Citrus Sinensis ID: 018429

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-------330-------340-------350------
MSPSSGINSNGGANGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGYSNILQSLESLRTESSKKGSLATGTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLIHKSKSLVNGFLHENGATDDYVPLAEAGEGEGEKSNEKSVRRRQKAEADSRVGTPERLLKEENSGGSSGFSPATGKGLAMRPKSASRTSTSDSESGWLSSIPVGLGDSIMTDGPVGFRKSSSTPSFIDQDSSSSSIWPTSKWSLKPDLQALSTVAITRPIFDGLPKPSRRGKAALD
cccccccccccccccccEEEEEccccccHHHHHHHHcccHHHHHHHHccccccccccccEEEEcccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccc
ccccccccccccccccEEEEEEccccccHHHHEEEccEEHHHHHHHHcccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccHHHHHHHHHcccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccEccccccccccccHHcccccccccccccHHHccHccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccHHHHcHccccccccccccccHHHHHHHcc
mspssginsnggangwnYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKtlhiplpgrhppspslsdgssssgensmertpprlgySNILQSLESLRtesskkgslatgtSQKVSSAMSNLQKyyglrspngkgkdegtEMAVYRtgssghfdnglfpkaspvshpfanlIHKSKSLVNgflhengatddyvplaeagegegeksneKSVRRRQKAeadsrvgtperllkeensggssgfspatgkglamrpksasrtstsdsesgwlssipvglgdsimtdgpvgfrkssstpsfidqdsssssiwptskwslkpdlqaLSTVAitrpifdglpkpsrrgkaald
mspssginsnggaNGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGYSNILQSLESLRTesskkgslatgtsqkvssAMSNLQKyyglrspngkgkdeGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLIHKSKSLVNGFLHENGATDDYVPLAeagegegeksneksvrrrqkaeadsrvgtperllkeensggssgfspatgkglamrpksasrtstsdsesgwlSSIPVGLGDSIMTDGPVGFRKSSSTPSFIDQDSSSSSIWPTSKWSLKPDLQALSTVAitrpifdglpkpsrrgkaald
MspssginsnggangwnYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHppspslsdgssssGENSMERTPPRLGYSNILQSLESLRTESSKKGSLATGTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLIHKSKSLVNGFLHENGATDDYVPLaeagegegeKSNEKSVRRRQKAEADSRVGTPERLLKEENSGGSSGFSPATGKGLAMRPKsasrtstsdsesGWLSSIPVGLGDSIMTDGPVGFRKssstpsfidqdsssssiwptskwsLKPDLQALSTVAITRPIFDGLPKPSRRGKAALD
*************NGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIP**************************************************************************************************************HPFANLIHKSKSLVNGFLHENGAT**Y***********************************************************************************************************************KWSLKPDLQALSTVAITRPIF***************
******************IEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPL*****************************************************************************************************************************FLHENGA********************************************************TGKGL***************************************************************WSLKPDLQALSTVAITRPIFDGLPKPSRRG*****
*********NGGANGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHP********************PPRLGYSNILQSLES**********************MSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLIHKSKSLVNGFLHENGATDDYVPLAEA*************************GTPERL***************************************LSSIPVGLGDSIMTDGPVGFR*******************PTSKWSLKPDLQALSTVAITRPIFDGLPKP*********
*************NGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGR********************************************************SSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSS*****GLFPKA**************************************************************************GGSSGFS******L*****************GWLSSIPVGLGDSIMTDGPVGFRK******************PTSKWSLKPDLQALSTVAITRPIFDGLPKPSRRG*****
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MSPSSGINSNGGANGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGYSNILQSLESLRTESSKKGSLATGTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLIHKSKSLVNGFLHENGATDDYVPLAEAGEGEGEKSNEKSVRRRQKAEADSRVGTPERLLKEENSGGSSGFSPATGKGLAMRPKSASRTSTSDSESGWLSSIPVGLGDSIMTDGPVGFRKSSSTPSFIDQDSSSSSIWPTSKWSLKPDLQALSTVAITRPIFDGLPKPSRRGKAALD
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 ?
Query356 2.2.26 [Sep-21-2011]
A0JNI1225 LysM and putative peptido yes no 0.132 0.208 0.553 1e-07
Q9D0E3226 LysM and putative peptido yes no 0.132 0.207 0.531 4e-07
Q5HZA4227 LysM and putative peptido yes no 0.132 0.207 0.531 4e-07
Q96S90227 LysM and putative peptido yes no 0.132 0.207 0.531 9e-07
Q9N012227 LysM and putative peptido N/A no 0.132 0.207 0.531 9e-07
Q6DEF4208 LysM and putative peptido yes no 0.143 0.245 0.470 1e-06
Q8IV50215 LysM and putative peptido no no 0.148 0.246 0.471 1e-06
Q1JQA8215 LysM and putative peptido no no 0.148 0.246 0.471 1e-06
Q6P606267 LysM and putative peptido no no 0.359 0.479 0.294 2e-06
Q9D7V2215 LysM and putative peptido no no 0.151 0.251 0.462 3e-06
>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 = 57.8 bits (138), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 35/47 (74%)

