D-I-TASSER Q96CS3

D-I-TASSER results for Q96CS3

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

Summary of the Protein

Uniprot ID: Q96CS3
Protein Name: FAS-associated factor 2
Gene Name: FAF2

Input Sequence in FASTA format

>Q96CS3 (445 residues)
MAAPEERDLTQEQTEKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNEQEGVPSV
FNPPPSRPLQVNTADHRIYSYVVSRPQPRGLLGWGYYLIMLPFRFTYYTILDIFRFALRF
IRPDPRSRVTDPVGDIVSFMHSFEEKYGRAHPVFYQGTYSQALNDAKRELRFLLVYLHGD
DHQDSDEFCRNTLCAPEVISLINTRMLFWACSTNKPEGYRVSQALRENTYPFLAMIMLKD
RRMTVVGRLEGLIQPDDLINQLTFIMDANQTYLVSERLEREERNQTQVLRQQQDEAYLAS
LRADQEKERKKREERERKRRKEEEVQQQKLAEERRRQNLQEEKERKLECLPPEPSPDDPE
SVKIIFKLPNDSRVERRFHFSQSLTVIHDFLFSLKESPEKFQIEANFPRRVLPCIPSEEW
PNPPTLQEAGLSHTEVLFVQDLTDE

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	Q96CS3-D1	1-128	128		MAAPEERDLTQEQTEKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNEQEGVPSVFNPPPSRPLQVNTADHRIYSYVVSRPQPRGLLGWGYYLIMLPFRFTYYTILDIFRFALRFIRPDPRSR
2	Q96CS3-D2	129-350	222		VTDPVGDIVSFMHSFEEKYGRAHPVFYQGTYSQALNDAKRELRFLLVYLHGDDHQDSDEFCRNTLCAPEVISLINTRMLFWACSTNKPEGYRVSQALRENTYPFLAMIMLKDRRMTVVGRLEGLIQPDDLINQLTFIMDANQTYLVSERLEREERNQTQVLRQQQDEAYLASLRADQEKERKKREERERKRRKEEEVQQQKLAEERRRQNLQEEKERKLECL
3	Q96CS3-D3	351-445	95		PPEPSPDDPESVKIIFKLPNDSRVERRFHFSQSLTVIHDFLFSLKESPEKFQIEANFPRRVLPCIPSEEWPNPPTLQEAGLSHTEVLFVQDLTDE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.49

(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	2xt6A	0.40	7.30	0.032	0.672	model1_2xt6A.pdb.gz
2	5u1sA	0.40	7.42	0.040	0.683	model1_5u1sA.pdb.gz
3	6z2wE	0.39	7.84	0.046	0.699	model1_6z2wE.pdb.gz
4	7kveB	0.39	7.10	0.044	0.656	model1_7kveB.pdb.gz
5	5twvB	0.39	7.27	0.061	0.643	model1_5twvB.pdb.gz
6	5hb4B	0.39	7.12	0.045	0.640	model1_5hb4B.pdb.gz
7	6v22A	0.39	7.33	0.052	0.647	model1_6v22A.pdb.gz
8	3p8cA	0.39	7.20	0.032	0.636	model1_3p8cA.pdb.gz
9	5yz0A	0.39	7.64	0.042	0.667	model1_5yz0A.pdb.gz
10	6g2dC	0.39	6.65	0.049	0.607	model1_6g2dC.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:0019899	0.73	enzyme binding
GO:0043130	0.69	ubiquitin binding
GO:0031625	0.67	ubiquitin protein ligase binding
GO:0030234	0.61	enzyme regulator activity
GO:0055102	0.54	lipase inhibitor activity
GO:0035473	0.54	lipase 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:0009987	0.87	cellular process
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.81	primary metabolic process
GO:0043170	0.80	macromolecule metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0019538	0.73	protein metabolic process
GO:0006508	0.65	proteolysis
GO:0006511	0.61	ubiquitin-dependent protein catabolic process
GO:0043161	0.60	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0030433	0.56	ER-associated ubiquitin-dependent protein catabolic process

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.91	cytoplasmic part
GO:0043226	0.84	organelle
GO:0043229	0.83	intracellular organelle
GO:0043227	0.83	membrane-bounded organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0044422	0.74	organelle part
GO:0044446	0.71	intracellular organelle part
GO:0044425	0.69	membrane part
GO:0044432	0.64	endoplasmic reticulum part
GO:0032991	0.64	macromolecular complex
GO:0043234	0.63	protein complex
GO:0098796	0.61	membrane protein complex
GO:0034098	0.57	VCP-NPL4-UFD1 AAA ATPase complex
GO:0005783	0.55	endoplasmic reticulum

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	3h0gA	0.319	6.68	0.045	0.497	2.7.7.6	213,224
2	0.060	1mc0A	0.240	7.08	0.048	0.396	3.1.4.17	NA
3	0.060	1s46A	0.271	7.54	0.032	0.470	2.4.1.4	NA
4	0.060	1z0hB	0.248	7.45	0.047	0.418	3.4.24.69	233
5	0.060	2vuaA	0.242	7.55	0.034	0.418	3.4.24.69	249

	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	2nm1A	0.238	7.25	0.033	0.393	0.22	III	complex1.pdb.gz	155,156,173,178
2	0.01	3cmvD	0.332	7.60	0.039	0.575	0.17	ANP	complex2.pdb.gz	179,218,221
3	0.01	3cmvE	0.299	7.27	0.044	0.508	0.30	ANP	complex3.pdb.gz	214,215,218,233
4	0.01	2xt6A	0.401	7.30	0.032	0.672	0.13	TPP	complex4.pdb.gz	218,221,222
5	0.01	2y0pA	0.242	8.16	0.042	0.458	0.13	ACO	complex5.pdb.gz	211,218,219,220,221
6	0.01	2np0A	0.347	7.63	0.031	0.596	0.15	III	complex6.pdb.gz	219,229,230
7	0.01	3cmvF	0.331	7.70	0.037	0.582	0.16	ANP	complex7.pdb.gz	214,215,218
8	0.01	2y0pA	0.242	8.16	0.042	0.458	0.15	TD7	complex8.pdb.gz	179,180,228,229,230

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.