D-I-TASSER Q53RD9-D3

D-I-TASSER results for Q53RD9-D3

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

Input Sequence in FASTA format

>Q53RD9 (96 residues)
QTAAPEGSVAGDSAFSRAPRCAQVERAQHCSCEAGFHLSGAAGDSVCQDVNECELYGQEG
RPRLCMHACVNTPGSYRCTCPGGYRTLADGKSCEDV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| QTAAPEGSVAGDSAFSRAPRCAQVERAQHCSCEAGFHLSGAAGDSVCQDVNECELYGQEGRPRLCMHACVNTPGSYRCTCPGGYRTLADGKSCEDV
Prediction	CCCCCCCCSCCCCCCCCCCSSSCCCCCSSSSCCCCCSSCCCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSSCCCCSSSSCCCCCSSCCCCCCSSCC
Confidence	988888442479999988671916993498748881254789997150322534899998888753292936993399848992688999912747
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| QTAAPEGSVAGDSAFSRAPRCAQVERAQHCSCEAGFHLSGAAGDSVCQDVNECELYGQEGRPRLCMHACVNTPGSYRCTCPGGYRTLADGKSCEDV
Prediction	833375252046651445241321421042424541414556654333000002444664543314344341541442434641414744544668
	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                  60                  80

                   |                   |                   |                   |

SS
Seq

CCCCCCCCSCCCCCCCCCCSSSCCCCCSSSSCCCCCSSCCCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSSCCCCSSSSCCCCCSSCCCCCCSSCC
QTAAPEGSVAGDSAFSRAPRCAQVERAQHCSCEAGFHLSGAAGDSVCQDVNECELYGQEGRPRLCMHACVNTPGSYRCTCPGGYRTLADGKSCEDV

6pogB1

0.30

0.26

7.89

2.51

SPARKS-K

-------DFCSERHCMENSICRNLNDRAVCSCRDGFRALRED-NAYCEDIDECA-----EGRHYCNTMCVNTPGSFMCICKTGYI-RIDDYSCTEH

1hz8A

0.29

0.25

7.60

2.21

MUSTER

-----GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQL---VAQRRCEDIDEC------QDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV

1hz8A

0.29

0.25

7.60

1.32

HHsearch

-----GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLV---AQRRCEDIDECQD------PDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV

6polB

0.29

0.23

6.98

3.04

CNFpred

-------------KCGENSECKNWNTKATCECKSGYISVQ-GDSAYCEDIDECAAK-----MHYCHTVCVNLPGLYRCDCVPGYIRVD-DFSCTEH

2vj3A

0.26

0.20

6.11

1.00

DEthreader

------VDECLANPCEHAGKCINTLGSFECQCLQGYTG--P---RCEIDVNECV-------SNPCQATCLDQIGEFQCICMPGYEG----VHCEVN

1hz8A

0.29

0.25

7.60

2.27

SPARKS-K

-----GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRR---CEDIDEC------QDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV

