D-I-TASSER P54762-D4

D-I-TASSER results for P54762-D4

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

Input Sequence in FASTA format

>P54762 (58 residues)
RNVISIVNETSIILEWHPPRETGGRDDVTYNIICKKCRADRRSCSRCDDNVEFVPRQL

Predicted Secondary Structure

Sequence	20 40 \| \| RNVISIVNETSIILEWHPPRETGGRDDVTYNIICKKCRADRRSCSRCDDNVEFVPRQL
Prediction	CCSSSSSCCCSSSSSSCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSCCCCCSSCCCCC
Confidence	9707985086899997698878998526999997404899953262699847823579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| RNVISIVNETSIILEWHPPRETGGRDDVTYNIICKKCRADRRSCSRCDDNVEFVPRQL
Prediction	8534442453304030431475443641302020441557754154137604243568
	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

                   |                   |

SS
Seq

CCSSSSSCCCSSSSSSCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSCCCCCSSCCCCC
RNVISIVNETSIILEWHPPRETGGRDDVTYNIICKKCRADRRSCSRCDDNVEFVPRQL

3fl7A

0.23

0.22

7.03

1.27

SPARKS-K

HYLTAVGMGAKVELRWTPPQDSGGREDIVYSVTCEQCWPSGEC-GPCEASVRYSEPPH

3fl7A2

0.25

0.24

7.50

1.02

MUSTER

HYLTAVGMGAKVELRWTPPQDSGGREDIVYSVTCEQCWPSG-ECGPCEASVRYSEPPH

7k7jA

0.40

11.71

2.33

HHsearch

QELWFEVQGSALMLHWRLPRELGGRGDLLFNVVCKECEGRGGTCHRCRDEVHFDPRQR

4bk4A

0.50

14.50

1.15

CNFpred

LNLISNVNETSVNLEWSSPQNTGGRQDISYNVVCKKCGAGPSKCRPCGSGVHYTPQQN

3fbqA2

0.06

0.05

2.26

1.00

DEthreader

IKANMEKVAFILYYNQEVSARKEWD-SVDVELTVKDDL-----GNDYS--GEGNGGRW

7k7jA

0.40

11.71

1.15

SPARKS-K

QELWFEVQGSALMLHWRLPRELGGRGDLLFNVVCKECEGRQGTCHRCRDEVHFDPRQR

3tspA

0.05

2.36

0.47

MapAlign

ALTIGMGENGALWGGECLRVNYRECEHLGLPAVALPGAAKQPWRNAAP--LASSCGRL

2coyA

0.10

3.79

0.48

CEthreader

VGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDGTVQGRKYFTCDEGHGIFVRQSQ

2jllA4

0.17

5.66

0.99

MUSTER

GVKIIELSQTTAKVSFNKPDSHGGVPIHHYQVDVKEVASEIWKIVRSGVQTMVVLNNL

3fl7A

0.25

0.24

7.50

2.01

HHsearch

HYLTAVGMGAKVELRWTPPQDSGGREDIVYSVTCEQCWP-SGECGPCEASVRYSEPPH

(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	0.5632

(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	7k7jA2	0.63	2.92	0.310	1.000	model1_7k7jA2.pdb.gz
2	3fl7A	0.62	2.83	0.193	0.983	model1_3fl7A.pdb.gz
3	5mrc12	0.57	3.08	0.093	0.914	model1_5mrc12.pdb.gz
4	5t98A	0.57	2.90	0.060	0.862	model1_5t98A.pdb.gz
5	1vw41	0.56	3.10	0.093	0.914	model1_1vw41.pdb.gz
6	2yuxA	0.55	3.21	0.212	0.879	model1_2yuxA.pdb.gz
7	4bk4A	0.55	3.20	0.466	0.983	model1_4bk4A.pdb.gz
8	1cn4B2	0.54	3.00	0.154	0.862	model1_1cn4B2.pdb.gz
9	1x5kA	0.50	3.35	0.196	0.845	model1_1x5kA.pdb.gz
10	1x5iA	0.49	3.12	0.163	0.793	model1_1x5iA.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	0.95	catalytic activity
GO:0016301	0.94	kinase activity
GO:0004672	0.92	protein kinase activity
GO:0004872	0.71	receptor activity
GO:0004871	0.71	signal transducer activity
GO:0004714	0.70	transmembrane receptor protein tyrosine kinase activity
GO:0005003	0.68	ephrin receptor 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:0065007	0.98	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0009987	0.92	cellular process
GO:0050794	0.88	regulation of cellular process
GO:0044699	0.77	single-organism process
GO:0008152	0.76	metabolic process
GO:0048518	0.75	positive regulation of biological process
GO:0044237	0.75	cellular metabolic process
GO:0071704	0.72	organic substance metabolic process
GO:0044238	0.72	primary metabolic process
GO:0007165	0.71	signal transduction
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0006796	0.69	phosphate-containing compound metabolic process
GO:0016310	0.68	phosphorylation
GO:0007166	0.68	cell surface receptor signaling pathway
GO:0044763	0.67	single-organism cellular process
GO:0007167	0.67	enzyme linked receptor protein signaling pathway
GO:0048013	0.66	ephrin receptor signaling pathway
GO:0032502	0.65	developmental process
GO:0019538	0.65	protein metabolic process
GO:0051128	0.64	regulation of cellular component organization
GO:0006464	0.64	cellular protein modification process
GO:0044767	0.63	single-organism developmental process
GO:0006468	0.63	protein phosphorylation
GO:0048522	0.57	positive regulation of cellular process
GO:0006928	0.57	movement of cell or subcellular component
GO:0051239	0.53	regulation of multicellular organismal process
GO:2000026	0.52	regulation of multicellular organismal development
GO:0065009	0.52	regulation of molecular function
GO:0050790	0.51	regulation of catalytic activity
GO:0048856	0.51	anatomical structure development
GO:0009653	0.51	anatomical structure morphogenesis
GO:0044087	0.50	regulation of cellular component biogenesis

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	1.00	cell part
GO:0044424	0.87	intracellular part
GO:0044425	0.74	membrane part
GO:0044459	0.71	plasma membrane part
GO:0031224	0.70	intrinsic component of membrane
GO:0016021	0.69	integral component of membrane
GO:0005887	0.67	integral component of plasma membrane
GO:0016020	0.66	membrane
GO:0044444	0.60	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	2gg1A	0.462	3.35	0.020	0.845	2.7.7.48 3.4.21.91	NA
2	0.060	2obvA	0.481	2.99	0.058	0.741	2.5.1.6	NA
3	0.060	2v5yA	0.534	3.09	0.161	0.828	3.1.3.48	22
4	0.060	1gxsA	0.477	3.09	0.102	0.845	4.1.2.11	NA
5	0.060	2dlhA	0.514	3.38	0.157	0.862	3.1.3.48	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:

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	1vh50	0.538	3.23	0.017	1.000	0.10	III	complex1.pdb.gz	16,17,18,29,30,31,32

	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.