D-I-TASSER Q9ULE0

D-I-TASSER results for Q9ULE0

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q9ULE0
Protein Name: Protein WWC3
Gene Name: WWC3

Input Sequence in FASTA format

>Q9ULE0 (1092 residues)
MDHINKLTQIEDPREQWRREQERMLKEYLIVAQEALNAKKEIYQIKQQRFELAQEEYQQL
HKMCEDDSRSYASSFSGYSTNTKYDPHQIKAEIASRRDRLSRLKRELTQMKQELQYKEKG
VETLQEIDRKMSSTHTSYKLDEAQAIMSELRTIKKAICTGEKERRDLMHSLAKLTDSFKN
SCSVTDSLVDFPHHVGVPGDAGVPQQFCDAGSQTDIIGEFVFDDKTRLVDRVRLNWQYEE
ARKRVANIQQQLARLDNESWPSTAEADRDRLQLIKEKEALLQELQLIIAQRRSAGDVARL
EEERERLEEELRRARATSAQGATERILLQEKRNCLLMQLEEATRLTSYLQSQLKSLCAST
LTVSSGSSRGSLASSRGSLASSRGSLSSVSFTDIYGLPQYEKPDAEGSQLLRFDLIPFDS
LGRDAPFSEPPGPSGFHKQRRSLDTPQSLASLSSRSSLSSLSPPSSPLDTPFLPASRDSP
LAQLADSCEGPGLGALDRLRAHASAMGDEDLPGMAALQPHGVPGDGEGPHERGPPPASAP
VGGTVTLREDSAKRLERRARRISACLSDYSLASDSGVFEPLTKRNEDAEEPAYGDTASNG
DPQIHVGLLRDSGSECLLVHVLQLKNPAGLAVKEDCKVHIRVYLPPLDSGTPNTYCSKAL
EFQVPLVFNEVFRIPVHSSALTLKSLQLYVCSVTPQLQEELLGIAQINLADYDSLSEMQL
RWHSVQVFTSSEPSRTREAGCAGESSARDPAHTISISGKTDAVTVLLARTTAQLQAVERE
LAEERAKLEYTEEEVLEMERKEEQAEAISERSWQADSVDSGCSNCTQTSPPYPEPCCMGI
DSILGHPFAAQAGPYSPEKFQPSPLKVDKETNTEDLFLEEAASLVKERPSRRARGSPFVR
SGTIVRSQTFSPGARSQYVCRLYRSDSDSSTLPRKSPFVRNTLERRTLRYKQSCRSSLAE
LMARTSLDLELDLQASRTRQRQLNEELCALRELRQRLEDAQLRGQTDLPPWVLRDERLRG
LLREAERQTRQTKLDYRHEQAAEKMLKKASKEIYQLRGQSHKEPIQVQTFREKIAFFTRP
RINIPPLPADDV

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9ULE0-D1	1-636,677-865	825		MDHINKLTQIEDPREQWRREQERMLKEYLIVAQEALNAKKEIYQIKQQRFELAQEEYQQLHKMCEDDSRSYASSFSGYSTNTKYDPHQIKAEIASRRDRLSRLKRELTQMKQELQYKEKGVETLQEIDRKMSSTHTSYKLDEAQAIMSELRTIKKAICTGEKERRDLMHSLAKLTDSFKNSCSVTDSLVDFPHHVGVPGDAGVPQQFCDAGSQTDIIGEFVFDDKTRLVDRVRLNWQYEEARKRVANIQQQLARLDNESWPSTAEADRDRLQLIKEKEALLQELQLIIAQRRSAGDVARLEEERERLEEELRRARATSAQGATERILLQEKRNCLLMQLEEATRLTSYLQSQLKSLCASTLTVSSGSSRGSLASSRGSLASSRGSLSSVSFTDIYGLPQYEKPDAEGSQLLRFDLIPFDSLGRDAPFSEPPGPSGFHKQRRSLDTPQSLASLSSRSSLSSLSPPSSPLDTPFLPASRDSPLAQLADSCEGPGLGALDRLRAHASAMGDEDLPGMAALQPHGVPGDGEGPHERGPPPASAPVGGTVTLREDSAKRLERRARRISACLSDYSLASDSGVFEPLTKRNEDAEEPAYGDTASNGDPQIHVGLLRDSGSECLLVHVLQLKNPAGLAVKEDCHSSALTLKSLQLYVCSVTPQLQEELLGIAQINLADYDSLSEMQLRWHSVQVFTSSEPSRTREAGCAGESSARDPAHTISISGKTDAVTVLLARTTAQLQAVERELAEERAKLEYTEEEVLEMERKEEQAEAISERSWQADSVDSGCSNCTQTSPPYPEPCCMGIDSILGHPFAAQAGPYSPEKFQPSPL
2	Q9ULE0-D2	637-676	40		KVHIRVYLPPLDSGTPNTYCSKALEFQVPLVFNEVFRIPV
3	Q9ULE0-D3	866-913	48		KVDKETNTEDLFLEEAASLVKERPSRRARGSPFVRSGTIVRSQTFSPG
4	Q9ULE0-D4	914-1092	179		ARSQYVCRLYRSDSDSSTLPRKSPFVRNTLERRTLRYKQSCRSSLAELMARTSLDLELDLQASRTRQRQLNEELCALRELRQRLEDAQLRGQTDLPPWVLRDERLRGLLREAERQTRQTKLDYRHEQAAEKMLKKASKEIYQLRGQSHKEPIQVQTFREKIAFFTRPRINIPPLPADDV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.36

