Citrus Sinensis ID: 024891

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-
MGCCGEQNDAEEELQNHLLSSSSSSASSFTDPSTVISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGALA
ccccccccccHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHcccHHHHHHHHccccccccccccEEEEccccccccccccccccccccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccc
ccccccccccHHHHHHHccccccccccccccccccccccccHHHHccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccHHHHHHHHHccccccccccccccccccccccccEEEEEEEEcccccHHHHHEHcccEHHHHHHHHccccccccEHHcEEEEccccHHHHHccEEEEEEcccccEEEEEEEcccccccccHHHccHHHHHHcccHHHHHHccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccc
MGCCGEQNDAEEELQNHllssssssassftdpstvispmnshfsalacPDTLRLILSNLSVTDLARASCVCRawssvasdnnMIVLAFMApwklkevvgmplngsfwrdngigkFAISHRLARGDTVASLAVKYSVQVMDIKRLNnmmsdhgiysrerllipisspellidgicyiefdtYAKREVAVLYLegapekkpscllnrvtsvhGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGALA
MGCCGEQNDAEEELQNHLLSSSSSSASSFTDPSTVISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWssvasdnnMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYlegapekkpscllnrvtsvhgrrriinslrrsmqvddETAQYYLSISNGNLRAALSEFSADLEWERQGALA
MGCCGEQNDAEEELQNHLLssssssassFTDPSTVISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERllipisspelliDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGALA
*****************************************HFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEF*************
*********************************************LACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLA***************************FAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLI******************************************************VDDETAQYYLSISNGNLRAALSEFSADLEWERQ****
********************************STVISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADL*********
**********E***********************VISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEG****************************SMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQG***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGCCGEQNDAEEELQNHLLSSSSSSASSFTDPSTVISPMNSHFSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGALA
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 ?
Query261 2.2.26 [Sep-21-2011]
Q9FZ32221 F-box protein At1g55000 O yes no 0.827 0.977 0.666 1e-82
A0JNI1225 LysM and putative peptido yes no 0.218 0.253 0.413 4e-05
Q9D0E3226 LysM and putative peptido yes no 0.218 0.252 0.413 4e-05
Q96S90227 LysM and putative peptido yes no 0.218 0.251 0.396 6e-05
Q5HZA4227 LysM and putative peptido yes no 0.218 0.251 0.396 7e-05
Q9N012227 LysM and putative peptido N/A no 0.218 0.251 0.396 8e-05
Q8IV50215 LysM and putative peptido no no 0.340 0.413 0.298 8e-05
Q6DEF4208 LysM and putative peptido yes no 0.206 0.259 0.388 0.0001
Q9D7V2215 LysM and putative peptido no no 0.233 0.283 0.370 0.0003
Q1JQA8215 LysM and putative peptido no no 0.256 0.311 0.338 0.0003
>sp|Q9FZ32|FB60_ARATH F-box protein At1g55000 OS=Arabidopsis thaliana GN=At1g55000 PE=1 SV=1 Back     alignment and function desciption
 Score =  306 bits (783), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 146/219 (66%), Positives = 177/219 (80%), Gaps = 3/219 (1%)

Query: 45  ALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNG 104
           AL C DTL +I   L+V DLARASCVC+ W+SVA++++++V AF APW++KE+VG P + 
Sbjct: 2   ALYCRDTLIIIFQKLTVADLARASCVCKVWNSVATEDDLVVSAFTAPWRIKELVGRPASV 61

Query: 105 SFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164
           SFWRDNGI KFAISHR+ RGD+V SLAVKY+VQVMDIKRLNNMMSDHGIYSR+RLLIPIS
Sbjct: 62  SFWRDNGIWKFAISHRICRGDSVTSLAVKYAVQVMDIKRLNNMMSDHGIYSRDRLLIPIS 121

Query: 165 SPELLIDGICYIEFDTYAKREVAVLYLEGAPEKK---PSCLLNRVTSVHGRRRIINSLRR 221
           +PE+L +  CY+E D YAKREVAVLYLEGAP+++   P        S  G+RR+I SLRR
Sbjct: 122 NPEILANTTCYVELDKYAKREVAVLYLEGAPKREQPVPGTNQQSNLSADGKRRLIESLRR 181