Query: 19 IEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPL 65
          +EHQ++  DTLAG+A+KYGV +  IKR N L T+  +F  KTLHIP+
Sbjct: 40 LEHQLAPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLHIPI 86

Bos taurus (taxid: 9913)
>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|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|Q6DEF4|LYSM2_DANRE LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Danio rerio GN=lysmd2 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|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|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

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 ?
Query356
225457497366 PREDICTED: uncharacterized protein LOC10 0.949 0.923 0.658 1e-117
224118088340 predicted protein [Populus trichocarpa] 0.935 0.979 0.661 1e-117
118487763359 unknown [Populus trichocarpa] 0.924 0.916 0.666 1e-116
449439507352 PREDICTED: uncharacterized protein LOC10 0.963 0.974 0.561 2e-96
225423753398 PREDICTED: uncharacterized protein LOC10 0.915 0.819 0.556 3e-90
224083910336 predicted protein [Populus trichocarpa] 0.912 0.967 0.565 3e-89
356560027354 PREDICTED: uncharacterized protein LOC10 0.904 0.909 0.576 3e-89
296087994 495 unnamed protein product [Vitis vinifera] 0.794 0.571 0.552 1e-87
359807357349 uncharacterized protein LOC100786430 [Gl 0.904 0.922 0.570 2e-86
255546898261 conserved hypothetical protein [Ricinus 0.702 0.957 0.669 4e-86
>gi|225457497|ref|XP_002267776.1| PREDICTED: uncharacterized protein LOC100266699 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  429 bits (1102), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 237/360 (65%), Positives = 270/360 (75%), Gaps = 22/360 (6%)

Query: 4   SSGINSNGGANGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHI 63
            +  NSN   NG NYI H VSKMDTLAGVAIKYGVEVADIKR+NGLATDLQMFALK+L I
Sbjct: 22  CAATNSNSHVNGVNYILHTVSKMDTLAGVAIKYGVEVADIKRMNGLATDLQMFALKSLQI 81

Query: 64  PLPGRHPPSPSLSDGSSSSGENSMERTPPRLGYSNILQSLESLRTESSKKGSLATGTSQK 123
           PLPGRHPPSP LS+ S+SSGE S E TP  L +SN+L+SL+SL  ++ +K         K
Sbjct: 82  PLPGRHPPSPVLSNASTSSGERSTEETPLHLSHSNVLESLQSLGLKTPQK---------K 132

Query: 124 VSSAMSNLQKYYGLRS--PNGKGKDEGTEMAVYRTGSSGHFDNGLFPKASPVSHPFANLI 181
           VS AMS LQ YYGL+S   N  G  EG EM VY  G    FD GL PKA P+S P +N  
Sbjct: 133 VSPAMSTLQNYYGLKSQDKNQNGGAEGMEMTVYGAGKPHGFDFGLLPKALPISEPSSNQD 192

Query: 182 HKSKSLVNGFLHENGATDDYVPLAEAGEGEGEKSNEKSVRRRQKAEADSRVGTPERLLKE 241
           HKS++L NGF  ENG     VP++EAG+GEGE+SNEKSVRRRQK+EADS  G PERLLKE
Sbjct: 193 HKSRNLANGFFAENGTVAADVPISEAGDGEGERSNEKSVRRRQKSEADSGAG-PERLLKE 251

Query: 242 ENSGGSSGFSPATGKGLAMRPKSASRTSTS-DSESGWLSSIPVGLGDSIMTDGPVGFRKS 300
           ENSGGSSGFS  TGKGLA+RPKSASRT+ S D+ES WL++IPVGLGDSIM +G    RKS
Sbjct: 252 ENSGGSSGFSAITGKGLALRPKSASRTALSADAESSWLNAIPVGLGDSIMPEGLTSVRKS 311

