D-I-TASSER Q8NFQ6-D3

D-I-TASSER results for Q8NFQ6-D3

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

Input Sequence in FASTA format

>Q8NFQ6 (149 residues)
NVTLSTEEISNHFVQNSQGLGNVLSRIAEIYILSQPFMVRIMATEPPIINLQPGNFTLDI
PASIMMLTQPKNSTVETIVSMDFVASTSVGLVILGQRLVCSLSLNRFRLALPESNRSNIE
VLRFENILSSILHFGVLPLANAKLQQGFP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NVTLSTEEISNHFVQNSQGLGNVLSRIAEIYILSQPFMVRIMATEPPIINLQPGNFTLDIPASIMMLTQPKNSTVETIVSMDFVASTSVGLVILGQRLVCSLSLNRFRLALPESNRSNIEVLRFENILSSILHFGVLPLANAKLQQGFP
Prediction	CCCCCCCSCCCCCCCCHHHHHHHHHHHHHHCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSSSSSSSSSSCCCCCCSSSSSSSSSSSSSSSSSSSCCSSSSSSSSCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	96667651566676667899999999999689999779999966998899955978999999999999879997117999999999999999977889999996307999865267666769999999999998224888877215899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NVTLSTEEISNHFVQNSQGLGNVLSRIAEIYILSQPFMVRIMATEPPIINLQPGNFTLDIPASIMMLTQPKNSTVETIVSMDFVASTSVGLVILGQRLVCSLSLNRFRLALPESNRSNIEVLRFENILSSILHFGVLPLANAKLQQGFP
Prediction	84515666267423231520240013007412774403030305430403045741303030302010135763322001031314140303046530203032540403044262460426304420330043001120153176438
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSCCCCCCCCHHHHHHHHHHHHHHCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSSSSSSSSSSCCCCCCSSSSSSSSSSSSSSSSSSSCCSSSSSSSSCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
NVTLSTEEISNHFVQNSQGLGNVLSRIAEIYILSQPFMVRIMATEPPIINLQPGNFTLDIPASIMMLTQPKNSTVETIVSMDFVASTSVGLVILGQRLVCSLSLNRFRLALPESNRSNIEVLRFENILSSILHFGVLPLANAKLQQGFP

4m4dA

0.20

0.19

6.24

1.50

DEthreader

NFSITDDMLPHGIRLNTKAFRPFTPQIYKKYPD-MKLELLGTVVS-APILNVSGNLSLAPQMEIEGFVILPTSAREPVFRLGVVTNVFASLTFNNSKVTGMLHPDKAQVRLIESKVGMFNVNLFQAFLNYYLLNSLYPDVNAELAQGFP

1bp1A2

0.27

0.26

8.05

2.41

SPARKS-K

-MTLRDDMIPSKFRLTTKFFGTFLPEVAKKFPN-MKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFP

4m4dA2

0.22

0.21

6.79

1.42

MapAlign

NFSITDDMLDSGIRLNTKAFRPFTPQIYKKY-PDMKLELLGTVVSAPILNVSPGNLSLAPQMEIEGFVILPTSAREPVFRLGVVTNVFASLTFNNSKVTGMLHPDKAQVRLIESKVGMFNVNLFQAFLNYYLLNSLYPDVNAELAQGFP

4m4dA2

0.22

0.21

6.79

1.46

CEthreader

NFSITDDMLPSGIRLNTKAFRPFTPQIYKKYPD-MKLELLGTVVSAPILNVSPGNLSLAPQMEIEGFVILPTSAREPVFRLGVVTNVFASLTFNNSKVTGMLHPDKAQVRLIESKVGMFNVNLFQAFLNYYLLNSLYPDVNAELAQGFP

1bp1A2

0.27

0.26

8.05

2.26

MUSTER

-MTLRDDMIPKKFRLTTKFFGTFLPEVAKKFPN-MKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFP

4m4dA2

0.22

0.21

6.79

4.26

HHsearch

NFSITDDMLPSGIRLNTKAFRPFTPQIYKKYPD-MKLELLGTVVSAPILNVSPGNLSLAPQMEIEGFVILPTSAREPVFRLGVVTNVFASLTFNNSKVTGMLHPDKAQVRLIESKVGMFNVNLFQAFLNYYLLNSLYPDVNAELAQGFP

1bp1A2

0.27

0.26

8.05

2.17

FFAS-3D

-MTLRDDMIPKKFRLTTKFFGTFLPEVAKKFP-NMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFP

1bp1A2

0.23

7.15

1.33

EigenThreader

TLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPN-MKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKG-F

1ewfA

0.26

8.06

2.21

CNFpred

KMTLRDDMIPKKFRLTTKFFGTFLPEVAKKFPN-MKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFP

4m4dA2

0.20

0.19

6.24

1.50

DEthreader

NFSITDDMLPHGIRLNTKAFRPFTPQIYKKYPD-MKLELLGTVVS-APILNVSGNLSLAPQMEIEGFVILPTSAREPVFRLGVVTNVFASLTFNNSKVTGMLHPDKAQVRLIESKVGMFNVNLFQAFLNYYLLNSLYPDVNAELAQGFP

