D-I-TASSER O14757-D3

D-I-TASSER results for O14757-D3

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

Input Sequence in FASTA format

>O14757 (180 residues)
NLDFSPVNSASSEENVKYSSSQPEPRTGLSLWDTSPSYIDKLVQGISFSQPTCPDHMLLN
SQLLGTPGSSQNPWQRLVKRMTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTIST
TDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NLDFSPVNSASSEENVKYSSSQPEPRTGLSLWDTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPWQRLVKRMTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTISTTDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCCCCCCHHHHHHHCCCSSSSCCCHHHHHHHHHHHHHHHCCCSSSCCCCSSSSSSSCCCCCSSSSSSSSSSSCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHSSCCCCCCCCC
Confidence	986332356655667875345778998877667770445544225666788882135553224579876677678765302148854999999999999999919946853786799997527885389999999939928999997479817899999999987544054488667789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NLDFSPVNSASSEENVKYSSSQPEPRTGLSLWDTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPWQRLVKRMTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTISTTDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT
Prediction	856454354345656330111013355454436444541553465222322343731232143464454445314510431010104241630052035006616051445453312031444452302020202424540001013254232202410440163042002457332368
	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                 100                 120                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCCCCCCHHHHHHHCCCSSSSCCCHHHHHHHHHHHHHHHCCCSSSCCCCSSSSSSSCCCCCSSSSSSSSSSSCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHSSCCCCCCCCC
NLDFSPVNSASSEENVKYSSSQPEPRTGLSLWDTSPSYIDKLVQGISFSQPTCPDHMLLNSQLLGTPGSSQNPWQRLVKRMTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTISTTDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT

5wu1A

0.10

0.08

3.10

1.00

DEthreader

------HNSLS-VYLRAWAQGRG-LTLVIYLLSLPSLRLGPLNTSRVAGR-LQ-NCCRAAN-D-GLLPLQP--SSPSSLLSAPIPLLAPFTQLTAALVQVFEALGCHIE-Q-SASWRCALWHRTEPLLSFVASVSPA--DRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIR---------

2ehbD

0.17

0.12

3.84

1.71

SPARKS-K

---------------------------------EGPLMMNA-FEMITLSQGLNLSALFDRRQDFVKRQ-------------TRFVSRREPSEIIANIEAVANSMGFKSHTR-NFKTRLEGLSSIAGQLAVVIEIYEVAPLFMVDVRKAAGETLEYHKFYKKLCSKLENIIWR--------

6c9dA

0.07

2.72

1.05

MapAlign

--KTIGKGNFAKVKLARHVLTGREVAVKIIDKTQLNPTSLQKLFREVRIMKILNHPNIVKLFEVIETEKTLYLVMEGEVFDVKTTSSMDPNDMMREIRKVLDANNCDYEQKERFLLFCVHGDRQDSLVQWEMEVCSLLSLNGVRFKRISGTSIAFKNIASKIANEL-KL-----------

3osmA

0.13

0.08

2.71

0.84

CEthreader

---------------------------------------------------------------KPPNSVLLKKFSKGKILELEIHAKIPEKRLYEGLHKLLEGWGLKNLVFNIMIITGKLVNDFLRSTLFEIMVLPNDGRSLIKFNKKTGSTKTLTKLATEIQIILQKEGVLD-------

2ehbD

0.19

0.13

4.29

1.51

MUSTER

---------------------------------EGPLMMN-AFEMITLSQGLNLSALFD-------------RRQDFVKRQTRFVSRREPSEIIANIEAVANSMGFKSHTRNFKTRLEGLSSIKAGQLAVVIEIYEVAPSFMVDVRKAAGETLEYHKFYKKLCSKLENIIWR--------

2ehbD

0.19

0.13

4.29

3.90

HHsearch

---------------------------------EGPLMMN-AFEMITLSQGLNLSALFDRRQ-------------DFVKRQTRFVSRREPSEIIANIEAVANSMGFKSHTR-NFKTRLEGSSIKAGQLAVVIEIYEVAPSFMVDVRKAAGETLEYHKFYKKLCSKLENIIWR--------

5wi2A

1.00

0.51

14.31

1.65

FFAS-3D

--------------------------------------------------------------------------------MTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTISTTDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSS--------

1v5sA

0.10

0.07

2.46

0.90

EigenThreader

----MKDHLIHNVHKEEHAHAHNKD------------------------YDIPT------------------------TENLYFQGSSSSGDMMREIRKVLGANNCDYER---FLLFCVHGDGHENLVQWEMEVCKLLSLNGVRFKRISGTSIAFKNIASKIANEL--KLSGPSSG----

5wi2A

1.00

0.51

14.31

1.64

CNFpred

--------------------------------------------------------------------------------MTRFFTKLDADKSYQCLKETCEKLGYQWKKSCMNQVTISTTDRRNNKLIFKVNLLEMDDKILVDFRLSKGDGLEFKRHFLKIKGKLIDIVSS--------

