D-I-TASSER Q8NFU3-D1

D-I-TASSER results for Q8NFU3-D1

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

Input Sequence in FASTA format

>Q8NFU3 (115 residues)
MAGAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQ
ALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAGAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES
Prediction	CCCCCSSCHHHHHHHHHCCCSSSSSCCCHHHHHCCCCCCCSSCCHHHHHHHHCCCCHHHHHHHHHCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHCCCCSSSCCCCHHHHHHHCC
Confidence	9998541999999999649959997799899971958996774767877775168478888642114778998699987998899999999999099975875785999997029
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAGAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES
Prediction	7573571416304611757511001033564165241430320225404732544465146425563564663400001214310330042047261640341523155546678
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSCHHHHHHHHHCCCSSSSSCCCHHHHHCCCCCCCSSCCHHHHHHHHCCCCHHHHHHHHHCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHCCCCSSSCCCCHHHHHHHCC
MAGAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

0.95

0.91

25.62

1.33

DEthreader

---APTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALY-SAEKPKEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

1.00

0.98

27.51

2.46

SPARKS-K

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

3utnX

0.23

0.22

6.82

1.00

MapAlign

--AWEIVDYEEMFQLVKAKKFNAFDARSLGRFESGHIPGTQPLPYGSLLYPI---HATLEKALKDFHCTLPSKPTICSCGTGVSGVIIKTALELAGVPNVRLYDGSWTEWVLKS-

3utnX

0.23

7.34

0.57

CEthreader

FQDKEIVDYEEMFQLVKSGELNAFDARSLGRFESGHIPGTQPLPYGSLLEAGEAIHATLEKALKDFCTLDPSKPTICSCGTGVSGVIIKTALELAGVPNVRLYDGSWTEWVLKSG

6bevA

1.00

0.98

27.51

2.22

MUSTER

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

1.00

0.98

27.51

1.26

HHsearch

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

1.00

0.98

27.51

2.12

FFAS-3D

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

1.00

0.98

27.51

0.83

EigenThreader

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6bevA

1.00

0.98

27.51

1.68

CNFpred

--GAPTVSLPELRSLLASGRARLFDVRSREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPKLEDEHLVFFCQMGKRGLQATQLARSLGYTGARNYAGAYREWLEKES

6k6rA

0.29

8.73

1.33

DEthreader

TKAPKIYTFDQVRNLVHPNDKLLVDVREPKEVKDYKMPTTINIPVNSAPGALGLPEKEFHKVF-QFAKPPHDKELIFLA-KGVRAKTAEELARSYGYENTGIYPGSITEWLAKGG

(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	0.8948

(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	6bevA	0.90	1.28	0.991	0.974	model1_6bevA.pdb.gz
2	6k6rA	0.83	1.87	0.292	0.983	model1_6k6rA.pdb.gz
3	3d1pA	0.81	1.91	0.273	0.957	model1_3d1pA.pdb.gz
4	3tp9A	0.80	1.34	0.330	0.870	model1_3tp9A.pdb.gz
5	3utnX	0.80	2.53	0.212	0.983	model1_3utnX.pdb.gz
6	1orbA	0.80	2.46	0.218	0.957	model1_1orbA.pdb.gz
7	3olhA	0.79	2.46	0.245	0.957	model1_3olhA.pdb.gz
8	2hhgA	0.79	2.35	0.206	0.930	model1_2hhgA.pdb.gz
9	1urhA1	0.77	2.39	0.185	0.939	model1_1urhA1.pdb.gz
10	1h4kX	0.77	2.67	0.264	0.957	model1_1h4kX.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	0.95	catalytic activity
GO:0016740	0.88	transferase activity
GO:0016783	0.83	sulfurtransferase activity
GO:0004792	0.80	thiosulfate sulfurtransferase activity
GO:0016772	0.51	transferase activity, transferring phosphorus-containing groups
GO:0016779	0.50	nucleotidyltransferase 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	0.94	cellular process
GO:0008152	0.90	metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0071704	0.86	organic substance metabolic process
GO:0044238	0.82	primary metabolic process
GO:0043170	0.79	macromolecule metabolic process
GO:0006807	0.74	nitrogen compound metabolic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0019538	0.71	protein metabolic process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0046483	0.69	heterocycle metabolic process
GO:0043412	0.67	macromolecule modification
GO:0034641	0.66	cellular nitrogen compound metabolic process
GO:0006725	0.64	cellular aromatic compound metabolic process
GO:0006464	0.63	cellular protein modification process
GO:0006139	0.63	nucleobase-containing compound metabolic process
GO:0090304	0.60	nucleic acid metabolic process
GO:0016070	0.59	RNA metabolic process
GO:0006399	0.57	tRNA metabolic process
GO:0006396	0.57	RNA processing
GO:0008033	0.56	tRNA processing
GO:0006400	0.55	tRNA modification
GO:0002098	0.54	tRNA wobble uridine modification
GO:0034227	0.53	tRNA thio-modification
GO:0070647	0.52	protein modification by small protein conjugation or removal
GO:0044699	0.51	single-organism process
GO:0032447	0.51	protein urmylation
GO:0002143	0.51	tRNA wobble position uridine thiolation

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.85	cytoplasmic part
GO:0005829	0.54	cytosol

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	0.356	1gn0A	0.766	2.28	0.178	0.878	2.8.1.1	40,88
2	0.356	2jtqA	0.613	1.99	0.222	0.704	2.8.1.1	40,42,44,79,82,102,105
3	0.247	2vswB	0.755	3.09	0.195	0.983	3.1.3.16 3.1.3.48	23,31,104
4	0.210	3f4aB	0.728	2.34	0.176	0.870	3.1.3.16	84
5	0.165	1cwsA	0.740	2.45	0.223	0.887	3.1.3.48	79,105

	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	0.21	1qxnB	0.698	2.57	0.252	0.887	1.16	PS5	complex1.pdb.gz	27,79,82,83,84,106,107,108
2	0.06	3etnB	0.553	3.45	0.130	0.809	0.52	CMK	complex2.pdb.gz	26,27,28,79,80,81,83,86
3	0.05	1qxnA	0.695	2.39	0.257	0.870	1.14	PS5	complex3.pdb.gz	27,79,105,106,107
4	0.04	1kqfA	0.550	3.73	0.106	0.887	0.46	SF4	complex4.pdb.gz	25,81,82,84,85
5	0.01	1siwA	0.540	4.32	0.083	0.913	0.53	SF4	complex5.pdb.gz	77,78,79,85,105

	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.