D-I-TASSER Q9NUM3

D-I-TASSER results for Q9NUM3

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

Summary of the Protein

Uniprot ID: Q9NUM3
Protein Name: Zinc transporter ZIP9
Gene Name: SLC39A9

Input Sequence in FASTA format

>Q9NUM3 (307 residues)
MDDFISISLLSLAMLVGCYVAGIIPLAVNFSEERLKLVTVLGAGLLCGTALAVIVPEGVH
ALYEDILEGKHHQASETHNVIASDKAAEKSVVHEHEHSHDHTQLHAYIGVSLVLGFVFML
LVDQIGNSHVHSTDDPEAARSSNSKITTTLGLVVHAAADGVALGAAASTSQTSVQLIVFV
AIMLHKAPAAFGLVSFLMHAGLERNRIRKHLLVFALAAPVMSMVTYLGLSKSSKEALSEV
NATGVAMLFSAGTFLYVATVHVLPEVGGIGHSHKPDATGGRGLSRLEVAALVLGCLIPLI
LSVGHQH

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	Q9NUM3-D1	1-30,133-233	131		MDDFISISLLSLAMLVGCYVAGIIPLAVNFTDDPEAARSSNSKITTTLGLVVHAAADGVALGAAASTSQTSVQLIVFVAIMLHKAPAAFGLVSFLMHAGLERNRIRKHLLVFALAAPVMSMVTYLGLSKSS
2	Q9NUM3-D2	31-132,234-307	176		SEERLKLVTVLGAGLLCGTALAVIVPEGVHALYEDILEGKHHQASETHNVIASDKAAEKSVVHEHEHSHDHTQLHAYIGVSLVLGFVFMLLVDQIGNSHVHSKEALSEVNATGVAMLFSAGTFLYVATVHVLPEVGGIGHSHKPDATGGRGLSRLEVAALVLGCLIPLILSVGHQH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	5tsaA	0.59	3.42	0.129	0.697	model1_5tsaA.pdb.gz
2	7ccsB	0.54	5.25	0.074	0.785	model1_7ccsB.pdb.gz
3	7cmhB	0.53	5.56	0.040	0.798	model1_7cmhB.pdb.gz
4	4djiA	0.53	4.92	0.126	0.749	model1_4djiA.pdb.gz
5	6kkrA	0.53	5.44	0.068	0.798	model1_6kkrA.pdb.gz
6	6y5rA	0.53	5.11	0.072	0.765	model1_6y5rA.pdb.gz
7	6irsB	0.53	5.48	0.049	0.785	model1_6irsB.pdb.gz
8	6f2gA	0.53	5.33	0.077	0.769	model1_6f2gA.pdb.gz
9	6li9B	0.53	5.59	0.041	0.788	model1_6li9B.pdb.gz
10	6nplA1	0.52	5.17	0.080	0.769	model1_6nplA1.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:0005385	1.00	zinc ion transmembrane transporter 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:0006829	1.00	zinc II ion transport
GO:0055085	0.96	transmembrane transport
GO:0071577	0.94	zinc II ion transmembrane transport
GO:0065007	0.78	biological regulation
GO:0065008	0.73	regulation of biological quality
GO:0055076	0.72	transition metal ion homeostasis
GO:0072507	0.71	divalent inorganic cation homeostasis
GO:0046916	0.71	cellular transition metal ion homeostasis
GO:0006882	0.70	cellular zinc ion homeostasis

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:0044464	0.99	cell part
GO:0016020	0.96	membrane
GO:0044425	0.90	membrane part
GO:0016021	0.89	integral component of membrane
GO:0005886	0.80	plasma membrane
GO:0044424	0.69	intracellular part
GO:0044459	0.66	plasma membrane part
GO:0005887	0.60	integral component of plasma membrane

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	2iukB	0.432	5.96	0.060	0.671	1.13.11.12	NA
2	0.060	1jqoA	0.374	6.52	0.034	0.642	4.1.1.31	NA
3	0.060	1g87B	0.382	5.50	0.039	0.577	3.2.1.4	NA
4	0.060	2qykB	0.317	5.57	0.052	0.469	3.1.4.17	NA
5	0.060	2p0mA	0.423	5.61	0.064	0.635	1.13.11.33	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	0.03	3l1lA	0.495	5.81	0.092	0.778	0.54	ARG	complex1.pdb.gz	46,47,50,51,54,255
2	0.01	3gjcA	0.485	6.36	0.068	0.814	0.70	NA	complex2.pdb.gz	160,161,162,163,164
3	0.01	3f3aA	0.489	6.30	0.060	0.814	0.49	TRP	complex3.pdb.gz	155,159,187,192
4	0.01	3gjdA	0.483	6.36	0.043	0.814	0.60	BOG	complex4.pdb.gz	157,158,160,163
5	0.01	1loxA	0.416	5.91	0.063	0.661	0.43	RS7	complex5.pdb.gz	151,155,159,162,181,185,189,254
6	0.01	1hu9A	0.431	5.95	0.060	0.668	0.45	4HM	complex6.pdb.gz	148,151,155,193,195
7	0.01	2qjuA	0.480	6.22	0.046	0.791	0.43	DSM	complex7.pdb.gz	45,49,50,54,257
8	0.01	2qeiA	0.484	6.35	0.046	0.818	0.55	CXX	complex8.pdb.gz	34,38,41,42,45,185
9	0.01	2p0mB	0.376	5.98	0.056	0.586	0.42	RS7	complex9.pdb.gz	151,185,189,193,197,259
10	0.01	3f4jA	0.480	6.33	0.042	0.808	0.40	GLY	complex10.pdb.gz	48,49,50,254

	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.