2ehbD

0.19

0.12

3.78

0.83

DEthreader

------------------------------------------A----M---I--LSQGLNLSA--L-----FDRRQFVKRQTRFVSRREPSEIIANIEAVANSMGFKSHT-RNFKTRLEGLSSIKAQLAVVIEIYEVPSLFMVDVRKAAGETLEYHKFYKKLCSKLENIIWR--------

(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	0.7326

(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	5wu1A	0.57	4.48	0.078	0.828	model1_5wu1A.pdb.gz
2	2ehbD	0.53	2.70	0.168	0.617	model1_2ehbD.pdb.gz
3	4gyrA	0.52	5.03	0.074	0.828	model1_4gyrA.pdb.gz
4	2gi3A	0.52	5.15	0.075	0.833	model1_2gi3A.pdb.gz
5	6te4A	0.52	4.72	0.046	0.778	model1_6te4A.pdb.gz
6	3kfuE	0.52	4.83	0.063	0.800	model1_3kfuE.pdb.gz
7	5i8iA1	0.52	5.13	0.056	0.839	model1_5i8iA1.pdb.gz
8	4qg5A	0.52	4.13	0.074	0.761	model1_4qg5A.pdb.gz
9	1m21A	0.52	4.88	0.029	0.794	model1_1m21A.pdb.gz
10	6v04A	0.52	4.64	0.045	0.783	model1_6v04A.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:0004674	1.00	protein serine/threonine kinase activity
GO:0035402	0.76	histone kinase activity (H3-T11 specific)

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:0050794	1.00	regulation of cellular process
GO:0009987	1.00	cellular process
GO:0008152	0.98	metabolic process
GO:0006468	0.97	protein phosphorylation
GO:0051726	0.87	regulation of cell cycle
GO:0048523	0.87	negative regulation of cellular process
GO:0022402	0.87	cell cycle process
GO:0045930	0.86	negative regulation of mitotic cell cycle
GO:0031570	0.86	DNA integrity checkpoint
GO:0010948	0.86	negative regulation of cell cycle process
GO:0051716	0.84	cellular response to stimulus
GO:0006950	0.84	response to stress
GO:0000077	0.83	DNA damage checkpoint
GO:0031572	0.70	G2 DNA damage checkpoint
GO:0016043	0.70	cellular component organization
GO:0009314	0.67	response to radiation
GO:0080090	0.66	regulation of primary metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0048518	0.66	positive regulation of biological process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0048522	0.65	positive regulation of cellular process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0019219	0.64	regulation of nucleobase-containing compound metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0048583	0.63	regulation of response to stimulus
GO:0045935	0.63	positive regulation of nucleobase-containing compound metabolic process
GO:0031399	0.63	regulation of protein modification process
GO:0006355	0.63	regulation of transcription, DNA-templated
GO:2001020	0.62	regulation of response to DNA damage stimulus
GO:0051052	0.62	regulation of DNA metabolic process
GO:0045893	0.62	positive regulation of transcription, DNA-templated
GO:0033043	0.62	regulation of organelle organization
GO:0006357	0.62	regulation of transcription from RNA polymerase II promoter
GO:0006325	0.62	chromatin organization
GO:2000615	0.61	regulation of histone H3-K9 acetylation
GO:0048096	0.61	chromatin-mediated maintenance of transcription
GO:0046602	0.61	regulation of mitotic centrosome separation
GO:0045839	0.61	negative regulation of mitotic nuclear division
GO:0018107	0.61	peptidyl-threonine phosphorylation
GO:0010767	0.61	regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
GO:0010569	0.61	regulation of double-strand break repair via homologous recombination
GO:0006975	0.61	DNA damage induced protein phosphorylation

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:0043231	0.99	intracellular membrane-bounded organelle
GO:0044446	0.86	intracellular organelle part
GO:0044428	0.84	nuclear part
GO:0005634	0.79	nucleus
GO:0032991	0.66	macromolecular complex
GO:0005654	0.61	nucleoplasm
GO:0044427	0.60	chromosomal part
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0044430	0.58	cytoskeletal part
GO:0005813	0.57	centrosome
GO:0000794	0.57	condensed nuclear chromosome
GO:0000785	0.57	chromatin

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	0.072	2v8qA	0.470	1.78	0.130	0.511	2.7.11.1	145,148,155
2	0.060	3a1kA	0.490	4.99	0.042	0.800	3.5.1.4	NA
3	0.060	2zfdB	0.461	3.44	0.115	0.606	2.7.11.1	116
4	0.060	2qmxB	0.478	4.65	0.067	0.728	4.2.1.51	NA
5	0.060	1hr9F	0.464	4.47	0.045	0.706	3.4.24.64	131

	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	1pp9A	0.476	4.54	0.067	0.717	0.43	AZI	complex1.pdb.gz	79,148,149,150,154
2	0.01	2qmxB	0.482	4.46	0.067	0.717	0.54	PHE	complex2.pdb.gz	149,150,155,156
3	0.01	1sqpA	0.475	4.54	0.067	0.717	0.43	PLX	complex3.pdb.gz	128,151,153
4	0.01	1ppjA	0.472	3.97	0.035	0.661	0.55	AZI	complex4.pdb.gz	146,150,156

	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.