D-I-TASSER A6NEE1-D1

D-I-TASSER results for A6NEE1-D1

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

Input Sequence in FASTA format

>A6NEE1 (118 residues)
MFTSKSNSVSPSPSLEQADSDALDISTKVQLYGVLWKRPFGRPSAKWSRRFFIIKESFLL
YYSESEKKSFETNKYFNIHPKGVIPLGGCLVEPKEEPSMPYAMKISHQDFHGNILLAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MFTSKSNSVSPSPSLEQADSDALDISTKVQLYGVLWKRPFGRPSAKWSRRFFIIKESFLLYYSESEKKSFETNKYFNIHPKGVIPLGGCLVEPKEEPSMPYAMKISHQDFHGNILLAA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSCCCSSSSSCCCCCCCSSSSSSCCCCCCSSSSSC
Confidence	9656667767887667776010378983215548864257987775067699992989999932544444444556788517998687299974688996389996478872699809
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MFTSKSNSVSPSPSLEQADSDALDISTKVQLYGVLWKRPFGRPSAKWSRRFFIIKESFLLYYSESEKKSFETNKYFNIHPKGVIPLGGCLVEPKEEPSMPYAMKISHQDFHGNILLAA
Prediction	7344664645344565564364142465143402022354646455043010003522000034556553555554544020002034040443757734100302276243210303
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSSSSCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSCCCSSSSSCCCCCCCSSSSSSCCCCCCSSSSSC
MFTSKSNSVSPSPSLEQADSDALDISTKVQLYGVLWKRPFGRPSAKWSRRFFIIKESFLLYYSESEKKSFETNKYFNIHPKGVIPLGGCLVEPKEEPSMPYAMKISHQDFHGNILLAA

