D-I-TASSER Q03468-D3

D-I-TASSER results for Q03468-D3

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

Input Sequence in FASTA format

>Q03468 (71 residues)
EVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGTQIPQKQEKKPRK
IMLNEASGFEK

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| EVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGTQIPQKQEKKPRKIMLNEASGFEK
Prediction	CSSSSSCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCC
Confidence	91454100233356898953244320421378999999857877787758764333326665202334469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| EVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGTQIPQKQEKKPRKIMLNEASGFEK
Prediction	83524264352666564335222422332564415412642534434461466666433413155365368
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60

                   |                   |                   |

SS
Seq

CSSSSSCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCC
EVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGTQIPQKQEKKPRKIMLNEASGFEK

2ivwA

0.10

3.66

0.59

CEthreader

KETLEKFSLENMRYVGILKSGQKVSGFIEAEGYVYTVGVGNYLGQNYGRIESITDDSIVLNELIEDSTGNW

1vzaA2

0.03

1.72

0.55

EigenThreader

KKVLDEGGTYSIFGFPLLTTK---KVPFGLIKSDLLWFLHGDVYGSQWRAWSKGDTQLGDVIEQIKTHPYS

3d5gB

0.22

0.14

4.45

0.31

FFAS-3D

--------------ADPALADVCRTKLPSQAQDTLALIAKNGPYPYGVVFENRESRLPKK-----------

3hgfC

0.07

2.90

1.06

SPARKS-K

KIENIVTKIDKKKYIYKKLLNEIAEIEKDKTSEEVKNINMSYGKSLNKLFLEKIKKKSENMMEKYIKDLDE

1vrqA

0.35

0.10

2.94

0.38

CNFpred

------------------------------LQVWEDVYAAGNITPYGTET---------------------

1xi5A

0.07

2.85

1.00

DEthreader

---GSAQVVFPVIIIVCVEENLAG-AEELFARKFNALFAQGNYSSPQYFGESLECSENVNYKKDEEALSEL

4ui9A1

0.00

0.96

0.82

MapAlign

---EKCICILQSSCINMHSIEGKDYIASLPFQVANVWYGLLFERSPTMFSMLHPLDEITPLVCKVQYVVDH

6gsiI

0.14

4.79

0.61

MUSTER

-QQIELDKAALGQQRELALKKLDHQALNNQVEQFNKILEQRVQGPISVRLARAAGFRVDPYSYTDQNFYDD

3p12A

0.16

0.13

4.23

0.60

HHsearch

EIKEHNPTQLQQKQLISSEIEIIFIMSNLAHPLNKGNIRTGETTPYSNIALESNV------------TF--

1vt4I3

0.07

2.90

0.54

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

(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	0.4671

(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	5jcaL	0.49	3.62	0.109	0.859	model1_5jcaL.pdb.gz
2	6sp2A	0.49	3.85	0.043	0.873	model1_6sp2A.pdb.gz
3	2x0oA	0.49	3.50	0.050	0.789	model1_2x0oA.pdb.gz
4	6dwoA	0.49	3.61	0.070	0.803	model1_6dwoA.pdb.gz
5	2rdyA	0.48	3.82	0.063	0.873	model1_2rdyA.pdb.gz
6	6s8bK	0.48	3.57	0.061	0.859	model1_6s8bK.pdb.gz
7	2vn4A1	0.48	4.12	0.030	0.887	model1_2vn4A1.pdb.gz
8	4ufcA	0.46	3.87	0.114	0.873	model1_4ufcA.pdb.gz
9	2f6dA	0.44	3.87	0.032	0.887	model1_2f6dA.pdb.gz
10	2w02B3	0.43	4.09	0.062	0.831	model1_2w02B3.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:0047485	1.00	protein N-terminus binding
GO:0032403	1.00	protein complex binding
GO:0030296	1.00	protein tyrosine kinase activator activity
GO:0008094	1.00	DNA-dependent ATPase activity
GO:0008022	1.00	protein C-terminus binding
GO:0005524	1.00	ATP binding
GO:0003682	1.00	chromatin binding
GO:0003677	1.00	DNA binding
GO:0003678	0.53	DNA helicase 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:0006974	1.00	cellular response to DNA damage stimulus
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.74	primary metabolic process
GO:0044237	0.74	cellular metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0065007	0.71	biological regulation
GO:0006139	0.70	nucleobase-containing compound metabolic process
GO:0090304	0.69	nucleic acid metabolic process
GO:0050794	0.69	regulation of cellular process
GO:0044249	0.67	cellular biosynthetic process
GO:0016070	0.67	RNA metabolic process
GO:0009059	0.67	macromolecule biosynthetic process
GO:0032774	0.66	RNA biosynthetic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0080090	0.64	regulation of primary metabolic process
GO:0048522	0.64	positive regulation of cellular process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.63	regulation of macromolecule biosynthetic process
GO:0010468	0.63	regulation of gene expression
GO:1902680	0.62	positive regulation of RNA biosynthetic process
GO:0010628	0.62	positive regulation of gene expression
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0045893	0.61	positive regulation of transcription, DNA-templated
GO:0006259	0.61	DNA metabolic process
GO:0009628	0.60	response to abiotic stimulus
GO:0006281	0.60	DNA repair
GO:0032786	0.59	positive regulation of DNA-templated transcription, elongation
GO:0009411	0.59	response to UV
GO:0006979	0.59	response to oxidative stress
GO:0006284	0.59	base-excision repair
GO:0006283	0.59	transcription-coupled nucleotide-excision repair

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:0008023	1.00	transcription elongation factor complex
GO:0005730	1.00	nucleolus
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus

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	1ksdA	0.474	3.64	0.033	0.817	3.2.1.4	NA
2	0.060	1u60C	0.473	3.79	0.016	0.859	3.5.1.2	NA
3	0.060	1hlgB	0.452	3.80	0.069	0.775	3.1.1.3	NA
4	0.060	1i8qA	0.455	3.55	0.033	0.732	4.2.2.1	NA
5	0.060	2z8kC	0.455	3.04	0.118	0.704	2.3.2.2	11

	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:

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
	1	0.01	3shyA	0.453	3.78	0.049	0.761	0.64	5FO	complex1.pdb.gz	34,37,38,41,45

	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.