D-I-TASSER Q9H9A7-D2

D-I-TASSER results for Q9H9A7-D2

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

Input Sequence in FASTA format

>Q9H9A7 (124 residues)
LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEAQVTPKPW
EAKPSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENV
KVLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEAQVTPKPWEAKPSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG
Prediction	CCCCCHHHCCSSSSCCCSSSSSSSSSSCCHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCSSSSSSSSSSCCCCCCCCCCCSSSSSSCCCSSSSCSSSSCCCCSSSSC
Confidence	9897621275059669879999747871512799999974877544434422124555678888617999981798499999974336566789996799995896688128995699189939
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEAQVTPKPWEAKPSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG
Prediction	7227515535545061300000330340032134204614755554644555564466646543321020203335440300124315504541200010103460402200000357305228
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHCCSSSSCCCSSSSSSSSSSCCHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCSSSSSSSSSSCCCCCCCCCCCSSSSSSCCCSSSSCSSSSCCCCSSSSC
LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEAQVTPKPWEAKPSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

1.00

0.76

21.23

1.17

DEthreader

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYS---------------------------AKPSR-L-LQLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.96

0.86

24.19

2.32

SPARKS-K

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKAQV----------TPKPWEAKPSRLL--QLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.77

0.69

19.40

0.89

MapAlign

LLPDGILEIPKGELNGFYALQINSLVDVS--QPAYSQIQK---------LRGKAQVTPKPWEAKPSRL-LQLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.86

0.77

21.80

0.90

CEthreader

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKAQVTPK------------PWEAKPSRLLQLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.99

0.89

24.85

1.41

MUSTER

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGK----------AQVTPKPWEAKPSRL--LQLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.96

0.86

24.19

4.65

HHsearch

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKAQV----------TPKPWEAKPSRL--LQLTDGIVQIQG-EYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.86

0.77

21.58

1.45

FFAS-3D

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKA------------QVTPKPWEAKPSRLLQLTDGIVQI-QGEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

3nbiA

0.80

0.72

20.27

1.27

EigenThreader

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGK------------AQVTPKPWEAKPSRLLQLTDGIVQIQGEYQP-IPILHSDLPPGTKILIYGNISFRLGVLLLKPENVLGGE

4cgyB

1.00

0.92

25.74

2.94

CNFpred

LLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEA----------PSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLG

5gvdA

0.35

0.25

7.46

1.00

DEthreader

FLPSDINSGKVEKLEGPCVLQIQKIRN------------------------------------APRMLRLQMTDGHISCTAVEFSYMSKISLNTPPGTKVKLSGIVDIKNGFLLLNDSNTTVLG

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7586

(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	3nbiA	0.79	1.15	0.928	0.831	model1_3nbiA.pdb.gz
2	5gvdA	0.62	1.80	0.352	0.710	model1_5gvdA.pdb.gz
3	1miuA	0.60	3.62	0.139	0.863	model1_1miuA.pdb.gz
4	2i46A	0.57	3.03	0.102	0.742	model1_2i46A.pdb.gz
5	2b3gA	0.57	2.26	0.188	0.685	model1_2b3gA.pdb.gz
6	3kf8A	0.57	2.85	0.143	0.734	model1_3kf8A.pdb.gz
7	2m9vA	0.56	2.30	0.128	0.694	model1_2m9vA.pdb.gz
8	1x54A1	0.56	2.09	0.098	0.661	model1_1x54A1.pdb.gz
9	1eqrA1	0.56	2.26	0.110	0.661	model1_1eqrA1.pdb.gz
10	4h02A1	0.55	2.26	0.094	0.685	model1_4h02A1.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:0097159	0.72	organic cyclic compound binding
GO:1901363	0.71	heterocyclic compound binding
GO:0044877	0.62	macromolecular complex binding
GO:0003682	0.61	chromatin binding
GO:0035064	0.60	methylated histone binding
GO:0003713	0.60	transcription coactivator activity
GO:0036094	0.59	small molecule binding
GO:0000166	0.58	nucleotide 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	0.81	cellular process
GO:0065007	0.75	biological regulation
GO:0008152	0.70	metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044238	0.61	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0043170	0.60	macromolecule metabolic process
GO:0044699	0.59	single-organism process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:1901360	0.58	organic cyclic compound metabolic process
GO:0034641	0.58	cellular nitrogen compound metabolic process
GO:0090304	0.57	nucleic acid metabolic process
GO:0006259	0.56	DNA metabolic process
GO:0050789	0.52	regulation of biological process
GO:0050896	0.50	response to stimulus
GO:0050794	0.50	regulation of cellular 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:0043231	1.00	intracellular membrane-bounded organelle
GO:0005634	0.96	nucleus
GO:0044446	0.85	intracellular organelle part
GO:0044428	0.82	nuclear part
GO:0032991	0.63	macromolecular complex
GO:0043234	0.62	protein 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	2r93G	0.442	3.73	0.061	0.645	2.7.7.6	16,71,75
2	0.060	1hnkA	0.263	5.48	0.106	0.516	2.3.1.180 2.3.1.41	NA
3	0.060	2qx1A	0.436	5.11	0.033	0.806	2.3.1.180	NA
4	0.060	3bjuA	0.548	2.33	0.141	0.685	6.1.1.6	NA
5	0.060	3il3A	0.453	5.08	0.067	0.823	2.3.1.180	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	0.05	1qzhB	0.554	3.11	0.140	0.742	0.53	QNA	complex1.pdb.gz	25,27,28,67,107,114,115,116,117
2	0.05	1qzhA	0.554	3.10	0.129	0.742	0.64	QNA	complex2.pdb.gz	80,82,86,109,112,114,115,116
3	0.03	2i460	0.573	3.03	0.102	0.742	0.72	III	complex3.pdb.gz	17,18,21,73,74,75,99,101,103,119
4	0.02	2vw9A	0.505	2.58	0.101	0.629	0.74	QNA	complex4.pdb.gz	21,22,73,96,97

	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.