D-I-TASSER P25685-D2

D-I-TASSER results for P25685-D2

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

Input Sequence in FASTA format

>P25685 (75 residues)
SGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGG
FTNVNFGRSRSAQEP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| SGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEP
Prediction	CCCCCCCCCSSSSSCCCHHHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	998889982478971898999999919999178972789986656667876667777777788888887778998
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| SGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEP
Prediction	856567454231313232452045214473223412444545461534432443443442244654556456658
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSSCCCHHHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
SGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGFTNVNFGRSRSAQEP

3bogA

0.15

0.13

4.48

2.06

SPARKS-K

AHGVGCPGTAGAAGSV---------GGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGGRGGKGGSGTPKGADGA

3pbiA

0.12

0.11

3.77

1.11

MapAlign

QGPSKGVDSGANTVGFDCSGLVRYAIPRSGDQYLIFYGPGGGQHVTLYLGMLEASGSAGKVTVSPVR--------

6z5nA

1.00

0.40

11.20

1.77

HHsearch

SGGGANGTSFSYTFHGDPHAMFAEFFGGRN---------------------------------------------

3pbiA

0.08

3.16

0.75

CEthreader

GGSLQGPSKGVDSGANTVGFDCSGLVRFSGRGDLIFYGPGGGQHVTLYLQMLEASGSAGKVTVSPVRKAGMTPFV

3nv9A3

0.08

3.16

0.58

EigenThreader

EQRAVAKTQFGNNSVGFPGILKGALIVRARAADVAMQAIKDGVALTWQQVYDIAEHDIKEARESAQLLQDSKHIV

5yqjA

0.12

0.08

2.81

0.33

FFAS-3D

------------TIHASLGRVVNILFGKDVSYIMAILKAQKNSDISPIPVLVDSPTVSEGK--------------

3boiA

0.15

0.13

4.48

1.87

SPARKS-K

HGVNGCPGTAGAAGSV---------GGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGGRGGKGGSGTPKGADGA

5yqiA

0.04

0.01

0.71

0.51

CNFpred

-----------ANINAPLGKVVNLLYGEDVYYERILK--------------------------------------

4uc1A

0.04

2.05

1.00

DEthreader

DPRWVFPWTLLMLAAMRVAQLEGSGQAL-AFYAAQLAFN-LWVVMLVAATMWAFFQLDTWAGVLFVPYWATLNEM

4ogdA2

0.08

0.07

2.59

0.66

MapAlign

SQVIADKRVVGVCLTGSERGGASIAEKKTTLELLPFGGIKHSGYGRELSELGFTSFVNE----------------

(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	0.5332

(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	2uv9D	0.48	3.78	0.062	0.840	model1_2uv9D.pdb.gz
2	3jpzA	0.48	4.03	0.041	0.920	model1_3jpzA.pdb.gz
3	6k8xA	0.47	4.13	0.070	0.893	model1_6k8xA.pdb.gz
4	3l8qA	0.47	3.95	0.113	0.853	model1_3l8qA.pdb.gz
5	1tyjA	0.45	3.86	0.071	0.840	model1_1tyjA.pdb.gz
6	1zv9A	0.43	3.98	0.087	0.813	model1_1zv9A.pdb.gz
7	2b59A	0.41	3.92	0.028	0.813	model1_2b59A.pdb.gz
8	1w0iA	0.40	4.68	0.015	0.840	model1_1w0iA.pdb.gz
9	3ghpA	0.38	4.58	0.074	0.800	model1_3ghpA.pdb.gz
10	1e8uB	0.38	4.54	0.014	0.853	model1_1e8uB.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:0051087	0.93	chaperone binding
GO:0051082	0.70	unfolded protein binding
GO:0098772	0.50	molecular function regulator

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	0.80	cellular process
GO:0065007	0.76	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0050896	0.68	response to stimulus
GO:0048523	0.68	negative regulation of cellular process
GO:0006950	0.67	response to stress
GO:0006457	0.64	protein folding
GO:0010033	0.59	response to organic substance
GO:0006986	0.58	response to unfolded protein
GO:0050790	0.57	regulation of catalytic activity
GO:0070389	0.56	chaperone cofactor-dependent protein refolding
GO:0051345	0.56	positive regulation of hydrolase activity
GO:0051128	0.56	regulation of cellular component organization
GO:0090084	0.55	negative regulation of inclusion body assembly
GO:0032781	0.55	positive regulation of ATPase 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 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:0043226	0.92	organelle
GO:0043227	0.89	membrane-bounded organelle
GO:0043229	0.82	intracellular organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005634	0.78	nucleus
GO:0044444	0.60	cytoplasmic part
GO:0044422	0.51	organelle part
GO:0044446	0.50	intracellular organelle 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

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	1ga0A	0.450	4.20	0.068	0.920	3.5.2.6	NA
2	0.060	1h2aL	0.381	4.46	0.043	0.853	1.12.2.1	NA
3	0.060	2zc7A	0.450	4.22	0.081	0.933	3.5.2.6	NA
4	0.060	1mroB	0.391	4.39	0.077	0.853	2.8.4.1	28
5	0.060	2uv8G	0.421	4.12	0.078	0.800	2.3.1.86	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	0.01	1l2sA	0.447	4.20	0.108	0.907	0.38	STC	complex1.pdb.gz	18,22,25
2	0.01	2hduA	0.374	4.85	0.122	0.840	0.21	F12	complex2.pdb.gz	20,23,32
3	0.01	1llbB	0.342	4.71	0.053	0.747	0.13	PCN	complex3.pdb.gz	54,55,56,57
4	0.01	2r9wB	0.323	4.48	0.081	0.707	0.10	UUU	complex4.pdb.gz	52,53,54
5	0.01	1kvlA	0.451	4.23	0.095	0.933	0.22	KCP	complex5.pdb.gz	18,19,22
6	0.01	1i5qA	0.448	4.42	0.122	0.947	0.14	MOX	complex6.pdb.gz	16,25,26,27
7	0.01	1fcmB	0.414	4.58	0.097	0.840	0.11	CXU	complex7.pdb.gz	17,26,27
8	0.01	2hduB	0.347	4.36	0.056	0.707	0.38	F12	complex8.pdb.gz	16,20,27
9	0.01	3jq3A	0.459	4.37	0.055	0.920	0.13	ADP	complex9.pdb.gz	19,28,32

	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.