D-I-TASSER O00267-D3

D-I-TASSER results for O00267-D3

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

Input Sequence in FASTA format

>O00267 (88 residues)
IDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKG
FLFKSFAMSAVITEGVKPTLSELEKFED

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| IDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFED
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCSSSCCCSSSSSCCSSSSCCSSSSSSSSSSSSSCCCCCCHHHHHHHHC
Confidence	9865334432357665444468999966889999998599324328848982987720671899998447997498999999998619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| IDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFED
Prediction	7526444651646767554445533354324473057344624763421313455134401122414153042760413352155258
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCSSSCCCSSSSSCCSSSSCCSSSSSSSSSSSSSCCCCCCHHHHHHHHC
IDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFED

6b3rA1

0.03

0.02

1.51

0.83

DEthreader

RLLDLAASFSAVLTRIQVFVRRLLLHKLALYTVWVALKEVVNL------LLV-VLWAFALPRASCT--AVYRQEYQPQANFFYSQWQF

5oikZ1

0.73

0.72

20.31

2.78

SPARKS-K

YVEPSQNTISLKMIPRIDYDRIKAPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKF--

5a1uG1

0.06

2.43

0.82

MapAlign

TCTDAEFRQM---WAEFEWENKVTVNTNMTDLNYLQHTNMKCLEKFMAANLYAANVSIEKTGHIRIRAKSQGM------ALSLGDKIN

5oikZ1

0.74

0.73

20.61

0.67

CEthreader

LKRGIYKDDIAQMIPRIDYDRIKAPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKF--

5oikZ

0.97

0.80

22.30

1.78

MUSTER

IDYDRIKA----------------PPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFRE

4ytkA

0.28

0.24

7.31

3.16

HHsearch

LDYGKFDE---------RPTFAHRAPPQLFNPTMALRLDQANKRDDRHFTYKNEDY-IDGYLYKSFRIQHVETKNIQPTVEELARF--

5oikZ1

0.94

0.72

20.09

1.15

FFAS-3D

-------------------DRIKAPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKF--

5oikZ

0.82

0.67

18.92

0.67

EigenThreader

PRID--------------YDRIKAPPQRLFDAEKIRSLGGDSDG--DFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFRE

5oikZ

1.00

0.80

22.27

2.33

CNFpred

IDYDRIKA----------------PPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKF--

