D-I-TASSER Q3C1V9

D-I-TASSER results for Q3C1V9

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

Summary of the Protein

Uniprot ID: Q3C1V9
Protein Name: Putative uncharacterized protein ENSP00000334305
Gene Name: YJU2

Input Sequence in FASTA format

>Q3C1V9 (767 residues)
MTPPPPSPLLGTQVKEDRADYKEFQDFSSLPDTHNIAWDHSFYPFQEEEEHGVKGVESVL
EKGVLDEGVLEAWGCCRRCRHAGWNRSQPSPELAGAVIHARAPAVGCRQRSGHLHVRLKQ
RLLERPCQEPLGKKYQLELPPLYERARKPEGSKNLPADGQGLRAVRADAALPVWPGGPGR
PGPHAPEAGAEGQHQGQWPPADTRHLRTPKWPYKVATEEKPEAEEAEKKRQAKVQEKRLP
PWKKRTLNQVHRVPWGQHRACQVMLLVSTKQLQRYLHFEKPAKPANMGQDPDCFGKSEGE
LATCLCGGESVVGETEAPGVRPDPRPEKDAKPAVSGCQEESWLQSEYDEMHPREEMNVPS
LRSGSGCQVSGSPLAKGLHPLQPCHPHYMMWECCLFTLTLGTQACFEVCARRLKLAHFCP
DTSLWSCGGQSPPVLCQLLDIISVSRDKVIGSHEKKPSSNPNQDDFHSSEYAYRCGIAEA
VGLPSIPVHPIGYYDAEKLLEYESLLLQVSEPVNPELSAGPITGLLDRLSGFRDHGPPGS
SCRSQRKGNGVETKDQAHRNRDPRGFQGGVLTARLFKMQVSLELFCGHQEHYLTRPVLAP
GYPVHLGKAGTHWEQGPNMPTPEQHGTWGNRHLFAVLPLLFYTSLEIMSIGYSVVMAGRN
VWQPTKGQMPHQPEQSCQTLALPMTIRHSWEGGAIRESSGWVSWKCHLKATEASQNPCVR
ATALRVGCSAVTYGVLGQAQGSAPWTSAFKTFSAGIAGLERHAWETM

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	Q3C1V9-D1	1-222	222		MTPPPPSPLLGTQVKEDRADYKEFQDFSSLPDTHNIAWDHSFYPFQEEEEHGVKGVESVLEKGVLDEGVLEAWGCCRRCRHAGWNRSQPSPELAGAVIHARAPAVGCRQRSGHLHVRLKQRLLERPCQEPLGKKYQLELPPLYERARKPEGSKNLPADGQGLRAVRADAALPVWPGGPGRPGPHAPEAGAEGQHQGQWPPADTRHLRTPKWPYKVATEEKPE
2	Q3C1V9-D2	223-580	358		AEEAEKKRQAKVQEKRLPPWKKRTLNQVHRVPWGQHRACQVMLLVSTKQLQRYLHFEKPAKPANMGQDPDCFGKSEGELATCLCGGESVVGETEAPGVRPDPRPEKDAKPAVSGCQEESWLQSEYDEMHPREEMNVPSLRSGSGCQVSGSPLAKGLHPLQPCHPHYMMWECCLFTLTLGTQACFEVCARRLKLAHFCPDTSLWSCGGQSPPVLCQLLDIISVSRDKVIGSHEKKPSSNPNQDDFHSSEYAYRCGIAEAVGLPSIPVHPIGYYDAEKLLEYESLLLQVSEPVNPELSAGPITGLLDRLSGFRDHGPPGSSCRSQRKGNGVETKDQAHRNRDPRGFQGGVLTARLFKMQV
3	Q3C1V9-D3	581-767	187		SLELFCGHQEHYLTRPVLAPGYPVHLGKAGTHWEQGPNMPTPEQHGTWGNRHLFAVLPLLFYTSLEIMSIGYSVVMAGRNVWQPTKGQMPHQPEQSCQTLALPMTIRHSWEGGAIRESSGWVSWKCHLKATEASQNPCVRATALRVGCSAVTYGVLGQAQGSAPWTSAFKTFSAGIAGLERHAWETM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.38