(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	0.8628

(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	4m4dA2	0.95	0.98	0.204	0.987	model1_4m4dA2.pdb.gz
2	1bp1A	0.85	2.03	0.264	0.993	model1_1bp1A.pdb.gz
3	2obdA	0.63	3.76	0.086	0.893	model1_2obdA.pdb.gz
4	3epmA	0.37	5.57	0.048	0.711	model1_3epmA.pdb.gz
5	1tc5A	0.35	5.58	0.091	0.678	model1_1tc5A.pdb.gz
6	3cf1B2	0.32	5.81	0.062	0.658	model1_3cf1B2.pdb.gz
7	3mz1A1	0.29	4.74	0.041	0.497	model1_3mz1A1.pdb.gz
8	3zq4A2	0.29	3.19	0.068	0.389	model1_3zq4A2.pdb.gz
9	4kp1A	0.28	5.70	0.036	0.564	model1_4kp1A.pdb.gz
10	2qckA	0.28	5.53	0.009	0.517	model1_2qckA.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:0008289	0.89	lipid binding
GO:0097367	0.88	carbohydrate derivative binding
GO:0001530	0.87	lipopolysaccharide binding
GO:0005543	0.76	phospholipid 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	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0009987	0.81	cellular process
GO:0048518	0.77	positive regulation of biological process
GO:0044699	0.77	single-organism process
GO:0050794	0.75	regulation of cellular process
GO:0050896	0.74	response to stimulus
GO:0044763	0.73	single-organism cellular process
GO:0002376	0.73	immune system process
GO:0051239	0.69	regulation of multicellular organismal process
GO:0032879	0.66	regulation of localization
GO:0006952	0.66	defense response
GO:0051179	0.62	localization
GO:0051050	0.62	positive regulation of transport
GO:0043207	0.62	response to external biotic stimulus
GO:0002682	0.62	regulation of immune system process
GO:0001817	0.62	regulation of cytokine production
GO:0051240	0.61	positive regulation of multicellular organismal process
GO:0048519	0.61	negative regulation of biological process
GO:0032680	0.61	regulation of tumor necrosis factor production
GO:0048522	0.58	positive regulation of cellular process
GO:0002694	0.57	regulation of leukocyte activation
GO:0043030	0.55	regulation of macrophage activation
GO:1903557	0.54	positive regulation of tumor necrosis factor superfamily cytokine production
GO:0010033	0.54	response to organic substance
GO:0006810	0.54	transport
GO:0002275	0.54	myeloid cell activation involved in immune response
GO:1901700	0.52	response to oxygen-containing compound
GO:0032677	0.52	regulation of interleukin-8 production
GO:0032675	0.52	regulation of interleukin-6 production
GO:0019222	0.52	regulation of metabolic process
GO:0006928	0.52	movement of cell or subcellular component
GO:1901701	0.51	cellular response to oxygen-containing compound
GO:0071396	0.51	cellular response to lipid
GO:0071219	0.51	cellular response to molecule of bacterial origin
GO:0032496	0.51	response to lipopolysaccharide
GO:0009966	0.51	regulation of signal transduction
GO:0051704	0.50	multi-organism process
GO:0051128	0.50	regulation of cellular component organization
GO:0034143	0.50	regulation of toll-like receptor 4 signaling pathway
GO:0002696	0.50	positive regulation of leukocyte activation

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:0044424	0.86	intracellular part
GO:0044421	0.81	extracellular region part
GO:0043226	0.71	organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0005615	0.56	extracellular space
GO:0031988	0.53	membrane-bounded vesicle
GO:0070062	0.52	extracellular exosome
GO:0044444	0.50	cytoplasmic part
GO:0005737	0.50	cytoplasm

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	2de6B	0.458	4.18	0.045	0.698	1.14.12.-	NA
2	0.060	1wqlA	0.484	4.22	0.062	0.718	1.14.12.-	NA
3	0.060	3imhA	0.447	4.57	0.051	0.718	5.1.3.3	76
4	0.060	2x4mA	0.523	4.21	0.056	0.792	3.4.23.48	47,50
5	0.060	3b9jJ	0.378	4.56	0.056	0.617	1.17.1.4 1.17.3.2	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	2obdA	0.625	3.76	0.086	0.893	0.62	UUU	complex1.pdb.gz	18,20,21,22,26,27
2	0.03	1fo4A	0.564	3.58	0.058	0.778	0.62	FES	complex2.pdb.gz	18,19,20,21,24
3	0.01	2ckjD	0.523	4.13	0.050	0.799	0.71	FES	complex3.pdb.gz	18,19,20,21,25,31
4	0.01	2ckjD	0.523	4.13	0.050	0.799	0.62	FES	complex4.pdb.gz	19,21,29,30,31
5	0.01	2ckjA	0.468	5.20	0.031	0.839	0.68	FES	complex5.pdb.gz	18,20,22,25,26,27,28

	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.