Query: 222 SMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGAL 260
           SMQVDD TA YYL+I+ G+ R+ALSEFSADL WERQ  L
Sbjct: 182 SMQVDDGTALYYLAIAEGDPRSALSEFSADLRWERQAGL 220
Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.
Arabidopsis thaliana (taxid: 3702)
>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 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|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|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|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|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|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|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

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 ?
Query261
296088355321 unnamed protein product [Vitis vinifera] 0.988 0.803 0.680 1e-101
225450917266 PREDICTED: F-box protein At1g55000-like 0.988 0.969 0.680 1e-101
255542644260 conserved hypothetical protein [Ricinus 0.984 0.988 0.666 4e-98
356576783260 PREDICTED: F-box protein At1g55000-like 0.984 0.988 0.630 3e-89
358248284263 uncharacterized protein LOC100803417 [Gl 0.992 0.984 0.616 7e-88
449442811269 PREDICTED: F-box protein At1g55000-like 0.988 0.959 0.610 4e-87
449482840269 PREDICTED: F-box protein At1g55000-like 0.988 0.959 0.606 9e-87
383100920 547 peptidoglycan-binding LysM domain-contai 0.873 0.416 0.676 2e-86
357441673262 F-box protein [Medicago truncatula] gi|3 0.977 0.973 0.615 5e-85
388513159262 unknown [Medicago truncatula] 0.977 0.973 0.611 8e-85
>gi|296088355|emb|CBI36800.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 183/269 (68%), Positives = 210/269 (78%), Gaps = 11/269 (4%)

Query: 1   MGCCGEQNDAEEELQNHLLSS--------SSSSASSFTDPSTVISPMNSHFSALACPDTL 52
           MGCCG   D EEE   HL+ +        S+  AS+  D   VIS MNSHFSAL C D L
Sbjct: 56  MGCCG---DEEEEFLKHLMPNFSETLTLGSTFQASTSGDSDAVISAMNSHFSALTCQDVL 112

Query: 53  RLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGI 112
           R I   L V DLARASCVCR W+ VASD  + V AF APWKLK+VVG+P +GSFWRD+ +
Sbjct: 113 RGIFERLPVADLARASCVCRVWNLVASDRGIQVRAFRAPWKLKDVVGIPSSGSFWRDDSL 172

Query: 113 GKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDG 172
           GKFAISHRL RGD+VASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIP+S P++LI+ 
Sbjct: 173 GKFAISHRLVRGDSVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPVSKPDILINA 232

Query: 173 ICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRVTSVHGRRRIINSLRRSMQVDDETAQY 232
           ICYIE D+YAKREVAVLYLEG P+KK + LLN+V+S  GRRR+I SL+RSMQ+DD TAQY
Sbjct: 233 ICYIELDSYAKREVAVLYLEGGPDKKLNSLLNKVSSEQGRRRVIESLKRSMQIDDGTAQY 292

Query: 233 YLSISNGNLRAALSEFSADLEWERQGALA 261
           YLSISNG+ RAA+SEFS DL WER   L+
Sbjct: 293 YLSISNGDPRAAISEFSEDLRWERHAGLS 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225450917|ref|XP_002284540.1| PREDICTED: F-box protein At1g55000-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|255542644|ref|XP_002512385.1| conserved hypothetical protein [Ricinus communis] gi|223548346|gb|EEF49837.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|356576783|ref|XP_003556509.1| PREDICTED: F-box protein At1g55000-like [Glycine max] Back     alignment and taxonomy information
>gi|358248284|ref|NP_001240110.1| uncharacterized protein LOC100803417 [Glycine max] gi|255642335|gb|ACU21432.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|449442811|ref|XP_004139174.1| PREDICTED: F-box protein At1g55000-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449482840|ref|XP_004156419.1| PREDICTED: F-box protein At1g55000-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|383100920|emb|CCD74465.1| peptidoglycan-binding LysM domain-containing protein [Arabidopsis halleri subsp. halleri] Back     alignment and taxonomy information
>gi|357441673|ref|XP_003591114.1| F-box protein [Medicago truncatula] gi|355480162|gb|AES61365.1| F-box protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|388513159|gb|AFK44641.1| unknown [Medicago truncatula] 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 ?
Query261
TAIR|locus:2011020221 AT1G55000 "AT1G55000" [Arabido 0.827 0.977 0.630 8e-69
TAIR|locus:2011020 AT1G55000 "AT1G55000" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 698 (250.8 bits), Expect = 8.0e-69, P = 8.0e-69
 Identities = 138/219 (63%), Positives = 169/219 (77%)