Query: 301 SSTPSFI--DQDSSSSSIWPTSKWSLKPDLQALSTVAITRPIFDGLPKP--SRRGKAALD 356
           SSTPS    DQ++SSSS+WPTS W+LKPDLQALS     RPIFDGLPKP   R+ KAALD
Sbjct: 312 SSTPSLQEHDQNNSSSSVWPTS-WNLKPDLQALS----ARPIFDGLPKPITGRKNKAALD 366

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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
>gi|449439507|ref|XP_004137527.1| PREDICTED: uncharacterized protein LOC101205794 [Cucumis sativus] gi|449503083|ref|XP_004161826.1| PREDICTED: uncharacterized protein LOC101231173 [Cucumis sativus] Back     alignment and taxonomy information
>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
>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|356560027|ref|XP_003548297.1| PREDICTED: uncharacterized protein LOC100816543 [Glycine max] Back     alignment and taxonomy information
>gi|296087994|emb|CBI35277.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|359807357|ref|NP_001241636.1| uncharacterized protein LOC100786430 [Glycine max] gi|255638670|gb|ACU19640.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|255546898|ref|XP_002514507.1| conserved hypothetical protein [Ricinus communis] gi|223546406|gb|EEF47907.1| conserved hypothetical protein [Ricinus communis] 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 ?
Query356
TAIR|locus:2181539409 AT5G08200 "AT5G08200" [Arabido 0.898 0.782 0.397 2.3e-48
TAIR|locus:2178272397 AT5G23130 "AT5G23130" [Arabido 0.901 0.808 0.400 6e-48
RGD|1561865227 Lysmd1 "LysM, putative peptido 0.415 0.651 0.314 6.3e-07
UNIPROTKB|A0JNI1225 LYSMD1 "LysM and putative pept 0.132 0.208 0.553 1.4e-06
DICTYBASE|DDB_G0292322290 DDB_G0292322 "peptidoglycan-bi 0.407 0.5 0.238 1.5e-06
UNIPROTKB|E1BT57195 LYSMD2 "Uncharacterized protei 0.134 0.246 0.520 4.7e-06
UNIPROTKB|F1MNB9225 LYSMD1 "LysM and putative pept 0.132 0.208 0.531 7.7e-06
UNIPROTKB|E2RD13227 LYSMD1 "Uncharacterized protei 0.132 0.207 0.531 8e-06
UNIPROTKB|F1SSY1227 LYSMD1 "Uncharacterized protei 0.132 0.207 0.531 8e-06
UNIPROTKB|Q96S90227 LYSMD1 "LysM and putative pept 0.132 0.207 0.531 1.1e-05
TAIR|locus:2181539 AT5G08200 "AT5G08200" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 140/352 (39%), Positives = 178/352 (50%)

Query:    18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHXXXXXXXX 77
             YIEH++SK DTLAGVAIKYGVEVAD+K++N L TDLQMFALK+L IPLPGRH        
Sbjct:    77 YIEHRISKFDTLAGVAIKYGVEVADVKKMNNLVTDLQMFALKSLQIPLPGRHPPSPCLSN 136

Query:    78 XXXXXGENSMERTP--PRLGYSNILQSLESLRTESSKKGSLATGTSQKVSSAMSNLQKYY 135
                  GE      P  P      +  S +SLR +SS+K         KVS AM +LQ YY
Sbjct:   137 GSLNHGEGCSCHEPESPNHSEQEVFDSFQSLRLKSSEK---------KVSPAMYSLQGYY 187

Query:   136 GLRSPNGKGKDEGT-EMAVYRTGSSGH-FDNGL--FPKASPVSHPFANLIHKSKSLVNGF 191
             GL+  +    D G  EM  Y+T +S H F+NG   + +  P ++   N   KS+SLVN  
Sbjct:   188 GLKPADRTVSDGGCFEMGNYKTETSHHIFNNGDNGYLRPFPSTNTPLNHHRKSRSLVNAL 247

Query:   192 LHENGATDDYVPLXXXXXXXXXKSNEKSVRRRQKAEADSRVGTPERLLKEENSGGSSGFS 251
             + E   + D              +++K +RRRQK+EAD    TPE +LKEEN   + GF 
Sbjct:   248 IEEVNQSPD--------NNTQEPTSDKFMRRRQKSEADFSSRTPELVLKEENGSSNGGFL 299

