D-I-TASSER O75312-D3

D-I-TASSER results for O75312-D3

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

Input Sequence in FASTA format

>O75312 (156 residues)
VEPLGTRITLHITDASDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRE
LVTKNPFTLGDSSNPGQTERLQEFSQKMDQIIEGNMKAHFIMDDPAGNSYLQNVYAPEDD
PEMKVERYKRTFDQNEELGLNDMKTEGYEAGLAPQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VEPLGTRITLHITDASDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPGQTERLQEFSQKMDQIIEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEELGLNDMKTEGYEAGLAPQR
Prediction	CCCCCSSSSSSSCCHHHCCCSSSSCCCCSSSSSSSSSSSCCCCCCCSSSSHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSCCCHHHHHHHCCCCCCCCCCCCCCCCCC
Confidence	999877999997896654304786398559852132574688654277629999999999998563112456899999999999999999993999769999769999665588998889983799933898899986976466556545556789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VEPLGTRITLHITDASDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPGQTERLQEFSQKMDQIIEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEELGLNDMKTEGYEAGLAPQR
Prediction	867533302030535720312023065030403205142542343032220330043025205733343443447722630450153055026364501000102433231354644652650434406135523561415415265276645678
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSSSSCCHHHCCCSSSSCCCCSSSSSSSSSSSCCCCCCCSSSSHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSCCCHHHHHHHCCCCCCCCCCCCCCCCCC
VEPLGTRITLHITDASDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPGQTERLQEFSQKMDQIIEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEELGLNDMKTEGYEAGLAPQR

2qkdA

0.31

0.28

8.32

1.33

DEthreader

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFQKG-ALTTVEGLISRAISGLEQDQTRRAVEG-A-IAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

2qkdA4

0.31

0.28

8.33

3.97

SPARKS-K

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQ-DQPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

2qkdA4

0.32

0.28

8.51

1.55

MapAlign

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTRR-AVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

2qkdA

0.28

8.61

1.75

CEthreader

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTR-RAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGLEEDLRNEVLQFNTNCP

2qkdA4

0.32

0.28

8.51

3.22

MUSTER

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTR-RAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

2qkdA

0.29

0.28

8.60

5.10

HHsearch

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEDQPTRR--AVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGLEEDLRNELQFNTNCPE

2qkdA4

0.31

0.28

8.33

2.39

FFAS-3D

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQD-QPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

2qkdA

0.29

0.28

8.60

1.60

EigenThreader

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTEGLISRAISGLEQ--DQPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGLEEDLRNECPECNAPAQ

2qkdA

0.94

0.83

23.21

2.03

CNFpred

VEPLGTRITLHITDPSDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPDQSEKLQEFSQKLGQIIEGKMKAHFIMNDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEE-------------------

2qkdA4

0.31

0.28

8.32

1.33

DEthreader

IQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFQKG-ALTTVEGLISRAISGLEQDQTRRAVEG-A-IAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------------

(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	0.8244

(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	2qkdA4	0.84	1.41	0.317	0.891	model1_2qkdA4.pdb.gz
2	3poyA	0.48	4.69	0.070	0.788	model1_3poyA.pdb.gz
3	2wjsA	0.47	4.51	0.045	0.756	model1_2wjsA.pdb.gz
4	2jd4A	0.46	4.59	0.054	0.744	model1_2jd4A.pdb.gz
5	3hfwA	0.46	4.71	0.056	0.718	model1_3hfwA.pdb.gz
6	3asiA3	0.44	4.13	0.132	0.641	model1_3asiA3.pdb.gz
7	1h30A2	0.43	4.63	0.057	0.705	model1_1h30A2.pdb.gz
8	1kdkA	0.42	4.04	0.029	0.647	model1_1kdkA.pdb.gz
9	2r16A	0.41	4.35	0.075	0.635	model1_2r16A.pdb.gz
10	1dykA1	0.40	4.49	0.074	0.635	model1_1dykA1.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:0031369	0.85	translation initiation factor 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:0044699	1.00	single-organism process
GO:0065007	0.96	biological regulation
GO:0009987	0.96	cellular process
GO:0050789	0.92	regulation of biological process
GO:0044763	0.92	single-organism cellular process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0048518	0.86	positive regulation of biological process
GO:0032879	0.85	regulation of localization
GO:0010628	0.85	positive regulation of gene expression
GO:0006996	0.85	organelle organization
GO:0061564	0.84	axon development
GO:0042307	0.84	positive regulation of protein import into nucleus
GO:0030576	0.84	Cajal body organization
GO:0008283	0.84	cell proliferation
GO:0008152	0.67	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0044238	0.64	primary metabolic process
GO:0050794	0.62	regulation of cellular process
GO:0044260	0.62	cellular macromolecule metabolic process
GO:0006807	0.62	nitrogen compound metabolic process
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0032502	0.60	developmental process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:0016070	0.59	RNA metabolic process
GO:0050896	0.57	response to stimulus
GO:0051716	0.55	cellular response to stimulus
GO:0010033	0.55	response to organic substance
GO:0048856	0.54	anatomical structure development
GO:1901576	0.53	organic substance biosynthetic process
GO:0044249	0.53	cellular biosynthetic process
GO:0080090	0.52	regulation of primary metabolic process
GO:0034645	0.52	cellular macromolecule biosynthetic process
GO:0031323	0.52	regulation of cellular metabolic process
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0048523	0.50	negative regulation of cellular process
GO:0045935	0.50	positive regulation of nucleobase-containing compound metabolic process

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:0044424	1.00	intracellular part
GO:0005737	0.99	cytoplasm
GO:0043229	0.94	intracellular organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0005634	0.92	nucleus

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	3f41A	0.421	5.59	0.090	0.776	3.1.3.8	44,106
2	0.060	1yrqI	0.416	4.92	0.041	0.705	1.12.2.1	NA
3	0.060	2b0cA	0.341	5.28	0.121	0.603	3.1.3.-	NA
4	0.060	2j9pA	0.419	5.29	0.088	0.756	3.4.16.4	40
5	0.060	2yr4A	0.435	4.89	0.083	0.699	1.13.12.9	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	0.02	2r1dH	0.432	4.13	0.162	0.641	0.40	III	complex1.pdb.gz	46,50,54,55

	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.