Query:    45 ALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNG 104
             AL C DTL +I   L+V DLARASCVC+ W+SVA++++++V AF APW++KE+VG P + 
Sbjct:     2 ALYCRDTLIIIFQKLTVADLARASCVCKVWNSVATEDDLVVSAFTAPWRIKELVGRPASV 61

Query:   105 SFWRDNGIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERXXXXXX 164
             SFWRDNGI KFAISHR+ RGD+V SLAVKY+VQVMDIKRLNNMMSDHGIYSR+R      
Sbjct:    62 SFWRDNGIWKFAISHRICRGDSVTSLAVKYAVQVMDIKRLNNMMSDHGIYSRDRLLIPIS 121

Query:   165 XXXXXXDGICYIEFDTYAKREVAVLYLEGAPEKK-PSCLLNRVT--SVHGRRRIINSLRR 221
                   +  CY+E D YAKREVAVLYLEGAP+++ P    N+ +  S  G+RR+I SLRR
Sbjct:   122 NPEILANTTCYVELDKYAKREVAVLYLEGAPKREQPVPGTNQQSNLSADGKRRLIESLRR 181

Query:   222 SMQVDDETAQYYLSISNGNLRAALSEFSADLEWERQGAL 260
             SMQVDD TA YYL+I+ G+ R+ALSEFSADL WERQ  L
Sbjct:   182 SMQVDDGTALYYLAIAEGDPRSALSEFSADLRWERQAGL 220


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.133   0.397    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      261       240   0.00093  113 3  11 22  0.40    33
                                                     32  0.44    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  615 (65 KB)
  Total size of DFA:  196 KB (2111 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  17.34u 0.12s 17.46t   Elapsed:  00:00:00
  Total cpu time:  17.34u 0.12s 17.46t   Elapsed:  00:00:00
  Start:  Sat May 11 06:05:25 2013   End:  Sat May 11 06:05:25 2013
GO:0003674 "molecular_function" evidence=ND
GO:0016998 "cell wall macromolecule catabolic process" evidence=IEA;ISS

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9FZ32FB60_ARATHNo assigned EC number0.66660.82750.9773yesno

