------ccCceEEEecCCCcHHHHHHH-hcCCCCC--HHHHHHhcCCCc---ccCCCCCEEEEcCCC
Confidence                   0112345679999999999 7 888  99  999999999764   569999999998654
>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A* Back     alignment and structure
>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Back     alignment and structure
>1e0g_A Membrane-bound lytic murein transglycosylase D; cell WALL, hydrolase, glycosidase, lipoprotein, outer membrane, multigene family; NMR {Escherichia coli} SCOP: d.7.1.1 Back     alignment and structure
>2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae} Back     alignment and structure
>4a1k_A Putative L, D-transpeptidase YKUD; transferase, peptidoglycan synthesis; HET: CME; 1.75A {Bacillus subtilis} PDB: 4a1j_A 4a1i_A* 1y7m_A 3zqd_A 4a52_A* Back     alignment and structure
>2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae} Back     alignment and structure
>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3slu_A M23 peptidase domain protein; outer membrane, hydrolase; 2.41A {Neisseria meningitidis} Back     alignment and structure
>1e0g_A Membrane-bound lytic murein transglycosylase D; cell WALL, hydrolase, glycosidase, lipoprotein, outer membrane, multigene family; NMR {Escherichia coli} SCOP: d.7.1.1 Back     alignment and structure
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 324
d1e0ga_48 d.7.1.1 (A:) Membrane-bound lytic murein transclyc 2e-08
d1y7ma248 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term 7e-08
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Length = 48 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

 Score = 47.7 bits (114), Expect = 2e-08
 Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPL 77
          I ++V K D+L+ IA ++GV++ D+ + N  + +LQ      L + +
Sbjct: 3  ITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTANLQ--PGDKLTLFV 47
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]} Length = 48 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query324
d1e0ga_48 Membrane-bound lytic murein transclycosylase D, Ml 99.53
d1y7ma248 Hypothetical protein YkuD, N-terminal domain {Baci 99.51
d1e0ga_48 Membrane-bound lytic murein transclycosylase D, Ml 98.0
d1y7ma248 Hypothetical protein YkuD, N-terminal domain {Baci 96.95
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

Probab=99.53  E-value=2.9e-15  Score=105.72  Aligned_cols=46  Identities=26%  Similarity=0.345  Sum_probs=42.8

Q ss_pred             eEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCC
Q 038519           30 IIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPL   77 (324)
Q Consensus        30 ~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~   77 (324)
                      .+.|+|++|||||.||++|||++++|+++|++.+  .|++||.|+||+
T Consensus         2 ~v~y~V~~GDTl~~IA~~y~vs~~~i~~~N~l~~--~l~~Gq~L~i~v   47 (48)
T d1e0ga_           2 SITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTA--NLQPGDKLTLFV   47 (48)
T ss_dssp             CCEEEECTTCCHHHHHHHHTCCHHHHHHHCSCGG--GCCTTEEEECCC
T ss_pred             cEEEEECCCCCHHHHHHHHCCCHHHHHHHcCCcc--cCcCCCEEEEEe
Confidence            4689999999999999999999999999999953  599999999997
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure