D-I-TASSER Q9P2Y4-D3

D-I-TASSER results for Q9P2Y4-D3

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

Input Sequence in FASTA format

>Q9P2Y4 (112 residues)
PLSSALPARARRHRAEEPEEEEEVVEAEEETWARGRSLGSLASLHPRPGEGPGHSASAAG
AQARSTATQEENGLLVGGTRPEGGRGATGKDCPFCGKSFRSAHHLKVHLRVH

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| PLSSALPARARRHRAEEPEEEEEVVEAEEETWARGRSLGSLASLHPRPGEGPGHSASAAGAQARSTATQEENGLLVGGTRPEGGRGATGKDCPFCGKSFRSAHHLKVHLRVH
Prediction	CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCSSSSSSCC
Confidence	9864333323222346875122111243333223566433467898888888876765444456665311320112552432135887653761110112322124666529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| PLSSALPARARRHRAEEPEEEEEVVEAEEETWARGRSLGSLASLHPRPGEGPGHSASAAGAQARSTATQEENGLLVGGTRPEGGRGATGKDCPFCGKSFRSAHHLKVHLRVH
Prediction	8446424462534557575556434534655354455464445454444644456445455446745444644463555455456554554042025414442304223448
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCSSSSSSCC
PLSSALPARARRHRAEEPEEEEEVVEAEEETWARGRSLGSLASLHPRPGEGPGHSASAAGAQARSTATQEENGLLVGGTRPEGGRGATGKDCPFCGKSFRSAHHLKVHLRVH

2b63I

0.08

0.06

2.43

0.54

CEthreader

-----------------------------TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETALPRSDRECPKCHSRENVFFFFVCLSCSH

