D-I-TASSER Q5TC82

D-I-TASSER results for Q5TC82

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

Summary of the Protein

Uniprot ID: Q5TC82
Protein Name: Roquin-1
Gene Name: RC3H1

Input Sequence in FASTA format

>Q5TC82 (1133 residues)
MPVQAPQWTDFLSCPICTQTFDETIRKPISLGCGHTVCKMCLNKLHRKACPFDQTTINTD
IELLPVNSALLQLVGAQVPEQQPITLCSGVEDTKHYEEAKKCVEELALYLKPLSSARGVG
LNSTTQSVLSRPMQRKLVTLVHCQLVEEEGRIRAMRAARSLGERTVTELILQHQNPQQLS
SNLWAAVRARGCQFLGPAMQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKT
SIGHVVQLLYRASCFKVTKRDEDSSLMQLKEEFRTYEALRREHDSQIVQIAMEAGLRIAP
DQWSSLLYGDQSHKSHMQSIIDKLQTPASFAQSVQELTIALQRTGDPANLNRLRPHLELL
ANIDPSPDAPPPTWEQLENGLVAVRTVVHGLVDYIQNHSKKGADQQQPPQHSKYKTYMCR
DMKQRGGCPRGASCTFAHSQEELEKFRKMNKRLVPRRPLSASLGQLNEVGLPSAAILPDE
GAVDLPSRKPPALPNGIVSTGNTVTQLIPRGTDPSYDSSLKPGKIDHLSSSAPGSPPDLL
ESVPKSISALPVNPHSIPPRGPADLPPMPVTKPLQMVPRGSQLYPAQQTDVYYQDPRGAA
PPFEPAPYQQGMYYTPPPQCVSRFVRPPPSAPEPAPPYLDHYPPYLQERVVNSQYGTQPQ
QYPPIYPSHYDGRRVYPAPSYTREEIFRESPIPIEIPPAAVPSYVPESRERYQQIESYYP
VAPHPTQIRPSYLREPPYSRLPPPPQPHPSLDELHRRRKEIMAQLEERKVISPPPFAPSP
TLPPTFHPEEFLDEDLKVAGKYKGNDYSQYSPWSCDTIGSYIGTKDAKPKDVVAAGSVEM
MNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTSKTIYQGAGPMQAMA
PQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERISMSEVASHGKPLPS
AEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQSQPPPPPPPKWPGMI
SSEQLSLELHQVEREIGKRTRELSMENQCSLDMKSKLNTSKQAENGQPEPQNKVPAEDLT
LTFSDVPNGSALTQENISLLSNKTSSLNLSEDPEGGGDNNDSQRSGVTPSSAP

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	Q5TC82-D1	1-826,1021-1133	939		MPVQAPQWTDFLSCPICTQTFDETIRKPISLGCGHTVCKMCLNKLHRKACPFDQTTINTDIELLPVNSALLQLVGAQVPEQQPITLCSGVEDTKHYEEAKKCVEELALYLKPLSSARGVGLNSTTQSVLSRPMQRKLVTLVHCQLVEEEGRIRAMRAARSLGERTVTELILQHQNPQQLSSNLWAAVRARGCQFLGPAMQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKTSIGHVVQLLYRASCFKVTKRDEDSSLMQLKEEFRTYEALRREHDSQIVQIAMEAGLRIAPDQWSSLLYGDQSHKSHMQSIIDKLQTPASFAQSVQELTIALQRTGDPANLNRLRPHLELLANIDPSPDAPPPTWEQLENGLVAVRTVVHGLVDYIQNHSKKGADQQQPPQHSKYKTYMCRDMKQRGGCPRGASCTFAHSQEELEKFRKMNKRLVPRRPLSASLGQLNEVGLPSAAILPDEGAVDLPSRKPPALPNGIVSTGNTVTQLIPRGTDPSYDSSLKPGKIDHLSSSAPGSPPDLLESVPKSISALPVNPHSIPPRGPADLPPMPVTKPLQMVPRGSQLYPAQQTDVYYQDPRGAAPPFEPAPYQQGMYYTPPPQCVSRFVRPPPSAPEPAPPYLDHYPPYLQERVVNSQYGTQPQQYPPIYPSHYDGRRVYPAPSYTREEIFRESPIPIEIPPAAVPSYVPESRERYQQIESYYPVAPHPTQIRPSYLREPPYSRLPPPPQPHPSLDELHRRRKEIMAQLEERKVISPPPFAPSPTLPPTFHPEEFLDEDLKVAGKYKGNDYSQYSPWSCDTIGSYIGTKDSSEQLSLELHQVEREIGKRTRELSMENQCSLDMKSKLNTSKQAENGQPEPQNKVPAEDLTLTFSDVPNGSALTQENISLLSNKTSSLNLSEDPEGGGDNNDSQRSGVTPSSAP
2	Q5TC82-D2	827-1020	194		AKPKDVVAAGSVEMMNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTSKTIYQGAGPMQAMAPQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERISMSEVASHGKPLPSAEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQSQPPPPPPPKWPGMI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.35

