D-I-TASSER Q8IWU6

D-I-TASSER results for Q8IWU6

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

Summary of the Protein

Uniprot ID: Q8IWU6
Protein Name: Extracellular sulfatase Sulf-1
Gene Name: SULF1

Input Sequence in FASTA format

>Q8IWU6 (871 residues)
MKYSCCALVLAVLGTELLGSLCSTVRSPRFRGRIQQERKNIRPNIILVLTDDQDVELGSL
QVMNKTRKIMEHGGATFINAFVTTPMCCPSRSSMLTGKYVHNHNVYTNNENCSSPSWQAM
HEPRTFAVYLNNTGYRTAFFGKYLNEYNGSYIPPGWREWLGLIKNSRFYNYTVCRNGIKE
KHGFDYAKDYFTDLITNESINYFKMSKRMYPHRPVMMVISHAAPHGPEDSAPQFSKLYPN
ASQHITPSYNYAPNMDKHWIMQYTGPMLPIHMEFTNILQRKRLQTLMSVDDSVERLYNML
VETGELENTYIIYTADHGYHIGQFGLVKGKSMPYDFDIRVPFFIRGPSVEPGSIVPQIVL
NIDLAPTILDIAGLDTPPDVDGKSVLKLLDPEKPGNRFRTNKKAKIWRDTFLVERGKFLR
KKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKGPS
DLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLRNQGTPKYKPRFVHT
RQTRSLSVEFEGEIYDINLEEEEELQVLQPRNIAKRHDEGHKGPRDLQASSGGNRGRMLA
DSSNAVGPPTTVRVTHKCFILPNDSIHCERELYQSARAWKDHKAYIDKEIEALQDKIKNL
REVRGHLKRRKPEECSCSKQSYYNKEKGVKKQEKLKSHLHPFKEAAQEVDSKLQLFKENN
RRRKKERKEKRRQRKGEECSLPGLTCFTHDNNHWQTAPFWNLGSFCACTSSNNNTYWCLR
TVNETHNFLFCEFATGFLEYFDMNTDPYQLTNTVHTVERGILNQLHVQLMELRSCQGYKQ
CNPRPKNLDVGNKDGGSYDLHRGQLWDGWEG

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	Q8IWU6-D1	1-418,675-871	615		MKYSCCALVLAVLGTELLGSLCSTVRSPRFRGRIQQERKNIRPNIILVLTDDQDVELGSLQVMNKTRKIMEHGGATFINAFVTTPMCCPSRSSMLTGKYVHNHNVYTNNENCSSPSWQAMHEPRTFAVYLNNTGYRTAFFGKYLNEYNGSYIPPGWREWLGLIKNSRFYNYTVCRNGIKEKHGFDYAKDYFTDLITNESINYFKMSKRMYPHRPVMMVISHAAPHGPEDSAPQFSKLYPNASQHITPSYNYAPNMDKHWIMQYTGPMLPIHMEFTNILQRKRLQTLMSVDDSVERLYNMLVETGELENTYIIYTADHGYHIGQFGLVKGKSMPYDFDIRVPFFIRGPSVEPGSIVPQIVLNIDLAPTILDIAGLDTPPDVDGKSVLKLLDPEKPGNRFRTNKKAKIWRDTFLVERGKFCSCSKQSYYNKEKGVKKQEKLKSHLHPFKEAAQEVDSKLQLFKENNRRRKKERKEKRRQRKGEECSLPGLTCFTHDNNHWQTAPFWNLGSFCACTSSNNNTYWCLRTVNETHNFLFCEFATGFLEYFDMNTDPYQLTNTVHTVERGILNQLHVQLMELRSCQGYKQCNPRPKNLDVGNKDGGSYDLHRGQLWDGWEG
2	Q8IWU6-D2	419-526	108		LRKKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKGPSDLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLR
3	Q8IWU6-D3	527-674	148		NQGTPKYKPRFVHTRQTRSLSVEFEGEIYDINLEEEEELQVLQPRNIAKRHDEGHKGPRDLQASSGGNRGRMLADSSNAVGPPTTVRVTHKCFILPNDSIHCERELYQSARAWKDHKAYIDKEIEALQDKIKNLREVRGHLKRRKPEE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.41

