D-I-TASSER Q99784

D-I-TASSER results for Q99784

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

Summary of the Protein

Uniprot ID: Q99784
Protein Name: Noelin
Gene Name: OLFM1

Input Sequence in FASTA format

>Q99784 (485 residues)
MSVPLLKIGVVLSTMAMITNWMSQTLPSLVGLNTTKLSAAGGGTLDRSTGVLPTNPEESW
QVYSSAQDSEGRCICTVVAPQQTMCSRDARTKQLRQLLEKVQNMSQSIEVLDRRTQRDLQ
YVEKMENQMKGLESKFKQVEESHKQHLARQFKAIKAKMDELRPLIPVLEEYKADAKLVLQ
FKEEVQNLTSVLNELQEEIGAYDYDELQSRVSNLEERLRACMQKLACGKLTGISDPVTVK
TSGSRFGSWMTDPLAPEGDNRVWYMDGYHNNRFVREYKSMVDFMNTDNFTSHRLPHPWSG
TGQVVYNGSIYFNKFQSHIIIRFDLKTETILKTRSLDYAGYNNMYHYAWGGHSDIDLMVD
ESGLWAVYATNQNAGNIVVSRLDPVSLQTLQTWNTSYPKRSAGEAFIICGTLYVTNGYSG
GTKVHYAYQTNASTYEYIDIPFQNKYSHISMLDYNPKDRALYAWNNGHQILYNVTLFHVI
RSDEL

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	Q99784-D1	1-130	130		MSVPLLKIGVVLSTMAMITNWMSQTLPSLVGLNTTKLSAAGGGTLDRSTGVLPTNPEESWQVYSSAQDSEGRCICTVVAPQQTMCSRDARTKQLRQLLEKVQNMSQSIEVLDRRTQRDLQYVEKMENQMK
2	Q99784-D2	131-225	95		GLESKFKQVEESHKQHLARQFKAIKAKMDELRPLIPVLEEYKADAKLVLQFKEEVQNLTSVLNELQEEIGAYDYDELQSRVSNLEERLRACMQKL
3	Q99784-D3	226-244,401-485	104		ACGKLTGISDPVTVKTSGSSAGEAFIICGTLYVTNGYSGGTKVHYAYQTNASTYEYIDIPFQNKYSHISMLDYNPKDRALYAWNNGHQILYNVTLFHVIRSDEL
4	Q99784-D4	245-336	92		RFGSWMTDPLAPEGDNRVWYMDGYHNNRFVREYKSMVDFMNTDNFTSHRLPHPWSGTGQVVYNGSIYFNKFQSHIIIRFDLKTETILKTRSL
5	Q99784-D5	337-400	64		DYAGYNNMYHYAWGGHSDIDLMVDESGLWAVYATNQNAGNIVVSRLDPVSLQTLQTWNTSYPKR

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.54

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4wxqA	0.46	1.85	0.376	0.480	model1_4wxqA.pdb.gz
2	5afbA2	0.45	2.29	0.393	0.476	model1_5afbA2.pdb.gz
3	4d77A	0.44	2.15	0.320	0.468	model1_4d77A.pdb.gz
4	5amoA	0.44	2.29	0.846	0.464	model1_5amoA.pdb.gz
5	1kitA	0.42	5.37	0.039	0.550	model1_1kitA.pdb.gz
6	3bykA	0.42	4.35	0.055	0.509	model1_3bykA.pdb.gz
7	6m0dA	0.42	4.20	0.081	0.505	model1_6m0dA.pdb.gz
8	1w18B	0.42	4.18	0.073	0.505	model1_1w18B.pdb.gz
9	5wbiA	0.41	5.80	0.051	0.573	model1_5wbiA.pdb.gz
10	4d47A	0.41	4.02	0.072	0.493	model1_4d47A.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:0004872	0.35	receptor activity
GO:0099600	0.33	transmembrane receptor activity
GO:0004871	0.31	signal transducer activity
GO:0038023	0.30	signaling receptor 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	0.96	cellular process
GO:0044699	0.95	single-organism process
GO:0044763	0.94	single-organism cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0044767	0.85	single-organism developmental process
GO:0050794	0.84	regulation of cellular process
GO:0048869	0.82	cellular developmental process
GO:0016043	0.81	cellular component organization
GO:0048518	0.80	positive regulation of biological process
GO:0051094	0.79	positive regulation of developmental process
GO:0048522	0.77	positive regulation of cellular process
GO:0045595	0.73	regulation of cell differentiation
GO:0051128	0.72	regulation of cellular component organization
GO:0045597	0.72	positive regulation of cell differentiation
GO:0051130	0.71	positive regulation of cellular component organization
GO:0048519	0.68	negative regulation of biological process
GO:0009653	0.68	anatomical structure morphogenesis
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0051239	0.67	regulation of multicellular organismal process
GO:0032989	0.67	cellular component morphogenesis
GO:0010770	0.67	positive regulation of cell morphogenesis involved in differentiation
GO:2000026	0.66	regulation of multicellular organismal development
GO:0051240	0.66	positive regulation of multicellular organismal process
GO:0060317	0.59	cardiac epithelial to mesenchymal transition
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0010468	0.59	regulation of gene expression
GO:0009892	0.59	negative regulation of metabolic process
GO:0010718	0.58	positive regulation of epithelial to mesenchymal transition
GO:0010629	0.58	negative regulation of gene expression
GO:0010628	0.58	positive regulation of gene expression
GO:0003190	0.58	atrioventricular valve formation

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	0.80	cell part
GO:0005623	0.64	cell
GO:0044424	0.56	intracellular part

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

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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	1s0kA	0.366	4.67	0.065	0.462	3.2.1.18	361
2	0.060	1uv4A	0.374	4.01	0.121	0.454	3.2.1.99	311
3	0.060	3beqB	0.361	4.45	0.032	0.445	3.2.1.18	NA
4	0.060	1usrA	0.370	5.08	0.040	0.484	3.2.1.18	NA
5	0.060	1ingA	0.359	4.26	0.044	0.437	3.2.1.18	215

	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

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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	3gvjA	0.376	4.73	0.073	0.470	0.30	UUU	complex1.pdb.gz	248,250,251,262
2	0.01	1w2tC	0.379	4.06	0.053	0.460	0.34	UUU	complex2.pdb.gz	247,248,303,452
3	0.01	1w2tA	0.379	4.06	0.053	0.460	0.18	UUU	complex3.pdb.gz	365,366,411,430
4	0.01	3ldkA	0.379	4.17	0.067	0.462	0.37	SUC	complex4.pdb.gz	247,265,302,355,464
5	0.01	3akhA	0.388	3.59	0.073	0.458	0.17	AHR	complex5.pdb.gz	336,363,365,367

	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.