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:
GSVIVG00022802001
SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (223 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 ?
Query261
cd0011845 cd00118, LysM, Lysine Motif is a small domain invo 1e-06
pfam1293747 pfam12937, F-box-like, F-box-like 3e-06
pfam0147643 pfam01476, LysM, LysM domain 3e-05
smart0025641 smart00256, FBOX, A Receptor for Ubiquitination Ta 2e-04
pfam0064648 pfam00646, F-box, F-box domain 2e-04
smart0025744 smart00257, LysM, Lysin motif 0.002
PRK13914 481 PRK13914, PRK13914, invasion associated secreted e 0.003
>gnl|CDD|212030 cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan Back     alignment and domain information 
 Score = 44.0 bits (105), Expect = 1e-06
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLI 161
            ++ +  GDT+ S+A KY V V ++   N +++   IY  ++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|221867 pfam12937, F-box-like, F-box-like Back     alignment and domain information
>gnl|CDD|144899 pfam01476, LysM, LysM domain Back     alignment and domain information
>gnl|CDD|197608 smart00256, FBOX, A Receptor for Ubiquitination Targets Back     alignment and domain information
>gnl|CDD|201368 pfam00646, F-box, F-box domain Back     alignment and domain information
>gnl|CDD|197609 smart00257, LysM, Lysin motif Back     alignment and domain information
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 261
PF0147644 LysM: LysM domain; InterPro: IPR018392 This domain 99.35
PRK06347592 autolysin; Reviewed 99.26
PRK10783456 mltD membrane-bound lytic murein transglycosylase 99.19
PRK06347592 autolysin; Reviewed 99.11
PRK14125103 cell division suppressor protein YneA; Provisional 99.09
TIGR0289944 spore_safA spore coat assembly protein SafA. in wh 99.02
cd0011846 LysM Lysin domain, found in a variety of enzymes i 98.98
PF1293747 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 98.88
TIGR02907338 spore_VI_D stage VI sporulation protein D. SpoVID, 98.87
PRK10871 319 nlpD lipoprotein NlpD; Provisional 98.82
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 98.71
smart0025744 LysM Lysin motif. 98.63
PRK13914 481 invasion associated secreted endopeptidase; Provis 98.61
smart0025641 FBOX A Receptor for Ubiquitination Targets. 98.58
PRK11198147 LysM domain/BON superfamily protein; Provisional 98.53
PRK13914 481 invasion associated secreted endopeptidase; Provis 98.49
PF0064648 F-box: F-box domain; InterPro: IPR001810 The F-box 98.48
PRK10783456 mltD membrane-bound lytic murein transglycosylase 98.28
KOG2997366 consensus F-box protein FBX9 [General function pre 98.07
KOG2850186 consensus Predicted peptidoglycan-binding protein, 97.88
PF1455543 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 97.7
PF0422585 OapA: Opacity-associated protein A LysM-like domai 96.98
KOG2850186 consensus Predicted peptidoglycan-binding protein, 96.9
TIGR0350574 FimV_core FimV N-terminal domain. This region is f 96.85
COG1652269 XkdP Uncharacterized protein containing LysM domai 96.61
PRK10190 310 L,D-transpeptidase; Provisional 96.56
PRK10260 306 L,D-transpeptidase; Provisional 96.5
COG3858 423 Predicted glycosyl hydrolase [General function pre 96.14
KOG2120 419 consensus SCF ubiquitin ligase, Skp2 component [Po 96.03
COG3858 423 Predicted glycosyl hydrolase [General function pre 96.02
PLN03215 373 ascorbic acid mannose pathway regulator 1; Provisi 95.88
PF0548960 Phage_tail_X: Phage Tail Protein X; InterPro: IPR0 94.57
PRK11649 439 putative peptidase; Provisional 93.91
COG1388124 LytE FOG: LysM repeat [Cell envelope biogenesis, o 93.12
PF0394351 TAP_C: TAP C-terminal domain; InterPro: IPR005637 90.77
COG0739 277 NlpD Membrane proteins related to metalloendopepti 87.5
smart0080463 TAP_C C-terminal domain of vertebrate Tap protein. 85.39
KOG4341 483 consensus F-box protein containing LRR [General fu 84.11
KOG4408 386 consensus Putative Mg2+ and Co2+ transporter CorD 81.66
>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 
Probab=99.35  E-value=9.2e-13  Score=88.22  Aligned_cols=43  Identities=35%  Similarity=0.569  Sum_probs=36.9

Q ss_pred             EEccCCCcHHHHHHHhCCCHHHHHHHh-CCCCCcCccCCCEEEec
Q 024891          119 HRLARGDTVASLAVKYSVQVMDIKRLN-NMMSDHGIYSRERLLIP  162 (261)
Q Consensus       119 h~V~~GDTL~~IA~rYgvsv~~I~~~N-~L~s~~~i~~gq~L~IP  162 (261)
                      |+|++||||++||.+||+++++|+++| ++..+. |++||+|.||
T Consensus         1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~-l~~G~~l~iP   44 (44)
T PF01476_consen    1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDN-LQPGQKLCIP   44 (44)
T ss_dssp             EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGC-GGTTEEEEEC
T ss_pred             CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCccc-CCCCCEEEeC
Confidence            899999999999999999999999999 887765 9999999998

