D-I-TASSER Q9NWS0

D-I-TASSER results for Q9NWS0

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

Summary of the Protein

Uniprot ID: Q9NWS0
Protein Name: PIH1 domain-containing protein 1
Gene Name: PIH1D1

Input Sequence in FASTA format

>Q9NWS0 (290 residues)
MANPKLLGMGLSEAEAIGADSARFEELLLQASKELQQAQTTRPESTQIQPQPGFCIKTNS
SEGKVFINICHSPSIPPPADVTEEELLQMLEEDQAGFRIPMSLGEPHAELDAKGQGCTAY
DVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKNRPFMGSISQQNIR
SEQRPRIQELGDLYTPAPGRAESGPEKPHLNLWLEAPDLLLAEVDLPKLDGALGLSLEIG
ENRLVMGGPQQLYHLDAYIPLQINSHESKAAFHRKRKQLMVAMPLLPVPS

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	Q9NWS0-D1	1-290	290		MANPKLLGMGLSEAEAIGADSARFEELLLQASKELQQAQTTRPESTQIQPQPGFCIKTNSSEGKVFINICHSPSIPPPADVTEEELLQMLEEDQAGFRIPMSLGEPHAELDAKGQGCTAYDVAVNSDFYRRMQNSDFLRELVITIAREGLEDKYNLQLNPEWRMMKNRPFMGSISQQNIRSEQRPRIQELGDLYTPAPGRAESGPEKPHLNLWLEAPDLLLAEVDLPKLDGALGLSLEIGENRLVMGGPQQLYHLDAYIPLQINSHESKAAFHRKRKQLMVAMPLLPVPS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5027

(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	4chhA	0.46	2.10	0.257	0.493	model1_4chhA.pdb.gz
2	4psfA	0.42	2.28	0.933	0.462	model1_4psfA.pdb.gz
3	7bwmA2	0.41	6.38	0.057	0.690	model1_7bwmA2.pdb.gz
4	1gqiA2	0.40	6.53	0.039	0.690	model1_1gqiA2.pdb.gz
5	2hfzA	0.40	5.75	0.066	0.628	model1_2hfzA.pdb.gz
6	5bqnA	0.39	6.26	0.029	0.648	model1_5bqnA.pdb.gz
7	6xd0A	0.39	5.95	0.060	0.634	model1_6xd0A.pdb.gz
8	6k31A	0.39	6.51	0.061	0.703	model1_6k31A.pdb.gz
9	2j0wA	0.39	6.21	0.086	0.669	model1_2j0wA.pdb.gz
10	4wieA	0.39	6.04	0.047	0.648	model1_4wieA.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	0.88	enzyme binding
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0003676	0.76	nucleic acid binding
GO:0003677	0.68	DNA binding
GO:0051219	0.66	phosphoprotein binding
GO:0051117	0.66	ATPase binding
GO:0042393	0.66	histone binding
GO:0019901	0.66	protein kinase binding
GO:0001164	0.66	RNA polymerase I CORE element sequence-specific DNA 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	1.00	cellular process
GO:0034622	0.93	cellular macromolecular complex assembly
GO:0065007	0.81	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0000492	0.76	box C/D snoRNP assembly
GO:0048583	0.74	regulation of response to stimulus
GO:0044699	0.71	single-organism process
GO:0080090	0.68	regulation of primary metabolic process
GO:0048522	0.68	positive regulation of cellular process
GO:0044763	0.68	single-organism cellular process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0010468	0.68	regulation of gene expression
GO:2000112	0.67	regulation of cellular macromolecule biosynthetic process
GO:0051252	0.67	regulation of RNA metabolic process
GO:0051234	0.67	establishment of localization
GO:0048523	0.67	negative regulation of cellular process
GO:0032006	0.67	regulation of TOR signaling
GO:0031325	0.67	positive regulation of cellular metabolic process
GO:0010604	0.67	positive regulation of macromolecule metabolic process
GO:0072594	0.66	establishment of protein localization to organelle
GO:0065008	0.66	regulation of biological quality
GO:0051129	0.66	negative regulation of cellular component organization
GO:0045893	0.66	positive regulation of transcription, DNA-templated
GO:0044087	0.66	regulation of cellular component biogenesis
GO:0043085	0.66	positive regulation of catalytic activity
GO:0033044	0.66	regulation of chromosome organization
GO:0033036	0.66	macromolecule localization
GO:0032270	0.66	positive regulation of cellular protein metabolic process
GO:0032008	0.66	positive regulation of TOR signaling
GO:0031400	0.66	negative regulation of protein modification process
GO:0030162	0.66	regulation of proteolysis
GO:0010638	0.66	positive regulation of organelle organization
GO:2001268	0.65	negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:2000619	0.65	negative regulation of histone H4-K16 acetylation
GO:2000617	0.65	positive regulation of histone H3-K9 acetylation
GO:1904263	0.65	positive regulation of TORC1 signaling
GO:1902661	0.65	positive regulation of glucose mediated signaling pathway
GO:1901838	0.65	positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter
GO:1900113	0.65	negative regulation of histone H3-K9 trimethylation
GO:1900110	0.65	negative regulation of histone H3-K9 dimethylation
GO:0090240	0.65	positive regulation of histone H4 acetylation
GO:0071902	0.65	positive regulation of protein serine/threonine kinase activity
GO:0071169	0.65	establishment of protein localization to chromatin
GO:0051569	0.65	regulation of histone H3-K4 methylation
GO:0048254	0.65	snoRNA localization
GO:0031334	0.65	positive regulation of protein complex assembly
GO:0006338	0.65	chromatin remodeling

