D-I-TASSER Q6NTF9-D2

D-I-TASSER results for Q6NTF9-D2

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

Input Sequence in FASTA format

>Q6NTF9 (111 residues)
TPVAFAMLGVTTVRSRMRRALVFGMVVPSVLVPWLLLGASWLIPQTSFLSNVCGLSIGLA
YGLTYCYSIDLSERVALKLDQTFPFSLMRRISVFKYVSGSSAERRAAQSRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| TPVAFAMLGVTTVRSRMRRALVFGMVVPSVLVPWLLLGASWLIPQTSFLSNVCGLSIGLAYGLTYCYSIDLSERVALKLDQTFPFSLMRRISVFKYVSGSSAERRAAQSRK
Prediction	CCHHHHHHHHHHHHCCCCCCSSSSSSCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHHCHHHHHHCCCCCSSCCCCHHHHHHHHHCC
Confidence	931367677877641775407999975717998999999996777168999999999899971102211680999999982614889853886077178735655565159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| TPVAFAMLGVTTVRSRMRRALVFGMVVPSVLVPWLLLGASWLIPQTSFLSNVCGLSIGLAYGLTYCYSIDLSERVALKLDQTFPFSLMRRISVFKYVSGSSAERRAAQSRK
Prediction	632121101131244444311010133333332333033032224233212110212131323330310323540043046412130044244343143444544446668
	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                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHCCCCCCSSSSSSCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHHCHHHHHHCCCCCSSCCCCHHHHHHHHHCC
TPVAFAMLGVTTVRSRMRRALVFGMVVPSVLVPWLLLGASWLIPQTSFLSNVCGLSIGLAYGLTYCYSIDLSERVALKLDQTFPFSLMRRISVFKYVSGSSAERRAAQSRK

