D-I-TASSER Q13422-D3

D-I-TASSER results for Q13422-D3

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

Input Sequence in FASTA format

>Q13422 (74 residues)
SNVAKRKSSMPQKFLGDKGLSDTPYDSSASYEKENEMMKSHVMDQAINNAINYLGAESLR
PLVQTPPGGSEVVP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| SNVAKRKSSMPQKFLGDKGLSDTPYDSSASYEKENEMMKSHVMDQAINNAINYLGAESLRPLVQTPPGGSEVVP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Confidence	96221467897434567778767666777752145553144204554334442152224665569998767799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| SNVAKRKSSMPQKFLGDKGLSDTPYDSSASYEKENEMMKSHVMDQAINNAINYLGAESLRPLVQTPPGGSEVVP
Prediction	86456455444451336542451426444525454523554334432443143233731332353445446448
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
SNVAKRKSSMPQKFLGDKGLSDTPYDSSASYEKENEMMKSHVMDQAINNAINYLGAESLRPLVQTPPGGSEVVP

5yfpE6

0.12

0.09

3.31

1.06

SPARKS-K

-------TVNYDKEINKRVLLD-KYKEKLSHLYILEILKIMFLGI-VDSYMEIALEVAYWKICKV---------

6ycxA

0.10

0.08

3.01

1.00

DEthreader

------ELKYVQLGYKQEGAKILIREKLVEWENCVSVIEAAILKHKYKQKVNKN-IPSLLQHIRMVAQ------

2hguG

0.10

0.09

3.53

0.49

CEthreader

KAAQELALITGQKPAVTRAKKPIGLRVTLRRDRMWIFLEKNSFDGRGNYNTTAETDEEARALLELLGFPFRK--

5araT

0.04

2.09

0.60

EigenThreader

YIVKKYGASVGEFADKLNEQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQKRHYLFDVQRNNIAMALEVTYRE

6pasA4

0.11

3.89

0.25

FFAS-3D

-IFCEELDVYKVETIGDAYCVASGLHRKVETHAPQIAWMALRMVETCAQHLTHEGNPKMRIGLHTGTVLAGVV-

5yfpE1

0.07

2.82

0.99

SPARKS-K

KTDNFLGGLTVNEFVQKDHRNDVLIDANTKNTNEKDQDAIREAIWKQLDPKPYIRTFESTLKELKNLNEETLNK

5cqcA

0.30

0.14

4.09

0.59

CNFpred

------------------------------LVKEVDCLMDSSLGKLVQFHLKNLGAESLQKLV-----------

4y21A

0.07

2.81

1.00

DEthreader

KSDCLNVG-KYVAFRVPEADPQIGDAEASGTLKELQVKLNNVLDELSHVFATSFQPHIVTMTIVLLYTQATDLL

6j27A2

0.07

2.82

0.79

MapAlign

DQGYVTPESTLARVALAWNWGDLEGKEVLVLGDDVVLDADPRIVRFLERAAKAEGLPLEAHVHDLREPLPEAWV

1m0fB

0.12

0.11

3.82

0.71

MUSTER

EQLTKNQRKKRDEIEAGKSYCSRRFGGATCDDKSAQIYAR--FDK---NDWRIQPAEFYRFHDAEVNTFGYF--

(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	0.4148

(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	2wyeB2	0.45	3.78	0.076	0.878	model1_2wyeB2.pdb.gz
2	1e3aB3	0.45	3.72	0.060	0.865	model1_1e3aB3.pdb.gz
3	4yf9C	0.45	3.72	0.062	0.865	model1_4yf9C.pdb.gz
4	3k3wB2	0.44	3.88	0.059	0.865	model1_3k3wB2.pdb.gz
5	4hsrB2	0.42	4.01	0.045	0.878	model1_4hsrB2.pdb.gz
6	1oqzB2	0.37	4.28	0.069	0.716	model1_1oqzB2.pdb.gz
7	1ru3A1	0.36	4.10	0.088	0.716	model1_1ru3A1.pdb.gz
8	1o12A	0.36	4.08	0.000	0.689	model1_1o12A.pdb.gz
9	3op0A3	0.32	4.24	0.132	0.662	model1_3op0A3.pdb.gz
10	1lp3A	0.31	4.55	0.127	0.703	model1_1lp3A.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:0003677	1.00	DNA binding
GO:0044212	0.99	transcription regulatory region DNA binding
GO:0003700	0.99	transcription factor activity, sequence-specific DNA 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:0065007	0.94	biological regulation
GO:0050789	0.94	regulation of biological process
GO:0050794	0.93	regulation of cellular process
GO:0006355	0.91	regulation of transcription, DNA-templated
GO:0048518	0.89	positive regulation of biological process
GO:0006357	0.89	regulation of transcription from RNA polymerase II promoter
GO:0045893	0.88	positive regulation of transcription, DNA-templated
GO:0045944	0.87	positive regulation of transcription from RNA polymerase II promoter
GO:0009987	0.51	cellular 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:0043229	1.00	intracellular organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0044446	0.60	intracellular organelle part
GO:0032991	0.51	macromolecular complex

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	2v4uA	0.419	3.97	0.074	0.811	6.3.4.2	NA
2	0.060	5pfkA	0.410	4.30	0.029	0.797	2.7.1.11	17,55
3	0.060	2qymA	0.403	4.20	0.045	0.797	3.1.4.17	47
4	0.060	1wd4A	0.422	3.98	0.090	0.838	3.2.1.55	63
5	0.060	2vf3B	0.408	4.23	0.057	0.797	2.7.1.148	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	1wwzB	0.415	3.67	0.070	0.730	0.16	ACO	complex1.pdb.gz	17,18,19,37,38,64,66
2	0.01	3srcB	0.452	3.78	0.076	0.878	0.19	28N	complex2.pdb.gz	15,16,19
3	0.01	3l91B	0.450	3.84	0.091	0.878	0.15	OCA	complex3.pdb.gz	1,16,53,54,55
4	0.01	3b9xC	0.320	4.55	0.015	0.676	0.17	NOS	complex4.pdb.gz	18,48,51
5	0.01	2aw45	0.369	3.70	0.034	0.689	0.37	III	complex5.pdb.gz	14,19,47,51
6	0.01	1p6dA	0.435	4.49	0.044	0.905	0.19	3PC	complex6.pdb.gz	6,12,51,60,61
7	0.01	1kieB	0.411	4.30	0.072	0.892	0.13	AD3	complex7.pdb.gz	18,48,51
8	0.01	3mknB	0.318	4.42	0.017	0.662	0.20	DNB	complex8.pdb.gz	18,48,51
9	0.01	1kicA	0.409	4.26	0.075	0.865	0.31	NOS	complex9.pdb.gz	53,54,55
10	0.01	3epxB	0.429	4.24	0.043	0.892	0.10	IMQ	complex10.pdb.gz	20,22,54,59

	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.