D-I-TASSER Q86W25

D-I-TASSER results for Q86W25

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

Summary of the Protein

Uniprot ID: Q86W25
Protein Name: NACHT, LRR and PYD domains-containing protein 13
Gene Name: NLRP13

Input Sequence in FASTA format

>Q86W25 (1043 residues)
MNFSVITCPNGGTNQGLLPYLMALDQYQLEEFKLCLEPQQLMDFWSAPQGHFPRIPWANL
RAADPLNLSFLLDEHFPKGQAWKVVLGIFQTMNLTSLCEKVRAEMKENVQTQELQDPTQE
DLEMLEAAAGNMQTQGCQDPNQEELDELEEETGNVQAQGCQDPNQEEPEMLEEADHRRKY
RENMKAELLETWDNISWPKDHVYIRNTSKDEHEELQRLLDPNRTRAQAQTIVLVGRAGVG
KTTLAMQAMLHWANGVLFQQRFSYVFYLSCHKIRYMKETTFAELISLDWPDFDAPIEEFM
SQPEKLLFIIDGFEEIIISESRSESLDDGSPCTDWYQELPVTKILHSLLKKELVPLATLL
ITIKTWFVRDLKASLVNPCFVQITGFTGDDLRVYFMRHFDDSSEVEKILQQLRKNETLFH
SCSAPMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQW
RALCSLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQ
EFFAAMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIAREL
EDTLHCKISPRVMEELLKWGEELGKAESASLQFHILRLFHCLHESQEEDFTKKMLGRIFE
VDLNILEDEELQASSFCLKHCKRLNKLRLSVSSHILERDLEILETSKFDSRMHAWNSICS
TLVTNENLHELDLSNSKLHASSVKGLCLALKNPRCKVQKLTCKSVTPEWVLQDLIIALQG
NSKLTHLNFSSNKLGMTVPLILKALRHSACNLKYLCLEKCNLSAASCQDLALFLTSIQHV
TRLCLGFNRLQDDGIKLLCAALTHPKCALERLELWFCQLAAPACKHLSDALLQNRSLTHL
NLSKNSLRDEGVKFLCEALGRPDGNLQSLNLSGCSFTREGCGELANALSHNHNVKILDLG
ENDLQDDGVKLLCEALKPHRALHTLGLAKCNLTTACCQHLFSVLSSSKSLVNLNLLGNEL
DTDGVKMLCKALKKSTCRLQKLG

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 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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q86W25-D1	1-424,625-691	491		MNFSVITCPNGGTNQGLLPYLMALDQYQLEEFKLCLEPQQLMDFWSAPQGHFPRIPWANLRAADPLNLSFLLDEHFPKGQAWKVVLGIFQTMNLTSLCEKVRAEMKENVQTQELQDPTQEDLEMLEAAAGNMQTQGCQDPNQEELDELEEETGNVQAQGCQDPNQEEPEMLEEADHRRKYRENMKAELLETWDNISWPKDHVYIRNTSKDEHEELQRLLDPNRTRAQAQTIVLVGRAGVGKTTLAMQAMLHWANGVLFQQRFSYVFYLSCHKIRYMKETTFAELISLDWPDFDAPIEEFMSQPEKLLFIIDGFEEIIISESRSESLDDGSPCTDWYQELPVTKILHSLLKKELVPLATLLITIKTWFVRDLKASLVNPCFVQITGFTGDDLRVYFMRHFDDSSEVEKILQQLRKNETLFHSCSAKAESASLQFHILRLFHCLHESQEEDFTKKMLGRIFEVDLNILEDEELQASSFCLKHCKRLNKLRLSV
2	Q86W25-D2	425-624	200		PMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQWRALCSLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQEFFAAMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIARELEDTLHCKISPRVMEELLKWGEELG
3	Q86W25-D3	692-1043	352		SSHILERDLEILETSKFDSRMHAWNSICSTLVTNENLHELDLSNSKLHASSVKGLCLALKNPRCKVQKLTCKSVTPEWVLQDLIIALQGNSKLTHLNFSSNKLGMTVPLILKALRHSACNLKYLCLEKCNLSAASCQDLALFLTSIQHVTRLCLGFNRLQDDGIKLLCAALTHPKCALERLELWFCQLAAPACKHLSDALLQNRSLTHLNLSKNSLRDEGVKFLCEALGRPDGNLQSLNLSGCSFTREGCGELANALSHNHNVKILDLGENDLQDDGVKLLCEALKPHRALHTLGLAKCNLTTACCQHLFSVLSSSKSLVNLNLLGNELDTDGVKMLCKALKKSTCRLQKLG

