D-I-TASSER Q96J84-D4

D-I-TASSER results for Q96J84-D4

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

Input Sequence in FASTA format

>Q96J84 (84 residues)
APRIVVDPKPTTTDIGSDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADA
GTYTCRAIVPRIGVAEREVPLYVN

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| APRIVVDPKPTTTDIGSDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADAGTYTCRAIVPRIGVAEREVPLYVN
Prediction	CCSSSSCCCCSSSCCCCCSSSSSSSSSCCCCSSSSSSCCSSSSSCCCCSSSSCCCCHHHCSSSSSSSSCCCCCSSSSSSSSSSC
Confidence	984997688789908932999999953279889999999666875999799966674657799999961899718999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| APRIVVDPKPTTTDIGSDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADAGTYTCRAIVPRIGVAEREVPLYVN
Prediction	855344526634154456145525054445141464467562433754554465145635545333043474454434156458
	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

                   |                   |                   |                   |

SS
Seq

CCSSSSCCCCSSSCCCCCSSSSSSSSSCCCCSSSSSSCCSSSSSCCCCSSSSCCCCHHHCSSSSSSSSCCCCCSSSSSSSSSSC
APRIVVDPKPTTTDIGSDVTLTCVWVGNPPLTLTWTKKDSNMVLSNSNQLLLKSVTQADAGTYTCRAIVPRIGVAEREVPLYVN