(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	6s21A	0.46	2.88	0.187	0.489	model1_6s21A.pdb.gz
2	6j66A	0.46	2.89	0.176	0.487	model1_6j66A.pdb.gz
3	5g2vA	0.46	2.69	0.264	0.482	model1_5g2vA.pdb.gz
4	6pt4B	0.45	3.43	0.192	0.491	model1_6pt4B.pdb.gz
5	4upiA	0.45	3.13	0.197	0.488	model1_4upiA.pdb.gz
6	4uplA	0.45	3.14	0.179	0.488	model1_4uplA.pdb.gz
7	4upkA	0.45	3.37	0.214	0.490	model1_4upkA.pdb.gz
8	2vqrA	0.45	3.32	0.189	0.487	model1_2vqrA.pdb.gz
9	4uphA	0.45	3.30	0.189	0.484	model1_4uphA.pdb.gz
10	4ug4A	0.45	3.14	0.191	0.480	model1_4ug4A.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	1.00	catalytic activity
GO:0016787	0.99	hydrolase activity
GO:0008484	0.98	sulfuric ester hydrolase activity
GO:0004065	0.84	arylsulfatase activity
GO:0008449	0.81	N-acetylglucosamine-6-sulfatase 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	0.98	cellular process
GO:0044699	0.92	single-organism process
GO:0008152	0.92	metabolic process
GO:0065007	0.90	biological regulation
GO:0044763	0.90	single-organism cellular process
GO:0071704	0.89	organic substance metabolic process
GO:0050789	0.89	regulation of biological process
GO:0044237	0.89	cellular metabolic process
GO:0050794	0.88	regulation of cellular process
GO:1901135	0.87	carbohydrate derivative metabolic process
GO:0043170	0.87	macromolecule metabolic process
GO:0032502	0.86	developmental process
GO:0048856	0.85	anatomical structure development
GO:0048519	0.85	negative regulation of biological process
GO:0051239	0.84	regulation of multicellular organismal process
GO:0048523	0.84	negative regulation of cellular process
GO:0044767	0.84	single-organism developmental process
GO:0006790	0.84	sulfur compound metabolic process
GO:0048731	0.83	system development
GO:0044707	0.83	single-multicellular organism process
GO:0048869	0.82	cellular developmental process
GO:0007166	0.82	cell surface receptor signaling pathway
GO:0003008	0.82	system process
GO:2000026	0.81	regulation of multicellular organismal development
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0032879	0.80	regulation of localization
GO:0048518	0.78	positive regulation of biological process
GO:0030334	0.78	regulation of cell migration
GO:0048522	0.77	positive regulation of cellular process
GO:0048583	0.76	regulation of response to stimulus
GO:0045995	0.76	regulation of embryonic development
GO:0030336	0.76	negative regulation of cell migration
GO:0030201	0.76	heparan sulfate proteoglycan metabolic process
GO:0009968	0.75	negative regulation of signal transduction
GO:0009967	0.74	positive regulation of signal transduction
GO:0090288	0.73	negative regulation of cellular response to growth factor stimulus
GO:0048513	0.73	animal organ development
GO:0030111	0.73	regulation of Wnt signaling pathway
GO:0060384	0.72	innervation
GO:0060348	0.72	bone development
GO:0051216	0.72	cartilage development
GO:0048706	0.72	embryonic skeletal system development
GO:0040037	0.72	negative regulation of fibroblast growth factor receptor signaling pathway
GO:0035860	0.72	glial cell-derived neurotrophic factor receptor signaling pathway
GO:0030177	0.72	positive regulation of Wnt signaling pathway
GO:0014846	0.72	esophagus smooth muscle contraction
GO:0002063	0.72	chondrocyte development
GO:0001822	0.72	kidney development
GO:2000027	0.70	regulation of organ morphogenesis
GO:0050678	0.70	regulation of epithelial cell proliferation
GO:0080090	0.69	regulation of primary metabolic process
GO:0060255	0.69	regulation of macromolecule metabolic process
GO:0031323	0.69	regulation of cellular metabolic process
GO:0090092	0.68	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0006355	0.68	regulation of transcription, DNA-templated
GO:0060686	0.67	negative regulation of prostatic bud formation
GO:0048010	0.67	vascular endothelial growth factor receptor signaling pathway
GO:0030513	0.67	positive regulation of BMP signaling pathway
GO:0016525	0.67	negative regulation of angiogenesis
GO:0001937	0.67	negative regulation of endothelial cell proliferation
GO:0009653	0.65	anatomical structure morphogenesis
GO:0048661	0.63	positive regulation of smooth muscle cell proliferation
GO:0036022	0.63	limb joint morphogenesis
GO:0007155	0.63	cell adhesion
GO:0001502	0.63	cartilage condensation

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	0.99	cell part
GO:0044424	0.97	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0043227	0.95	membrane-bounded organelle
GO:0044421	0.92	extracellular region part
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0016020	0.85	membrane
GO:0005615	0.83	extracellular space
GO:0009986	0.82	cell surface
GO:0005783	0.82	endoplasmic reticulum
GO:0044425	0.78	membrane part
GO:0005794	0.75	Golgi apparatus
GO:0045121	0.74	membrane raft

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	1n2lA	0.409	3.34	0.188	0.447	3.1.6.8	NA
2	0.060	1b0pA	0.303	7.79	0.033	0.442	1.2.7.1	NA
3	0.060	2vz8B	0.288	8.34	0.021	0.441	2.3.1.85	NA
4	0.060	1p49A	0.408	4.28	0.184	0.462	3.1.6.2	131,136
5	0.060	1qbaA	0.283	8.65	0.033	0.447	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:

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.