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 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	4kxfK	0.63	4.93	0.125	0.734	model1_4kxfK.pdb.gz
2	6npyA	0.53	6.25	0.199	0.673	model1_6npyA.pdb.gz
3	5irlA	0.51	6.26	0.179	0.645	model1_5irlA.pdb.gz
4	6b5bA	0.48	6.35	0.095	0.620	model1_6b5bA.pdb.gz
5	6eqoA	0.41	9.05	0.054	0.642	model1_6eqoA.pdb.gz
6	6reyc	0.39	8.53	0.063	0.584	model1_6reyc.pdb.gz
7	1vt4I	0.38	8.35	0.043	0.561	model1_1vt4I.pdb.gz
8	4k17A	0.38	5.01	0.156	0.443	model1_4k17A.pdb.gz
9	3wpbA	0.38	5.92	0.102	0.464	model1_3wpbA.pdb.gz
10	1dfjI	0.38	2.87	0.286	0.400	model1_1dfjI.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:1901363	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0097367	0.53	carbohydrate derivative 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	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0009987	0.80	cellular process
GO:0050794	0.77	regulation of cellular process
GO:0050896	0.73	response to stimulus
GO:0019222	0.73	regulation of metabolic process
GO:0048518	0.72	positive regulation of biological process
GO:0044699	0.72	single-organism process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0080090	0.69	regulation of primary metabolic process
GO:0044763	0.66	single-organism cellular process
GO:0006950	0.66	response to stress
GO:0006952	0.65	defense response
GO:0048583	0.64	regulation of response to stimulus
GO:0065009	0.63	regulation of molecular function
GO:0010468	0.62	regulation of gene expression
GO:0050790	0.60	regulation of catalytic activity
GO:2000112	0.59	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.59	regulation of nitrogen compound metabolic process
GO:0048522	0.59	positive regulation of cellular process
GO:0048519	0.59	negative regulation of biological process
GO:0044238	0.58	primary metabolic process
GO:0043170	0.58	macromolecule metabolic process
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0006355	0.58	regulation of transcription, DNA-templated
GO:0051336	0.57	regulation of hydrolase activity
GO:0048584	0.57	positive regulation of response to stimulus
GO:0043207	0.57	response to external biotic stimulus
GO:0010941	0.57	regulation of cell death
GO:0002376	0.57	immune system process
GO:0048523	0.56	negative regulation of cellular process
GO:0044093	0.56	positive regulation of molecular function
GO:0042981	0.56	regulation of apoptotic process
GO:0031347	0.56	regulation of defense response
GO:0009893	0.56	positive regulation of metabolic process
GO:0002682	0.56	regulation of immune system process
GO:0050776	0.55	regulation of immune response
GO:0043281	0.55	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0010604	0.55	positive regulation of macromolecule metabolic process
GO:0051707	0.54	response to other organism
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:0098542	0.53	defense response to other organism
GO:0050778	0.53	positive regulation of immune response
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0051090	0.52	regulation of sequence-specific DNA binding transcription factor activity
GO:0044092	0.52	negative regulation of molecular function
GO:0051239	0.51	regulation of multicellular organismal process
GO:0009617	0.51	response to bacterium
GO:0007165	0.51	signal transduction

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:0043226	0.90	organelle
GO:0044444	0.88	cytoplasmic part
GO:0043227	0.88	membrane-bounded organelle
GO:0005737	0.88	cytoplasm
GO:0043229	0.82	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0032991	0.75	macromolecular complex
GO:0043234	0.74	protein complex
GO:0044446	0.67	intracellular organelle part
GO:0005634	0.63	nucleus
GO:0016020	0.54	membrane
GO:0005829	0.52	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	0.060	1ob2A	0.140	7.68	0.052	0.199	3.6.1.48	NA
2	0.060	2vz8A	0.288	8.52	0.057	0.423	2.3.1.85	NA
3	0.060	2qubA	0.267	8.07	0.048	0.389	3.1.1.3	274,364
4	0.060	2jfdA	0.142	7.33	0.025	0.197	2.3.1.85	268
5	0.060	1qbaA	0.265	8.70	0.026	0.402	3.2.1.52	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	0.01	3cigA	0.349	5.96	0.130	0.431	0.54	UUU	complex1.pdb.gz	239,242,243
2	0.01	3sfzA	0.381	8.55	0.078	0.568	0.43	GBL	complex2.pdb.gz	233,234,241,244
3	0.01	1z6tA	0.320	4.73	0.080	0.369	0.60	ADP	complex3.pdb.gz	202,238,239,240,241,242,243

	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.