2p0fA

0.16

0.12

3.97

1.00

DEthreader

-----------------------SH-E-VEKSGLLNMTKIAKLRKNWGPSWVVLTGNSLVFYRE-PP-PTAPSGWGPSRPESSVDLRGAALAHGRHSSRRNVLHIRTI-PGHEFLLQS

2p0fA

0.16

0.13

4.21

1.21

SPARKS-K

-------------------------SHEVEKSGLLNMTKIRKLRKNWGPSWVVLTGNSLVFYREPPPTAPSSGWGPASRPESSVDLRGAALAHRHLSSRRNVLHIRTIPG-HEFLLQS

1ntyA

0.13

0.10

3.50

0.55

MapAlign

------------------------SQGELILQESFQVWDPKTLIRKGRERHLFLFEMSLVFSKE----VKDSSGRSKYLYKSKLFTSELGVTEH-VEGDPCKFALWVGRTPNKIVLKA

1ntyA2

0.12

4.15

0.46

CEthreader

-SVPKRANDAMHLSMLEGFDENIESQGELILQESFQVWDPKTLIRKGRERHLFLFEMSLVFSKE----VKDSSGRSKYLYKSKLFTSELGVTE-HVEGDPCKFALWVGTSDNKIVLKA

2yryA

0.23

0.19

6.11

1.28

MUSTER

-------GSSGSSGGKRSHSMKRNPNAPVTKAGWLFKQA-SSGVKQWNKRWFVLVDRCLFYYKDEKEES----------ILGSIPLLSFRVAAVQPSSRKHTFKAEHAGVRTYFFSAE

2d9zA

0.13

0.09

3.22

1.37

HHsearch

---------------------GSSGSSGMVKEGWMVHY--TSRDNLRKRHYWRLDSKCLTLFQNES----------GSKYYKEIPLSEILRISSPRGSNPHCFEIITDT--MVYFVGE

2r09A2

0.27

0.18

5.47

1.20

FFAS-3D

---------------------------NPDREGWLLKL--GGRVKTWKRRWFILTDNCLYYFEYTTDK----------EPRGIIPLENLSIREVEDPRKPNCFELYNPSHKVVYRISA

4c0aA

0.10

0.09

3.48

0.70

EigenThreader

RGVDDGEDIPELKTNEDGLGCVLSLPHRRLVCYCRLFEVPDPQKLGLHQREIFLFNDLLVVT-KIFQKKKNSV---TYSFRQSFSLYGMQVLLFENQYYPNGIRLTSVPGALINFNAP

5l81A

0.18

0.13

4.13

1.38

CNFpred

----------------------------PELKDHLRIFRPRKTLKGYRQYWVVFKDTTLSYYKSQDEAPG--------DPTQQLNLKGCEVVPDVNVGQKFCIKLLVPSGMSEIYLRC

2dfkA

0.16

0.13

4.20

1.00

DEthreader

----------------EGDDIDRS--SELIYTGEMAWIYQ-PYG-RNQQRVFFLFDHQMVLCKKDLRRD----I---LYYKGRIDMDKYEVIDIEDGSMKNAFKLHNKETEEVHLFFA

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6985

(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 DeepPotential, 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	2p0fA	0.66	1.81	0.167	0.763	model1_2p0fA.pdb.gz
2	2otxA	0.65	2.03	0.163	0.754	model1_2otxA.pdb.gz
3	1x86A	0.63	2.62	0.163	0.780	model1_1x86A.pdb.gz
4	1xcgE2	0.62	3.08	0.172	0.805	model1_1xcgE2.pdb.gz
5	3odoA2	0.62	3.32	0.150	0.814	model1_3odoA2.pdb.gz
6	2pz1A	0.62	2.53	0.179	0.754	model1_2pz1A.pdb.gz
7	1uprA	0.62	2.38	0.256	0.729	model1_1uprA.pdb.gz
8	1ntyA	0.61	2.94	0.140	0.754	model1_1ntyA.pdb.gz
9	1x05A	0.61	2.45	0.255	0.720	model1_1x05A.pdb.gz
10	3a8pA	0.60	1.53	0.203	0.669	model1_3a8pA.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:0098772	0.70	molecular function regulator
GO:0097159	0.57	organic cyclic compound binding
GO:1901363	0.56	heterocyclic compound binding
GO:0030695	0.52	GTPase regulator activity
GO:0019899	0.52	enzyme binding
GO:0008047	0.52	enzyme activator activity
GO:0005543	0.52	phospholipid binding
GO:0043167	0.51	ion binding
GO:0035091	0.51	phosphatidylinositol 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:0009987	0.84	cellular process
GO:0065007	0.83	biological regulation
GO:0044699	0.80	single-organism process
GO:0050789	0.79	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0051179	0.74	localization
GO:0044763	0.74	single-organism cellular process
GO:0008152	0.74	metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044237	0.72	cellular metabolic process
GO:0044238	0.71	primary metabolic process
GO:0006810	0.71	transport
GO:0016043	0.67	cellular component organization
GO:0007165	0.65	signal transduction
GO:0048583	0.62	regulation of response to stimulus
GO:0044710	0.62	single-organism metabolic process
GO:0016192	0.62	vesicle-mediated transport
GO:0048518	0.60	positive regulation of biological process
GO:0009966	0.57	regulation of signal transduction
GO:0065009	0.56	regulation of molecular function
GO:0051128	0.55	regulation of cellular component organization
GO:0050790	0.55	regulation of catalytic activity
GO:0048584	0.55	positive regulation of response to stimulus
GO:0048523	0.55	negative regulation of cellular process
GO:0044765	0.55	single-organism transport
GO:0051336	0.54	regulation of hydrolase activity
GO:0032502	0.54	developmental process
GO:0006796	0.54	phosphate-containing compound metabolic process
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0048522	0.53	positive regulation of cellular process
GO:0044767	0.53	single-organism developmental process
GO:0019222	0.53	regulation of metabolic process
GO:0008104	0.53	protein localization
GO:0007166	0.53	cell surface receptor signaling pathway
GO:0006996	0.53	organelle organization
GO:0080090	0.52	regulation of primary metabolic process
GO:0071702	0.52	organic substance transport
GO:0065008	0.52	regulation of biological quality
GO:0043085	0.52	positive regulation of catalytic activity
GO:0033043	0.52	regulation of organelle organization
GO:0031323	0.52	regulation of cellular metabolic process
GO:0009968	0.52	negative regulation of signal transduction
GO:0051345	0.51	positive regulation of hydrolase activity
GO:0048869	0.51	cellular developmental process
GO:0048856	0.51	anatomical structure development
GO:0045184	0.51	establishment of protein localization
GO:0043087	0.51	regulation of GTPase activity
GO:0035556	0.51	intracellular signal transduction
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:1902532	0.50	negative regulation of intracellular signal transduction
GO:0051239	0.50	regulation of multicellular organismal process
GO:0030154	0.50	cell differentiation
GO:0019220	0.50	regulation of phosphate metabolic process
GO:0015031	0.50	protein transport
GO:0007010	0.50	cytoskeleton organization

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:0044424	1.00	intracellular part
GO:0016020	0.90	membrane
GO:0005737	0.85	cytoplasm
GO:0044444	0.81	cytoplasmic part
GO:0044446	0.73	intracellular organelle part
GO:0005886	0.70	plasma membrane
GO:0043226	0.67	organelle
GO:0043229	0.62	intracellular organelle
GO:0005829	0.60	cytosol
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.51	intracellular 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	1y7wA	0.443	4.85	0.073	0.805	4.2.1.1	95
2	0.060	2zkmX	0.512	2.91	0.051	0.652	3.1.4.11	NA
3	0.060	3d9wA	0.469	4.24	0.051	0.729	2.3.1.5	NA
4	0.060	1jnrA	0.461	4.86	0.065	0.839	1.8.99.2	NA
5	0.060	2vfbA	0.445	3.88	0.054	0.703	2.3.1.5	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	0.52	2i5cB	0.566	1.75	0.311	0.627	1.23	IP5	complex1.pdb.gz	37,39,40,41,50,61,81
2	0.23	2uvmA	0.609	2.33	0.176	0.720	1.09	GVF	complex2.pdb.gz	37,39,40,41,48,50,82,84,113
3	0.04	2p0hA	0.657	1.80	0.157	0.754	0.98	I3S	complex3.pdb.gz	45,47,99

	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.