(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	6gmhQ	0.74	1.62	0.050	0.758	model1_6gmhQ.pdb.gz
2	6tedQ	0.64	4.90	0.063	0.741	model1_6tedQ.pdb.gz
3	6af0A	0.55	6.24	0.054	0.690	model1_6af0A.pdb.gz
4	4bujB	0.45	7.20	0.050	0.601	model1_4bujB.pdb.gz
5	6z2wE	0.38	8.71	0.045	0.558	model1_6z2wE.pdb.gz
6	5fvmA	0.37	8.16	0.045	0.527	model1_5fvmA.pdb.gz
7	5u1sA	0.37	6.75	0.043	0.474	model1_5u1sA.pdb.gz
8	6sytA	0.36	7.87	0.039	0.496	model1_6sytA.pdb.gz
9	6emkA	0.35	8.84	0.047	0.524	model1_6emkA.pdb.gz
10	4uzyA	0.34	6.19	0.039	0.432	model1_4uzyA.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	0.96	heterocyclic compound binding
GO:0097159	0.96	organic cyclic compound binding
GO:0003723	0.95	RNA binding
GO:0044822	0.92	poly(A) RNA binding
GO:0003729	0.74	mRNA binding
GO:0003730	0.62	mRNA 3'-UTR binding
GO:0003824	0.60	catalytic activity
GO:0035613	0.58	RNA stem-loop binding
GO:0016740	0.57	transferase activity
GO:0004842	0.56	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:0009987	0.97	cellular process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0044238	0.94	primary metabolic process
GO:0065007	0.85	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0019222	0.80	regulation of metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0010468	0.76	regulation of gene expression
GO:0048518	0.75	positive regulation of biological process
GO:0065008	0.74	regulation of biological quality
GO:0010608	0.74	posttranscriptional regulation of gene expression
GO:0048522	0.73	positive regulation of cellular process
GO:0006139	0.70	nucleobase-containing compound metabolic process
GO:0048519	0.69	negative regulation of biological process
GO:0031323	0.69	regulation of cellular metabolic process
GO:0016070	0.69	RNA metabolic process
GO:0080090	0.68	regulation of primary metabolic process
GO:0050896	0.67	response to stimulus
GO:0048523	0.67	negative regulation of cellular process
GO:0009892	0.67	negative regulation of metabolic process
GO:2000112	0.66	regulation of cellular macromolecule biosynthetic process
GO:0051246	0.66	regulation of protein metabolic process
GO:0051171	0.66	regulation of nitrogen compound metabolic process
GO:0031324	0.66	negative regulation of cellular metabolic process
GO:0032268	0.65	regulation of cellular protein metabolic process
GO:0010605	0.65	negative regulation of macromolecule metabolic process
GO:0051248	0.64	negative regulation of protein metabolic process
GO:0051172	0.64	negative regulation of nitrogen compound metabolic process
GO:0031327	0.64	negative regulation of cellular biosynthetic process
GO:0016071	0.64	mRNA metabolic process
GO:0010629	0.64	negative regulation of gene expression
GO:0010558	0.64	negative regulation of macromolecule biosynthetic process
GO:2000113	0.63	negative regulation of cellular macromolecule biosynthetic process
GO:0032269	0.63	negative regulation of cellular protein metabolic process
GO:0006417	0.63	regulation of translation
GO:0061158	0.62	3'-UTR-mediated mRNA destabilization
GO:0010604	0.62	positive regulation of macromolecule metabolic process
GO:0051252	0.61	regulation of RNA metabolic process
GO:0042221	0.61	response to chemical
GO:0031325	0.61	positive regulation of cellular metabolic process
GO:0051173	0.60	positive regulation of nitrogen compound metabolic process
GO:0010033	0.60	response to organic substance
GO:0009896	0.60	positive regulation of catabolic process
GO:0070887	0.59	cellular response to chemical stimulus
GO:0051254	0.59	positive regulation of RNA metabolic process
GO:0034097	0.59	response to cytokine
GO:0000956	0.59	nuclear-transcribed mRNA catabolic process
GO:0071347	0.58	cellular response to interleukin-1
GO:0061014	0.58	positive regulation of mRNA catabolic process
GO:0000288	0.58	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0048583	0.56	regulation of response to stimulus
GO:0009966	0.55	regulation of 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	0.79	organelle
GO:0043229	0.77	intracellular organelle
GO:0044444	0.75	cytoplasmic part
GO:0032991	0.67	macromolecular complex
GO:0030529	0.64	intracellular ribonucleoprotein complex
GO:0043232	0.62	intracellular non-membrane-bounded organelle
GO:0010494	0.61	cytoplasmic stress granule
GO:0000932	0.55	cytoplasmic mRNA processing body
GO:0005737	0.52	cytoplasm

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	2ckjA	0.202	9.88	0.016	0.327	1.17.1.4 1.17.3.2	NA
2	0.060	2dqmA	0.237	7.72	0.016	0.326	3.4.11.2	NA
3	0.060	2ow6A	0.236	9.50	0.041	0.374	3.2.1.114	590
4	0.060	1llwA	0.259	9.13	0.035	0.393	1.4.7.1	NA
5	0.060	2qf7B	0.240	9.14	0.036	0.366	6.4.1.1	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:

No Binding sites was predicted

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

	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.