Query:   252 PATGKGLAMRPKXXXXXXXXXXXX-GWLSSIPVGLGDSIMTDGPVGFRKXXXXXXXXXXX 310
                GKGLA+R K             G  + + + L D+ ++D     RK           
Sbjct:   300 SIAGKGLALRSKASSRTNLAAESENGNFNPVSMNLMDAPVSDSFSSVRKSSSASSLQDPD 359

Query:   311 XXXXXXXXX----XXXXLKPDLQALSTVAITRPIFDGLPKP--SRRGKAALD 356
                              LKPDL  L+  AIT  IFDGLPKP   RR K ALD
Sbjct:   360 GNSNNGSLSLWPTSKWSLKPDL--LTPAAITSSIFDGLPKPLTGRRNKTALD 409
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
RGD|1561865 Lysmd1 "LysM, putative peptidoglycan-binding, domain containing 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|A0JNI1 LYSMD1 "LysM and putative peptidoglycan-binding domain-containing protein 1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0292322 DDB_G0292322 "peptidoglycan-binding LysM domain-containing protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|E1BT57 LYSMD2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1MNB9 LYSMD1 "LysM and putative peptidoglycan-binding domain-containing protein 1" [Bos taurus (taxid:9913)] 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|Q96S90 LYSMD1 "LysM and putative peptidoglycan-binding domain-containing protein 1" [Homo sapiens (taxid:9606)] 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:
gw1.XII.1240.1
SubName- Full=Putative uncharacterized protein; (340 aa)
(Populus trichocarpa)
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 ?
Query356
cd0011845 cd00118, LysM, Lysine Motif is a small domain invo 1e-06
pfam0147643 pfam01476, LysM, LysM domain 3e-04
smart0025744 smart00257, LysM, Lysin motif 0.001
>gnl|CDD|212030 cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan Back     alignment and domain information 
 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 14/45 (31%), Positives = 21/45 (46%)

Query: 19 IEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHI 63
            + V   DTL  +A 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 356
PRK06347592 autolysin; Reviewed 99.6
PRK10783456 mltD membrane-bound lytic murein transglycosylase 99.54
PRK06347592 autolysin; Reviewed 99.47
PF0147644 LysM: LysM domain; InterPro: IPR018392 This domain 99.3
PRK13914 481 invasion associated secreted endopeptidase; Provis 99.21
PRK14125103 cell division suppressor protein YneA; Provisional 99.1
cd0011846 LysM Lysin domain, found in a variety of enzymes i 98.99
TIGR0289944 spore_safA spore coat assembly protein SafA. in wh 98.96
TIGR02907338 spore_VI_D stage VI sporulation protein D. SpoVID, 98.85
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 98.76
PRK10871319 nlpD lipoprotein NlpD; Provisional 98.76
PRK10783456 mltD membrane-bound lytic murein transglycosylase 98.67
smart0025744 LysM Lysin motif. 98.65
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 98.54
PRK13914481 invasion associated secreted endopeptidase; Provis 98.47
PRK11198147 LysM domain/BON superfamily protein; Provisional 98.38
PF0147644 LysM: LysM domain; InterPro: IPR018392 This domain 97.44
PF0422585 OapA: Opacity-associated protein A LysM-like domai 97.07
COG3858 423 Predicted glycosyl hydrolase [General function pre 96.87
TIGR0350574 FimV_core FimV N-terminal domain. This region is f 96.8
KOG2850186 consensus Predicted peptidoglycan-binding protein, 96.43
PRK10190310 L,D-transpeptidase; Provisional 96.43
PRK10260306 L,D-transpeptidase; Provisional 96.3
PRK14125103 cell division suppressor protein YneA; Provisional 96.2
COG1652269 XkdP Uncharacterized protein containing LysM domai 96.09
TIGR0289944 spore_safA spore coat assembly protein SafA. in wh 95.87
PRK10871319 nlpD lipoprotein NlpD; Provisional 95.62
cd0011846 LysM Lysin domain, found in a variety of enzymes i 95.61
TIGR02907338 spore_VI_D stage VI sporulation protein D. SpoVID, 95.12
smart0025744 LysM Lysin motif. 94.75
PRK11649439 putative peptidase; Provisional 94.5
COG3858423 Predicted glycosyl hydrolase [General function pre 94.41
PF0548960 Phage_tail_X: Phage Tail Protein X; InterPro: IPR0 90.75
PRK11198147 LysM domain/BON superfamily protein; Provisional 89.85
COG0739277 NlpD Membrane proteins related to metalloendopepti 89.6
>PRK06347 autolysin; Reviewed Back     alignment and domain information 
Probab=99.60  E-value=2e-15  Score=157.62  Aligned_cols=113  Identities=19%  Similarity=0.248  Sum_probs=87.7