6ebuA

0.14

0.08

2.78

0.80

CEthreader

PSGDTAMAFTIAT--VLSHGEKLHIKAILFLYAFLIGYERIYAGVHFPLDVFVGALIGIICGIISLKY-------------------------------------------

4ybqA

0.09

3.43

0.62

EigenThreader

TFLAAFGSSFQYGYFGGFIGSLMVGICAGISSNVVPMYLGELAPKNLRGALGVVPQLFITVGILVAQLFGLRSVLASMAGQQLSGRNLLLIGFSTCLTACIVLTVALALQN

7czbA

0.23

0.13

3.96

0.63

FFAS-3D

IPLIMSVLYVWAQLNRDMIVSFWGTRFKACYLPWVILGFNYIIGG-SVINELIGNLVGHLYFF------------------------------------------------

5ed7A2

0.11

0.10

3.59

0.67

SPARKS-K

DALAAGTTAEQLLMFDL---------LPVQADSTALLRFIESQVISPEHVAYLGAFLSVLYATHTARLTGVLVLAVGDVDRLSAFDAGAASRRAAGYLDVLLTVRLARSQ-

5oqtA

0.13

0.11

3.72

0.72

CNFpred

GTGIFVLTGVAAAEHA-GPALVLSFILSCVFAALCYAEFASTVPVSGSAYTYSYATFGELIAWILGWDLILEYGVASSAVAVGWSGYFQG---------------------

6y83A1

0.12

0.11

3.85

1.00

DEthreader

VLAMLRHAGACIAHYTGKID-EIYNLQLS-HALHVTIFYMLSLSCGYGDDAVLALTSGLHSVTTGTRDALRVHDPARFCDIFEPDGNASQ-A-LHAFN--VA-CA-EPNRH

4a01A

0.10

3.65

0.76

MapAlign

FSTVSFLLGGVTSLAYARTEAKGVGKATSGLVLYIAINLFKIDDWGGLFEAITGYGLGGSSMALFGRVGGGIYTKAADVGA---DLVGKVERNIPEDPAVIADNVGDNVGD

3ivrA3

0.10

0.09

3.36

0.51

MUSTER

GNLLIAQSSLVDAWRLTEADVNLGM-LPGLGLMLTLQQASVIAAKFDPAQAARDIEAH-------VTVMAEFAPMLGNILDQAAPAQLASLRAVTGLTPETIERFEATCPN

7czbA

0.18

0.13

4.11

1.85

HHsearch

IPLIMSVLYVWAQLNRDMIVSFWFTRFKACYLPWVILGFNYIIGG-SVINELIGNLVGHLYFFL--MFRYPMDLG-----GRN---F---------LS-------------

1t5jA

0.08

0.07

2.82

0.61

CEthreader

AAMRIYPLGIVFHNN--------------LKKLKEEVIKASKITHNNKTAIAGALAIAFFVSSALKDRKDFSLDECYNYIKDIDEEFAKKLLEIKNFNNLDYIYDYFGTGV

(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	0.942

(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	3vvnA	0.58	3.90	0.091	0.892	model1_3vvnA.pdb.gz
2	5medA	0.55	3.66	0.052	0.865	model1_5medA.pdb.gz
3	7qe5A	0.54	3.95	0.078	0.883	model1_7qe5A.pdb.gz
4	7czbA	0.54	2.44	0.184	0.685	model1_7czbA.pdb.gz
5	2i3oD	0.53	3.88	0.041	0.874	model1_2i3oD.pdb.gz
6	2e0wB	0.53	3.92	0.020	0.865	model1_2e0wB.pdb.gz
7	7wb4I	0.53	3.84	0.030	0.847	model1_7wb4I.pdb.gz
8	4g32A2	0.52	3.92	0.095	0.856	model1_4g32A2.pdb.gz
9	5jm7A	0.52	4.24	0.058	0.874	model1_5jm7A.pdb.gz
10	7k7mA	0.52	3.94	0.106	0.847	model1_7k7mA.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	0.75	catalytic activity
GO:0016787	0.71	hydrolase activity
GO:0070011	0.69	peptidase activity, acting on L-amino acid peptides
GO:0004252	0.67	serine-type endopeptidase 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:0009987	0.89	cellular process
GO:0044699	0.88	single-organism process
GO:0008152	0.86	metabolic process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.85	primary metabolic process
GO:0044237	0.85	cellular metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0043170	0.84	macromolecule metabolic process
GO:0050794	0.83	regulation of cellular process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0044710	0.82	single-organism metabolic process
GO:0032502	0.81	developmental process
GO:0019538	0.81	protein metabolic process
GO:0080090	0.80	regulation of primary metabolic process
GO:0070887	0.80	cellular response to chemical stimulus
GO:0044767	0.80	single-organism developmental process
GO:0043066	0.80	negative regulation of apoptotic process
GO:0033554	0.80	cellular response to stress
GO:0031325	0.80	positive regulation of cellular metabolic process
GO:0010628	0.80	positive regulation of gene expression
GO:0006508	0.80	proteolysis
GO:0006464	0.80	cellular protein modification process
GO:2000254	0.79	regulation of male germ cell proliferation
GO:0051047	0.79	positive regulation of secretion
GO:0048515	0.79	spermatid differentiation
GO:0045732	0.79	positive regulation of protein catabolic process
GO:0043687	0.79	post-translational protein modification
GO:0036503	0.79	ERAD pathway
GO:0034644	0.79	cellular response to UV
GO:0034620	0.79	cellular response to unfolded protein
GO:0031293	0.79	membrane protein intracellular domain proteolysis
GO:0010954	0.79	positive regulation of protein processing

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:0044446	0.99	intracellular organelle part
GO:0044444	0.99	cytoplasmic part
GO:0016020	0.99	membrane
GO:0043231	0.97	intracellular membrane-bounded organelle
GO:0031090	0.95	organelle membrane
GO:0048471	0.94	perinuclear region of cytoplasm
GO:0005794	0.94	Golgi apparatus
GO:0000139	0.94	Golgi 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	2dhtA	0.480	4.85	0.010	0.865	1.1.1.42	NA
2	0.060	2p0mB	0.510	4.04	0.129	0.820	1.13.11.33	NA
3	0.060	2btuA	0.480	4.03	0.120	0.739	6.3.3.1	NA
4	0.060	3kb9A	0.477	4.43	0.062	0.829	4.2.3.37	61
5	0.060	1u0bB	0.488	4.41	0.029	0.847	6.1.1.16	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	1ga2A	0.461	5.02	0.087	0.919	0.45	BGC	complex1.pdb.gz	4,38,41,50
	2	0.01	3fg4C	0.484	4.16	0.053	0.856	0.67	ACD	complex2.pdb.gz	36,51,52,55

	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, 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.