D-I-TASSER A0A0G2JMS6

D-I-TASSER results for A0A0G2JMS6

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

Summary of the Protein

Uniprot ID: A0A0G2JMS6
Protein Name: Uncharacterized protein
Gene Name: NA

Input Sequence in FASTA format

>A0A0G2JMS6 (1433 residues)
MTGSHLSHDSWQYVLLIPSVLQEGSLDKACAQLFNLTESVVLTVSLNYGEVQTKIFEENV
TGENFFKCISFEVPQARSDPLAFITFSAKGATLNLEERRSVAIRSRENVVFVQTDKPTYK
PGQKDVNGIAQFFLDTYTFTYPNITLKDPQNNRIFQWQNVTSFRNITQLSFQLISEPMFG
DYWIVVKRNSRKTVTHQFAVKRYVLPKFEVTVNAPQTVTISDDEFQVDVCAKYTFGQPVQ
GKTQIRVCREYFSSSNCEKNDNEICEQFIAQLENGCVSQIVNTKVFQLYRSGLFMTFHVA
VIVTEFGTGNYCMQISEKTSVFITQLLGTVNFENMDTFYRRGISYFGTLKFSDPNNVPMV
NKLLQLELNDEFIGNYTTDENGEAQFSIDTSDIFDPEFNLKATYVRPKSCYLPSWLTPQY
LDAHFLVSRFYSRTNSFLKIVPEPKQLECNHQKVVTVHYSLNSEAYEDDSNVKFFYLVSL
SHDSGNFQHRISSSPIYTAWNGNFSFPLSISADLAPAAVLFVYTLHPSGEIVADSVRFQV
DKCFKHKVNIKFSNEQGLPGSNASLYLQAAPVLFCALGAVDGNVLLLKSEQQLSAESVYN
MVPSIEPYGYFYHGLNLDDGKEDPCIPQRDMFYNGLYYTPVSNYGDGDIYNIVRNMGLKV
FTNLHYRKPEVCVMERRLPLPKPLYLETENYGPMHSVPSRIACRGENADYVEQAIIQTVR
TNFPETWMWDLVSVDSSGSANLSFLIPDTITQWEASGFCVNGDVGFGISSTTTLEVSQPF
FIEIASPFSVVQNEQFDLIVNAFSYLNTCVEISVQVEESQNYEANINTWKINGSEVIQAG
GRKTNIWTIIPKKLGKVNITVVAESKQSSACPNEGMEQQKLNWKDTVVKSFLVEPEGIEK
ERTQSFLICTEGAKASKQGVLDLPNDVVEGSARGFFTVVGDILGLAMQNLVVLQMPYGGG
EQNAALLASDTYVLDYLKSTEQLTEEVQSKAFFLLSNGYQRQLSFKNSDGSYSVFWQQNQ
KGSIWLSALTFKTLERMKKFVFIDENVQKQTLIWLSSQQKTSGCFKNDGQLFNHAWEGGD
EEDISLTAYVVGMFFEAGLNSTFPALRNALFCLEAALDSGVTNGYNHAILAYAFALAGKE
KQVESLLQTLDQSATKLNNVIYWERERKPKTEEFPSFIPWAPSAQTEKSCYVLLAVISRK
IPDLTYASKIVQWLAQQMNSHGGFSSNQVINVGLILIAILGEEGLFSKNQNTVTFSSEGS
SEIFQVNGHNRLLVQRSEVTQAPGQYTVDVEGRGCTFIQATLKYNVLLPKKASGFSLSLE
IVKNYSLTVFDLTVNLKYTGIRNKSSMVVIDVKMLSGFTPTMSSIEELENKGQVMKTEVK
NDHVLFYLENVFGRADSFTFSVEQSNLVFNIQPAPGMVYDYYEKDGEAFLLTN