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6vr4A	0.29	9.58	0.039	0.467	model1_6vr4A.pdb.gz
2	7abiU	0.29	9.42	0.047	0.465	model1_7abiU.pdb.gz
3	7cpxA	0.29	8.86	0.035	0.440	model1_7cpxA.pdb.gz
4	6yejA	0.28	8.79	0.040	0.415	model1_6yejA.pdb.gz
5	6z2wE	0.27	8.79	0.040	0.412	model1_6z2wE.pdb.gz
6	5nrlA	0.27	9.47	0.031	0.436	model1_5nrlA.pdb.gz
7	5x6oC	0.27	8.75	0.041	0.409	model1_5x6oC.pdb.gz
8	5a22A	0.27	9.35	0.031	0.429	model1_5a22A.pdb.gz
9	5julA	0.27	8.89	0.033	0.409	model1_5julA.pdb.gz
10	6g7eB	0.27	8.38	0.046	0.393	model1_6g7eB.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0032947	0.90	protein complex scaffold
GO:0019900	0.90	kinase binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0065007	0.91	biological regulation
GO:0050794	0.90	regulation of cellular process
GO:0035330	0.87	regulation of hippo signaling
GO:0009987	0.59	cellular process
GO:0080090	0.58	regulation of primary metabolic process
GO:0048519	0.58	negative regulation of biological process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0010468	0.58	regulation of gene expression
GO:0048523	0.57	negative regulation of cellular process
GO:0006355	0.57	regulation of transcription, DNA-templated
GO:0051241	0.56	negative regulation of multicellular organismal process
GO:0051093	0.56	negative regulation of developmental process
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0010629	0.53	negative regulation of gene expression
GO:0009968	0.53	negative regulation of signal transduction
GO:0046621	0.52	negative regulation of organ growth
GO:0044699	0.52	single-organism process
GO:0035331	0.52	negative regulation of hippo signaling
GO:0000122	0.52	negative regulation of transcription from RNA polymerase II promoter

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	0.99	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0005829	0.90	cytosol

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2iukA	0.216	9.05	0.024	0.336	1.13.11.12	NA
2	0.060	1peuA	0.237	8.15	0.046	0.341	1.17.4.1	615
3	0.060	2vz8B	0.267	9.43	0.037	0.422	2.3.1.85	NA
4	0.060	2jfdA	0.168	6.86	0.037	0.223	2.3.1.85	NA
5	0.060	2iukB	0.212	9.21	0.033	0.333	1.13.11.12	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	1mhy3	0.102	4.81	0.039	0.119	0.13	III	complex1.pdb.gz	577,580,699,730
2	0.01	3sfzA	0.223	9.69	0.039	0.364	0.11	ADP	complex2.pdb.gz	606,626,627,877
3	0.01	2j6e2	0.104	6.30	0.105	0.133	0.30	III	complex3.pdb.gz	606,607,690
4	0.01	3izaA	0.255	9.07	0.032	0.392	0.13	ATP	complex4.pdb.gz	626,629,630,631,632,906
5	0.01	1i6vC	0.245	9.15	0.042	0.378	0.15	RFP	complex5.pdb.gz	608,609,610,611,704
6	0.01	2y3aA	0.254	8.58	0.054	0.377	0.22	GD9	complex6.pdb.gz	608,609,610,702,704,705,706
7	0.01	3q24A	0.248	8.60	0.031	0.365	0.24	POP	complex7.pdb.gz	606,607,702
8	0.01	2a6h8	0.104	6.47	0.044	0.133	0.11	III	complex8.pdb.gz	668,669,670,671,700
9	0.01	1ynjC	0.238	9.39	0.033	0.374	0.21	SRN	complex9.pdb.gz	608,610,611,643,705
10	0.01	1t3tA	0.263	8.96	0.034	0.401	0.13	ADP	complex10.pdb.gz	559,605,690

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.