D-I-TASSER Q9BXJ3

D-I-TASSER results for Q9BXJ3

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

Summary of the Protein

Uniprot ID: Q9BXJ3
Protein Name: Complement C1q tumor necrosis factor-related protein 4
Gene Name: C1QTNF4

Input Sequence in FASTA format

>Q9BXJ3 (329 residues)
MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGD
FDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQ
SAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYLVYADADADAPARGPPAPPEPRSAFS
AARTRSLVGSDAGPGPRHQPLAFDTEFVNIGGDFDAAAGVFRCRLPGAYFFSFTLGKLPR
KTLSVKLMKNRDEVQAMIYDDGASRRREMQSQSVMLALRRGDAVWLLSHDHDGYGAYSNH
GKYITFSGFLVYPDLAPAAPPGLGASELL

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 DeepPotential. 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	Q9BXJ3-D1	1-155	155		MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGDFDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQSAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYL
2	Q9BXJ3-D2	156-329	174		VYADADADAPARGPPAPPEPRSAFSAARTRSLVGSDAGPGPRHQPLAFDTEFVNIGGDFDAAAGVFRCRLPGAYFFSFTLGKLPRKTLSVKLMKNRDEVQAMIYDDGASRRREMQSQSVMLALRRGDAVWLLSHDHDGYGAYSNHGKYITFSGFLVYPDLAPAAPPGLGASELL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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 DeepPotential, 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	4douA	0.56	4.66	0.184	0.711	model1_4douA.pdb.gz
2	5kcaA	0.55	5.12	0.191	0.736	model1_5kcaA.pdb.gz
3	4zchA	0.52	5.47	0.071	0.736	model1_4zchA.pdb.gz
4	5hkjA	0.52	5.77	0.141	0.787	model1_5hkjA.pdb.gz
5	4gwmA	0.47	5.39	0.052	0.666	model1_4gwmA.pdb.gz
6	2pffA	0.43	6.72	0.078	0.739	model1_2pffA.pdb.gz
7	3hmjA	0.43	6.89	0.078	0.745	model1_3hmjA.pdb.gz
8	3k46A	0.43	5.65	0.042	0.638	model1_3k46A.pdb.gz
9	6ed2A	0.43	5.72	0.068	0.641	model1_6ed2A.pdb.gz
10	1bhgA	0.43	5.58	0.041	0.635	model1_1bhgA.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	0.62	catalytic activity
GO:0042802	0.57	identical protein 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:0044699	0.88	single-organism process
GO:0065007	0.85	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0009987	0.77	cellular process
GO:0008152	0.76	metabolic process
GO:0048518	0.75	positive regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0071704	0.73	organic substance metabolic process
GO:0048583	0.72	regulation of response to stimulus
GO:0050896	0.70	response to stimulus
GO:0044238	0.69	primary metabolic process
GO:0032502	0.69	developmental process
GO:0048584	0.68	positive regulation of response to stimulus
GO:0048856	0.65	anatomical structure development
GO:0048523	0.65	negative regulation of cellular process
GO:0044767	0.65	single-organism developmental process
GO:0002682	0.63	regulation of immune system process
GO:0051239	0.62	regulation of multicellular organismal process
GO:0016043	0.61	cellular component organization
GO:0031323	0.60	regulation of cellular metabolic process
GO:2000026	0.59	regulation of multicellular organismal development
GO:0048522	0.58	positive regulation of cellular process
GO:0045595	0.58	regulation of cell differentiation
GO:0043170	0.58	macromolecule metabolic process
GO:0006950	0.58	response to stress
GO:0080090	0.57	regulation of primary metabolic process
GO:0060255	0.57	regulation of macromolecule metabolic process
GO:0051241	0.57	negative regulation of multicellular organismal process
GO:0048513	0.57	animal organ development
GO:0023051	0.57	regulation of signaling
GO:0010646	0.57	regulation of cell communication
GO:0009966	0.56	regulation of signal transduction
GO:0044763	0.55	single-organism cellular process
GO:0042221	0.55	response to chemical
GO:0032268	0.55	regulation of cellular protein metabolic process
GO:0045649	0.54	regulation of macrophage differentiation
GO:0043933	0.54	macromolecular complex subunit organization
GO:0030852	0.54	regulation of granulocyte differentiation
GO:0022607	0.54	cellular component assembly
GO:0019538	0.54	protein metabolic process
GO:0002762	0.54	negative regulation of myeloid leukocyte differentiation
GO:0002376	0.54	immune system process
GO:0001932	0.54	regulation of protein phosphorylation
GO:0051240	0.53	positive regulation of multicellular organismal process
GO:0051128	0.53	regulation of cellular component organization
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0006955	0.53	immune response
GO:0006461	0.53	protein complex assembly
GO:0002252	0.53	immune effector process
GO:0031326	0.52	regulation of cellular biosynthetic process
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0023056	0.52	positive regulation of signaling
GO:0010647	0.52	positive regulation of cell communication
GO:0006956	0.52	complement activation
GO:0065009	0.51	regulation of molecular function
GO:0010468	0.51	regulation of gene expression
GO:0001934	0.51	positive regulation of protein phosphorylation
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0009967	0.50	positive regulation of signal transduction

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	0.94	cell part
GO:0044421	0.90	extracellular region part
GO:0005576	0.90	extracellular region
GO:0044424	0.86	intracellular part
GO:0043227	0.81	membrane-bounded organelle
GO:0005615	0.72	extracellular space
GO:0044444	0.69	cytoplasmic part
GO:0043234	0.60	protein complex
GO:0043229	0.59	intracellular organelle
GO:0016020	0.59	membrane
GO:0070062	0.58	extracellular exosome
GO:0043231	0.58	intracellular membrane-bounded 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	0.060	1tedA	0.387	6.52	0.079	0.644	2.3.1.74	NA
2	0.060	2gqdA	0.386	6.84	0.044	0.669	2.3.1.179	NA
3	0.060	3e1hB	0.385	6.47	0.081	0.641	2.3.1.74	123,154
4	0.060	3hmjA	0.431	6.89	0.078	0.745	2.3.1.86	NA
5	0.060	1k3iA	0.391	6.60	0.060	0.653	1.1.3.9	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:

Click to view	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	1p8jF	0.409	5.60	0.050	0.617	0.66	III	complex1.pdb.gz	75,76,77,78,154,155
	2	0.01	2d5hD	0.395	5.86	0.048	0.599	0.43	CO3	complex2.pdb.gz	32,151,153

	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.