D-I-TASSER P22223-D1

D-I-TASSER results for P22223-D1

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

Input Sequence in FASTA format

>P22223 (101 residues)
MGLPRGPLASLLLLQVCWLQCAASEPCRAVFREAEVTLEAGGAEQEPGQALGKVFMGCPG
QEPALFSTDNDDFTVRNGETVQERRSLKERNPLKIFPSKRI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MGLPRGPLASLLLLQVCWLQCAASEPCRAVFREAEVTLEAGGAEQEPGQALGKVFMGCPGQEPALFSTDNDDFTVRNGETVQERRSLKERNPLKIFPSKRI
Prediction	CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCSSSSSSSCCSSCCCCCCCCSSSCCCCCCCCCCSCCCCCCSSSSCCCSSSSSSCCCCCCCCSSSSSCCC
Confidence	99888725789999987553048888789876336999974600377520100101599995301004798289827964885411344888212210359
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MGLPRGPLASLLLLQVCWLQCAASEPCRAVFREAEVTLEAGGAEQEPGQALGKVFMGCPGQEPALFSTDNDDFTVRNGETVQERRSLKERNPLKIFPSKRI
Prediction	87347333110023311313235474244424544131414445154544243014514445442443644403124544143444156454342245568
	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                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCSSSSSSSCCSSCCCCCCCCSSSCCCCCCCCCCSCCCCCCSSSSCCCSSSSSSCCCCCCCCSSSSSCCC
MGLPRGPLASLLLLQVCWLQCAASEPCRAVFREAEVTLEAGGAEQEPGQALGKVFMGCPGQEPALFSTDNDDFTVRNGETVQERRSLKERNPLKIFPSKRI

