D-I-TASSER Q9NPP4-D1

D-I-TASSER results for Q9NPP4-D1

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

Input Sequence in FASTA format

>Q9NPP4 (82 residues)
MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILK
KGSESCNLFLKSLKEWNYPLFQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ
Prediction	CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCC
Confidence	9088999999999963121678999999974578999999997454479999999999872289999999999972813129
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ
Prediction	6531463243015305442044003301555114662263046463436403510420253145004201520374444228
	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

                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCC
MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ

6n1iA

0.95

26.68

1.50

DEthreader

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYLFLN

6n1iA

1.00

28.00

1.91

SPARKS-K

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ

2lwdA

0.16

0.15

4.88

1.11

MapAlign

RLLLKRLQPEFKTRI---IPTDIISDLS-E-CLINQECEEILICKGMMAGAEKLVECLLRSDENWPKTLKLALEKERNKFS-

2lwdA

0.16

0.15

4.89

0.80

CEthreader

RLLLKRLQPEFKTRI---IPTDIISDLSE--CLINQECEEILQIKGMMAGAEKLVECLLRSKENWPKTLKLALEKERNKFSE

6n1iA

1.00

28.00

1.86

MUSTER

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ

6drpA

1.00

28.00

1.73

HHsearch

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ

6drpA

1.00

28.00

1.38

FFAS-3D

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ

1dgnA

0.27

8.24

1.05

EigenThreader

DQLLRKKRRIFIHSVGAGTINALLDCLLEDEVISQEDMNKVRDNDTVMDKARVLIDLVTGKGPKSCCKFIKHLCEEDPQLAS

2n7zA

0.15

4.95

0.81

CNFpred

QQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQ

6drpA

0.95

26.68

1.50

DEthreader

MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYLFLN

(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	0.8608

(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	6n1iA	0.99	0.30	1.000	1.000	model1_6n1iA.pdb.gz
2	6k9fA	0.92	0.85	0.313	0.976	model1_6k9fA.pdb.gz
3	4dwnA	0.89	1.22	0.148	0.988	model1_4dwnA.pdb.gz
4	1dgnA	0.88	1.35	0.268	1.000	model1_1dgnA.pdb.gz
5	3t6pA	0.87	1.19	0.350	0.976	model1_3t6pA.pdb.gz
6	6n1hA	0.86	1.31	0.228	0.963	model1_6n1hA.pdb.gz
7	2dbdA	0.85	1.51	0.225	0.976	model1_2dbdA.pdb.gz
8	2n7zA	0.79	1.81	0.160	0.988	model1_2n7zA.pdb.gz
9	2l9mA	0.77	1.80	0.321	0.951	model1_2l9mA.pdb.gz
10	2kn6A	0.63	2.71	0.165	0.902	model1_2kn6A.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	0.98	catalytic activity
GO:0061134	0.85	peptidase regulator activity
GO:0016740	0.82	transferase activity
GO:0004869	0.81	cysteine-type endopeptidase inhibitor activity
GO:0004842	0.81	ubiquitin-protein transferase 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:0065007	0.99	biological regulation
GO:0050789	0.99	regulation of biological process
GO:0048583	0.96	regulation of response to stimulus
GO:0050794	0.87	regulation of cellular process
GO:0009987	0.87	cellular process
GO:0044699	0.84	single-organism process
GO:0042981	0.84	regulation of apoptotic process
GO:0048519	0.83	negative regulation of biological process
GO:0048523	0.82	negative regulation of cellular process
GO:0044763	0.82	single-organism cellular process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0016043	0.81	cellular component organization
GO:0009966	0.81	regulation of signal transduction
GO:0050790	0.80	regulation of catalytic activity
GO:0043066	0.80	negative regulation of apoptotic process
GO:0032268	0.80	regulation of cellular protein metabolic process
GO:0030162	0.80	regulation of proteolysis
GO:0022607	0.80	cellular component assembly
GO:0043281	0.79	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:1902589	0.78	single-organism organelle organization
GO:0044092	0.78	negative regulation of molecular function
GO:0031324	0.78	negative regulation of cellular metabolic process
GO:0022402	0.78	cell cycle process
GO:0010605	0.78	negative regulation of macromolecule metabolic process
GO:0010468	0.78	regulation of gene expression
GO:1990001	0.77	inhibition of cysteine-type endopeptidase activity involved in apoptotic process
GO:0090307	0.77	mitotic spindle assembly
GO:0050896	0.63	response to stimulus
GO:0006950	0.56	response to stress
GO:0031347	0.52	regulation of defense response
GO:0002376	0.52	immune system process
GO:0006952	0.51	defense response

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	0.99	intracellular part
GO:0043229	0.85	intracellular organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005634	0.82	nucleus
GO:0044446	0.81	intracellular organelle part
GO:0044444	0.80	cytoplasmic part
GO:0043234	0.77	protein complex
GO:0005876	0.76	spindle microtubule
GO:0044445	0.67	cytosolic part
GO:0061702	0.66	inflammasome complex
GO:0072557	0.62	IPAF inflammasome complex

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	3n0lA	0.544	3.58	0.042	0.817	2.1.2.1	NA
2	0.060	2jg2A	0.574	2.88	0.045	0.817	2.3.1.50	NA
3	0.060	1bt4A	0.544	3.13	0.062	0.793	2.6.1.52	NA
4	0.060	1x87A	0.550	3.32	0.092	0.866	4.2.1.49	NA
5	0.060	2zyjA	0.554	3.21	0.087	0.817	2.6.1.39	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	0.04	2nsn0	0.847	1.37	0.213	0.939	0.41	III	complex1.pdb.gz	10,11,14,15,16,20,66,67,70,71,72,73,74,75

	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.