D-I-TASSER Q5JS37

D-I-TASSER results for Q5JS37

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

Summary of the Protein

Uniprot ID: Q5JS37
Protein Name: NHL repeat-containing protein 3
Gene Name: NHLRC3

Input Sequence in FASTA format

>Q5JS37 (347 residues)
MARFWVCVAGAGFFLAFLVLHSRFCGSPVLRNFTFAVSWRTEKILYRLDVGWPKHPEYFT
GTTFCVAVDSLNGLVYIGQRGDNIPKILVFTEDGYFLRAWNYTVDTPHGIFAASTLYEQS
VWITDVGSGFFGHTVKKYSSFGDLVQVLGTPGKKGTSLNPLQFDNPAELYVEDTGDIYIV
DGDGGLNNRLIKLSQDFMILWLHGENGTGPAKFNIPHSVTLDSAGRVWVADRGNKRIQVF
DKDTGEWLGAWNNCFTEEGPSSVRFTPDGKYLIVAQLNLSRLSVVAAPPVGSIGECSVIS
TIQLADQVLPHLLEVDRKTGAVYVAEIGAKQVQKYVPLNSYVPSFGS

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	Q5JS37-D1	1-347	347		MARFWVCVAGAGFFLAFLVLHSRFCGSPVLRNFTFAVSWRTEKILYRLDVGWPKHPEYFTGTTFCVAVDSLNGLVYIGQRGDNIPKILVFTEDGYFLRAWNYTVDTPHGIFAASTLYEQSVWITDVGSGFFGHTVKKYSSFGDLVQVLGTPGKKGTSLNPLQFDNPAELYVEDTGDIYIVDGDGGLNNRLIKLSQDFMILWLHGENGTGPAKFNIPHSVTLDSAGRVWVADRGNKRIQVFDKDTGEWLGAWNNCFTEEGPSSVRFTPDGKYLIVAQLNLSRLSVVAAPPVGSIGECSVISTIQLADQVLPHLLEVDRKTGAVYVAEIGAKQVQKYVPLNSYVPSFGS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6957

(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	3fw0A	0.75	2.37	0.237	0.816	model1_3fw0A.pdb.gz
2	6d69A	0.73	2.34	0.189	0.790	model1_6d69A.pdb.gz
3	6fptA	0.72	2.73	0.166	0.790	model1_6fptA.pdb.gz
4	6qzhA	0.72	3.95	0.102	0.888	model1_6qzhA.pdb.gz
5	6mnjA	0.71	3.95	0.067	0.885	model1_6mnjA.pdb.gz
6	1kitA	0.71	4.18	0.071	0.893	model1_1kitA.pdb.gz
7	2vk7A1	0.71	3.60	0.060	0.859	model1_2vk7A1.pdb.gz
8	6gc1A	0.71	2.48	0.142	0.775	model1_6gc1A.pdb.gz
9	2dsoC	0.71	2.88	0.122	0.801	model1_2dsoC.pdb.gz
10	6fb3A	0.70	3.76	0.148	0.833	model1_6fb3A.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:0003824	0.94	catalytic activity
GO:0016740	0.85	transferase activity
GO:0097159	0.79	organic cyclic compound binding
GO:1901363	0.78	heterocyclic compound binding
GO:0043167	0.70	ion binding
GO:0046872	0.68	metal ion binding
GO:0004842	0.68	ubiquitin-protein transferase activity
GO:0046914	0.66	transition metal ion binding
GO:0000166	0.60	nucleotide binding
GO:0035639	0.56	purine ribonucleoside triphosphate binding
GO:0032555	0.56	purine ribonucleotide binding
GO:0032550	0.56	purine ribonucleoside binding
GO:0032559	0.52	adenyl ribonucleotide binding
GO:0004672	0.50	protein kinase activity

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:0009987	0.91	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0044237	0.85	cellular metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0050794	0.83	regulation of cellular process
GO:0044699	0.83	single-organism process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0044238	0.82	primary metabolic process
GO:0006464	0.77	cellular protein modification process
GO:0032502	0.74	developmental process
GO:0048856	0.72	anatomical structure development
GO:0044767	0.71	single-organism developmental process
GO:0080090	0.70	regulation of primary metabolic process
GO:0044763	0.70	single-organism cellular process
GO:0031326	0.70	regulation of cellular biosynthetic process
GO:0034641	0.67	cellular nitrogen compound metabolic process
GO:0048523	0.64	negative regulation of cellular process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0016070	0.63	RNA metabolic process
GO:2000112	0.62	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.62	regulation of nitrogen compound metabolic process
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0009890	0.62	negative regulation of biosynthetic process
GO:0010468	0.61	regulation of gene expression
GO:0050896	0.58	response to stimulus
GO:0032268	0.57	regulation of cellular protein metabolic process
GO:0048869	0.56	cellular developmental process
GO:0034248	0.56	regulation of cellular amide metabolic process
GO:0031327	0.56	negative regulation of cellular biosynthetic process
GO:0010608	0.56	posttranscriptional regulation of gene expression
GO:2000177	0.55	regulation of neural precursor cell proliferation
GO:0034660	0.55	ncRNA metabolic process
GO:0006950	0.55	response to stress
GO:2000113	0.54	negative regulation of cellular macromolecule biosynthetic process
GO:0034249	0.54	negative regulation of cellular amide metabolic process
GO:0032269	0.54	negative regulation of cellular protein metabolic process
GO:0010629	0.54	negative regulation of gene expression
GO:0006810	0.54	transport
GO:0032501	0.53	multicellular organismal process
GO:0051716	0.52	cellular response to stimulus
GO:0050790	0.52	regulation of catalytic activity
GO:0016567	0.52	protein ubiquitination
GO:0016043	0.52	cellular component organization
GO:0009605	0.52	response to external stimulus
GO:0051100	0.51	negative regulation of binding
GO:0051055	0.51	negative regulation of lipid biosynthetic process
GO:0048518	0.51	positive regulation of biological process
GO:0045922	0.51	negative regulation of fatty acid metabolic process
GO:0044093	0.51	positive regulation of molecular function
GO:0043393	0.51	regulation of protein binding
GO:0042304	0.51	regulation of fatty acid biosynthetic process
GO:0009267	0.51	cellular response to starvation
GO:0006351	0.51	transcription, DNA-templated
GO:0048468	0.50	cell development

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:0044464	0.93	cell part
GO:0044424	0.87	intracellular part
GO:0043226	0.82	organelle
GO:0044444	0.66	cytoplasmic part
GO:0043227	0.66	membrane-bounded organelle
GO:0043229	0.59	intracellular organelle

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	0.322	3fw0A	0.750	2.37	0.237	0.816	4.3.2.5	115,171,221
2	0.259	1rwlA	0.657	2.36	0.220	0.721	2.7.11.1	169,178
3	0.119	1pjxA	0.672	3.05	0.134	0.769	3.1.8.2	NA
4	0.109	1ri6A	0.699	3.12	0.102	0.816	3.1.1.31	NA
5	0.103	2f10A	0.690	3.65	0.055	0.827	3.2.1.18	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	0.03	1v0fD	0.687	3.40	0.049	0.824	0.69	SIA	complex1.pdb.gz	186,189,190,204,206
2	0.02	2f25A	0.685	3.87	0.074	0.842	0.41	DAN	complex2.pdb.gz	109,180,217,231,281
3	0.02	1v0fE	0.687	3.44	0.048	0.827	0.58	SIA	complex3.pdb.gz	189,205,207,214

	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.