D-I-TASSER Q9NP59-D2

D-I-TASSER results for Q9NP59-D2

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

Input Sequence in FASTA format

>Q9NP59 (115 residues)
WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNV
SVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR
Prediction	CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHSSSSC
Confidence	9305655456652886279999999999999997789999973475699999999999999999999999999543100133220699999999999999999999864313439
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR
Prediction	4500100101203343123100322043102000113004202635213002103332321211123100001134444444343323332233001112123112303401146
	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

CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHSSSSC
WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR

6w4sF

0.98

27.53

1.50

DEthreader

WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIRD

6w4sF

1.00

28.00

1.12

SPARKS-K

WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR

5aymA1

0.22

6.85

1.49

HHsearch

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLVRAG--GRESWLLSVLFIALALSGVMASLGSQITDISVGN

5aymA1

0.22

6.85

1.45

FFAS-3D

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDG--LVRAGGRESWLLSVLFIALALSGVMASLGSQITDISVGN

5aymA

0.22

6.85

1.33

DEthreader

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLVRAGGR--ESWLLSVLFIALALSGVMASLGSQITDISVND

5aymA

0.15

4.99

0.97

SPARKS-K

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLVRAGGRESLSVLFIALALSGVMASLGSQITDISVGNDLAP

5aymA

0.22

6.85

0.66

MapAlign

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLV--RAGGRESWLLSVLFIALALSGVMASLGSQITDISVGN

5aymA1

0.22

6.85

0.56

CEthreader

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLVRAGGRES--WLLSVLFIALALSGVMASLGSQITDISVGN

5aymA1

0.22

6.85

0.74

MUSTER

WDFVVPFALLVIFPGKLQVAAFYYLIVKIGTFLLTPSSGKWIDTHPRIQVVKWGVWLQFFAILAGMVFFGMLDGLVR--AGGRESWLLSVLFIALALSGVMASLGSQITDISVGN

6w4sF

1.00

28.00

1.46

HHsearch

WHFAVSVFLVELYGNSLLLTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHELLTMYHGWVLTSCYILIITIANIANLASTATAITIQR

(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	0.8066

(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	5aymA	0.93	1.06	0.221	0.983	model1_5aymA.pdb.gz
2	6w4sF	0.90	1.53	1.000	1.000	model1_6w4sF.pdb.gz
3	6thaA2	0.70	2.37	0.091	0.861	model1_6thaA2.pdb.gz
4	6ob6A	0.70	2.33	0.088	0.887	model1_6ob6A.pdb.gz
5	6h7dA	0.70	2.49	0.104	0.922	model1_6h7dA.pdb.gz
6	4pypA	0.70	2.42	0.091	0.861	model1_4pypA.pdb.gz
7	4gbyA	0.69	3.01	0.084	0.930	model1_4gbyA.pdb.gz
8	4ybqA2	0.66	2.58	0.059	0.878	model1_4ybqA2.pdb.gz
9	4ldsA1	0.64	2.40	0.138	0.817	model1_4ldsA1.pdb.gz
10	5c65A	0.64	2.58	0.112	0.852	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:0005381	1.00	iron ion transmembrane transporter activity
GO:0072509	0.52	divalent inorganic cation transmembrane transporter activity
GO:0004872	0.52	receptor activity
GO:0005261	0.51	cation channel activity
GO:0097689	0.50	iron channel activity
GO:0017046	0.50	peptide hormone binding
GO:0015093	0.50	ferrous iron transmembrane transporter 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:0000041	1.00	transition metal ion transport
GO:0006826	0.95	iron ion transport
GO:0009987	0.82	cellular process
GO:0044763	0.79	single-organism cellular process
GO:0065007	0.67	biological regulation
GO:0055085	0.59	transmembrane transport
GO:0072511	0.58	divalent inorganic cation transport
GO:0065008	0.55	regulation of biological quality
GO:0098662	0.53	inorganic cation transmembrane transport
GO:0055076	0.53	transition metal ion homeostasis

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	0.94	cell part
GO:0044425	0.87	membrane part
GO:0044424	0.85	intracellular part
GO:0016020	0.83	membrane
GO:0005886	0.73	plasma membrane
GO:0044459	0.62	plasma membrane part
GO:0044444	0.62	cytoplasmic part
GO:0016323	0.61	basolateral plasma membrane
GO:0005622	0.61	intracellular
GO:0016021	0.57	integral component of 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	0.136	1urfA	0.480	2.09	0.061	0.574	2.7.11.13	55,57,107
2	0.066	1yvwC	0.450	3.17	0.045	0.583	3.6.1.31	65
3	0.060	3bhgA	0.538	3.40	0.071	0.722	4.3.2.2	NA
4	0.060	1u7lA	0.569	3.59	0.059	0.844	3.6.3.14	98
5	0.060	1olpA	0.551	3.77	0.054	0.791	3.1.4.3	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	0.02	2nq24	0.603	3.45	0.167	0.887	0.22	III	complex1.pdb.gz	32,33,34,35,36,37,39,47,49
2	0.02	2nq21	0.603	3.45	0.167	0.887	0.17	III	complex2.pdb.gz	21,24,25,28,29,32,35,36,38,39,44,45
3	0.01	3taeD	0.550	3.60	0.062	0.809	0.29	QNA	complex3.pdb.gz	35,40,46
4	0.01	2dtuA	0.552	3.27	0.035	0.774	0.15	UUU	complex4.pdb.gz	6,91,92,93
5	0.01	2oyqB	0.441	4.26	0.038	0.704	0.22	QNA	complex5.pdb.gz	14,18,19,26
6	0.01	3kd5E	0.525	3.75	0.035	0.800	0.15	PPF	complex6.pdb.gz	35,38,39,41
7	0.01	1q9xA	0.535	3.70	0.035	0.852	0.21	DOC	complex7.pdb.gz	36,37,40,104
8	0.01	2nq22	0.453	4.67	0.078	0.852	0.21	III	complex8.pdb.gz	32,33,34,35,36,37,39,40
9	0.01	3tagD	0.536	3.86	0.044	0.870	0.27	QNA	complex9.pdb.gz	15,17,23

	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.