D-I-TASSER Q05397-D1

D-I-TASSER results for Q05397-D1

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

Input Sequence in FASTA format

>Q05397 (96 residues)
MAAAYLDPNLNHTPNSSTKTHLGTGMERSPGAMERVLKVFHYFESNSEPTTWASIIRHGD
ATDVRGIIQKIVDSHKVKHVACYGFRLSHLRSEEVH

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAAAYLDPNLNHTPNSSTKTHLGTGMERSPGAMERVLKVFHYFESNSEPTTWASIIRHGDATDVRGIIQKIVDSHKVKHVACYGFRLSHLRSEEVH
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCSSSSSSSSSSCCCCCCCCC
Confidence	974335899898989886445457756798529999999987524889998743112477302788999999975010578753354047644589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAAAYLDPNLNHTPNSSTKTHLGTGMERSPGAMERVLKVFHYFESNSEPTTWASIIRHGDATDVRGIIQKIVDSHKVKHVACYGFRLSHLRSEEVH
Prediction	754432444254445454444244436444432430130022134536544244314435344034104412534414211222121442557648
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCSSSSSSSSSSCCCCCCCCC
MAAAYLDPNLNHTPNSSTKTHLGTGMERSPGAMERVLKVFHYFESNSEPTTWASIIRHGDATDVRGIIQKIVDSHKVKHVACYGFRLSHLRSEEVH

6cgr8

0.11

0.10

3.78

1.00

DEthreader

LFNVAAADARVTY-GGLVILAFVDDALGGPGA-AFLYLVFTYRQRRDQELCCVYVIKSQLPPGLEPALERLFGRLITNT-ACTYAAFAELGRPGEW

6ty3A3

0.90

0.58

16.40

1.19

SPARKS-K

----------------------------------RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVH

6tgbA1

0.06

0.04

1.80

0.79

MapAlign

------------------------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGGGGGGGGGGGGGGGGGGGGG

2jxtA

0.12

0.08

2.95

0.64

CEthreader

-----------------------------MKMKTKIFRVKGKFLMGDKLQPFTKELNAIREEEIYERLYSEFGSHRVPRSKVKIEEIEEISPEEVQ

2j0kB

0.90

0.58

16.40

1.24

MUSTER

----------------------------------RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVH

6ty3A3

0.90

0.58

16.40

2.92

HHsearch

----------------------------------RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVH

6ty3A3

0.90

0.58

16.40

1.17

FFAS-3D

----------------------------------RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVH

4ekuA1

0.26

0.22

6.75

0.67

EigenThreader

-----ELGPAE-----PMVVVPV----DVEKEDVRILKVCFYSNSFNPGK-NFKLVKCTVQTEIREIITSILLSGRIRLAECYGLRLKHMKSDEIH

2j0jA

0.90

0.58

16.40

1.32

CNFpred

----------------------------------RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVH

6b438

0.10

0.09

3.49

1.00

DEthreader

FLTPTFTKVAWY--GPMLTLPCLVDDE-PAGLNVTIYASLVYLRVNQRPSMALTFFQSKGFAEVVAMIKDHFTDVRTKY-RLVFGAVCTLGACGPW

(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	0.6319

(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	6b438	0.58	3.57	0.085	0.885	model1_6b438.pdb.gz
2	6w2df	0.56	3.29	0.067	0.802	model1_6w2df.pdb.gz
3	5vkuj	0.55	3.82	0.096	0.896	model1_5vkuj.pdb.gz
4	6m6gS	0.55	3.75	0.077	0.865	model1_6m6gS.pdb.gz
5	6cgr8	0.55	3.85	0.098	0.885	model1_6cgr8.pdb.gz
6	7bqx5	0.55	3.20	0.067	0.802	model1_7bqx5.pdb.gz
7	5zapY	0.54	3.86	0.054	0.875	model1_5zapY.pdb.gz
8	6qbyA	0.53	3.98	0.063	0.896	model1_6qbyA.pdb.gz
9	6j4uA	0.53	3.95	0.063	0.896	model1_6j4uA.pdb.gz
10	5fwiC2	0.53	4.26	0.075	0.927	model1_5fwiC2.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:0004713	1.00	protein tyrosine kinase activity
GO:0005102	0.96	receptor binding
GO:0004715	0.95	non-membrane spanning protein tyrosine kinase 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:0044763	0.97	single-organism cellular process
GO:0065007	0.95	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0016043	0.89	cellular component organization
GO:0008152	0.89	metabolic process
GO:0007165	0.89	signal transduction
GO:0050896	0.88	response to stimulus
GO:0044767	0.88	single-organism developmental process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0044238	0.88	primary metabolic process
GO:0007166	0.88	cell surface receptor signaling pathway
GO:0046777	0.87	protein autophosphorylation
GO:0042127	0.87	regulation of cell proliferation
GO:0048869	0.84	cellular developmental process
GO:0045087	0.83	innate immune response
GO:0038083	0.83	peptidyl-tyrosine autophosphorylation
GO:0007173	0.83	epidermal growth factor receptor signaling pathway
GO:0048523	0.80	negative regulation of cellular process
GO:0043066	0.78	negative regulation of apoptotic process
GO:0030155	0.78	regulation of cell adhesion
GO:0001525	0.78	angiogenesis
GO:0030154	0.72	cell differentiation
GO:0007155	0.70	cell adhesion
GO:0007010	0.64	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:0044425	0.92	membrane part
GO:0031234	0.91	extrinsic component of cytoplasmic side of plasma membrane

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	2iveA	0.487	4.01	0.022	0.812	1.3.3.4	37
2	0.060	1l9mB	0.492	4.74	0.094	0.948	2.3.2.13	NA
3	0.060	1coyA	0.481	3.81	0.054	0.812	1.1.3.6	NA
4	0.060	1vlbA	0.478	4.16	0.049	0.844	1.2.99.7	61
5	0.060	1b37B	0.444	4.30	0.053	0.823	1.5.3.15 1.5.3.14	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	0.02	2v7xA	0.511	3.78	0.110	0.833	0.35	MET	complex1.pdb.gz	59,63,66
2	0.01	2cbxA	0.510	3.71	0.098	0.823	0.27	CC5	complex2.pdb.gz	26,59,67
3	0.01	2c5hC	0.503	3.81	0.096	0.833	0.25	3D1	complex3.pdb.gz	59,62,64,67
4	0.01	3ng7X	0.508	3.63	0.086	0.812	0.22	HNK	complex4.pdb.gz	62,63,65
5	0.01	2r45A	0.390	3.78	0.057	0.646	0.28	IMD	complex5.pdb.gz	58,66,67
6	0.01	2r45B	0.479	4.11	0.011	0.844	0.20	2PG	complex6.pdb.gz	25,55,56,58
7	0.01	2r4eA	0.511	3.73	0.011	0.812	0.24	PO4	complex7.pdb.gz	56,57,60
8	0.01	3nk1X	0.506	3.65	0.075	0.812	0.13	GP7	complex8.pdb.gz	52,68,69,72
9	0.01	2r45A	0.390	3.78	0.057	0.646	0.16	2PG	complex9.pdb.gz	27,56,57,59
10	0.01	3ng7X	0.508	3.63	0.086	0.812	0.21	GP7	complex10.pdb.gz	37,67,68,71

	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.