4o9dB

0.14

4.85

0.65

EigenThreader

KGN-LFLYTGAFDNYPEALEKGYSASLIEFSNFLGRSSDKVIIGYFHTNRGCLALFDASTASFVQKFTSSGTDNQRKPDKPLGKTKMAGINMGNLFVTGGSDGIVKVWDLRL

2eppA

0.36

0.12

3.46

0.50

FFAS-3D

----------------------------------------------------------------------------GSSGSSGLREAGILPCGLCGKVFTDANRLRQHEAQH

4a4zA

0.05

2.44

0.96

SPARKS-K

PEHEKQIKVLQEELQTKFMLAYKEATVNLMQEMVKSPKEGRLVAFRDPNDCLKFKVSLKDAVCVIMTTKPYKYFPKADGYRRRNFPKFQKTDFY-MEEVPVTIEVITKRKFA

2i13A

0.44

0.11

3.13

0.91

CNFpred

-------------------------------------------------------------------------------------GEKPYKCPECGKSFSREDNLHTHQRTH

2qt3A

0.06

0.05

2.29

0.83

DEthreader

SPGFVDAHTHMDKSYYATHEEIKRHVIEHAHMQVLHGTLYTR--IDYHIHSHAWFVLLEGINLGCASDIGNDQALIETQRL--------LIWKMITS-G------VLGIEYG

4gk9A1

0.06

2.66

0.87

MapAlign

---GFNNLQHVQNQWGGSSAPWHEGGMWVLGCRSGQNVVALNIKSGDGGRTLTGTMTYGEGPIGFRATLTQSNTYAVEIGCRVNQQVVALDIETLAGTMTYAGPIGFKSQQA

6ml2A

0.30

0.26

7.86

1.21

MUSTER

MDVSQLKKHLRTHTGEKPFTCEICGK----SFTAKSSLQTHIRIHR--GEKP-YSCSICGKCFSDSSAKRRHCILHTGKKP--------FSCPECGLQFARLDNLKAHLKIH

2eppA

0.28

0.09

2.73

0.93

HHsearch

---------------------------------------------------------------------------GSSGSSGLR-EAGILPCGLCGKVFTDANRLRQHEAQH

2ynpA4

0.06

0.04

1.55

0.51

CEthreader

----------------------------------------ESITSGKWVGDVFIFTTATNRLNYFVGGKTYN------LAHYTKEMYLLGYLARDNKVYLADREVHVYGYEI

(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	0.5662

(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	6at7B	0.51	4.01	0.057	0.812	model1_6at7B.pdb.gz
2	6tjvD	0.50	4.94	0.098	0.902	model1_6tjvD.pdb.gz
3	4he8N	0.49	4.28	0.099	0.839	model1_4he8N.pdb.gz
4	6v6hA	0.49	4.00	0.038	0.795	model1_6v6hA.pdb.gz
5	7d3uA	0.49	4.63	0.081	0.884	model1_7d3uA.pdb.gz
6	6xv8B	0.49	4.55	0.059	0.884	model1_6xv8B.pdb.gz
7	6y794	0.49	4.55	0.050	0.866	model1_6y794.pdb.gz
8	6krzA	0.49	4.43	0.105	0.812	model1_6krzA.pdb.gz
9	3unvA2	0.49	3.87	0.059	0.795	model1_3unvA2.pdb.gz
10	6nbqF	0.49	4.51	0.045	0.839	model1_6nbqF.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:0000982	0.99	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0044212	0.98	transcription regulatory region DNA binding
GO:0043565	0.98	sequence-specific DNA binding
GO:0001078	0.97	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific 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:0050794	0.99	regulation of cellular process
GO:0009987	0.96	cellular process
GO:0071704	0.95	organic substance metabolic process
GO:0044238	0.95	primary metabolic process
GO:0006351	0.94	transcription, DNA-templated
GO:0044699	0.87	single-organism process
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0007165	0.78	signal transduction
GO:0006355	0.78	regulation of transcription, DNA-templated
GO:0048523	0.77	negative regulation of cellular process
GO:0032502	0.77	developmental process
GO:0045892	0.76	negative regulation of transcription, DNA-templated
GO:0044767	0.76	single-organism developmental process
GO:0000122	0.73	negative regulation of transcription from RNA polymerase II promoter
GO:0048856	0.70	anatomical structure development
GO:0006366	0.69	transcription from RNA polymerase II promoter
GO:0007275	0.67	multicellular organism development

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	2z8kD	0.344	4.73	0.089	0.616	2.3.2.2	2,65
2	0.060	1b8fA	0.497	3.99	0.038	0.795	4.3.1.3	NA
3	0.060	1uyrA	0.430	4.96	0.018	0.839	6.4.1.2 6.3.4.14	65
4	0.060	1jn9D	0.365	4.85	0.082	0.732	3.4.19.5 3.5.1.1	NA
5	0.060	1wd9A	0.452	4.15	0.021	0.777	3.5.3.15	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	3omaA	0.395	5.02	0.019	0.759	0.13	HEA	complex1.pdb.gz	39,64,66,69,72,73
2	0.01	3hb3A	0.477	4.37	0.045	0.848	0.11	HEA	complex2.pdb.gz	8,9,56,62
3	0.01	1ocoA	0.458	4.71	0.027	0.830	0.13	UUU	complex3.pdb.gz	64,66,67,68,69,89,102,103
4	0.01	3rkoC	0.477	4.57	0.080	0.866	0.25	CA7	complex4.pdb.gz	92,95,96
5	0.01	1m56G	0.477	4.49	0.054	0.866	0.32	CA	complex5.pdb.gz	89,93,96,98
6	0.01	2zxwA	0.461	4.80	0.027	0.848	0.12	UUU	complex6.pdb.gz	4,6,8,66,67,86,91
7	0.01	3fyeA	0.391	4.08	0.058	0.643	0.10	HEA	complex7.pdb.gz	66,67,74,89,90,104,105
8	0.01	1ar1A	0.472	4.33	0.055	0.839	0.11	HEA	complex8.pdb.gz	63,68,90,96,97,102,103
9	0.01	2dysN	0.477	4.55	0.019	0.857	0.13	HEA	complex9.pdb.gz	8,64,67,68,69,89,90,103
10	0.01	2eijN	0.473	4.68	0.027	0.857	0.13	HEA	complex10.pdb.gz	8,64,66,67,68,69,89,103

	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.