YRC Public Data Repository - Protein Structure Prediction

Protein:	LCL3
Organism:	Saccharomyces cerevisiae
Length:	274 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for LCL3.

Description	E-value	Query Range	Subject Range
LCL3_YEAST - Probable endonuclease LCL3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LCL3 PE=1 SV=... LCL3_YEAS1 - Probable endonuclease LCL3 OS=Saccharomyces cerevisiae (strain RM11-1a) GN=LCL3 PE=3 SV=1 LCL3 - Putative protein of unknown function, has homology to Staphylococcus aureus nuclease; green fluoresc... LCL3_YEAS2 - Probable endonuclease LCL3 OS=Saccharomyces cerevisiae (strain JAY291) GN=LCL3 PE=3 SV=1 LCL3_YEAS7 - Probable endonuclease LCL3 OS=Saccharomyces cerevisiae (strain YJM789) GN=LCL3 PE=3 SV=1	2.0E-83	[1..274]	[1..274]
Y38K_CAPSE - Uncharacterized 38.1 kDa protein OS=Capnoides sempervirens PE=2 SV=1	2.0E-51	[50..273]	[141..333]
CAN1_ARATH - Staphylococcal-like nuclease CAN1 OS=Arabidopsis thaliana GN=CAN1 PE=1 SV=1	6.0E-49	[50..273]	[127..318]
gi\|14030876 - gi\|14030876\|gb\|AAK52082.1\| nuclease [Nicotiana tabacum]	1.0E-47	[50..273]	[132..323]
CAN1_ORYSJ - Probable staphylococcal-like nuclease CAN1 OS=Oryza sativa subsp. japonica GN=Os01g0166100 PE=2 SV=1	6.0E-45	[50..272]	[133..324]
LCL3_SCHPO - Probable endonuclease C19F8.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC19F8.0... SPBC19F8.04c - nuclease	1.0E-41	[18..274]	[10..230]
gi\|9507655, gi\|5... - gi\|9507655\|ref\|NP_052986.1\| hypothetical protein R100p106 [Plasmid R100], gi\|5103254\|dbj\|BAA78890.1\|... YFI3_ECOLX - Uncharacterized endonuclease OS=Escherichia coli PE=3 SV=1	5.0E-38	[107..273]	[1..152]
gi\|189366704, gi... - gi\|189366704\|gb\|EDU85120.1\| nuclease homolog [Escherichia coli O157:H7 str. EC4501], gi\|168763045\|re... gi\|168790170, gi... - gi\|189370335\|gb\|EDU88751.1\| nuclease homolog [Escherichia coli O157:H7 str. EC869], gi\|168790170\|ref... gi\|3337063, gi\|1... - gi\|3337063\|dbj\|BAA31822.1\| unnamed protein product [Escherichia coli O157:H7 str. Sakai], gi\|1095533... gi\|7435213, gi\|3... - gi\|7435213\|pir\|\|T00303 nuclease homolog - Escherichia coli plasmid pO157, gi\|3337063\|dbj\|BAA31822.1\|... gi\|75994450 - gi\|75994450\|ref\|YP_325563.1\| hypothetical protein L7003 [Escherichia coli O157:H7 EDL933] YFI3_ECO57 - Uncharacterized endonuclease OS=Escherichia coli O157:H7 GN=L7003 PE=3 SV=1	5.0E-38	[107..273]	[1..152]
gi\|149930788, gi... - gi\|37695776\|gb\|AAR00438.1\|AF401292_40 w0002 [Escherichia coli], gi\|149930788\|ref\|YP_001294666.1\| w00...	3.0E-37	[107..273]	[1..152]

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Predicted Domain #1

Region A:
Residues: [1-84]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MREGDSNSKK SADVAVLSII LTGSTLTLIY TYKRYLTQFK RTNDIPRRIF RKHWLYGKVT  60
   61 SVGDGDNFHF FHMPGGIRGG WGWL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.593	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.743	a.74.1	Cyclin-like
View	Download	0.751	d.95.2	Homing endonucleases
View	Download	0.715	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.751	d.95.2	Homing endonucleases
View	Download	0.743	a.74.1	Cyclin-like
View	Download	0.715	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.610	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.610	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.593	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.565	d.95.2	Homing endonucleases
View	Download	0.527	d.68.3	SirA-like
View	Download	0.515	b.85.5	Tlp20, baculovirus telokin-like protein
View	Download	0.489	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.463	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.461	a.74.1	Cyclin-like
View	Download	0.458	d.206.1	YggU-like
View	Download	0.446	d.68.7	R3H domain
View	Download	0.431	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.426	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.361	d.26.3	Chitinase insertion domain
View	Download	0.361	a.74.1	Cyclin-like
View	Download	0.352	d.26.3	Chitinase insertion domain
View	Download	0.334	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.319	a.26.1	4-helical cytokines
View	Download	0.304	d.68.3	SirA-like
View	Download	0.301	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.301	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.300	a.74.1	Cyclin-like
View	Download	0.297	a.4.12	TrpR-like
View	Download	0.295	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.273	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.269	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.265	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.258	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.256	d.68.7	R3H domain
View	Download	0.255	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.255	d.1.1	Microbial ribonucleases
View	Download	0.253	d.230.1	N-terminal, heterodimerisation domain of RBP4 (RpoE)
View	Download	0.253	a.112.1	Description not found.
View	Download	0.250	d.12.1	Ribosomal proteins L23 and L15e
View	Download	0.249	a.24.9	alpha-catenin/vinculin
View	Download	0.246	d.95.2	Homing endonucleases
View	Download	0.243	a.2.1	GreA transcript cleavage protein, N-terminal domain
View	Download	0.236	b.40.4	Nucleic acid-binding proteins
View	Download	0.231	a.4.2	Methylated DNA-protein cysteine methyltransferase, C-terminal domain
View	Download	0.230	a.24.17	Group V grass pollen allergen
View	Download	0.228	a.74.1	Cyclin-like
View	Download	0.227	d.68.1	Translation initiation factor IF3, C-terminal domain
View	Download	0.224	a.5.3	N-terminal domain of phosphatidylinositol transfer protein sec14p
View	Download	0.223	d.58.20	NAD-binding domain of HMG-CoA reductase
View	Download	0.223	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.222	a.4.1	Homeodomain-like
View	Download	0.220	c.30.1	PreATP-grasp domain
View	Download	0.218	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.218	d.99.1	Ribosomal protein L9 C-domain
View	Download	0.216	a.177.1	Sigma2 domain of RNA polymerase sigma factors
View	Download	0.213	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.212	a.1.1	Globin-like
View	Download	0.212	a.64.2	Bacteriocin AS-48
View	Download	0.206	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.205	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.204	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.201	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.201	c.47.1	Thioredoxin-like
View	Download	0.200	d.39.1	Dynein light chain 8 (DLC8)
View	Download	0.200	a.2.6	Effector domain of the protein kinase pkn/prk1

Predicted Domain #2

Region A:
Residues: [85-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPVPQMIKND STAEKLVGDS RNMRFFNFNW ITHGRSTKSK IQKAKSQFLK LNVPYKNRKN  60
   61 LPTIPIRLCG IDAPERAHFG NPAQPFGNEA LIWLQNRILG KKVWVKPLSI DQYNRCVARV 120
  121 SYWDWFGGWK DLSLEMLKDG LAVVYEGKVN TEFDDREDKY RYYEFLARSR KKGLWIQNKF 180
  181 ETPGEYKKRI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.0
Match:	1ey7A_
Description:	Staphylococcal nuclease
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits