D-I-TASSER Q15043

D-I-TASSER results for Q15043

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

Summary of the Protein

Uniprot ID: Q15043
Protein Name: Metal cation symporter ZIP14
Gene Name: SLC39A14

Input Sequence in FASTA format

>Q15043 (492 residues)
MKLLLLHPAFQSCLLLTLLGLWRTTPEAHASSLGAPAISAASFLQDLIHRYGEGDSLTLQ
QLKALLNHLDVGVGRGNVTQHVQGHRNLSTCFSSGDLFTAHNFSEQSRIGSSELQEFCPT
ILQQLDSRACTSENQENEENEQTEEGRPSAVEVWGYGLLCVTVISLCSLLGASVVPFMKK
TFYKRLLLYFIALAIGTLYSNALFQLIPEAFGFNPLEDYYVSKSAVVFGGFYLFFFTEKI
LKILLKQKNEHHHGHSHYASESLPSKKDQEEGVMEKLQNGDLDHMIPQHCSSELDGKAPM
VDEKVIVGSLSVQDLQASQSACYWLKGVRYSDIGTLAWMITLSDGLHNFIDGLAIGASFT
VSVFQGISTSVAILCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGILAG
SHFSANWIFALAGGMFLYISLADMFPEMNEVCQEDERKGSILIPFIIQNLGLLTGFTIMV
VLTMYSGQIQIG

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	Q15043-D1	1-133	133		MKLLLLHPAFQSCLLLTLLGLWRTTPEAHASSLGAPAISAASFLQDLIHRYGEGDSLTLQQLKALLNHLDVGVGRGNVTQHVQGHRNLSTCFSSGDLFTAHNFSEQSRIGSSELQEFCPTILQQLDSRACTSE
2	Q15043-D2	134-250,330-492	280		NQENEENEQTEEGRPSAVEVWGYGLLCVTVISLCSLLGASVVPFMKKTFYKRLLLYFIALAIGTLYSNALFQLIPEAFGFNPLEDYYVSKSAVVFGGFYLFFFTEKILKILLKQKNEYSDIGTLAWMITLSDGLHNFIDGLAIGASFTVSVFQGISTSVAILCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGILAGSHFSANWIFALAGGMFLYISLADMFPEMNEVCQEDERKGSILIPFIIQNLGLLTGFTIMVVLTMYSGQIQIG
3	Q15043-D3	251-329	79		HHHGHSHYASESLPSKKDQEEGVMEKLQNGDLDHMIPQHCSSELDGKAPMVDEKVIVGSLSVQDLQASQSACYWLKGVR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	0.45	0.98	0.213	0.457	model1_5tsaA.pdb.gz
2	5oybA	0.41	7.03	0.041	0.640	model1_5oybA.pdb.gz
3	4wisA	0.40	7.21	0.059	0.644	model1_4wisA.pdb.gz
4	5oc9A	0.40	7.08	0.061	0.628	model1_5oc9A.pdb.gz
5	6dz7B	0.39	7.03	0.053	0.616	model1_6dz7B.pdb.gz
6	6qp6A	0.39	6.62	0.032	0.589	model1_6qp6A.pdb.gz
7	1no3A	0.38	7.38	0.054	0.612	model1_1no3A.pdb.gz
8	4jspB	0.38	7.01	0.053	0.583	model1_4jspB.pdb.gz
9	5fvmA	0.37	7.18	0.050	0.585	model1_5fvmA.pdb.gz
10	6jxaA	0.37	7.38	0.060	0.602	model1_6jxaA.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	0.99	transmembrane transport
GO:0071577	0.98	zinc II ion transmembrane transport
GO:0065007	0.97	biological regulation
GO:0065008	0.96	regulation of biological quality
GO:0006882	0.95	cellular zinc ion homeostasis
GO:0071578	0.75	zinc II ion transmembrane import

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	1.00	cell part
GO:0044425	0.95	membrane part
GO:0044459	0.93	plasma membrane part
GO:0016021	0.93	integral component of membrane
GO:0005887	0.92	integral component of plasma membrane
GO:0044424	0.51	intracellular part

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	1ej6A	0.319	7.73	0.050	0.543	2.7.7.50	413
2	0.060	3h0gA	0.337	7.43	0.043	0.555	2.7.7.6	355
3	0.060	2vkzG	0.324	7.30	0.049	0.522	2.3.1.38 3.1.2.14	428
4	0.060	2hg4C	0.339	7.72	0.045	0.579	2.3.1.94	NA
5	0.060	2p0mA	0.366	7.17	0.061	0.573	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	0.01	1n38A	0.359	7.39	0.062	0.587	0.34	QNA	complex1.pdb.gz	199,200,205,434
2	0.01	2p0mB	0.374	7.09	0.037	0.585	0.25	RS7	complex2.pdb.gz	198,202,206
3	0.01	3b34A	0.324	7.61	0.036	0.543	0.23	PHE	complex3.pdb.gz	346,347,350
4	0.01	1no3A	0.380	7.38	0.054	0.612	0.23	4NC	complex4.pdb.gz	200,201,204,376
5	0.01	3dy5A	0.366	7.29	0.051	0.596	0.17	HEM	complex5.pdb.gz	406,409,410,413,414,417
6	0.01	1hu9A	0.382	7.48	0.042	0.624	0.24	4HM	complex6.pdb.gz	201,204,373,376
7	0.01	1n1hA	0.332	7.20	0.044	0.532	0.19	UUU	complex7.pdb.gz	170,171,194
8	0.01	3b2pA	0.324	7.60	0.051	0.543	0.15	ARG	complex8.pdb.gz	347,348,351
9	0.01	1jnqA	0.381	7.24	0.056	0.612	0.32	UUU	complex9.pdb.gz	191,194,195,198,376,380,383
10	0.01	2zxgA	0.352	7.88	0.047	0.612	0.16	S23	complex10.pdb.gz	352,355,356,365,366

	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.