(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	6z2wE	0.38	7.77	0.036	0.583	model1_6z2wE.pdb.gz
2	6zwmA	0.38	8.31	0.030	0.597	model1_6zwmA.pdb.gz
3	6jxaA	0.38	8.08	0.044	0.583	model1_6jxaA.pdb.gz
4	3a6pA	0.38	7.87	0.036	0.574	model1_3a6pA.pdb.gz
5	5yz0A	0.37	8.55	0.041	0.598	model1_5yz0A.pdb.gz
6	6r9tA	0.36	8.23	0.045	0.553	model1_6r9tA.pdb.gz
7	7k10A	0.35	8.15	0.035	0.551	model1_7k10A.pdb.gz
8	7cunG	0.35	8.09	0.046	0.536	model1_7cunG.pdb.gz
9	6lq9C	0.35	8.14	0.038	0.548	model1_6lq9C.pdb.gz
10	7dxjA	0.35	7.91	0.037	0.536	model1_7dxjA.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:0022892	0.52	substrate-specific transporter activity
GO:0008233	0.51	peptidase 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:0065007	0.70	biological regulation
GO:0050794	0.65	regulation of cellular process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0019219	0.59	regulation of nucleobase-containing compound metabolic process
GO:0043170	0.51	macromolecule metabolic 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:0044446	1.00	intracellular organelle part
GO:0043227	0.97	membrane-bounded organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0005737	0.92	cytoplasm
GO:0005634	0.86	nucleus
GO:0044428	0.84	nuclear part
GO:0016020	0.79	membrane
GO:0044425	0.78	membrane part
GO:0044444	0.76	cytoplasmic part
GO:0031090	0.70	organelle membrane
GO:0016021	0.70	integral component of membrane
GO:0031965	0.61	nuclear membrane
GO:0043234	0.57	protein complex

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	2q1fA	0.258	8.20	0.031	0.403	4.2.2.21	NA
2	0.060	1ygeA	0.263	8.79	0.035	0.433	1.13.11.12	NA
3	0.060	1gthA	0.300	8.68	0.043	0.495	1.3.1.2	NA
4	0.060	1llwA	0.295	8.56	0.027	0.478	1.4.7.1	NA
5	0.060	1vbgA	0.306	8.55	0.033	0.497	2.7.9.1	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	3tw6A	0.309	8.78	0.045	0.512	0.15	ADP	complex1.pdb.gz	56,70,131,132
2	0.01	2l1lB	0.103	4.48	0.042	0.123	0.32	III	complex2.pdb.gz	22,63,68,69,72,76,79
3	0.01	3ho8A	0.330	8.20	0.041	0.520	0.20	COA	complex3.pdb.gz	55,69,70,73
4	0.01	2ot8A	0.261	8.59	0.025	0.429	0.18	III	complex4.pdb.gz	71,74,75,78
5	0.01	3ho8D	0.322	8.52	0.047	0.518	0.19	COA	complex5.pdb.gz	68,70,74,75
6	0.01	3hb9A	0.323	8.43	0.050	0.515	0.12	ADP	complex6.pdb.gz	35,56,59,67
7	0.01	1gt8A	0.305	8.36	0.037	0.490	0.37	SF4	complex7.pdb.gz	36,37,41,79,84
8	0.01	2qf7B	0.340	8.26	0.039	0.531	0.16	SAP	complex8.pdb.gz	35,56,69,79
9	0.01	2uvbA	0.314	8.79	0.039	0.519	0.10	NAP	complex9.pdb.gz	43,45,72,73,83
10	0.01	3tw6C	0.307	8.90	0.039	0.514	0.18	ADP	complex10.pdb.gz	57,71,72,73,76

	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.