D-I-TASSER Q9NPP4

D-I-TASSER results for Q9NPP4

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

Summary of the Protein

Uniprot ID: Q9NPP4
Protein Name: NLR family CARD domain-containing protein 4
Gene Name: NLRC4

Input Sequence in FASTA format

>Q9NPP4 (1024 residues)
MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILK
KGSESCNLFLKSLKEWNYPLFQDLNGQSLFHQTSEGDLDDLAQDLKDLYHTPSFLNFYPL
GEDIDIIFNLKSTFTEPVLWRKDQHHHRVEQLTLNGLLQALQSPCIIEGESGKGKSTLLQ
RIAMLWGSGKCKALTKFKFVFFLRLSRAQGGLFETLCDQLLDIPGTIRKQTFMAMLLKLR
QRVLFLLDGYNEFKPQNCPEIEALIKENHRFKNMVIVTTTTECLRHIRQFGALTAEVGDM
TEDSAQALIREVLIKELAEGLLLQIQKSRCLRNLMKTPLFVVITCAIQMGESEFHSHTQT
TLFHTFYDLLIQKNKHKHKGVAASDFIRSLDHCGDLALEGVFSHKFDFELQDVSSVNEDV
LLTTGLLCKYTAQRFKPKYKFFHKSFQEYTAGRRLSSLLTSHEPEEVTKGNGYLQKMVSI
SDITSTYSSLLRYTCGSSVEATRAVMKHLAAVYQHGCLLGLSIAKRPLWRQESLQSVKNT
TEQEILKAININSFVECGIHLYQESTSKSALSQEFEAFFQGKSLYINSGNIPDYLFDFFE
HLPNCASALDFIKLDFYGGAMASWEKAAEDTGGIHMEEAPETYIPSRAVSLFFNWKQEFR
TLEVTLRDFSKLNKQDIRYLGKIFSSATSLRLQIKRCAGVAGSLSLVLSTCKNIYSLMVE
ASPLTIEDERHITSVTNLKTLSIHDLQNQRLPGGLTDSLGNLKNLTKLIMDNIKMNEEDA
IKLAEGLKNLKKMCLFHLTHLSDIGEGMDYIVKSLSSEPCDLEEIQLVSCCLSANAVKIL
AQNLHNLVKLSILDLSENYLEKDGNEALHELIDRMNVLEQLTALMLPWGCDVQGSLSSLL
KHLEEVPQLVKLGLKNWRLTDTEIRILGAFFGKNPLKNFQQLNLAGNRVSSDGWLAFMGV
FENLKQLVFFDFSTKEFLPDPALVRKLSQVLSKLTFLQEARLVGWQFDDDDLSVITGAFK
LVTA

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9NPP4-D1	1-82	82		MNFIKDNSRALIQRMGMTVIKQITDDLFVWNVLNREEVNIICCEKVEQDAARGIIHMILKKGSESCNLFLKSLKEWNYPLFQ
2	Q9NPP4-D2	83-112,353-450	128		DLNGQSLFHQTSEGDLDDLAQDLKDLYHTPEFHSHTQTTLFHTFYDLLIQKNKHKHKGVAASDFIRSLDHCGDLALEGVFSHKFDFELQDVSSVNEDVLLTTGLLCKYTAQRFKPKYKFFHKSFQEYT
3	Q9NPP4-D3	113-352,451-643,859-1024	599		SFLNFYPLGEDIDIIFNLKSTFTEPVLWRKDQHHHRVEQLTLNGLLQALQSPCIIEGESGKGKSTLLQRIAMLWGSGKCKALTKFKFVFFLRLSRAQGGLFETLCDQLLDIPGTIRKQTFMAMLLKLRQRVLFLLDGYNEFKPQNCPEIEALIKENHRFKNMVIVTTTTECLRHIRQFGALTAEVGDMTEDSAQALIREVLIKELAEGLLLQIQKSRCLRNLMKTPLFVVITCAIQMGESAGRRLSSLLTSHEPEEVTKGNGYLQKMVSISDITSTYSSLLRYTCGSSVEATRAVMKHLAAVYQHGCLLGLSIAKRPLWRQESLQSVKNTTEQEILKAININSFVECGIHLYQESTSKSALSQEFEAFFQGKSLYINSGNIPDYLFDFFEHLPNCASALDFIKLDFYGGAMASWEKAAEDTGGIHMEEAPETYYLEKDGNEALHELIDRMNVLEQLTALMLPWGCDVQGSLSSLLKHLEEVPQLVKLGLKNWRLTDTEIRILGAFFGKNPLKNFQQLNLAGNRVSSDGWLAFMGVFENLKQLVFFDFSTKEFLPDPALVRKLSQVLSKLTFLQEARLVGWQFDDDDLSVITGAFKLVTA
4	Q9NPP4-D4	644-858	215		IPSRAVSLFFNWKQEFRTLEVTLRDFSKLNKQDIRYLGKIFSSATSLRLQIKRCAGVAGSLSLVLSTCKNIYSLMVEASPLTIEDERHITSVTNLKTLSIHDLQNQRLPGGLTDSLGNLKNLTKLIMDNIKMNEEDAIKLAEGLKNLKKMCLFHLTHLSDIGEGMDYIVKSLSSEPCDLEEIQLVSCCLSANAVKILAQNLHNLVKLSILDLSEN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.52