This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
>PRK06347 autolysin; Reviewed Back     alignment and domain information
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Back     alignment and domain information
>PRK06347 autolysin; Reviewed 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
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B Back     alignment and domain information
>TIGR02907 spore_VI_D stage VI sporulation protein D Back     alignment and domain information
>PRK10871 nlpD lipoprotein NlpD; 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
>smart00256 FBOX A Receptor for Ubiquitination Targets Back     alignment and domain information
>PRK11198 LysM domain/BON superfamily protein; Provisional Back     alignment and domain information
>PRK13914 invasion associated secreted endopeptidase; Provisional Back     alignment and domain information
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ] Back     alignment and domain information
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Back     alignment and domain information
>KOG2997 consensus F-box protein FBX9 [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
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A 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
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only] 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
>PRK10190 L,D-transpeptidase; Provisional Back     alignment and domain information
>PRK10260 L,D-transpeptidase; Provisional Back     alignment and domain information
>COG3858 Predicted glycosyl hydrolase [General function prediction only] Back     alignment and domain information
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>COG3858 Predicted glycosyl hydrolase [General function prediction only] Back     alignment and domain information
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional 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
>PRK11649 putative peptidase; Provisional Back     alignment and domain information
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1) Back     alignment and domain information
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein Back     alignment and domain information
>KOG4341 consensus F-box protein containing LRR [General function prediction only] Back     alignment and domain information
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query261
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 1e-14
1fs1_A53 SKP2 F-BOX, cyclin A/CDK2-associated P19; F-BOX, L 5e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-06
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 2e-06
3l2o_B312 F-box only protein 4; small G protein fold, UBL co 6e-06
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 1e-04
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 3e-04
2ovr_B 445 FBW7, F-BOX/WD repeat protein 7, F-box PROT; WD40 6e-04
2e31_A297 FBS1, F-box only protein 2; ubiquitin, SCF, ubiqui 8e-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 = 66.4 bits (162), Expect = 1e-14
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISS 165
           + H+L  GDT+A LA+KY V +  IKR N + ++  I+ ++ L IPI +
Sbjct: 16  LEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPILT 64
>1fs1_A SKP2 F-BOX, cyclin A/CDK2-associated P19; F-BOX, LRR, leucine-rich repeat, SCF, ubiquitin, ubiquitin protein ligase; 1.80A {Homo sapiens} SCOP: a.158.1.1 PDB: 1ldk_E Length = 53 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 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 Length = 48 Back     alignment and structure
>3l2o_B F-box only protein 4; small G protein fold, UBL conjugation pathway, ubiquitin Pro ligase, protein binding-cell cycle complex; 2.80A {Homo sapiens} Length = 312 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
>2ovr_B FBW7, F-BOX/WD repeat protein 7, F-box PROT; WD40 domains, double phosphorylation, transcription-C complex; HET: TPO; 2.50A {Homo sapiens} SCOP: a.158.1.1 b.69.4.1 PDB: 2ovp_B* 2ovq_B* Length = 445 Back     alignment and structure
>2e31_A FBS1, F-box only protein 2; ubiquitin, SCF, ubiquitin ligase, FBS1; 2.40A {Mus musculus} PDB: 2e32_A Length = 297 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query261
2djp_A77 Hypothetical protein SB145; LYSM, structural genom 99.37
1e0g_A48 Membrane-bound lytic murein transglycosylase D; ce 99.33
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.25
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 99.21
4eby_A212 Chitin elicitor receptor kinase 1; pathogen-associ 99.13
1fs1_A53 SKP2 F-BOX, cyclin A/CDK2-associated P19; F-BOX, L 98.96
2e31_A297 FBS1, F-box only protein 2; ubiquitin, SCF, ubiqui 98.74
3l2o_B312 F-box only protein 4; small G protein fold, UBL co 98.55
2gu1_A 361 Zinc peptidase; alpha/beta, beta barrel, structura 98.49
4a1k_A165 Putative L, D-transpeptidase YKUD; transferase, pe 98.4
2gu1_A 361 Zinc peptidase; alpha/beta, beta barrel, structura 98.27
1p22_A 435 F-BOX/WD-repeat protein 1A; ubiquitination, degrad 98.08
3v7d_B 464 Cell division control protein 4; WD 40 domain, pho 98.04
2ovr_B 445 FBW7, F-BOX/WD repeat protein 7, F-box PROT; WD40 98.02
2ast_B 336 S-phase kinase-associated protein 2; SCF-substrate 97.64
2l9y_A167 CVNH-LYSM lectin; carbohydrate, sugar binding prot 97.49
1v92_A46 NSFL1 cofactor P47; 3-helix bundle, recombination; 97.17
2dam_A67 ETEA protein; KIAA0887, UBA-like domain, structura 97.02
3e21_A45 HFAF1, FAS-associated factor 1; UBA, alternative s 96.96
2dal_A62 Protein KIAA0794; FAS associted factor 1, UBA-like 96.92
3slu_A 371 M23 peptidase domain protein; outer membrane, hydr 96.86
2p1m_B 594 Transport inhibitor response 1 protein; F-BOX, leu 96.78
2dzl_A66 Protein FAM100B; UBA-like domain, structural genom 96.75
3ogk_B 592 Coronatine-insensitive protein 1; leucine rich rep 96.1
1oai_A59 Nuclear RNA export factor; nuclear transport, nucl 93.31
2jp7_A57 MRNA export factor MEX67; solution MEX67, UBA, tra 93.31
3bq3_A 270 Defective in cullin neddylation protein 1; ubiquit 92.99
4gew_A 362 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 86.55
1wj7_A104 Hypothetical protein (RSGI RUH-015); UBA domain, u 80.97
1z96_A40 DNA-damage, UBA-domain protein MUD1; ubiquitin, th 80.33
>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
Probab=99.37  E-value=5.7e-13  Score=98.62  Aligned_cols=51  Identities=39%  Similarity=0.673  Sum_probs=47.3