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	0.99	intracellular part
GO:0032991	0.84	macromolecular complex
GO:0043234	0.82	protein complex
GO:0005737	0.82	cytoplasm
GO:0044446	0.81	intracellular organelle part
GO:0043226	0.71	organelle
GO:0097255	0.70	R2TP complex
GO:0044428	0.70	nuclear part
GO:0043229	0.70	intracellular organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0030529	0.68	intracellular ribonucleoprotein complex
GO:0005634	0.65	nucleus
GO:0005730	0.63	nucleolus
GO:0070761	0.62	pre-snoRNP 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	3b2qA	0.376	6.33	0.025	0.634	3.6.3.14	NA
2	0.060	2o7qA	0.277	6.88	0.045	0.514	4.2.1.10 1.1.1.25	NA
3	0.060	1ytmA	0.387	5.97	0.035	0.641	4.1.1.49	NA
4	0.060	1skyB	0.358	6.37	0.087	0.621	3.6.3.14	NA
5	0.060	2ow6A	0.385	6.62	0.045	0.690	3.2.1.114	80,127

	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	0.05	3l76A	0.392	5.98	0.030	0.648	0.34	LYS	complex1.pdb.gz	53,55,56,169,170,171
2	0.01	1ce8A	0.380	6.32	0.031	0.648	0.19	IMP	complex2.pdb.gz	149,150,152,153
3	0.01	1m6vC	0.382	6.33	0.047	0.652	0.17	ADP	complex3.pdb.gz	69,104,105,106,107,108,211
4	0.01	1ce8A	0.380	6.32	0.031	0.648	0.22	ADP	complex4.pdb.gz	104,105,106,109,118,119,174
5	0.01	1a9xA	0.370	6.50	0.025	0.645	0.14	ADP	complex5.pdb.gz	51,104,108,120,121
6	0.01	2j0w0	0.394	6.21	0.086	0.669	0.13	III	complex6.pdb.gz	100,102,104
7	0.01	1ce8E	0.386	6.73	0.039	0.679	0.22	ADP	complex7.pdb.gz	104,105,109,119,120
8	0.01	2f7rA	0.380	6.27	0.057	0.648	0.11	SK3	complex8.pdb.gz	67,69,155
9	0.01	1bxrE	0.352	6.50	0.029	0.610	0.15	ANP	complex9.pdb.gz	49,51,107,173

	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.