D-I-TASSER Q6ZWI9

D-I-TASSER results for Q6ZWI9

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

Summary of the Protein

Uniprot ID: Q6ZWI9
Protein Name: Ret finger protein-like 4B
Gene Name: RFPL4B

Input Sequence in FASTA format

>Q6ZWI9 (263 residues)
MAKRLQAELSCPVCLDFFSCSISLSCTHVFCFDCIQRYILENHDFRAMCPLCRDVVKVPA
LEEWQVSVLTLMTKQHNSRLEQSLHVREELRHFREDVTLDAATASSLLVFSNDLRSAQCK
KIHHDLTKDPRLACVLGTPCFSSGQHYWEVEVGEVKSWSLGVCKEPADRKSNDLFPEHGF
WISMKAGAIHANTHLERIPASPRLRRVGIFLDADLEEIQFFDVDNNVLIYTHDGFFSLEL
LCPFFCLELLGEGESGNVLTICP

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	Q6ZWI9-D1	1-92	92		MAKRLQAELSCPVCLDFFSCSISLSCTHVFCFDCIQRYILENHDFRAMCPLCRDVVKVPALEEWQVSVLTLMTKQHNSRLEQSLHVREELRH
2	Q6ZWI9-D2	93-263	171		FREDVTLDAATASSLLVFSNDLRSAQCKKIHHDLTKDPRLACVLGTPCFSSGQHYWEVEVGEVKSWSLGVCKEPADRKSNDLFPEHGFWISMKAGAIHANTHLERIPASPRLRRVGIFLDADLEEIQFFDVDNNVLIYTHDGFFSLELLCPFFCLELLGEGESGNVLTICP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	4cg4A	0.69	2.80	0.283	0.764	model1_4cg4A.pdb.gz
2	2wl1A	0.65	1.67	0.343	0.681	model1_2wl1A.pdb.gz
3	3kb5A	0.63	1.93	0.242	0.677	model1_3kb5A.pdb.gz
4	4n7iA	0.63	1.76	0.343	0.669	model1_4n7iA.pdb.gz
5	2iwgB	0.63	1.15	0.304	0.650	model1_2iwgB.pdb.gz
6	2fbeC	0.62	1.74	0.360	0.665	model1_2fbeC.pdb.gz
7	4b8eA	0.61	2.06	0.251	0.662	model1_4b8eA.pdb.gz
8	4wvmA3	0.60	2.50	0.210	0.662	model1_4wvmA3.pdb.gz
9	2lm3A	0.59	2.15	0.249	0.639	model1_2lm3A.pdb.gz
10	4qolA	0.32	6.10	0.065	0.544	model1_4qolA.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	0.83	catalytic activity
GO:0016740	0.80	transferase activity
GO:0004842	0.79	ubiquitin-protein transferase activity
GO:0046872	0.69	metal ion binding
GO:0008270	0.68	zinc ion binding
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0008092	0.55	cytoskeletal protein binding
GO:0003676	0.55	nucleic acid 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	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0009987	0.92	cellular process
GO:0050794	0.91	regulation of cellular process
GO:0048518	0.86	positive regulation of biological process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0080090	0.83	regulation of primary metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0048522	0.82	positive regulation of cellular process
GO:0008152	0.82	metabolic process
GO:0071704	0.81	organic substance metabolic process
GO:0044238	0.81	primary metabolic process
GO:0044237	0.79	cellular metabolic process
GO:0043170	0.78	macromolecule metabolic process
GO:0048583	0.77	regulation of response to stimulus
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0050896	0.76	response to stimulus
GO:0044699	0.75	single-organism process
GO:0048519	0.74	negative regulation of biological process
GO:0019538	0.74	protein metabolic process
GO:0010468	0.74	regulation of gene expression
GO:0065009	0.73	regulation of molecular function
GO:0048523	0.73	negative regulation of cellular process
GO:2001141	0.72	regulation of RNA biosynthetic process
GO:0044093	0.72	positive regulation of molecular function
GO:0032268	0.72	regulation of cellular protein metabolic process
GO:0006355	0.71	regulation of transcription, DNA-templated
GO:0002376	0.71	immune system process
GO:0044267	0.70	cellular protein metabolic process
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0048584	0.69	positive regulation of response to stimulus
GO:0006464	0.69	cellular protein modification process
GO:0032270	0.68	positive regulation of cellular protein metabolic process
GO:0080134	0.67	regulation of response to stress
GO:0044763	0.67	single-organism cellular process
GO:0023051	0.67	regulation of signaling
GO:0010646	0.67	regulation of cell communication
GO:0009966	0.66	regulation of signal transduction
GO:0043900	0.65	regulation of multi-organism process
GO:0031347	0.65	regulation of defense response
GO:0016567	0.65	protein ubiquitination
GO:0002682	0.65	regulation of immune system process
GO:0050776	0.63	regulation of immune response
