D-I-TASSER A6NLU0

D-I-TASSER results for A6NLU0

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

Summary of the Protein

Uniprot ID: A6NLU0
Protein Name: Ret finger protein-like 4A
Gene Name: RFPL4A

Input Sequence in FASTA format

>A6NLU0 (287 residues)
MAEHFKQIIRCPVCLKDLEEAVQLKCGYACCLQCLNSLQKEPDGEGLLCRFCSVVSQKDD
IKPKYKLRALVSIIKELEPKLKSVLTMNPRMRKFQVDMTFDVDTANNYLIISEDLRSFRS
GDLSQNRKEQAERFDTALCVLGTPRFTSGRHYWEVDVGTSQVWDVGVCKESVNRQGKIVL
SSEHGFLTVGCREGKVFAASTVPMTPLWVSPQLHRVGIFLDVGMRSIAFYNVSDGCHIYT
FIEIPVCEPWRPFFAHKRGSQDDQSILSICSVINPSAASAPVSSEGK

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	A6NLU0-D1	1-87	87		MAEHFKQIIRCPVCLKDLEEAVQLKCGYACCLQCLNSLQKEPDGEGLLCRFCSVVSQKDDIKPKYKLRALVSIIKELEPKLKSVLTM
2	A6NLU0-D2	88-287	200		NPRMRKFQVDMTFDVDTANNYLIISEDLRSFRSGDLSQNRKEQAERFDTALCVLGTPRFTSGRHYWEVDVGTSQVWDVGVCKESVNRQGKIVLSSEHGFLTVGCREGKVFAASTVPMTPLWVSPQLHRVGIFLDVGMRSIAFYNVSDGCHIYTFIEIPVCEPWRPFFAHKRGSQDDQSILSICSVINPSAASAPVSSEGK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	2fbeC	0.65	1.57	0.944	0.683	model1_2fbeC.pdb.gz
2	4cg4A	0.64	1.73	0.286	0.669	model1_4cg4A.pdb.gz
3	2wl1A	0.63	1.21	0.374	0.652	model1_2wl1A.pdb.gz
4	4n7iA	0.62	1.48	0.368	0.645	model1_4n7iA.pdb.gz
5	3kb5A	0.61	1.76	0.270	0.645	model1_3kb5A.pdb.gz
6	2iwgB	0.61	1.05	0.430	0.624	model1_2iwgB.pdb.gz
7	4b8eA	0.59	1.71	0.246	0.624	model1_4b8eA.pdb.gz
8	4wvmA3	0.57	2.20	0.245	0.624	model1_4wvmA3.pdb.gz
9	2lm3A	0.56	2.09	0.269	0.603	model1_2lm3A.pdb.gz
10	4qolA	0.30	5.96	0.014	0.498	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:0046872	0.81	metal ion binding
GO:0008270	0.80	zinc ion binding
GO:0003824	0.75	catalytic activity
GO:0016740	0.73	transferase activity
GO:0004842	0.72	ubiquitin-protein transferase activity
GO:0004871	0.62	signal transducer activity
GO:0004872	0.61	receptor activity
GO:0038023	0.60	signaling receptor activity
GO:0038187	0.58	pattern recognition receptor activity
GO:0042802	0.55	identical protein binding
GO:0019899	0.53	enzyme binding
GO:0008092	0.53	cytoskeletal protein binding
GO:0046983	0.50	protein dimerization 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	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0009987	0.91	cellular process
GO:0050794	0.88	regulation of cellular process
GO:0071704	0.83	organic substance metabolic process
GO:0044238	0.83	primary metabolic process
GO:0048518	0.82	positive regulation of biological process
GO:0044237	0.82	cellular metabolic process
GO:0019222	0.82	regulation of metabolic process
GO:0043170	0.81	macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0080090	0.80	regulation of primary metabolic process
GO:0060255	0.80	regulation of macromolecule metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0048522	0.78	positive regulation of cellular process
GO:0048583	0.77	regulation of response to stimulus
GO:0019538	0.76	protein metabolic process
GO:0006464	0.74	cellular protein modification process
GO:0050896	0.73	response to stimulus
GO:0010468	0.73	regulation of gene expression
GO:2001141	0.72	regulation of RNA biosynthetic process
GO:0048519	0.72	negative regulation of biological process
GO:0048523	0.71	negative regulation of cellular process
GO:0016567	0.71	protein ubiquitination
GO:0006355	0.71	regulation of transcription, DNA-templated
GO:0065009	0.69	regulation of molecular function
GO:0032268	0.69	regulation of cellular protein metabolic process
GO:0044093	0.68	positive regulation of molecular function
GO:0009966	0.68	regulation of signal transduction
GO:0002376	0.68	immune system process
GO:0043900	0.67	regulation of multi-organism process
GO:0010604	0.67	positive regulation of macromolecule metabolic process
GO:0048584	0.66	positive regulation of response to stimulus
GO:0031325	0.66	positive regulation of cellular metabolic process
GO:0080134	0.65	regulation of response to stress
GO:0044699	0.65	single-organism process
GO:0031399	0.65	regulation of protein modification process
GO:0051090	0.64	regulation of sequence-specific DNA binding transcription factor activity
GO:0006950	0.64	response to stress
GO:0002682	0.64	regulation of immune system process
GO:1902531	0.63	regulation of intracellular signal transduction
GO:0051247	0.63	positive regulation of protein metabolic process
GO:0031347	0.63	regulation of defense response
GO:0031324	0.63	negative regulation of cellular metabolic process
