D-I-TASSER Q9H446

D-I-TASSER results for Q9H446

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

Summary of the Protein

Uniprot ID: Q9H446
Protein Name: RWD domain-containing protein 1
Gene Name: RWDD1

Input Sequence in FASTA format

>Q9H446 (243 residues)
MTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGENDETVQTTLKFTYSEKY
PDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKT
RREEEKKQKEKEAEEAEKQLFHGTPVTIENFLNWKAKFDAELLEIKKKRMKEEEQAGKNK
LSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDEDDPDYNPADPESD
SAD

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	Q9H446-D1	1-243	243		MTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGENDETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTRREEEKKQKEKEAEEAEKQLFHGTPVTIENFLNWKAKFDAELLEIKKKRMKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDEDDPDYNPADPESDSAD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.563

(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	2ebmA	0.48	1.09	1.000	0.498	model1_2ebmA.pdb.gz
2	3cegA	0.47	5.44	0.069	0.720	model1_3cegA.pdb.gz
3	5a4pA	0.47	5.37	0.085	0.708	model1_5a4pA.pdb.gz
4	2yz0A	0.46	2.24	0.309	0.506	model1_2yz0A.pdb.gz
5	1ukxA	0.44	2.01	0.279	0.477	model1_1ukxA.pdb.gz
6	2dmfA	0.44	2.58	0.276	0.486	model1_2dmfA.pdb.gz
7	1ylaA	0.43	4.33	0.110	0.576	model1_1ylaA.pdb.gz
8	2e2cA	0.43	3.61	0.119	0.539	model1_2e2cA.pdb.gz
9	2ediA	0.42	4.02	0.100	0.543	model1_2ediA.pdb.gz
10	1yh2A	0.42	4.02	0.124	0.539	model1_1yh2A.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	0.82	heterocyclic compound binding
GO:0097159	0.82	organic cyclic compound binding
GO:0003824	0.82	catalytic activity
GO:0016740	0.81	transferase activity
GO:0003676	0.74	nucleic acid binding
GO:0004842	0.63	ubiquitin-protein transferase activity
GO:0003723	0.58	RNA 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:0050794	0.95	regulation of cellular process
GO:0080090	0.92	regulation of primary metabolic process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0031323	0.92	regulation of cellular metabolic process
GO:0009987	0.91	cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0044237	0.81	cellular metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0044238	0.80	primary metabolic process
GO:2000112	0.73	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.73	regulation of nitrogen compound metabolic process
GO:0032268	0.73	regulation of cellular protein metabolic process
GO:0010468	0.73	regulation of gene expression
GO:0048522	0.71	positive regulation of cellular process
GO:0044267	0.68	cellular protein metabolic process
GO:0032270	0.66	positive regulation of cellular protein metabolic process
GO:0043412	0.65	macromolecule modification
GO:0006464	0.64	cellular protein modification process
GO:0044699	0.62	single-organism process
GO:0044763	0.59	single-organism cellular process
GO:0050896	0.56	response to stimulus
GO:0051716	0.55	cellular response to stimulus
GO:0070647	0.54	protein modification by small protein conjugation or removal
GO:0048583	0.54	regulation of response to stimulus
GO:0032446	0.53	protein modification by small protein conjugation
GO:0009267	0.53	cellular response to starvation
GO:0080134	0.51	regulation of response to stress
GO:0006417	0.51	regulation of translation
GO:0080135	0.50	regulation of cellular response to stress
GO:0031399	0.50	regulation of protein modification 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:0044424	1.00	intracellular part
GO:0043229	0.97	intracellular organelle
GO:0043227	0.92	membrane-bounded organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0005634	0.86	nucleus
GO:0032991	0.80	macromolecular complex
GO:0044444	0.73	cytoplasmic part
GO:0005737	0.72	cytoplasm
GO:0044446	0.70	intracellular organelle part
GO:0043234	0.56	protein complex
GO:0044428	0.54	nuclear part
GO:1990234	0.50	transferase 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	1pzvA	0.402	3.78	0.091	0.510	6.3.2.19	NA
2	0.060	1qcqA	0.410	3.74	0.099	0.518	6.3.2.19	NA
3	0.060	2gmiA	0.406	3.90	0.142	0.518	6.3.2.19	90
4	0.060	2uczA	0.409	3.97	0.103	0.527	6.3.2.19	NA
5	0.060	1ayzC	0.412	4.05	0.151	0.535	6.3.2.19	103

	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	2ag0A	0.408	5.62	0.038	0.679	0.12	TPP	complex1.pdb.gz	7,8,96,98
2	0.01	3d7kB	0.378	6.22	0.047	0.679	0.22	D7K	complex2.pdb.gz	5,6,7,58,64
3	0.01	1z8nA	0.415	5.61	0.079	0.683	0.14	TPP	complex3.pdb.gz	64,94,95,96,97
4	0.01	3iafA	0.376	6.48	0.042	0.704	0.19	TPP	complex4.pdb.gz	6,7,8,62
5	0.01	3iaeA	0.381	6.27	0.042	0.687	0.17	D7K	complex5.pdb.gz	5,6,96,97
6	0.01	2ag1A	0.379	6.23	0.046	0.683	0.25	TPP	complex6.pdb.gz	5,60,63,96
7	0.01	2ag1D	0.379	6.23	0.046	0.683	0.27	TPP	complex7.pdb.gz	5,60,62
8	0.01	3d7kA	0.376	6.24	0.041	0.679	0.25	D7K	complex8.pdb.gz	5,6,7,96

	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.