Q ss_pred             CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCc
Q 018429           17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGY   96 (356)
Q Consensus        17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq~~~~~   96 (356)
                      ....|+|++||||++||++|||++++|+++|+|.. +.|++||.|.||............. + .       ..+..   
T Consensus       478 ~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~~s~~~t~~~-s-~-------~~~~~---  544 (592)
T PRK06347        478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTTNNTNTAKP-S-T-------NKPSN---  544 (592)
T ss_pred             cceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecCcccccccccCC-c-c-------CCccC---
Confidence            45679999999999999999999999999999985 5799999999998643322110000 0 0       00000   


Q ss_pred             chhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEE
Q 018429           97 SNILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAV  153 (356)
Q Consensus        97 ~~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv  153 (356)
                          .....|+|++|  |+||. +++++|++  ..|..||+|.+   +.|++||.|.|
T Consensus       545 ----~~~~~Y~Vk~G--DTL~sIA~KygvSv--~~L~~~N~L~~---~~L~~GQ~L~I  591 (592)
T PRK06347        545 ----STVKTYTVKKG--DSLWAISRQYKTTV--DNIKAWNKLTS---NMIHVGQKLTI  591 (592)
T ss_pred             ----ccceeeecCCC--CcHHHHHHHhCCCH--HHHHHhcCCCc---ccCCCCCEEec
Confidence                01123999999  99999 99999988  99999999985   66999999987

>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
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation Back     alignment and domain information
>TIGR02899 spore_safA spore coat assembly protein SafA Back     alignment and domain information
>TIGR02907 spore_VI_D stage VI sporulation protein D Back     alignment and domain information
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PRK10871 nlpD lipoprotein NlpD; Provisional Back     alignment and domain information
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Back     alignment and domain information
>smart00257 LysM Lysin motif Back     alignment and domain information
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] 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
>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
>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
>COG3858 Predicted glycosyl hydrolase [General function prediction only] Back     alignment and domain information
>TIGR03505 FimV_core FimV N-terminal domain Back     alignment and domain information
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only] 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
>PRK14125 cell division suppressor protein YneA; Provisional Back     alignment and domain information
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown] 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
>TIGR02907 spore_VI_D stage VI sporulation protein D Back     alignment and domain information
>smart00257 LysM Lysin motif Back     alignment and domain information
>PRK11649 putative peptidase; Provisional Back     alignment and domain information
>COG3858 Predicted glycosyl hydrolase [General function prediction only] 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
>PRK11198 LysM domain/BON superfamily protein; Provisional Back     alignment and domain information
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] 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 ?
Query356
2djp_A77 The Solution Structure Of The Lysm Domain Of Human 2e-07
>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 34/47 (72%)
Query: 19 IEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPL 65
          +EHQ+   DTLAG+A+KYGV +  IKR 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 ?
Query356
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 2e-15
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 3e-08
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 2e-04
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 2e-04
>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 = 69.8 bits (171), Expect = 2e-15
 Identities = 29/65 (44%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLS 76
            +EHQ+   DTLAG+A+KYGV +  IKR N L T+  +F  KTL+IP+     P    +
Sbjct: 14 RRLEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPILTE--PRDLFN 71

Query: 77 DGSSS 81
           G SS
Sbjct: 72 SGPSS 76
>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
>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
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Length = 167 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query356
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.63
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.51
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 99.41
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 99.32
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 99.28
2gu1_A361 Zinc peptidase; alpha/beta, beta barrel, structura 99.27
4a1k_A165 Putative L, D-transpeptidase YKUD; transferase, pe 98.37
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 97.63
2gu1_A361 Zinc peptidase; alpha/beta, beta barrel, structura 97.47
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 97.17
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 97.13
3slu_A371 M23 peptidase domain protein; outer membrane, hydr 97.01
>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=99.63  E-value=9.7e-17  Score=146.61  Aligned_cols=109  Identities=11%  Similarity=0.095  Sum_probs=89.1