GO:0009967	0.63	positive regulation of signal transduction
GO:0000209	0.63	protein polyubiquitination
GO:0050776	0.62	regulation of immune response
GO:0032270	0.62	positive regulation of cellular protein metabolic process
GO:0051239	0.61	regulation of multicellular organismal process
GO:0032101	0.61	regulation of response to external stimulus
GO:0010605	0.61	negative regulation of macromolecule metabolic process
GO:1902533	0.60	positive regulation of intracellular signal transduction
GO:0001817	0.60	regulation of cytokine production
GO:0050792	0.59	regulation of viral process
GO:0043122	0.59	regulation of I-kappaB kinase/NF-kappaB signaling
GO:1903900	0.58	regulation of viral life cycle
GO:0045088	0.58	regulation of innate immune response
GO:0031401	0.58	positive regulation of protein modification process
GO:0010033	0.58	response to organic substance
GO:0006952	0.58	defense response
GO:0001932	0.58	regulation of protein phosphorylation
GO:0051128	0.57	regulation of cellular component organization
GO:0044763	0.57	single-organism cellular process
GO:0031327	0.57	negative regulation of cellular biosynthetic process
GO:0002684	0.57	positive regulation of immune system process
GO:0051241	0.56	negative regulation of multicellular organismal process
GO:0050778	0.56	positive regulation of immune response
GO:0002831	0.56	regulation of response to biotic stimulus
GO:1903901	0.55	negative regulation of viral life cycle
GO:0048585	0.55	negative regulation of response to stimulus
GO:0045089	0.55	positive regulation of innate immune response
GO:0043408	0.55	regulation of MAPK cascade
GO:0002253	0.55	activation of immune response
GO:0001934	0.55	positive regulation of protein phosphorylation
GO:0001818	0.55	negative regulation of cytokine production
GO:1902679	0.54	negative regulation of RNA biosynthetic process
GO:0051129	0.54	negative regulation of cellular component organization
GO:0032879	0.54	regulation of localization
GO:0030162	0.54	regulation of proteolysis
GO:0010629	0.54	negative regulation of gene expression
GO:0010506	0.54	regulation of autophagy
GO:0007165	0.54	signal transduction
GO:0002218	0.54	activation of innate immune response
GO:1902186	0.53	regulation of viral release from host cell
GO:0046782	0.53	regulation of viral transcription
GO:0034097	0.53	response to cytokine
GO:0050790	0.52	regulation of catalytic activity
GO:0046596	0.52	regulation of viral entry into host cell
GO:0043254	0.52	regulation of protein complex assembly
GO:1900225	0.51	regulation of NLRP3 inflammasome complex assembly
GO:0032651	0.51	regulation of interleukin-1 beta 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:0007166	0.51	cell surface receptor signaling pathway
GO:2000116	0.50	regulation of cysteine-type endopeptidase activity
GO:1900015	0.50	regulation of cytokine production involved in inflammatory response
GO:0071640	0.50	regulation of macrophage inflammatory protein 1 alpha production
GO:0032692	0.50	negative regulation of interleukin-1 production
GO:0032682	0.50	negative regulation of chemokine production
GO:0032655	0.50	regulation of interleukin-12 production
GO:0016043	0.50	cellular component organization
GO:0010950	0.50	positive regulation of endopeptidase 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 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	0.87	organelle
GO:0043229	0.81	intracellular organelle
GO:0044444	0.76	cytoplasmic part
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005737	0.66	cytoplasm
GO:0032991	0.58	macromolecular complex
GO:0005634	0.58	nucleus
GO:0044422	0.56	organelle part
GO:0044446	0.55	intracellular organelle part
GO:0043232	0.51	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	2ayhA	0.425	3.65	0.065	0.537	3.2.1.73	154,230
2	0.060	1o4zB	0.455	4.11	0.066	0.589	3.2.1.81	235
3	0.060	1wd4A	0.410	4.83	0.074	0.596	3.2.1.55	NA
4	0.060	1uaiA	0.418	3.84	0.083	0.540	4.2.2.11	116
5	0.060	3b9jJ	0.229	6.46	0.028	0.387	1.17.1.4 1.17.3.2	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	0.07	2vol2	0.605	1.07	0.421	0.620	0.96	III	complex1.pdb.gz	108,120,138,139,164,190
2	0.01	1lu1A	0.461	3.93	0.066	0.599	0.63	ADE	complex2.pdb.gz	142,167,169,186
3	0.01	1sbfA	0.448	3.95	0.071	0.582	0.48	UUU	complex3.pdb.gz	169,186,251

	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.