4qszA

0.07

0.06

2.45

0.83

DEthreader

EALAQTNAAAEFAEAALEAVRRQEFAARNVPRVVPPCII-ALEHVVNDYENL-HPPSDRPFQAQALHCTVR-L-L--LWFHHVQQSCIAV----------K

1op4A

0.21

0.17

5.36

0.92

SPARKS-K

------------------EASGEIALCKTGFPEDVYSAVLPKDV-HEGQPLLNVFSNCNRKRKVQYESSEPDFKVDEDGTVYAVRSFPLTAEQAKFLIYAQ

5jqmC

0.03

1.75

0.76

MapAlign

--TDFASVSRAFFSIDTISRNVDQEGNLRTTRLLKKSGKLVKPFLRGITETIIEVSVVNPAMKTYTRNGIMKVEEYTTYRVKFSSIKSKVEDWSRTKF---

6mitC

0.14

4.72

0.41

CEthreader

MSKTRRWVIILLSLVALILIGVNLDPTYKSDHSDTVVYSPEGA--LNYRLIAQHVEYFSDDGISWFTQPVDRAKLTNDRMLYLYGHVEVNALTADSQLRKI

1op4A

0.21

0.17

5.36

0.79

MUSTER

------------------EASGEIALCKTGFPEDVYSAVLPKD-VHEGQPLLNVFSNCNRKRKVQYESEPADFKVDEDGTVYAVRSFPLTAEQAKFLIYKE

1op4A

0.21

0.17

5.36

2.09

HHsearch

------------------EASGEIALCKTGFPEDVYSAVLPKD-VHEGQPLLNVFSNCNRKRKVQYESEPADFKVDEDGTVYAVRSFPLTAEQAKFLIYAQ

1op4A

0.19

0.15

4.77

0.91

FFAS-3D

---------------------GEIALCKTGFPEDVYSAVLPKDVHEGQPLLNVKFSNCNRKRKVQYESSEPDFKVDEDGTVYAVRSFPLTAEQAKFLI---

6cg7A

0.08

3.14

0.70

EigenThreader

SDSDEELTGRLDREQARDRATNRINDSEPRFLHGPYIGSVAELSPTGTSVMQVMASDADSSARLVYSVLEHHFTVDPKTGVIRTAVPDLDRQERYEVVIMA

1op4A

0.22

0.16

5.01

0.87

CNFpred

--------------------------CKTGFPEDVYSAVLPKD-VHEGQPLLNVKSNCNRKRKVQYESSEADFKVDEDGTVYAVRSFPLTAEQAKFLIYAQ

6ux2A1

0.02

1.34

0.83

DEthreader

KKIQETLNELDKRRKEVLDASKLGTTLELLLPKEEWKQQ---IDHG---LEQLETWFGALVLLLLAFVVQRTRLLVRL-GGLIW-DFG----T--------

(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	0.5135

(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	3q2vA4	0.54	2.80	0.104	0.762	model1_3q2vA4.pdb.gz
2	4xhzA	0.54	2.93	0.100	0.762	model1_4xhzA.pdb.gz
3	3ppeA	0.54	2.80	0.081	0.752	model1_3ppeA.pdb.gz
4	5cyxA	0.53	3.11	0.070	0.762	model1_5cyxA.pdb.gz
5	3q2wA	0.53	2.96	0.061	0.752	model1_3q2wA.pdb.gz
6	3k5sA	0.52	3.13	0.090	0.762	model1_3k5sA.pdb.gz
7	3k5rA	0.52	3.51	0.115	0.792	model1_3k5rA.pdb.gz
8	2qviA2	0.52	3.01	0.105	0.743	model1_2qviA2.pdb.gz
9	5vh2A	0.52	3.27	0.050	0.762	model1_5vh2A.pdb.gz
10	5wj8A1	0.52	2.87	0.068	0.713	model1_5wj8A1.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:0043169	0.59	cation 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	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0044699	0.86	single-organism process
GO:0050794	0.84	regulation of cellular process
GO:0048522	0.81	positive regulation of cellular process
GO:0060255	0.80	regulation of macromolecule metabolic process
GO:0031323	0.80	regulation of cellular metabolic process
GO:0048519	0.79	negative regulation of biological process
GO:0031328	0.79	positive regulation of cellular biosynthetic process
GO:0010604	0.79	positive regulation of macromolecule metabolic process
GO:0010468	0.79	regulation of gene expression
GO:2000026	0.78	regulation of multicellular organismal development
GO:0065008	0.78	regulation of biological quality
GO:0050790	0.78	regulation of catalytic activity
GO:0048584	0.78	positive regulation of response to stimulus
GO:0044707	0.78	single-multicellular organism process
GO:0010628	0.78	positive regulation of gene expression
GO:0009966	0.78	regulation of signal transduction
GO:0007165	0.78	signal transduction
GO:1902910	0.77	positive regulation of melanosome transport
GO:0060901	0.77	regulation of hair cycle by canonical Wnt signaling pathway
GO:0051796	0.77	negative regulation of catagen
GO:0048023	0.77	positive regulation of melanin biosynthetic process
GO:0043568	0.77	positive regulation of insulin-like growth factor receptor signaling pathway
GO:0032912	0.77	negative regulation of transforming growth factor beta2 production
GO:0032773	0.77	positive regulation of monophenol monooxygenase activity
GO:0031424	0.77	keratinization
GO:0022405	0.77	hair cycle process
GO:0010838	0.77	positive regulation of keratinocyte proliferation
GO:0007155	0.77	cell adhesion
GO:0001895	0.77	retina homeostasis
GO:0009987	0.72	cellular process
GO:0044763	0.67	single-organism cellular process
GO:0016043	0.62	cellular component organization
GO:0034330	0.59	cell junction organization
GO:0034332	0.54	adherens junction organization

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:0005886	1.00	plasma membrane
GO:0044424	0.58	intracellular 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	2dlhA	0.464	3.13	0.071	0.713	3.1.3.48	47
2	0.060	1bliA	0.433	4.13	0.025	0.762	3.2.1.1	NA
3	0.060	2wyhA	0.458	3.79	0.051	0.762	3.2.1.24	NA
4	0.060	3bc9A	0.488	3.72	0.061	0.792	3.2.1.1	NA
5	0.060	1c7sA	0.452	3.67	0.112	0.752	3.2.1.52	64

	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	2omy1	0.483	3.41	0.081	0.733	0.53	III	complex1.pdb.gz	32,33,34,36,49,53,55,58,72,80,84,85
2	0.01	1ncg0	0.465	3.19	0.086	0.693	0.69	III	complex2.pdb.gz	3,4,52,53,54,55,56,57,65,100,101
3	0.01	1uxaB	0.479	4.35	0.077	0.871	0.44	UUU	complex3.pdb.gz	49,81,83

	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.