D-I-TASSER O95405-D5

D-I-TASSER results for O95405-D5

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

Input Sequence in FASTA format

>O95405 (73 residues)
NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGI
LPNGEVADAAKLT

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLT
Prediction	CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCSSCCCSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCC
Confidence	9988312104698356654148899999711144122205798876776665278624777797313444579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLT
Prediction	8674446314434434434557546434332333222144474755457553301003333343423644748
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCSSCCCSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCC
NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLT

1devB

1.00

0.51

14.19

1.28

SPARKS-K

NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGV------------------------------------

1devB

1.00

0.51

14.19

1.10

CNFpred

NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGV------------------------------------

1devB

1.00

0.51

14.19

1.39

MUSTER

NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGV------------------------------------

1devB

1.00

0.51

14.19

2.36

HHsearch

NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGV------------------------------------

2f27B1

0.05

2.48

0.62

CEthreader

HPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGAYSDLQSMGTGPDGSPLFGCLYEANEIVFLMFTLKQAFP

7a6hG

0.10

3.58

0.53

EigenThreader

NKNVGLCICLFDITKLEDAYGASHTKVHFRCVVFHLIPDEAEQVWMDTGEEIRFRVLVGSISEPGLGL-LSWW

1devB

1.00

0.51

14.19

0.67

FFAS-3D

NPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGV------------------------------------

2ra1A2

0.13

0.12

4.29

0.79

SPARKS-K

NFNKPED--SAVDLTKYVDAAGNVIKSGFELEFTSSEKLTQGKFINTTGKK-SVIVNATVKTNVTTGNVILAV

3fhqA

0.24

0.07

2.14

0.74

CNFpred

----------------------------------------------------HIMWYDSMIDTGAIAWQNHLT

4xfkA

0.03

1.64

0.83

DEthreader

AS-T-GYGSAITDVRKYNL-RNKGKEVLYLNLGEPTPFNPSMAAEDKVTG-P-EPAA--FGLQLFSVKTMGFP

(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	0.4733

(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	6nbqD	0.46	3.76	0.015	0.822	model1_6nbqD.pdb.gz
2	4gbyA1	0.46	4.66	0.056	0.959	model1_4gbyA1.pdb.gz
3	2yxzA	0.46	4.52	0.127	0.945	model1_2yxzA.pdb.gz
4	1wp9A2	0.46	4.04	0.088	0.890	model1_1wp9A2.pdb.gz
5	4ol8A	0.45	4.11	0.062	0.849	model1_4ol8A.pdb.gz
6	4ybqA	0.44	3.93	0.104	0.863	model1_4ybqA.pdb.gz
7	2btuA	0.41	4.35	0.132	0.877	model1_2btuA.pdb.gz
8	4pypA	0.41	4.21	0.016	0.877	model1_4pypA.pdb.gz
9	4ldsA	0.41	4.30	0.104	0.877	model1_4ldsA.pdb.gz
10	5c65A	0.41	4.59	0.125	0.877	model1_5c65A.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:0005545	0.81	1-phosphatidylinositol 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:0009987	0.96	cellular process
GO:0044699	0.89	single-organism process
GO:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0006810	0.72	transport
GO:0006886	0.71	intracellular protein transport
GO:0072594	0.70	establishment of protein localization to organelle
GO:0033365	0.70	protein localization to organelle
GO:0007165	0.65	signal transduction
GO:0016043	0.64	cellular component organization
GO:0007178	0.64	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0048583	0.56	regulation of response to stimulus
GO:0007179	0.56	transforming growth factor beta receptor signaling pathway
GO:0044765	0.55	single-organism transport
GO:0009966	0.55	regulation of signal transduction
GO:0007184	0.54	SMAD protein import into nucleus
GO:0007183	0.54	SMAD protein complex assembly

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:0044444	1.00	cytoplasmic part
GO:0043229	0.75	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005768	0.68	endosome
GO:0016020	0.63	membrane
GO:0044422	0.61	organelle part
GO:0044446	0.60	intracellular organelle part
GO:0031090	0.57	organelle membrane
GO:0005769	0.57	early endosome
GO:0098805	0.56	whole membrane
GO:0098588	0.56	bounding membrane of organelle
GO:0010008	0.55	endosome membrane
GO:0031901	0.54	early endosome membrane

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	3kgxB	0.417	4.50	0.056	0.890	2.6.1.51 2.6.1.44	NA
2	0.060	1iruH	0.406	3.96	0.030	0.836	3.4.25.1	39
3	0.060	2h6jH	0.435	4.09	0.074	0.877	3.4.25.1	NA
4	0.060	1ug9A	0.413	3.90	0.045	0.726	3.2.1.70	NA
5	0.060	1rypV	0.426	3.68	0.030	0.808	3.4.25.1	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	1tyqA	0.420	4.09	0.074	0.836	0.13	ATP	complex1.pdb.gz	36,38,57,59,60
2	0.01	2j8u3	0.344	3.81	0.051	0.630	0.19	III	complex2.pdb.gz	8,9,60
3	0.01	2zcyN	0.430	3.93	0.029	0.836	0.26	SRG	complex3.pdb.gz	39,40,41,57,60,61
4	0.01	1eccA	0.316	4.90	0.059	0.685	0.34	ONL	complex4.pdb.gz	9,36,59
5	0.01	1ecgA	0.358	4.51	0.015	0.822	0.25	PIN	complex5.pdb.gz	7,62,63,64
6	0.01	2o8eA	0.365	4.33	0.016	0.794	0.24	ADP	complex6.pdb.gz	12,13,59,60,61
7	0.01	2o8cA	0.370	4.25	0.033	0.781	0.20	ADP	complex7.pdb.gz	35,65,66
8	0.01	3rkoN	0.445	3.93	0.031	0.849	0.35	LFA	complex8.pdb.gz	59,60,61,64
9	0.01	2r26C	0.424	3.69	0.047	0.726	0.21	CMC	complex9.pdb.gz	39,40,60,61,63,64
10	0.01	2p9nA	0.418	4.04	0.060	0.822	0.11	ADP	complex10.pdb.gz	36,37,64,65

	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.