D-I-TASSER P02749-D5

D-I-TASSER results for P02749-D5

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

Input Sequence in FASTA format

>P02749 (82 residues)
CKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVP
KCFKEHSSLAFWKTDASDVKPC

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| CKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC
Prediction	CCCCCSSSSSSSCCSSSSSCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCSSSCCCSCCCCCSCCCCSSSSSSCCHHHCCCC
Confidence	9556426799996889732013678731152899997586556688766346357232850133676268872482118899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| CKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC
Prediction	6736264130214354241563375314344302000335764252436441453615235015545314224443563658
	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

CCCCCSSSSSSSCCSSSSSCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCSSSCCCSCCCCCSCCCCSSSSSSCCHHHCCCC
CKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.68

0.60

17.01

1.00

DEthreader

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKN-KEKCSYTEDAQCIGTIEVPK--C--FK---E--HSSFWKTDV

1c1zA3

0.99

27.67

5.13

SPARKS-K

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA

0.99

27.67

0.87

MapAlign

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.99

27.67

0.85

CEthreader

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.99

27.67

3.14

MUSTER

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.99

27.67

5.17

HHsearch

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.99

27.67

1.60

FFAS-3D

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA3

0.99

27.67

0.75

EigenThreader

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1g4fA

0.99

27.67

2.88

CNFpred

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

1c1zA

0.68

0.60

17.01

1.00

DEthreader

CKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKN-KEKCSYTEDAQCIGTIEVPK--C--FK---E--HSSFWKTDV

(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	0.7493

(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	1c1zA	0.99	0.35	0.988	1.000	model1_1c1zA.pdb.gz
2	3gavA	0.51	3.61	0.120	0.780	model1_3gavA.pdb.gz
3	4pphA1	0.50	3.81	0.066	0.829	model1_4pphA1.pdb.gz
4	3aupA1	0.48	4.11	0.115	0.890	model1_3aupA1.pdb.gz
5	3vlaA	0.48	4.02	0.091	0.878	model1_3vlaA.pdb.gz
6	1ojyC1	0.43	3.33	0.094	0.622	model1_1ojyC1.pdb.gz
7	1ntjA1	0.43	3.00	0.132	0.622	model1_1ntjA1.pdb.gz
8	1gpzA1	0.42	3.41	0.175	0.646	model1_1gpzA1.pdb.gz
9	1ghqC2	0.41	3.49	0.211	0.585	model1_1ghqC2.pdb.gz
10	1m11R2	0.41	3.50	0.078	0.622	model1_1m11R2.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:0008289	1.00	lipid binding
GO:0097367	0.71	carbohydrate derivative binding
GO:0030234	0.70	enzyme regulator activity
GO:0042802	0.69	identical protein binding
GO:0060230	0.68	lipoprotein lipase activator activity
GO:0005543	0.68	phospholipid binding
GO:0001948	0.68	glycoprotein 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:0050896	1.00	response to stimulus
GO:0050878	1.00	regulation of body fluid levels
GO:0050794	1.00	regulation of cellular process
GO:0048519	1.00	negative regulation of biological process
GO:0048518	1.00	positive regulation of biological process
GO:0044699	1.00	single-organism process
GO:0009987	0.77	cellular process
GO:0008152	0.76	metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044763	0.73	single-organism cellular process
GO:0051239	0.72	regulation of multicellular organismal process
GO:0044710	0.72	single-organism metabolic process
GO:0044238	0.72	primary metabolic process
GO:0006810	0.72	transport
GO:0071702	0.71	organic substance transport
GO:0048583	0.71	regulation of response to stimulus
GO:0044765	0.71	single-organism transport
GO:0044237	0.71	cellular metabolic process
GO:0043170	0.71	macromolecule metabolic process
GO:0080134	0.70	regulation of response to stress
GO:0051241	0.70	negative regulation of multicellular organismal process
GO:0051240	0.70	positive regulation of multicellular organismal process
GO:0048523	0.70	negative regulation of cellular process
GO:0034197	0.70	triglyceride transport
GO:2000026	0.69	regulation of multicellular organismal development
GO:0051336	0.69	regulation of hydrolase activity
GO:0051093	0.69	negative regulation of developmental process
GO:0048584	0.69	positive regulation of response to stimulus
GO:0030195	0.69	negative regulation of blood coagulation
GO:0019538	0.69	protein metabolic process
GO:0006629	0.69	lipid metabolic process
GO:0051918	0.68	negative regulation of fibrinolysis
GO:0051006	0.68	positive regulation of lipoprotein lipase activity
GO:0034392	0.68	negative regulation of smooth muscle cell apoptotic process
GO:0033033	0.68	negative regulation of myeloid cell apoptotic process
GO:0031639	0.68	plasminogen activation
GO:0016525	0.68	negative regulation of angiogenesis
GO:0010596	0.68	negative regulation of endothelial cell migration
GO:0007597	0.68	blood coagulation, intrinsic pathway
GO:0006641	0.68	triglyceride metabolic process
GO:0001937	0.68	negative regulation of endothelial cell proliferation

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:0009986	1.00	cell surface
GO:0005615	1.00	extracellular space
GO:0044424	0.79	intracellular part
GO:0043227	0.73	membrane-bounded organelle
GO:0032991	0.71	macromolecular complex
GO:0070062	0.69	extracellular exosome
GO:0034358	0.69	plasma lipoprotein particle
GO:0031012	0.69	extracellular matrix
GO:0042627	0.68	chylomicron
GO:0034364	0.68	high-density lipoprotein particle
GO:0034361	0.68	very-low-density lipoprotein particle
GO:0005576	0.55	extracellular region
GO:0044444	0.51	cytoplasmic 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	0.060	2qk5A	0.467	3.91	0.063	0.744	3.4.23.46	NA
2	0.060	3en1A	0.436	3.61	0.062	0.720	1.14.12.11	29
3	0.060	1jawA	0.443	4.06	0.067	0.732	3.4.11.9	NA
4	0.060	2ofpB	0.442	4.14	0.037	0.793	1.1.1.169	22
5	0.060	1dq3A	0.483	3.80	0.080	0.817	1.17.4.1	61

	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	0.01	2q11A	0.466	4.12	0.064	0.756	0.14	XX4	complex1.pdb.gz	10,12,14
2	0.01	3l5dB	0.463	3.52	0.065	0.707	0.13	BDV	complex2.pdb.gz	13,34,35
3	0.01	3hvgA	0.413	4.18	0.095	0.768	0.13	EV0	complex3.pdb.gz	14,28,30,57
4	0.01	3nshA	0.458	3.68	0.064	0.720	0.11	957	complex4.pdb.gz	10,11,55
5	0.01	2ohrA	0.461	3.79	0.064	0.732	0.13	8IP	complex5.pdb.gz	19,24,28
6	0.01	3buhA	0.461	4.01	0.051	0.744	0.21	AED	complex6.pdb.gz	13,23,28,35
7	0.01	2q11C	0.463	3.87	0.064	0.732	0.16	XX4	complex7.pdb.gz	4,6,14,15
8	0.01	2zjjA	0.464	3.98	0.064	0.744	0.12	F1J	complex8.pdb.gz	12,13,27
9	0.01	3l59A	0.462	3.52	0.064	0.707	0.12	BDJ	complex9.pdb.gz	30,33,35
10	0.01	2jlsA	0.484	4.43	0.024	0.939	0.15	ADP	complex10.pdb.gz	12,13,14

	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.