(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	5irlA	0.52	4.41	0.152	0.587	model1_5irlA.pdb.gz
2	6npyA	0.47	4.94	0.116	0.550	model1_6npyA.pdb.gz
3	4kxfK	0.45	6.24	0.306	0.582	model1_4kxfK.pdb.gz
4	4xqkA	0.34	7.94	0.040	0.478	model1_4xqkA.pdb.gz
5	4k17A	0.34	4.42	0.082	0.382	model1_4k17A.pdb.gz
6	1dfjI	0.34	4.03	0.113	0.372	model1_1dfjI.pdb.gz
7	6j5tG	0.33	8.07	0.055	0.486	model1_6j5tG.pdb.gz
8	4ifqA	0.33	7.50	0.063	0.456	model1_4ifqA.pdb.gz
9	4perA	0.33	3.95	0.124	0.364	model1_4perA.pdb.gz
10	6b5bA	0.33	7.94	0.075	0.469	model1_6b5bA.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	0.91	catalytic activity
GO:0016740	0.89	transferase activity
GO:0004842	0.87	ubiquitin-protein transferase activity
GO:0098772	0.70	molecular function regulator
GO:0030234	0.69	enzyme regulator activity
GO:0061134	0.68	peptidase regulator activity
GO:0004857	0.68	enzyme inhibitor activity
GO:0004869	0.67	cysteine-type endopeptidase inhibitor 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	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0048583	0.91	regulation of response to stimulus
GO:0009966	0.87	regulation of signal transduction
GO:0009987	0.84	cellular process
GO:0019222	0.80	regulation of metabolic process
GO:0050896	0.79	response to stimulus
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0044699	0.78	single-organism process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0065009	0.76	regulation of molecular function
GO:0044763	0.75	single-organism cellular process
GO:0050790	0.74	regulation of catalytic activity
GO:0048519	0.73	negative regulation of biological process
GO:0032268	0.73	regulation of cellular protein metabolic process
GO:0010941	0.73	regulation of cell death
GO:0006950	0.73	response to stress
GO:0042981	0.72	regulation of apoptotic process
GO:0048523	0.71	negative regulation of cellular process
GO:0043281	0.71	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0010468	0.71	regulation of gene expression
GO:0006952	0.71	defense response
GO:0044092	0.69	negative regulation of molecular function
GO:0043066	0.68	negative regulation of apoptotic process
GO:0031324	0.68	negative regulation of cellular metabolic process
GO:0010605	0.68	negative regulation of macromolecule metabolic process
GO:0043154	0.67	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0016043	0.67	cellular component organization
GO:0022607	0.65	cellular component assembly
GO:0002376	0.65	immune system process
GO:1902589	0.63	single-organism organelle organization
GO:1903047	0.62	mitotic cell cycle process
GO:0070925	0.62	organelle assembly
GO:0010629	0.62	negative regulation of gene expression
GO:0000226	0.62	microtubule cytoskeleton organization
GO:1990001	0.61	inhibition of cysteine-type endopeptidase activity involved in apoptotic process
GO:0090307	0.61	mitotic spindle assembly
GO:0006955	0.57	immune response
GO:0045087	0.55	innate immune response
GO:0048518	0.52	positive regulation of biological process

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:0044444	0.84	cytoplasmic part
GO:0043227	0.82	membrane-bounded organelle
GO:0043229	0.79	intracellular organelle
GO:0043234	0.75	protein complex
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0044446	0.73	intracellular organelle part
GO:0005634	0.69	nucleus
GO:0044445	0.67	cytosolic part
GO:0061702	0.66	inflammasome complex
GO:0072557	0.64	IPAF inflammasome complex
GO:0044430	0.64	cytoskeletal part
GO:0005874	0.63	microtubule
GO:0005876	0.62	spindle microtubule

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	2vdcA	0.302	9.32	0.039	0.483	1.4.1.13	NA
2	0.060	1bxrA	0.290	8.97	0.036	0.453	6.3.5.5	NA
3	0.060	1yq2A	0.287	8.97	0.055	0.450	3.2.1.23	NA
4	0.060	3ecqB	0.320	8.81	0.051	0.486	3.2.1.97	668
5	0.060	1ug9A	0.268	8.52	0.032	0.401	3.2.1.70	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	3a79B	0.303	5.63	0.091	0.368	0.62	UUU	complex1.pdb.gz	169,171,724,726

	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.