Q ss_pred             cceEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891          114 KFAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS  164 (261)
Q Consensus       114 ~~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~  164 (261)
                      ..+..|+|++||||++||++||+++++|+++|++..++.|++||+|+||..
T Consensus        13 ~~~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~l~~~~~l~~Gq~l~iP~~   63 (77)
T 2djp_A           13 ERRLEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPIL   63 (77)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTCCHHHHHHHHTCCCSSCGGGSSCEEEEEE
T ss_pred             CCcEEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEEECCC
Confidence            357889999999999999999999999999999987778999999999975
>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
>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
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} 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* Back     alignment and structure
>1fs1_A SKP2 F-BOX, cyclin A/CDK2-associated P19; F-BOX, LRR, leucine-rich repeat, SCF, ubiquitin, ubiquitin protein ligase; 1.80A {Homo sapiens} SCOP: a.158.1.1 PDB: 1ldk_E Back     alignment and structure
>2e31_A FBS1, F-box only protein 2; ubiquitin, SCF, ubiquitin ligase, FBS1; 2.40A {Mus musculus} PDB: 2e32_A Back     alignment and structure
>3l2o_B F-box only protein 4; small G protein fold, UBL conjugation pathway, ubiquitin Pro ligase, protein binding-cell cycle complex; 2.80A {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
>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
>1p22_A F-BOX/WD-repeat protein 1A; ubiquitination, degradation, signaling protein; HET: SEP; 2.95A {Homo sapiens} SCOP: a.158.1.1 b.69.4.1 Back     alignment and structure
>3v7d_B Cell division control protein 4; WD 40 domain, phospho-peptide complex, E3 ubiquitin ligase, cell cycle, phospho binding protein, phosphorylation; HET: SEP; 2.31A {Saccharomyces cerevisiae} PDB: 1nex_B* 3mks_B* Back     alignment and structure
>2ovr_B FBW7, F-BOX/WD repeat protein 7, F-box PROT; WD40 domains, double phosphorylation, transcription-C complex; HET: TPO; 2.50A {Homo sapiens} SCOP: a.158.1.1 b.69.4.1 PDB: 2ovp_B* 2ovq_B* Back     alignment and structure
>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A Back     alignment and structure
>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Back     alignment and structure
>1v92_A NSFL1 cofactor P47; 3-helix bundle, recombination; NMR {Rattus norvegicus} SCOP: a.5.2.3 Back     alignment and structure
>2dam_A ETEA protein; KIAA0887, UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3e21_A HFAF1, FAS-associated factor 1; UBA, alternative splicing, apoptosis, nucleus, phosphoprotein; 1.73A {Homo sapiens} Back     alignment and structure
>2dal_A Protein KIAA0794; FAS associted factor 1, UBA-like domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3slu_A M23 peptidase domain protein; outer membrane, hydrolase; 2.41A {Neisseria meningitidis} Back     alignment and structure
>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B* Back     alignment and structure
>2dzl_A Protein FAM100B; UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B* Back     alignment and structure
>1oai_A Nuclear RNA export factor; nuclear transport, nuclear transport factor; 1.0A {Homo sapiens} SCOP: a.5.2.3 Back     alignment and structure
>2jp7_A MRNA export factor MEX67; solution MEX67, UBA, translation; NMR {Saccharomyces cerevisiae} PDB: 2khh_A Back     alignment and structure
>4gew_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; 2.35A {Caenorhabditis elegans} PDB: 4f1i_A Back     alignment and structure
>1wj7_A Hypothetical protein (RSGI RUH-015); UBA domain, ubiquitin associated domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.5.2.1 Back     alignment and structure
>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1 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 261
d1fs1a141 a.158.1.1 (A:109-149) Skp2 {Human (Homo sapiens) [ 7e-07
d1e0ga_48 d.7.1.1 (A:) Membrane-bound lytic murein transclyc 1e-06
d1y7ma248 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term 6e-06
d1p22a1118 a.158.1.1 (A:135-252) F-box/WD-repeat protein 1 (b 1e-05
d2ovrb1102 a.158.1.1 (B:2263-2364) F-box/WD repeat-containing 6e-04
d1nexb1100 a.158.1.1 (B:270-369) Cdc4 F-box and linker domain 0.002
>d1fs1a1 a.158.1.1 (A:109-149) Skp2 {Human (Homo sapiens) [TaxId: 9606]} Length = 41 Back     information, alignment and structure