GO:0032101	0.63	regulation of response to external stimulus
GO:0006950	0.63	response to stress
GO:0051090	0.61	regulation of sequence-specific DNA binding transcription factor activity
GO:0016043	0.61	cellular component organization
GO:0051239	0.60	regulation of multicellular organismal process
GO:0002684	0.60	positive regulation of immune system process
GO:0051128	0.59	regulation of cellular component organization
GO:0050778	0.59	positive regulation of immune response
GO:0009967	0.59	positive regulation of signal transduction
GO:1902531	0.58	regulation of intracellular signal transduction
GO:0010033	0.58	response to organic substance
GO:0002253	0.58	activation of immune response
GO:0001817	0.58	regulation of cytokine production
GO:0051129	0.57	negative regulation of cellular component organization
GO:0051241	0.56	negative regulation of multicellular organismal process
GO:0043933	0.56	macromolecular complex subunit organization
GO:1902533	0.55	positive regulation of intracellular signal transduction
GO:0048585	0.55	negative regulation of response to stimulus
GO:0010506	0.55	regulation of autophagy
GO:0007165	0.55	signal transduction
GO:0001818	0.55	negative regulation of cytokine production
GO:0043122	0.54	regulation of I-kappaB kinase/NF-kappaB signaling
GO:0034097	0.54	response to cytokine
GO:0032501	0.54	multicellular organismal process
GO:0006952	0.54	defense response
GO:0044087	0.53	regulation of cellular component biogenesis
GO:0030162	0.53	regulation of proteolysis
GO:0006955	0.53	immune response
GO:0050792	0.52	regulation of viral process
GO:0050790	0.52	regulation of catalytic activity
GO:0045087	0.52	innate immune response
GO:0044707	0.52	single-multicellular organism process
GO:0043254	0.52	regulation of protein complex assembly
GO:0032651	0.52	regulation of interleukin-1 beta production
GO:0032502	0.52	developmental process
GO:0022607	0.52	cellular component assembly
GO:0007166	0.52	cell surface receptor signaling pathway
GO:2000116	0.51	regulation of cysteine-type endopeptidase activity
GO:1903900	0.51	regulation of viral life cycle
GO:1900225	0.51	regulation of NLRP3 inflammasome complex assembly
GO:1900015	0.51	regulation of cytokine production involved in inflammatory response
GO:0071640	0.51	regulation of macrophage inflammatory protein 1 alpha production
GO:0051179	0.51	localization
GO:0032692	0.51	negative regulation of interleukin-1 production
GO:0032682	0.51	negative regulation of chemokine production
GO:0032655	0.51	regulation of interleukin-12 production
GO:0032102	0.51	negative regulation of response to external stimulus
GO:0031348	0.51	negative regulation of defense response
GO:0031333	0.51	negative regulation of protein complex assembly
GO:0010950	0.51	positive regulation of endopeptidase activity
GO:0044765	0.50	single-organism transport
GO:0006461	0.50	protein complex assembly

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:0043226	0.89	organelle
GO:0043229	0.84	intracellular organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0044444	0.78	cytoplasmic part
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005737	0.70	cytoplasm
GO:0044446	0.65	intracellular organelle part
GO:0032991	0.65	macromolecular complex
GO:0005634	0.64	nucleus
GO:0043232	0.57	intracellular non-membrane-bounded organelle

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	1st8A	0.481	4.33	0.073	0.643	3.2.1.80	217
2	0.060	1umzA	0.457	3.47	0.066	0.578	2.4.1.207	NA
3	0.060	2agsA	0.432	4.18	0.021	0.586	3.2.1.18	143
4	0.060	1uaiA	0.441	4.16	0.036	0.593	4.2.2.11	115
5	0.060	2aeyA	0.482	4.44	0.077	0.650	3.2.1.80	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	0.05	2iwg3	0.630	1.15	0.304	0.650	0.75	III	complex1.pdb.gz	121,132,159,173,183,249
2	0.01	1y9mA	0.482	4.48	0.046	0.646	0.41	UUU	complex2.pdb.gz	109,136,137
3	0.01	3azzB	0.477	4.13	0.059	0.635	0.42	LGC	complex3.pdb.gz	159,161,179,181,183

	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.