D-I-TASSER P40189-D4

D-I-TASSER results for P40189-D4

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

Input Sequence in FASTA format

>P40189 (95 residues)
DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVN
ATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA
Prediction	CCCCCCCCSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSSCCCCSSSSSSCCCSSSSSSCCCCSSSSSSSSSCCCCCCCSSSSCCC
Confidence	99999997348802154799727999974699654773088799999938974177973798799994797489999999378628985884689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA
Prediction	86357424102414465476433020103415646241402413031444755444242544414140476312000102034443442514258
	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

CCCCCCCCSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSSCCCCSSSSSSCCCSSSSSSCCCCSSSSSSSSSCCCCCCCSSSSCCC
DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5iA1

1.00

28.00

1.50

DEthreader

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5iA1

1.00

28.00

1.72

SPARKS-K

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

1uenA

0.18

0.17

5.49

0.39

MapAlign

DLPMVAPGVRVNVVN-----STLAEVHWDPVPLKSIRGHLQGYRIYYWKTHIEKKILTFQGTHGMLPLPFSHYTLNVRVVNGKGEGPASDRVFNT

3l5hA

1.00

28.00

0.34

CEthreader

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5hA2

1.00

28.00

1.78

MUSTER

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5hA2

1.00

28.00

0.99

HHsearch

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5iA1

1.00

28.00

1.84

FFAS-3D

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5hA2

1.00

28.00

0.52

EigenThreader

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5iA

1.00

28.00

1.64

CNFpred

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

3l5iA

1.00

28.00

1.50

DEthreader

DRPSKAPSFWYKIDPSHTQGYRTVQLVWKTLPPFEANGKILDYEVTLTRWKSHLQNYTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPA

(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	0.8583

(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	3l5iA	0.99	0.42	1.000	1.000	model1_3l5iA.pdb.gz
2	3l5hA2	0.95	0.94	1.000	1.000	model1_3l5hA2.pdb.gz
3	3f7pE	0.83	1.38	0.264	0.916	model1_3f7pE.pdb.gz
4	2ed9A	0.82	1.52	0.167	0.947	model1_2ed9A.pdb.gz
5	5oj2A	0.82	1.72	0.209	0.958	model1_5oj2A.pdb.gz
6	6xfiA2	0.81	1.83	0.143	0.958	model1_6xfiA2.pdb.gz
7	2yrzA	0.81	1.45	0.138	0.916	model1_2yrzA.pdb.gz
8	4hljA	0.81	1.62	0.191	0.937	model1_4hljA.pdb.gz
9	1x5hA	0.81	1.63	0.189	0.947	model1_1x5hA.pdb.gz
10	2dlhA	0.81	1.83	0.227	0.926	model1_2dlhA.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:0004871	0.71	signal transducer activity
GO:0004872	0.70	receptor activity
GO:0004888	0.69	transmembrane signaling receptor activity
GO:0004896	0.68	cytokine receptor activity
GO:0005102	0.64	receptor binding
GO:0019838	0.61	growth factor binding
GO:0004924	0.60	oncostatin-M receptor activity
GO:0005126	0.57	cytokine receptor binding
GO:0004923	0.53	leukemia inhibitory factor 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:0050794	1.00	regulation of cellular process
GO:0048522	0.95	positive regulation of cellular process
GO:0050896	0.88	response to stimulus
GO:0042221	0.86	response to chemical
GO:0007165	0.83	signal transduction
GO:0007166	0.82	cell surface receptor signaling pathway
GO:0019221	0.81	cytokine-mediated signaling pathway
GO:0010033	0.72	response to organic substance
GO:0034097	0.65	response to cytokine
GO:0008284	0.65	positive regulation of cell proliferation
GO:0038165	0.64	oncostatin-M-mediated signaling pathway
GO:0048583	0.63	regulation of response to stimulus
GO:0048584	0.61	positive regulation of response to stimulus
GO:0051239	0.56	regulation of multicellular organismal process
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0023051	0.55	regulation of signaling
GO:0010646	0.55	regulation of cell communication
GO:0045595	0.53	regulation of cell differentiation
GO:0009987	0.53	cellular process
GO:0070102	0.52	interleukin-6-mediated signaling pathway
GO:0045597	0.52	positive regulation of cell differentiation
GO:0070120	0.50	ciliary neurotrophic factor-mediated signaling pathway
GO:0048861	0.50	leukemia inhibitory factor signaling pathway

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	0.96	cell part
GO:0044459	0.92	plasma membrane part
GO:0032991	0.83	macromolecular complex
GO:0043235	0.82	receptor complex
GO:0016020	0.75	membrane
GO:0043226	0.69	organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0044421	0.67	extracellular region part
GO:0098802	0.66	plasma membrane receptor complex
GO:0005900	0.65	oncostatin-M receptor complex
GO:0070062	0.63	extracellular exosome

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	0.107	2dleA	0.703	2.56	0.115	0.895	3.1.3.48	NA
2	0.103	2dlhA	0.807	1.83	0.227	0.926	3.1.3.48	33,35,40
3	0.067	2amuA	0.715	2.66	0.124	0.905	1.15.1.2	NA
4	0.067	1u2hA	0.571	3.32	0.062	0.853	2.7.11.1	NA
5	0.067	2bk8A	0.593	2.90	0.123	0.853	2.7.11.1	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.03	1tdq0	0.752	1.74	0.179	0.884	0.14	III	complex1.pdb.gz	42,55,58,59,60
2	0.03	1bp31	0.776	2.08	0.156	0.947	0.15	III	complex2.pdb.gz	6,32,33,34,36,37,38,82,83
3	0.03	1y6m1	0.727	2.08	0.174	0.905	0.11	III	complex3.pdb.gz	33,77,78,79,84,85
4	0.03	2b5i5	0.719	2.36	0.148	0.926	0.17	III	complex4.pdb.gz	38,39,62
5	0.03	1pvh0	0.712	2.53	0.146	0.937	0.28	III	complex5.pdb.gz	77,78,80,85,87
6	0.03	2qbwA	0.725	2.41	0.153	0.895	0.15	III	complex6.pdb.gz	37,38,39,40,43,44
7	0.02	2amu0	0.715	2.66	0.124	0.905	0.15	III	complex7.pdb.gz	76,77,78,79,81,83
8	0.01	2vdqA	0.383	5.04	0.032	0.747	0.25	III	complex8.pdb.gz	40,42,43
9	0.01	3mbw0	0.517	3.39	0.081	0.800	0.19	III	complex9.pdb.gz	39,40,41,81

	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.