Q ss_pred             CeEEEEecCCCCHHHHHHHhCCCH--------HHHHHHh-CCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCc
Q 018429           17 NYIEHQVSKMDTLAGVAIKYGVEV--------ADIKRLN-GLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSM   87 (356)
Q Consensus        17 ~~i~H~VkkGDTL~~IA~KYgVsV--------~dIKraN-nL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~   87 (356)
                      .|..|+|++||||+.||++|||++        ++|+++| +|...+.|++||.|+||......      . . .      
T Consensus         8 a~~~Y~V~~GDTL~~IA~~~~vsv~~~~~~~~~~I~~~Np~l~~~~~l~~Gq~L~IP~~~~~~------~-~-~------   73 (212)
T 4eby_A            8 ALASYYLENGTTLSVINQNLNSSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVPFPCECQ------P-G-D------   73 (212)
T ss_dssp             EEEEEECCTTCCHHHHHHHTCCSSSCCCSSCCHHHHTTCTTCSCTTSCCTTCEEEEEECCEEE------T-T-T------
T ss_pred             ceEEEEeCCCCCHHHHHHHHCCCchhccccCHHHHHHhccCCCCcCccCCCCEEEEecccccc------C-C-c------
Confidence            578899999999999999999999        9999999 99766789999999999752110      0 0 0      


Q ss_pred             ccCCCCCCcchhhhhcccccccCCCCCCCcc-c-cccc--cChhHHHHHHHhCCCCCCCCCCCCCceEEEeeCC
Q 018429           88 ERTPPRLGYSNILQSLESLRTESSKKGSLAT-G-TSQK--VSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTG  157 (356)
Q Consensus        88 ~~aq~~~~~~~~le~~~s~~vKsg~~dsLw~-g-q~~k--VSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~~~  157 (356)
                                 .......|+|++|  |+||. + +++.  |++  ..|+.||++.+   +.+.+||+|.|....
T Consensus        74 -----------~~~~~~~Y~V~~G--DTL~~IA~~~y~~lvt~--~~L~~~N~~~~---~~l~~Gq~L~IP~~~  129 (212)
T 4eby_A           74 -----------FLGHNFSYSVRQE--DTYERVAISNYANLTTM--ESLQARNPFPA---TNIPLSATLNVLVNC  129 (212)
T ss_dssp             -----------EEEEEEEEECCTT--CCHHHHHHTTTTTSSCH--HHHHHHCCSCT---TCCCTTCEEEEEEEC
T ss_pred             -----------cccCceEEEecCC--CcHHHHHHHhcCCCCCH--HHHHHhcCCCc---ccCCCCCEEEEcCCC
Confidence                       0001124999999  99999 9 8999  988  99999999765   679999999997643
>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
>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
>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
>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} 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
>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
>3slu_A M23 peptidase domain protein; outer membrane, hydrolase; 2.41A {Neisseria meningitidis} 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 356
d1e0ga_48 d.7.1.1 (A:) Membrane-bound lytic murein transclyc 1e-08
d1y7ma248 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term 9e-06
>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 = 48.1 bits (115), Expect = 1e-08
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQ 54
          + I ++V K D+L+ +A ++GV + D+ R N    +LQ
Sbjct: 1  DSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTANLQ 38
>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 ?
Query356
d1e0ga_48 Membrane-bound lytic murein transclycosylase D, Ml 99.48
d1y7ma248 Hypothetical protein YkuD, N-terminal domain {Baci 99.47
d1e0ga_48 Membrane-bound lytic murein transclycosylase D, Ml 98.14
d1y7ma248 Hypothetical protein YkuD, N-terminal domain {Baci 97.71
>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=99.48  E-value=1.6e-14  Score=103.24  Aligned_cols=47  Identities=26%  Similarity=0.325  Sum_probs=43.3

Q ss_pred             eEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCC
Q 018429           18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLP   66 (356)
Q Consensus        18 ~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~   66 (356)
                      .+.|+|++||||+.||++|||++++|+++|++. + .|++||.|.||+.
T Consensus         2 ~v~y~V~~GDTl~~IA~~y~vs~~~i~~~N~l~-~-~l~~Gq~L~i~vk   48 (48)
T d1e0ga_           2 SITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDT-A-NLQPGDKLTLFVK   48 (48)
T ss_dssp             CCEEEECTTCCHHHHHHHHTCCHHHHHHHCSCG-G-GCCTTEEEECCCC
T ss_pred             cEEEEECCCCCHHHHHHHHCCCHHHHHHHcCCc-c-cCcCCCEEEEEeC
Confidence            467999999999999999999999999999995 3 5999999999974
>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