D-I-TASSER P17020-D1

D-I-TASSER results for P17020-D1

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

Input Sequence in FASTA format

>P17020 (58 residues)
MPSLRTRREEAEMELSVPGPSPWTPAAQARVRDAPAVTHPGSAACGTPCCSDTELEAI

Predicted Secondary Structure

Sequence	20 40 \| \| MPSLRTRREEAEMELSVPGPSPWTPAAQARVRDAPAVTHPGSAACGTPCCSDTELEAI
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCC
Confidence	9862358422322337999999997765434678755588412128876688887879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MPSLRTRREEAEMELSVPGPSPWTPAAQARVRDAPAVTHPGSAACGTPCCSDTELEAI
Prediction	7664654476362534244454434435343653433334443244331245453757
	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 DeepPotential. 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

                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCC
MPSLRTRREEAEMELSVPGPSPWTPAAQARVRDAPAVTHPGSAACGTPCCSDTELEAI

3czjA2

0.07

2.86

0.59

CEthreader

LLQCTADTLLITTAHAWQHQGKTLFISRKTYRIAITVDVEVASDTPHPARIGLNCQLA

3ga9S

0.08

0.07

2.72

0.55

EigenThreader

FAPTVLKGETIGIGSPGKVSPAFFGGVQALIKNVITGAGDGR-----RNGTWKSN---

1b1yA

0.26

0.21

6.38

0.26

FFAS-3D

APLPRSGPEEMILQAAQPQPFPFQEHTDLPVGPTGGM---GGQAEGPTC---------

3gawA1

0.09

3.26

1.32

SPARKS-K

-TSCVNPPTVQNAYIVSRQMSKYPSGERVRYQCRSPYEMFGD---EEVMCLNGNWTEP

3gkhA

0.25

0.05

1.60

0.86

CNFpred

----------------------------------------------SLCCDVRQLQTL

3frmC

0.08

0.07

2.69

0.83

DEthreader

GNKITE-DSRKAI-YLLPPQPLKYASNTWIYPQKDIVKHLSSYH--LS------FSFH

7abhE

0.05

2.38

0.68

MapAlign

-FSVAVCDWYVLVGVAKDLILSVAGGFVYTYKLHKTPVAAIAPFQGRVLIGVGKLLRV

1sqqI

0.17

0.16

5.12

0.75

MUSTER

MLSVAARSGPFALSATSRGAGALRPLVQAAVPATSESPVL--DLKRSVLCRESLRG--

5nd1A

0.28

0.26

7.91

0.39

HHsearch

VADTRTRPGEVYTVPRVSGL-ALRPYERSCVRDASTL---HSMLCGPLLYGGGEPMKL

7lbeC1

0.05

2.40

0.48

CEthreader

LAGPIRNDSITYLWFDFYSTRKPAKYVYSQYNHTITFRPPSCGTVPSMTCLSEMLNVS

(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	0.6138

(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 DeepPotential, 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	3pqsA1	0.56	3.17	0.036	0.931	model1_3pqsA1.pdb.gz
2	2ervA	0.55	3.06	0.091	0.948	model1_2ervA.pdb.gz
3	6myiA	0.52	2.82	0.059	0.845	model1_6myiA.pdb.gz
4	5ek8A	0.52	3.15	0.071	0.879	model1_5ek8A.pdb.gz
5	6rtvA	0.51	3.21	0.018	0.879	model1_6rtvA.pdb.gz
6	3bzhA	0.51	2.87	0.059	0.879	model1_3bzhA.pdb.gz
7	2d1tA	0.51	3.63	0.018	0.948	model1_2d1tA.pdb.gz
8	3jrqA	0.51	3.10	0.170	0.897	model1_3jrqA.pdb.gz
9	6b7lA2	0.51	3.27	0.018	0.914	model1_6b7lA2.pdb.gz
10	5f0eA	0.51	3.50	0.107	0.914	model1_5f0eA.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:0003700	1.00	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:0031323	1.00	regulation of cellular metabolic process
GO:0009987	0.79	cellular process
GO:0080090	0.72	regulation of primary metabolic process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0051171	0.71	regulation of nitrogen compound metabolic process
GO:0031326	0.71	regulation of cellular biosynthetic process
GO:0010468	0.71	regulation of gene expression
GO:0006355	0.70	regulation of transcription, DNA-templated
GO:0048518	0.69	positive regulation of biological process
GO:0048522	0.68	positive regulation of cellular process
GO:0050896	0.67	response to stimulus
GO:0031325	0.67	positive regulation of cellular metabolic process
GO:0065008	0.66	regulation of biological quality
GO:0048523	0.66	negative regulation of cellular process
GO:0042325	0.66	regulation of phosphorylation
GO:2000026	0.65	regulation of multicellular organismal development
GO:1901987	0.65	regulation of cell cycle phase transition
GO:1901700	0.65	response to oxygen-containing compound
GO:0071310	0.65	cellular response to organic substance
GO:0051240	0.65	positive regulation of multicellular organismal process
GO:0051094	0.65	positive regulation of developmental process
GO:0045597	0.65	positive regulation of cell differentiation
GO:0043069	0.65	negative regulation of programmed cell death
GO:0042981	0.65	regulation of apoptotic process
GO:0033674	0.65	positive regulation of kinase activity
GO:0002684	0.65	positive regulation of immune system process
GO:1901989	0.64	positive regulation of cell cycle phase transition
GO:0072707	0.64	cellular response to sodium dodecyl sulfate
GO:0045654	0.64	positive regulation of megakaryocyte differentiation
GO:0045648	0.64	positive regulation of erythrocyte differentiation
GO:0043066	0.64	negative regulation of apoptotic process
GO:0008284	0.64	positive regulation of cell proliferation

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:0005634	1.00	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	1llnA	0.488	2.63	0.041	0.776	3.2.2.22	NA
2	0.060	1x6mA	0.478	3.24	0.089	0.879	4.4.1.22 4.4.-.-	NA
3	0.060	2aqsA	0.500	2.45	0.059	0.776	1.15.1.1	NA
4	0.060	3b9jC	0.333	4.16	0.037	0.776	1.17.3.2 1.17.1.4	NA
5	0.060	1rl0A	0.494	3.31	0.058	0.845	3.2.2.22	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	1jglH	0.443	3.36	0.020	0.810	0.63	EST	complex1.pdb.gz	42,43,46,48
2	0.01	2zpkH	0.478	3.39	0.078	0.845	0.50	III	complex2.pdb.gz	38,39,40,41,44,47,49,50,51
3	0.01	2ervB	0.414	3.50	0.067	0.724	0.44	CXE	complex3.pdb.gz	17,19,27,40
4	0.01	1zeaH	0.482	3.16	0.078	0.828	0.45	III	complex4.pdb.gz	38,39,40,47,49,50

	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.