class: All alpha proteins
fold: F-box domain
superfamily: F-box domain
family: F-box domain
domain: Skp2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (101), Expect = 7e-07
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 49 PDTLRLILSNLSVTDLARASCVCRAWSSVASDN 81
           + L  I S L + +L + S VC+ W  +ASD 
Sbjct: 6  DELLLGIFSCLCLPELLKVSGVCKRWYRLASDE 38
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Length = 48 Back     information, alignment and structure
>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
>d1p22a1 a.158.1.1 (A:135-252) F-box/WD-repeat protein 1 (beta-TRCP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 118 Back     information, alignment and structure
>d2ovrb1 a.158.1.1 (B:2263-2364) F-box/WD repeat-containing protein 7, FBXW7 {Human (Homo sapiens) [TaxId: 9606]} Length = 102 Back     information, alignment and structure
>d1nexb1 a.158.1.1 (B:270-369) Cdc4 F-box and linker domains {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 100 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 ?
Query261
d1y7ma248 Hypothetical protein YkuD, N-terminal domain {Baci 99.53
d1e0ga_48 Membrane-bound lytic murein transclycosylase D, Ml 99.51
d1fs1a141 Skp2 {Human (Homo sapiens) [TaxId: 9606]} 99.14
d2ovrb1102 F-box/WD repeat-containing protein 7, FBXW7 {Human 98.9
d1nexb1100 Cdc4 F-box and linker domains {Baker's yeast (Sacc 98.71
d1p22a1118 F-box/WD-repeat protein 1 (beta-TRCP1) {Human (Hom 98.45
d1v92a_46 NSFL1 (p97 ATPase) cofactor p47, UBA-like domain { 97.62
d1oaia_59 FG-binding, C-terminal domain of TAP {Human (Homo 91.55
d1auaa193 N-terminal domain of phosphatidylinositol transfer 85.57
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Hypothetical protein YkuD, N-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.53  E-value=7.8e-16  Score=104.64  Aligned_cols=47  Identities=19%  Similarity=0.443  Sum_probs=44.0

Q ss_pred             eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecC
Q 024891          116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPI  163 (261)
Q Consensus       116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~  163 (261)
                      ++.|+|++||||++||+|||+++++|+++|++.++ .|++||+|+||+
T Consensus         1 ~i~y~V~~GDTL~~IA~~y~v~~~~i~~~N~~~~~-~l~~Gq~L~IPg   47 (48)
T d1y7ma2           1 MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQA-GLTAGQSIVIPG   47 (48)
T ss_dssp             CEEEECCTTCCHHHHHHHTTSCCCCCCCTSCTTCS-SCCTTCEEEETT
T ss_pred             CEEEEECCCCCHHHHHHHhCCCHHHHHHHcCCCCC-CCCCCCEEEeCC
Confidence            46899999999999999999999999999999775 699999999995
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1fs1a1 a.158.1.1 (A:109-149) Skp2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ovrb1 a.158.1.1 (B:2263-2364) F-box/WD repeat-containing protein 7, FBXW7 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nexb1 a.158.1.1 (B:270-369) Cdc4 F-box and linker domains {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1p22a1 a.158.1.1 (A:135-252) F-box/WD-repeat protein 1 (beta-TRCP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1v92a_ a.5.2.3 (A:) NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1oaia_ a.5.2.3 (A:) FG-binding, C-terminal domain of TAP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1auaa1 a.5.3.1 (A:4-96) N-terminal domain of phosphatidylinositol transfer protein sec14p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure