D-I-TASSER P09430

D-I-TASSER results for P09430

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

Summary of the Protein

Uniprot ID: P09430
Protein Name: Spermatid nuclear transition protein 1
Gene Name: TNP1

Input Sequence in FASTA format

>P09430 (55 residues)
MSTSRKLKSHGMRRSKSRSPHKGVKRGGSKRKYRKGNLKSRKRGDDANRNYRSHL

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	P09430-D1	1-55	55		MSTSRKLKSHGMRRSKSRSPHKGVKRGGSKRKYRKGNLKSRKRGDDANRNYRSHL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.606

(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	5ejqA1	0.46	3.71	0.098	0.891	model1_5ejqA1.pdb.gz
2	1rw9A1	0.46	3.13	0.038	0.818	model1_1rw9A1.pdb.gz
3	1i8qA	0.45	3.09	0.019	0.836	model1_1i8qA.pdb.gz
4	3o0yA2	0.45	3.07	0.056	0.764	model1_3o0yA2.pdb.gz
5	3pvlA1	0.45	3.94	0.058	0.946	model1_3pvlA1.pdb.gz
6	1n7qA1	0.42	3.87	0.018	0.855	model1_1n7qA1.pdb.gz
7	1rlkA	0.38	2.57	0.088	0.600	model1_1rlkA.pdb.gz
8	2w47A	0.38	4.06	0.037	0.909	model1_2w47A.pdb.gz
9	3pzdA1	0.34	3.12	0.106	0.618	model1_3pzdA1.pdb.gz
10	1hmwA1	0.34	4.13	0.042	0.691	model1_1hmwA1.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:0003677	1.00	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:0007290	1.00	spermatid nucleus elongation
GO:0006338	1.00	chromatin remodeling
GO:0044699	0.76	single-organism process
GO:0065007	0.71	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0008152	0.69	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0044763	0.68	single-organism cellular process
GO:0044238	0.68	primary metabolic process
GO:0032502	0.68	developmental process
GO:0048856	0.67	anatomical structure development
GO:0044767	0.67	single-organism developmental process
GO:0044237	0.67	cellular metabolic process
GO:0050794	0.66	regulation of cellular process
GO:0050896	0.65	response to stimulus
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0006139	0.65	nucleobase-containing compound metabolic process
GO:0090304	0.64	nucleic acid metabolic process
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0044702	0.64	single organism reproductive process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0051704	0.63	multi-organism process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0071822	0.62	protein complex subunit organization
GO:0007281	0.62	germ cell development
GO:0006950	0.62	response to stress
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0030317	0.61	sperm motility
GO:0019953	0.61	sexual reproduction
GO:0007286	0.61	spermatid development
GO:0006342	0.61	chromatin silencing
GO:0006337	0.61	nucleosome disassembly
GO:0000012	0.61	single strand break repair

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:0000786	1.00	nucleosome
GO:0043229	0.94	intracellular organelle
GO:0005634	0.93	nucleus
GO:0001673	0.91	male germ cell nucleus

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	2h3qA	0.368	3.33	0.000	0.727	3.1.26.4	37
2	0.060	1pv9A	0.384	3.61	0.063	0.818	3.4.13.9	NA
3	0.060	1gpeB	0.329	3.72	0.049	0.636	1.1.3.4	36
4	0.060	2gamC	0.409	3.66	0.059	0.818	2.4.1.102	NA
5	0.060	2o0rA	0.403	3.95	0.019	0.855	2.6.1.-	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	2h3zA	0.360	3.48	0.048	0.764	0.28	PBU	complex1.pdb.gz	12,23,48
2	0.01	2j5xB	0.276	4.57	0.000	0.746	0.11	GSP	complex2.pdb.gz	23,25,26
3	0.01	2c1uD	0.343	4.14	0.063	0.782	0.16	HEC	complex3.pdb.gz	7,11,51
4	0.01	3o0gB	0.291	4.90	0.040	0.782	0.19	3O0	complex4.pdb.gz	11,21,23,24
5	0.01	3o0rC	0.417	2.96	0.043	0.691	0.23	HEC	complex5.pdb.gz	10,30,51
6	0.01	2h3qA	0.368	3.33	0.000	0.727	0.26	PBU	complex6.pdb.gz	46,47,50,51
7	0.01	3nizA	0.270	4.15	0.082	0.691	0.18	ADP	complex7.pdb.gz	4,8,11,12,48
8	0.01	2a5gA	0.266	4.57	0.064	0.746	0.13	GTP	complex8.pdb.gz	10,11,12,13,14
9	0.01	1zzhA	0.296	3.88	0.025	0.618	0.15	HEC	complex9.pdb.gz	10,13,14,22,23,24,39,47
10	0.01	3pcrB	0.289	3.79	0.047	0.564	0.12	GTP	complex10.pdb.gz	4,5,6,32,33,47

	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.