6dldA

0.29

8.70

1.50

DEthreader

PARIVNISSPVTVNEGGNVNLLCLAVGRPEPTVTWRQLRDGFTS-EGEILEISDIQRGQAGEYECVTHNGVSAPDSRRVLVTVN

5uv6A2

0.28

0.27

8.37

1.18

SPARKS-K

PPQIMNISSDITVNEGSSVTLLCLAIGRPEPTVTWRHLSGFVSEDE--YLEISDIKRDQSGEYECSALNDVAAPDVRKVKITVN

1nunB2

0.33

0.32

9.65

0.42

MapAlign

RPILQL-PANASTVVGGDVEFVCKVYSDAQPHIQWIKHPYLKVLKHSEVLALFNVTEADAGEYICKVSN-YIGQANQSAWLTVL

1cs6A3

0.31

9.35

0.30

CEthreader

APSIKAKFADTYALTGQMVTLECFAFGNPVPQIKWRKLDGSKWLSSEPLLHIQNVDFEDEGTYECEAEN-IKGRDTYQGRIIIH

5uv6A2

0.29

8.69

1.25

MUSTER

PPQIMNISSDITVNEGSSVTLLCLAIGRPEPTVTWRHLSG--FVSEDEYLEISDIKRDQSGEYECSALNDVAAPDVRKVKITVN

6iaaA2

0.30

9.02

0.41

HHsearch

PPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLVSPTGDLTITNIQRSDAGYYICQALT-VAGSILAKAQLEVT

5o5gA4

0.28

0.27

8.38

1.58

FFAS-3D

PPHFVVKPRDQVVALGRTVTFQCEATGNPQPAIFWRREGSQFSVSQTGDLTITNVQRSDVGYYICQTL-NVAGSIITKAYLEVT

6dldB2

0.30

9.04

0.28

EigenThreader

PPKIYDISNDMTVNEGTNVTLTCLATGKPEPSISWRHISSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVRKVKVVVN

5lfrA

0.34

0.33

9.98

1.46

CNFpred

PPVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREA-SLYLDLEEVTPGEDGVYACLAENA-YGQDNRTVELSVM

6dldA2

0.29

8.70

1.50

DEthreader

PARIVNISSPVTVNEGGNVNLLCLAVGRPEPTVTWRQLRDGFTS-EGEILEISDIQRGQAGEYECVTHNGVSAPDSRRVLVTVN

(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	0.92

(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	6dldA	0.92	0.98	0.289	0.988	model1_6dldA.pdb.gz
2	1cs6A	0.92	1.27	0.325	0.988	model1_1cs6A.pdb.gz
3	6dldB	0.91	1.21	0.286	1.000	model1_6dldB.pdb.gz
4	5uv6A	0.90	1.04	0.293	0.976	model1_5uv6A.pdb.gz
5	6nrrB2	0.90	1.16	0.289	0.988	model1_6nrrB2.pdb.gz
6	5e4iA3	0.90	1.52	0.277	0.988	model1_5e4iA3.pdb.gz
7	5noiA1	0.90	1.21	0.301	0.988	model1_5noiA1.pdb.gz
8	5o5gA4	0.90	1.27	0.277	0.988	model1_5o5gA4.pdb.gz
9	3s97C2	0.90	1.57	0.289	0.988	model1_3s97C2.pdb.gz
10	6eg0B2	0.90	1.20	0.253	0.988	model1_6eg0B2.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:0042802	0.48	identical protein binding
GO:0004872	0.43	receptor activity
GO:0038023	0.37	signaling receptor activity
GO:0004888	0.36	transmembrane signaling receptor activity
GO:0042803	0.33	protein homodimerization 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:0044699	0.91	single-organism process
GO:0009987	0.89	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0065007	0.71	biological regulation
GO:0032502	0.70	developmental process
GO:0050789	0.69	regulation of biological process
GO:0044767	0.67	single-organism developmental process
GO:0050794	0.66	regulation of cellular process
GO:0048856	0.55	anatomical structure development
GO:0048869	0.50	cellular developmental 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:0044464	0.97	cell part
GO:0044424	0.71	intracellular part
GO:0044444	0.53	cytoplasmic part
GO:0044425	0.51	membrane part
GO:0016020	0.48	membrane
GO:0043226	0.46	organelle
GO:0016021	0.44	integral component of membrane
GO:0044459	0.43	plasma membrane part
GO:0043227	0.41	membrane-bounded organelle
GO:0005887	0.38	integral component of plasma membrane
GO:0097458	0.37	neuron part
GO:0043005	0.34	neuron projection
GO:0005886	0.34	plasma membrane
GO:0044422	0.33	organelle part
GO:0043229	0.33	intracellular organelle
GO:0030424	0.32	axon
GO:0044446	0.31	intracellular organelle part
GO:0044421	0.31	extracellular region 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	0.226	2edwA	0.760	1.80	0.208	0.917	2.7.11.1	NA
2	0.148	2bk8A	0.826	1.69	0.207	0.976	2.7.11.1	34,62
3	0.102	1rv6Y	0.699	2.51	0.162	0.941	2.7.10.1	26,32,34
4	0.088	1zvhA	0.761	2.16	0.181	0.964	3.2.1.17	NA
5	0.076	1zvyA	0.757	2.02	0.207	0.952	3.2.1.17	73

	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	0.06	2iep0	0.875	1.46	0.262	1.000	0.77	III	complex1.pdb.gz	5,6,9,20,22,24,26,49
2	0.06	1gl41	0.853	1.89	0.253	0.988	0.91	III	complex2.pdb.gz	30,31,32,34,48,66,68,69,70,73,74
3	0.05	1cbvL	0.790	2.09	0.134	0.976	0.99	QNA	complex3.pdb.gz	27,32,68,69,74
4	0.04	3hujG	0.816	2.05	0.183	0.976	0.84	AGH	complex4.pdb.gz	30,31,69,70
5	0.04	2gsiE	0.806	1.76	0.162	0.952	0.67	III	complex5.pdb.gz	16,55,56,60
6	0.04	2r0wL	0.785	1.99	0.160	0.964	0.61	III	complex6.pdb.gz	27,28,32,68,69,74
7	0.04	1ehlL	0.782	2.19	0.146	0.976	0.67	QNA	complex7.pdb.gz	20,22,82

	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.