D-I-TASSER P29460-D3

D-I-TASSER results for P29460-D3

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

Input Sequence in FASTA format

>P29460 (97 residues)
IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFT
DKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS
Prediction	CCCCCCCCCSSSSSCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSSSSCCCCSSSSSSCCCSSSSSSSCCCSSSSSSSSCCCCCCCCCCCCCCCCCC
Confidence	9778999516999926898189999499988787755889999999987887158962133079986389449999997079999978743255169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS
Prediction	7453543551403337555403030531642744432130302030345647424444446434340426560200010366445141031143628
	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

CCCCCCCCCSSSSSCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSSSSCCCCSSSSSSCCCSSSSSSSCCCSSSSSSSSCCCCCCCCCCCCCCCCCC
IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS

1uc6A

0.27

8.23

1.33

DEthreader

PVKPDPPENVVARPVPSNRRLEVTWQTPSTWPDPE-SFPLKFFLRYRPLILDQWQHVELGTAHTITAYAGKEYIIQVAAKDNIGTWSDWSVAAHATP

1f42A2

0.92

0.87

24.32

1.56

SPARKS-K

--KPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKRRVFTDKT----SATVICRKNASISVRAQDRYYSSSWSEWASVPCS

1n26A

0.24

0.23

7.08

0.37

MapAlign

ILQPDPPANITVTAVRNPRWLSVTWQDPHSW--NSSFYRLRFELRYRAERSKTFTTWMVLHHCVIHAWSGLRHVVQLRAQEEGEWSEWSPEA-MGT-

1uc6A

0.30

9.06

0.26

CEthreader

SVKPDPPENVVARPVPSPRRLEVTWQTPSTWPDP-ESFPLKFFLRYRPLILDQWQHVELTAHTITDAYAGKEYIIQVAAKDNETWSDWSVAAHATPW

1f42A

0.99

0.95

26.57

1.24

MUSTER

IIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKRR----VFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS

2erjC

0.22

0.21

6.49

0.96

HHsearch

LVIPWAPENLTLHKLSE-SQLELNWNNRFL--N----HCLEHLVQYRTDWDHSWTEQSVHKFSLPSVDGQKRYTFRVRSRFNPLAQHWSEWSHPIHW

1f42A2

0.97

0.91

25.43

1.68

FFAS-3D

--KPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKRRVF----TDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS

3hhrB2

0.18

5.70

0.53

EigenThreader

---PDPPIALNWTLLLTGIHIQVRWEAPRNADIQKGWMVLEYELQYKEVNETKWKMMDPISVPVYSLKVDKEYEVRVRSKQRNSGNYGEFSEVLYVT

1n26A

0.23

7.10

1.44

CNFpred

ILQPDPPANITVTAVANPRWLSVTWQDPHSWNS--SFYRLRFELRYRAERSKTFTTWMVHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMG

6xfiA2

0.12

0.11

4.03

1.33

DEthreader

GLYPGKVREARCQASVHEARLTVSWQIPWNLKYL-KVREVKYEVWLQEQG-ENTYPYILLQNHTFTIKPFTTYLVWVRCIFNILLG-PFADVLVCNT

(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	0.8135

(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	1n26A	0.87	1.36	0.189	0.979	model1_1n26A.pdb.gz
2	6o4pA	0.87	1.41	0.242	0.979	model1_6o4pA.pdb.gz
3	4i18R	0.86	1.72	0.168	0.979	model1_4i18R.pdb.gz
4	1uc6A	0.86	1.47	0.274	0.979	model1_1uc6A.pdb.gz
5	3hhrB	0.86	1.64	0.198	0.990	model1_3hhrB.pdb.gz
6	1cn4B	0.86	1.59	0.149	0.969	model1_1cn4B.pdb.gz
7	6xfiA2	0.85	1.76	0.115	0.990	model1_6xfiA2.pdb.gz
8	3ew3B	0.85	1.76	0.156	0.990	model1_3ew3B.pdb.gz
9	3qt2A	0.82	1.83	0.141	0.949	model1_3qt2A.pdb.gz
10	3di2D2	0.82	2.14	0.137	0.979	model1_3di2D2.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:0019955	0.98	cytokine binding
GO:0042164	0.89	interleukin-12 alpha subunit binding
GO:0005102	0.85	receptor binding
GO:0005126	0.79	cytokine receptor binding
GO:0070851	0.78	growth factor receptor binding
GO:0005143	0.75	interleukin-12 receptor binding
GO:0008083	0.66	growth factor activity
GO:0045519	0.65	interleukin-23 receptor 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:0050794	0.98	regulation of cellular process
GO:0048518	0.96	positive regulation of biological process
GO:0048522	0.95	positive regulation of cellular process
GO:0008284	0.89	positive regulation of cell proliferation
GO:0032946	0.85	positive regulation of mononuclear cell proliferation
GO:0051239	0.82	regulation of multicellular organismal process
GO:0051240	0.81	positive regulation of multicellular organismal process
GO:0002682	0.78	regulation of immune system process
GO:0080090	0.77	regulation of primary metabolic process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0002684	0.77	positive regulation of immune system process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0010604	0.76	positive regulation of macromolecule metabolic process
GO:0001819	0.76	positive regulation of cytokine production
GO:0051246	0.75	regulation of protein metabolic process
GO:0050870	0.75	positive regulation of T cell activation
GO:0050671	0.75	positive regulation of lymphocyte proliferation
GO:0051247	0.74	positive regulation of protein metabolic process
GO:0031326	0.74	regulation of cellular biosynthetic process
GO:0010556	0.74	regulation of macromolecule biosynthetic process
GO:0010557	0.73	positive regulation of macromolecule biosynthetic process
GO:0031328	0.72	positive regulation of cellular biosynthetic process
GO:0046634	0.71	regulation of alpha-beta T cell activation
GO:0042035	0.71	regulation of cytokine biosynthetic process
GO:0046635	0.70	positive regulation of alpha-beta T cell activation
GO:0045078	0.70	positive regulation of interferon-gamma biosynthetic process
GO:0051135	0.69	positive regulation of NK T cell activation
GO:0032816	0.69	positive regulation of natural killer cell activation
GO:0002376	0.61	immune system process
GO:0044699	0.58	single-organism process
GO:0050896	0.57	response to stimulus
GO:0009987	0.57	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:0044421	0.98	extracellular region part
GO:0043234	0.98	protein complex
GO:0043514	0.91	interleukin-12 complex
GO:0044464	0.68	cell part
GO:0070743	0.66	interleukin-23 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	0.105	2dlhA	0.782	2.13	0.154	0.938	3.1.3.48	NA
2	0.066	2bk8A	0.564	3.18	0.049	0.835	2.7.11.1	NA
3	0.066	1u2hA	0.540	3.43	0.074	0.835	2.7.11.1	NA
4	0.066	2djmA	0.617	2.59	0.070	0.845	3.2.1.3	NA
5	0.066	2edtA	0.558	2.73	0.039	0.794	2.7.11.1	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.