6b3rA

0.03

0.02

1.51

0.83

DEthreader

RLLDLAASFSAVLTRIQVFVRRLLLHKLALYTVWVALKEVVNL------LLV-VLWAFALPRASCT--AVYRQEYQPQANFFYSQWQF

(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	0.5628

(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	5oikZ1	0.55	2.87	0.709	0.795	model1_5oikZ1.pdb.gz
2	4ytkA	0.52	3.74	0.182	0.818	model1_4ytkA.pdb.gz
3	1q5fA	0.51	3.17	0.096	0.784	model1_1q5fA.pdb.gz
4	2f6dA	0.50	3.87	0.063	0.886	model1_2f6dA.pdb.gz
5	5xonW2	0.49	3.76	0.257	0.784	model1_5xonW2.pdb.gz
6	4u1cC	0.49	4.13	0.052	0.852	model1_4u1cC.pdb.gz
7	5hb4B3	0.49	3.72	0.091	0.818	model1_5hb4B3.pdb.gz
8	2vn4A	0.49	4.05	0.063	0.886	model1_2vn4A.pdb.gz
9	3o0yA1	0.49	3.95	0.035	0.841	model1_3o0yA1.pdb.gz
10	1lf9A	0.43	4.16	0.042	0.807	model1_1lf9A.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:1901363	0.89	heterocyclic compound binding
GO:0097159	0.89	organic cyclic compound binding
GO:0003676	0.82	nucleic acid binding
GO:0046983	0.68	protein dimerization activity
GO:0046982	0.67	protein heterodimerization activity
GO:0003723	0.58	RNA binding
GO:0044822	0.54	poly(A) RNA binding
GO:0019899	0.53	enzyme 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:2000112	0.96	regulation of cellular macromolecule biosynthetic process
GO:0051252	0.96	regulation of RNA metabolic process
GO:0010468	0.96	regulation of gene expression
GO:0006357	0.95	regulation of transcription from RNA polymerase II promoter
GO:0009987	0.91	cellular process
GO:0048522	0.90	positive regulation of cellular process
GO:0045944	0.89	positive regulation of transcription from RNA polymerase II promoter
GO:0071704	0.87	organic substance metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0044238	0.86	primary metabolic process
GO:0044260	0.85	cellular macromolecule metabolic process
GO:0034641	0.85	cellular nitrogen compound metabolic process
GO:0006139	0.83	nucleobase-containing compound metabolic process
GO:0090304	0.82	nucleic acid metabolic process
GO:0016070	0.81	RNA metabolic process
GO:1901576	0.77	organic substance biosynthetic process
GO:0044271	0.77	cellular nitrogen compound biosynthetic process
GO:0009059	0.76	macromolecule biosynthetic process
GO:0034654	0.74	nucleobase-containing compound biosynthetic process
GO:0032774	0.73	RNA biosynthetic process
GO:0051172	0.71	negative regulation of nitrogen compound metabolic process
GO:0032784	0.71	regulation of DNA-templated transcription, elongation
GO:0031327	0.71	negative regulation of cellular biosynthetic process
GO:0010629	0.71	negative regulation of gene expression
GO:0000122	0.70	negative regulation of transcription from RNA polymerase II promoter
GO:0032786	0.65	positive regulation of DNA-templated transcription, elongation
GO:0032785	0.65	negative regulation of DNA-templated transcription, elongation
GO:0006368	0.65	transcription elongation from RNA polymerase II promoter
GO:0044699	0.50	single-organism 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:0044424	1.00	intracellular part
GO:0044428	0.97	nuclear part
GO:0032991	0.88	macromolecular complex
GO:0043234	0.86	protein complex
GO:0044451	0.84	nucleoplasm part
GO:0032044	0.83	DSIF complex
GO:0043229	0.75	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0005634	0.57	nucleus

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	1bwzA	0.407	4.67	0.072	0.864	5.1.1.7	NA
2	0.060	1ayxA	0.497	3.88	0.063	0.886	3.2.1.3	52
3	0.060	1wzzA	0.457	3.97	0.056	0.818	3.2.1.4	NA
4	0.060	1gz3A	0.382	4.52	0.026	0.761	1.1.1.38	NA
5	0.060	1khvB	0.446	4.07	0.081	0.784	2.7.7.48	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	1u1wA	0.497	3.83	0.053	0.841	0.15	3HA	complex1.pdb.gz	56,59,64
2	0.01	1q5kA	0.389	4.68	0.069	0.807	0.14	TMU	complex2.pdb.gz	54,55,56,57,58
3	0.01	3zrkB	0.346	4.04	0.016	0.648	0.18	III	complex3.pdb.gz	46,58,63
4	0.01	3l1sB	0.325	4.53	0.045	0.693	0.12	Z92	complex4.pdb.gz	30,32,56
5	0.01	3l1sA	0.421	4.70	0.060	0.898	0.11	Z92	complex5.pdb.gz	35,46,47,48,49,51,53
6	0.01	2f6dA	0.498	3.87	0.063	0.886	0.27	ACR	complex6.pdb.gz	47,48,49,51,60,61
7	0.01	3o7wA	0.469	4.11	0.072	0.852	0.11	SAM	complex7.pdb.gz	25,26,74,75
8	0.01	1q4lB	0.456	4.34	0.059	0.852	0.15	679	complex8.pdb.gz	59,60,61,62,65
9	0.01	1pyxB	0.412	4.37	0.104	0.807	0.29	ANP	complex9.pdb.gz	43,45,46,50,54,56
10	0.01	2ow3A	0.403	4.73	0.070	0.807	0.18	BIM	complex10.pdb.gz	54,55,56,57,59,62

	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.