D-I-TASSER Q96M63

D-I-TASSER results for Q96M63

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

Summary of the Protein

Uniprot ID: Q96M63
Protein Name: Coiled-coil domain-containing protein 114
Gene Name: CCDC114

Input Sequence in FASTA format

>Q96M63 (670 residues)
MEGERRAYSKEVHQRINKQLEEIRRLEEVRGDLQVQISAAQNQVKRLRDSQRLENMDRLL
KGRAQVQAEIEELQEQTRALDKQIQEWETRIFTHSKNVRSPGFILDQKVKIRRRIRILEN
QLDRVTCHFDNQLVRNAALREELDLLRIDRNRYLNVDRKLKKEIHHLHHLVSTLILSSTS
AYAVREEAKAKMGLLRERAEKEEAQSEMEAQVLQRQILHLEQLHHFLKLKNNDRQPDPDV
LEKREKQAGEVAEGVWKTSQERLVLCYEDALNKLSQLMGESDPDLLVQKYLEIEERNFAE
FNFINEQNLELEHVQEEIKEMQEALVSARASKDDQHLLQEQQQKVLQQRMDKVHSEAERL
EARFQDVRGQLEKLKADIQLLFTKAHCDSSMIDDLLGVKTSMGDRDMGLFLSLIEKRLVE
LLTVQAFLHAQSFTSLADAALLVLGQSLEDLPKKMAPLQPPDTLEDPPGFEASDDYPMSR
EELLSQVEKLVELQEQAEAQRQKDLAAAAAKLDGTLSVDLASTQRAGSSTVLVPTRHPHA
IPGSILSHKTSRDRGSLGHVTFGGLSSSTGHLPSHITHGDPNTGHVTFGSTSASSGGHVT
FRPVSASSYLGSTGYVGSSRGGENTEGGVESGGTASDSSGGLGSSRDHVSSTGPASSTGP
GSSTSKDSRG

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	Q96M63-D1	1-113	113		MEGERRAYSKEVHQRINKQLEEIRRLEEVRGDLQVQISAAQNQVKRLRDSQRLENMDRLLKGRAQVQAEIEELQEQTRALDKQIQEWETRIFTHSKNVRSPGFILDQKVKIRR
2	Q96M63-D2	114-235	122		RIRILENQLDRVTCHFDNQLVRNAALREELDLLRIDRNRYLNVDRKLKKEIHHLHHLVSTLILSSTSAYAVREEAKAKMGLLRERAEKEEAQSEMEAQVLQRQILHLEQLHHFLKLKNNDRQ
3	Q96M63-D3	236-337	102		PDPDVLEKREKQAGEVAEGVWKTSQERLVLCYEDALNKLSQLMGESDPDLLVQKYLEIEERNFAEFNFINEQNLELEHVQEEIKEMQEALVSARASKDDQHL
4	Q96M63-D4	338-670	333		LQEQQQKVLQQRMDKVHSEAERLEARFQDVRGQLEKLKADIQLLFTKAHCDSSMIDDLLGVKTSMGDRDMGLFLSLIEKRLVELLTVQAFLHAQSFTSLADAALLVLGQSLEDLPKKMAPLQPPDTLEDPPGFEASDDYPMSREELLSQVEKLVELQEQAEAQRQKDLAAAAAKLDGTLSVDLASTQRAGSSTVLVPTRHPHAIPGSILSHKTSRDRGSLGHVTFGGLSSSTGHLPSHITHGDPNTGHVTFGSTSASSGGHVTFRPVSASSYLGSTGYVGSSRGGENTEGGVESGGTASDSSGGLGSSRDHVSSTGPASSTGPGSSTSKDSRG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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	5yz0A	0.34	7.74	0.036	0.525	model1_5yz0A.pdb.gz
2	6z2wE	0.34	7.35	0.044	0.507	model1_6z2wE.pdb.gz
3	6eqoA	0.32	7.64	0.044	0.500	model1_6eqoA.pdb.gz
4	5x6oC	0.32	8.42	0.038	0.536	model1_5x6oC.pdb.gz
5	6g7eB	0.32	7.82	0.039	0.504	model1_6g7eB.pdb.gz
6	6fijA	0.32	7.73	0.045	0.498	model1_6fijA.pdb.gz
7	4f91B	0.32	8.08	0.057	0.510	model1_4f91B.pdb.gz
8	4bedA	0.32	8.29	0.027	0.516	model1_4bedA.pdb.gz
9	2pffA	0.30	8.04	0.032	0.495	model1_2pffA.pdb.gz
10	4bgdA	0.30	8.55	0.051	0.516	model1_4bgdA.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:1901363	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0035639	0.72	purine ribonucleoside triphosphate binding
GO:0032555	0.72	purine ribonucleotide binding
GO:0032550	0.72	purine ribonucleoside binding
GO:0032559	0.71	adenyl ribonucleotide binding
GO:0003824	0.62	catalytic activity
GO:0017111	0.60	nucleoside-triphosphatase 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:0044767	1.00	single-organism developmental process
GO:0044763	1.00	single-organism cellular process
GO:0016043	0.81	cellular component organization
GO:0010927	0.79	cellular component assembly involved in morphogenesis
GO:0070286	0.78	axonemal dynein complex assembly
GO:0036158	0.77	outer dynein arm assembly
GO:0007017	0.64	microtubule-based process
GO:0006928	0.64	movement of cell or subcellular component
GO:0007018	0.62	microtubule-based movement
GO:0003341	0.59	cilium movement

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:0044441	1.00	ciliary part
GO:0044430	1.00	cytoskeletal part
GO:0043234	0.85	protein complex
GO:0043226	0.84	organelle
GO:0036157	0.84	outer dynein arm
GO:0005929	0.80	cilium
GO:0005930	0.76	axoneme

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	2pffA	0.304	8.04	0.026	0.495	2.3.1.41 2.3.1.86	NA
2	0.060	1jqmB	0.237	8.18	0.061	0.387	3.6.5.3	NA
3	0.060	3b8eA	0.235	7.66	0.038	0.363	3.6.3.9	NA
4	0.060	2vz8B	0.238	8.32	0.045	0.396	2.3.1.85	NA
5	0.060	3dy5A	0.243	8.06	0.028	0.385	1.13.11.40 4.2.1.92	272

	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	3s90B	0.155	5.25	0.075	0.196	0.16	III	complex1.pdb.gz	8,12,21,24,27
2	0.01	1zw3A	0.117	3.94	0.021	0.134	0.16	III	complex2.pdb.gz	15,16,20,21,27,28,31
3	0.01	1rke0	0.146	6.13	0.041	0.199	0.18	III	complex3.pdb.gz	3,4,5,27,28,74,78
4	0.01	1t01A	0.155	5.42	0.046	0.199	0.17	III	complex4.pdb.gz	10,11,15,18,19,30
5	0.01	1ydiA	0.156	4.90	0.035	0.193	0.13	III	complex5.pdb.gz	20,22,25,28,29,33
6	0.01	2vu9A	0.147	7.19	0.052	0.219	0.20	UUU	complex6.pdb.gz	17,103,104
7	0.01	3s90A	0.126	3.22	0.024	0.139	0.13	III	complex7.pdb.gz	16,19,20,22,23
8	0.01	1syqA	0.151	5.40	0.044	0.193	0.16	III	complex8.pdb.gz	11,19,22,23,25,26,29
9	0.01	1bg3B	0.255	7.87	0.036	0.396	0.20	G6P	complex9.pdb.gz	9,99,101

	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.