D-I-TASSER Q00653-D2

D-I-TASSER results for Q00653-D2

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

Input Sequence in FASTA format

>Q00653 (95 residues)
DKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPP
YHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| DKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPL
Prediction	CCCCCSCCCCCSSSSSSCCCCCCCCSSSSSSCCCCCCSSSSSSCHHHCCCCCSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCSCCCSCSSSSCC
Confidence	98220448993899993453679839999966999818988819887245506999769988987799769999999889996027613599619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| DKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPL
Prediction	85441405434201000440457403020125677315341504564125420000201524366145404030203135665435436043447
	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                  80

                   |                   |                   |                   |

SS
Seq

CCCCCSCCCCCSSSSSSCCCCCCCCSSSSSSCCCCCCSSSSSSCHHHCCCCCSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCSCCCSCSSSSCC
DKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPL

2o61B

0.60

17.20

1.33

DEthreader

MRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEEGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B2

0.62

17.77

2.47

SPARKS-K

DRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B2

0.60

0.59

16.91

0.74

MapAlign

-RTAGCVTGGEEIYLLCDKVQKDDIQIRFYEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B2

0.62

17.77

0.66

CEthreader

DRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B2

0.62

17.77

2.44

MUSTER

DRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B

0.62

17.77

3.07

HHsearch

DRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

2o61B2

0.61

0.60

17.19

1.86

FFAS-3D

DRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYP-

2o61B2

0.59

16.92

0.67

EigenThreader

IRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

1a3qA

1.00

0.99

27.71

1.87

CNFpred

DKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYP-

2o61B2

0.60

17.20

1.33

DEthreader

MRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEEGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPE

(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	0.8441

(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	2o61B2	0.95	0.90	0.611	1.000	model1_2o61B2.pdb.gz
2	2o61A	0.93	0.72	0.522	0.968	model1_2o61A.pdb.gz
3	1gjiA2	0.92	0.81	0.571	0.958	model1_1gjiA2.pdb.gz
4	3do7A	0.91	1.02	0.511	0.968	model1_3do7A.pdb.gz
5	1imhC2	0.85	1.86	0.297	0.958	model1_1imhC2.pdb.gz
6	1bvoA	0.60	3.52	0.075	0.926	model1_1bvoA.pdb.gz
7	4bn2A	0.49	4.43	0.057	0.863	model1_4bn2A.pdb.gz
8	4k4kA1	0.48	3.57	0.082	0.810	model1_4k4kA1.pdb.gz
9	1zkaA	0.45	1.76	0.232	0.484	model1_1zkaA.pdb.gz
10	4asmB	0.42	4.82	0.045	0.905	model1_4asmB.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:0003700	0.97	transcription factor activity, sequence-specific DNA binding
GO:0003676	0.96	nucleic acid binding
GO:0003677	0.95	DNA binding
GO:0000975	0.94	regulatory region DNA binding
GO:0000981	0.92	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0044212	0.89	transcription regulatory region DNA binding
GO:0000977	0.88	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003682	0.87	chromatin 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	0.99	regulation of cellular process
GO:0048518	0.99	positive regulation of biological process
GO:0048522	0.98	positive regulation of cellular process
GO:0048523	0.96	negative regulation of cellular process
GO:0010628	0.94	positive regulation of gene expression
GO:0006357	0.94	regulation of transcription from RNA polymerase II promoter
GO:0045893	0.93	positive regulation of transcription, DNA-templated
GO:0000122	0.91	negative regulation of transcription from RNA polymerase II promoter
GO:0050896	0.90	response to stimulus
GO:0006950	0.89	response to stress
GO:0045944	0.88	positive regulation of transcription from RNA polymerase II promoter
GO:0010033	0.88	response to organic substance
GO:0007165	0.88	signal transduction
GO:0035556	0.87	intracellular signal transduction
GO:0034097	0.87	response to cytokine
GO:0006952	0.87	defense response
GO:0002376	0.87	immune system process
GO:0006955	0.86	immune response
GO:0045087	0.85	innate immune response
GO:0038061	0.85	NIK/NF-kappaB signaling
GO:0006954	0.85	inflammatory response
GO:0007249	0.84	I-kappaB kinase/NF-kappaB signaling

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:0044424	1.00	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0032991	0.90	macromolecular complex
GO:0043234	0.89	protein complex
GO:0005829	0.89	cytosol
GO:0033256	0.88	I-kappaB/NF-kappaB 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	0.067	2b3rB	0.615	3.07	0.102	0.926	2.7.1.154	76
2	0.067	2djmA	0.563	3.04	0.072	0.874	3.2.1.3	14
3	0.067	1k85A	0.574	2.63	0.079	0.800	3.2.1.14	3,71
4	0.066	2j73A	0.545	3.50	0.073	0.863	3.2.1.41	54
5	0.066	2dlhA	0.555	2.94	0.138	0.842	3.1.3.48	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	0.17	1bfs0	0.948	0.95	0.611	1.000	1.19	III	complex1.pdb.gz	1,12,14,16,17,47,49,53,55
2	0.09	1gjiB	0.919	0.82	0.571	0.958	0.53	QNA	complex2.pdb.gz	28,72,74
3	0.09	3gutE	0.933	0.75	0.522	0.968	0.59	QNA	complex3.pdb.gz	4,5,10,11,12
4	0.09	1le9A	0.932	0.76	0.522	0.968	0.55	QNA	complex4.pdb.gz	11,13,41
5	0.09	3do7A	0.906	1.02	0.511	0.968	0.63	QNA	complex5.pdb.gz	5,8,10,12

	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.