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	A0A0G2JMS6-D1	1-622,719-777	681		MTGSHLSHDSWQYVLLIPSVLQEGSLDKACAQLFNLTESVVLTVSLNYGEVQTKIFEENVTGENFFKCISFEVPQARSDPLAFITFSAKGATLNLEERRSVAIRSRENVVFVQTDKPTYKPGQKDVNGIAQFFLDTYTFTYPNITLKDPQNNRIFQWQNVTSFRNITQLSFQLISEPMFGDYWIVVKRNSRKTVTHQFAVKRYVLPKFEVTVNAPQTVTISDDEFQVDVCAKYTFGQPVQGKTQIRVCREYFSSSNCEKNDNEICEQFIAQLENGCVSQIVNTKVFQLYRSGLFMTFHVAVIVTEFGTGNYCMQISEKTSVFITQLLGTVNFENMDTFYRRGISYFGTLKFSDPNNVPMVNKLLQLELNDEFIGNYTTDENGEAQFSIDTSDIFDPEFNLKATYVRPKSCYLPSWLTPQYLDAHFLVSRFYSRTNSFLKIVPEPKQLECNHQKVVTVHYSLNSEAYEDDSNVKFFYLVSLSHDSGNFQHRISSSPIYTAWNGNFSFPLSISADLAPAAVLFVYTLHPSGEIVADSVRFQVDKCFKHKVNIKFSNEQGLPGSNASLYLQAAPVLFCALGAVDGNVLLLKSEQQLSAESVYNMVPSIEPYGYFYHGLNLDDGKEVRTNFPETWMWDLVSVDSSGSANLSFLIPDTITQWEASGFCVNGDVGFGISSTTTLEVS
2	A0A0G2JMS6-D2	623-718,778-1433	752		DPCIPQRDMFYNGLYYTPVSNYGDGDIYNIVRNMGLKVFTNLHYRKPEVCVMERRLPLPKPLYLETENYGPMHSVPSRIACRGENADYVEQAIIQTQPFFIEIASPFSVVQNEQFDLIVNAFSYLNTCVEISVQVEESQNYEANINTWKINGSEVIQAGGRKTNIWTIIPKKLGKVNITVVAESKQSSACPNEGMEQQKLNWKDTVVKSFLVEPEGIEKERTQSFLICTEGAKASKQGVLDLPNDVVEGSARGFFTVVGDILGLAMQNLVVLQMPYGGGEQNAALLASDTYVLDYLKSTEQLTEEVQSKAFFLLSNGYQRQLSFKNSDGSYSVFWQQNQKGSIWLSALTFKTLERMKKFVFIDENVQKQTLIWLSSQQKTSGCFKNDGQLFNHAWEGGDEEDISLTAYVVGMFFEAGLNSTFPALRNALFCLEAALDSGVTNGYNHAILAYAFALAGKEKQVESLLQTLDQSATKLNNVIYWERERKPKTEEFPSFIPWAPSAQTEKSCYVLLAVISRKIPDLTYASKIVQWLAQQMNSHGGFSSNQVINVGLILIAILGEEGLFSKNQNTVTFSSEGSSEIFQVNGHNRLLVQRSEVTQAPGQYTVDVEGRGCTFIQATLKYNVLLPKKASGFSLSLEIVKNYSLTVFDLTVNLKYTGIRNKSSMVVIDVKMLSGFTPTMSSIEELENKGQVMKTEVKNDHVLFYLENVFGRADSFTFSVEQSNLVFNIQPAPGMVYDYYEKDGEAFLLTN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.62

(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	3cu7A	0.79	4.97	0.147	0.890	model1_3cu7A.pdb.gz
2	2b39A	0.73	5.65	0.184	0.867	model1_2b39A.pdb.gz
3	2pn5A	0.65	6.36	0.163	0.778	model1_2pn5A.pdb.gz
4	6tavA	0.55	6.35	0.223	0.653	model1_6tavA.pdb.gz
5	4u48A	0.55	6.84	0.081	0.675	model1_4u48A.pdb.gz
6	4acqA	0.53	5.08	0.230	0.596	model1_4acqA.pdb.gz
7	3prxB	0.51	5.74	0.138	0.586	model1_3prxB.pdb.gz
8	6ysqA	0.50	5.91	0.122	0.583	model1_6ysqA.pdb.gz
9	7ad7A	0.46	2.37	0.193	0.477	model1_7ad7A.pdb.gz
10	4fxgB	0.39	3.29	0.172	0.416	model1_4fxgB.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:0030414	0.62	peptidase inhibitor activity
GO:0005102	0.58	receptor binding
GO:0004866	0.51	endopeptidase inhibitor activity
GO:0001664	0.51	G-protein coupled receptor 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:0050896	0.76	response to stimulus
GO:0044699	0.70	single-organism process
GO:0065007	0.65	biological regulation
GO:0050789	0.64	regulation of biological process
GO:0048583	0.60	regulation of response to stimulus
GO:0006950	0.60	response to stress
GO:0019222	0.59	regulation of metabolic process
GO:0051246	0.58	regulation of protein metabolic process
GO:0050794	0.56	regulation of cellular process
GO:0002682	0.55	regulation of immune system process
GO:0050776	0.54	regulation of immune response
GO:0048518	0.54	positive regulation of biological process
GO:0048584	0.53	positive regulation of response to stimulus
GO:0032268	0.53	regulation of cellular protein metabolic process
GO:0032101	0.53	regulation of response to external stimulus
GO:0030162	0.53	regulation of proteolysis
GO:0006955	0.53	immune response
GO:0080134	0.52	regulation of response to stress
GO:0044767	0.52	single-organism developmental process
GO:0048856	0.51	anatomical structure development
GO:0009987	0.51	cellular process
GO:2000257	0.50	regulation of protein activation cascade
GO:0070613	0.50	regulation of protein processing
GO:0032501	0.50	multicellular organismal process
GO:0009966	0.50	regulation of signal transduction
GO:0006959	0.50	humoral immune response
GO:0002920	0.50	regulation of humoral immune response
GO:0002697	0.50	regulation of immune effector process
GO:0002673	0.50	regulation of acute inflammatory response
GO:0002252	0.50	immune effector process

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:0044421	0.89	extracellular region part
GO:0005615	0.78	extracellular space
GO:0005576	0.71	extracellular region
GO:0044464	0.67	cell part
GO:0043227	0.65	membrane-bounded organelle
GO:0070062	0.62	extracellular exosome

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	2e1qA	0.208	10.08	0.030	0.322	1.17.3.2 1.17.1.4	NA
2	0.060	3hmjA	0.232	10.12	0.036	0.363	2.3.1.86	NA
3	0.060	1ug9A	0.227	7.18	0.063	0.287	3.2.1.70	NA
4	0.060	2uv8G	0.234	10.17	0.039	0.365	2.3.1.86	NA
5	0.060	2fhcA	0.219	9.68	0.064	0.334	3.2.1.41	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.