D-I-TASSER Q6ZNE9-D4

D-I-TASSER results for Q6ZNE9-D4

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

Input Sequence in FASTA format

>Q6ZNE9 (35 residues)
LRKAEEQAQRQEQLLREQEGELQALREQLSRCQEE

Predicted Secondary Structure

Sequence	20 \| LRKAEEQAQRQEQLLREQEGELQALREQLSRCQEE
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	62589999999999999876899999999987309
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| LRKAEEQAQRQEQLLREQEGELQALREQLSRCQEE
Prediction	75546753544553156574535414642551588
	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

                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
LRKAEEQAQRQEQLLREQEGELQALREQLSRCQEE

1vw42

0.09

3.31

1.67

DEthreader

TIEKCWSIYQQQQRERRNLQLELQYKSIERSMNLL

3lecA3

0.14

4.86

1.01

SPARKS-K

KEKWQNELNKLTFALNSIPNERAILEDKIQDIKEV

3javA

0.03

1.77

1.03

MapAlign

FAARVIYDLLFFFMVIIIVLNLIFGVIIDTFADLR

1zxaA

0.39

0.37

10.97

1.42

MUSTER

LMLKEERIKELEKRLSEKEEEIQELKRKLHKCQ--

6r17A

0.06

2.54

1.67

DEthreader

YQIYNDHNKIIQEKLQEFTQKMAKISHLETELKQV

5ymaA1

0.31

9.49

0.97

SPARKS-K

LGAIKKRARAIERLLKELERELKAHKERIKDIEFK

3feyA

0.12

0.11

4.06

0.55

MapAlign

-PWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFT

2tmaA1

0.20

6.40

0.38

CEthreader

ATDAEADVASLNRRIQLVEEELDRAQERLATALQK

3a2aA

0.20

6.40

1.05

MUSTER

LKQMNVQLAAKIQHLEFSCSEKEQEIERLNKLLRQ

1zxaA

0.39

0.37

10.97

0.42

HHsearch

LMLKEERIKELEKRLSEKEEEIQELKRKLHKCQ--

(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	0.6754

(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	6rwbA2	0.95	0.37	0.114	1.000	model1_6rwbA2.pdb.gz
2	6lthN2	0.95	0.37	0.086	1.000	model1_6lthN2.pdb.gz
3	6yvuB	0.94	0.40	0.057	1.000	model1_6yvuB.pdb.gz
4	6rw9A	0.94	0.40	0.057	1.000	model1_6rw9A.pdb.gz
5	6rw8A	0.94	0.41	0.114	1.000	model1_6rw8A.pdb.gz
6	6vy1A	0.94	0.42	0.143	1.000	model1_6vy1A.pdb.gz
7	6vhfA	0.93	0.42	0.114	1.000	model1_6vhfA.pdb.gz
8	6l7eA	0.93	0.44	0.114	1.000	model1_6l7eA.pdb.gz
9	1ztmC	0.93	0.43	0.114	1.000	model1_1ztmC.pdb.gz
10	5xauC	0.93	0.44	0.086	1.000	model1_5xauC.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:0003824	0.62	catalytic activity
GO:0046872	0.60	metal ion binding
GO:0046914	0.59	transition metal ion binding
GO:0016740	0.58	transferase activity
GO:0046983	0.55	protein dimerization activity
GO:0019899	0.55	enzyme binding
GO:0019787	0.55	ubiquitin-like protein transferase activity
GO:0044389	0.54	ubiquitin-like protein ligase binding
GO:0005198	0.54	structural molecule activity
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound binding
GO:0003682	0.52	chromatin binding
GO:0005102	0.51	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:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0050794	0.71	regulation of cellular process
GO:0009987	0.69	cellular process
GO:0008152	0.67	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044699	0.65	single-organism process
GO:0044238	0.65	primary metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0044763	0.62	single-organism cellular process
GO:0048518	0.61	positive regulation of biological process
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0044260	0.60	cellular macromolecule metabolic process
GO:0048583	0.59	regulation of response to stimulus
GO:0048522	0.59	positive regulation of cellular process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0048584	0.58	positive regulation of response to stimulus
GO:0048523	0.58	negative regulation of cellular process
GO:0090304	0.57	nucleic acid metabolic process
GO:0031326	0.57	regulation of cellular biosynthetic process
GO:0031324	0.57	negative regulation of cellular metabolic process
GO:2000113	0.56	negative regulation of cellular macromolecule biosynthetic process
GO:0080134	0.56	regulation of response to stress
GO:0051179	0.56	localization
GO:0044267	0.56	cellular protein metabolic process
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0002376	0.56	immune system process
GO:0044767	0.55	single-organism developmental process
GO:0006996	0.55	organelle organization
GO:0006464	0.55	cellular protein modification process
GO:2001022	0.54	positive regulation of response to DNA damage stimulus
GO:1903047	0.54	mitotic cell cycle process
GO:0070534	0.54	protein K63-linked ubiquitination
GO:0051054	0.54	positive regulation of DNA metabolic process
GO:0048515	0.54	spermatid differentiation
GO:0043044	0.54	ATP-dependent chromatin remodeling
GO:0034728	0.54	nucleosome organization
GO:0034243	0.54	regulation of transcription elongation from RNA polymerase II promoter
GO:0033522	0.54	histone H2A ubiquitination
GO:0032785	0.54	negative regulation of DNA-templated transcription, elongation
GO:0019941	0.54	modification-dependent protein catabolic process
GO:0009314	0.54	response to radiation
GO:0007281	0.54	germ cell development
GO:0006282	0.54	regulation of DNA repair
GO:0002312	0.54	B cell activation involved in immune response
GO:0002204	0.54	somatic recombination of immunoglobulin genes involved in immune response
GO:0000726	0.54	non-recombinational repair
GO:0000280	0.54	nuclear division
GO:1902578	0.51	single-organism localization

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	0.93	cell part
GO:0044424	0.88	intracellular part
GO:0043226	0.72	organelle
GO:0043229	0.70	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0044446	0.68	intracellular organelle part
GO:0032991	0.68	macromolecular complex
GO:0043234	0.66	protein complex
GO:0016020	0.65	membrane
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0005634	0.59	nucleus
GO:0044428	0.55	nuclear part
GO:0044444	0.53	cytoplasmic part
GO:0044427	0.53	chromosomal part
GO:0005667	0.50	transcription factor complex
GO:0000790	0.50	nuclear chromatin

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	0.400	1ybzA	0.770	0.99	0.029	1.000	5.4.99.5	26
2	0.175	1ecmB	0.846	0.77	0.143	1.000	4.2.1.51 5.4.99.5	26
3	0.145	1z8yN	0.732	1.11	0.057	1.000	3.4.21.90	NA
4	0.105	3brvC	0.679	1.08	0.152	0.914	2.7.11.10	NA
5	0.102	3brtA	0.693	1.09	0.121	0.943	2.7.11.10	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, 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.