1lmjA

0.25

0.21

6.47

0.63

MapAlign

--------CRISPDLCGRGQCVNTPGDFECKCDEGYESGFM-MMKNCMDIDECQRD----PLLCRGGVCHNTEGSYRCECPPGHQLSPNISACI--

1lmjA

0.23

0.21

6.52

0.59

CEthreader

---TDIDECRISPDLCGRGQCVNTPGDFECKCDEGYESGF-MMMKNCMDIDECQRDPL----LCRGGVCHNTEGSYRCECPPGHQLSPNISACI--

1z6cA

0.30

0.26

7.91

2.15

MUSTER

---KDVDECSLKPSICGTAVCKNIPGDFECECPEGYRYNL--KSKSCEDIDECS-------ENMCAQLCVNYPGGYTCYCDGGFKLAQDQKSCEVV

1pfxL

0.23

0.20

6.22

1.29

HHsearch

WKQYVDGDQCEPNPCLNGGLCKD-INSYECWCQVGFEG------KNCELDATCNIK-----NGRCKQFCKTGDSKVLCSCTTGYRLAPDQKSCKPA

(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	0.5562

(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	6polB	0.63	2.91	0.267	0.875	model1_6polB.pdb.gz
2	6pogB	0.61	3.01	0.298	0.875	model1_6pogB.pdb.gz
3	2vj3A	0.61	2.42	0.247	0.792	model1_2vj3A.pdb.gz
4	5mwbA	0.60	2.23	0.200	0.781	model1_5mwbA.pdb.gz
5	5uk5A	0.58	2.81	0.222	0.812	model1_5uk5A.pdb.gz
6	4xbmB	0.58	2.45	0.198	0.792	model1_4xbmB.pdb.gz
7	4d90A	0.57	2.55	0.203	0.760	model1_4d90A.pdb.gz
8	1emnA	0.56	2.86	0.215	0.781	model1_1emnA.pdb.gz
9	1yo8A	0.56	2.95	0.253	0.823	model1_1yo8A.pdb.gz
10	5b4xB	0.56	2.91	0.265	0.823	model1_5b4xB.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:0046872	0.87	metal ion binding
GO:0005509	0.86	calcium ion binding
GO:0005201	0.74	extracellular matrix structural constituent
GO:0005102	0.72	receptor binding
GO:0032403	0.70	protein complex binding
GO:0050839	0.68	cell adhesion molecule binding
GO:0005179	0.67	hormone activity
GO:0005178	0.67	integrin binding
GO:0030023	0.66	extracellular matrix constituent conferring elasticity
GO:0003824	0.57	catalytic activity
GO:0097367	0.53	carbohydrate derivative 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	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0044699	0.91	single-organism process
GO:0009987	0.90	cellular process
GO:0050794	0.89	regulation of cellular process
GO:0044763	0.85	single-organism cellular process
GO:0032502	0.84	developmental process
GO:0007165	0.81	signal transduction
GO:0044767	0.78	single-organism developmental process
GO:0048856	0.77	anatomical structure development
GO:0016043	0.75	cellular component organization
GO:0009653	0.75	anatomical structure morphogenesis
GO:0071704	0.74	organic substance metabolic process
GO:0048583	0.74	regulation of response to stimulus
GO:0051179	0.73	localization
GO:0048518	0.73	positive regulation of biological process
GO:0044238	0.73	primary metabolic process
GO:0048519	0.72	negative regulation of biological process
GO:0019222	0.72	regulation of metabolic process
GO:0080090	0.71	regulation of primary metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0050896	0.71	response to stimulus
GO:0048523	0.71	negative regulation of cellular process
GO:0048522	0.71	positive regulation of cellular process
GO:0031323	0.71	regulation of cellular metabolic process
GO:0065008	0.70	regulation of biological quality
GO:0048513	0.70	animal organ development
GO:0023051	0.70	regulation of signaling
GO:0010646	0.70	regulation of cell communication
GO:0010468	0.70	regulation of gene expression
GO:0090287	0.69	regulation of cellular response to growth factor stimulus
GO:0051246	0.69	regulation of protein metabolic process
GO:0030198	0.69	extracellular matrix organization
GO:0009966	0.69	regulation of signal transduction
GO:0006355	0.69	regulation of transcription, DNA-templated
GO:0048731	0.68	system development
GO:0048585	0.68	negative regulation of response to stimulus
GO:0044710	0.68	single-organism metabolic process
GO:0031325	0.68	positive regulation of cellular metabolic process
GO:0010604	0.68	positive regulation of macromolecule metabolic process
GO:0001932	0.68	regulation of protein phosphorylation
GO:1901700	0.67	response to oxygen-containing compound
GO:0051716	0.67	cellular response to stimulus
GO:0050790	0.67	regulation of catalytic activity
GO:0044281	0.67	small molecule metabolic process
GO:0044093	0.67	positive regulation of molecular function
GO:0035556	0.67	intracellular signal transduction
GO:0010033	0.67	response to organic substance
GO:0009968	0.67	negative regulation of signal transduction
GO:0009887	0.67	organ morphogenesis
GO:0006357	0.67	regulation of transcription from RNA polymerase II promoter
GO:0001934	0.67	positive regulation of protein phosphorylation
GO:1901701	0.66	cellular response to oxygen-containing compound
GO:0071310	0.66	cellular response to organic substance
GO:0048562	0.66	embryonic organ morphogenesis
GO:0042593	0.66	glucose homeostasis
GO:0032147	0.66	activation of protein kinase activity
GO:0022617	0.66	extracellular matrix disassembly
GO:0017015	0.66	regulation of transforming growth factor beta receptor signaling pathway
GO:0010243	0.66	response to organonitrogen compound
GO:0009886	0.66	post-embryonic morphogenesis
GO:0006006	0.66	glucose metabolic process
GO:0001822	0.66	kidney development
GO:0001501	0.66	skeletal system development
GO:1990314	0.65	cellular response to insulin-like growth factor stimulus
GO:0048050	0.65	post-embryonic eye morphogenesis
GO:0048048	0.65	embryonic eye morphogenesis
GO:0043010	0.65	camera-type eye development
GO:0035583	0.65	sequestering of TGFbeta in extracellular matrix
GO:0035582	0.65	sequestering of BMP in extracellular matrix
GO:0034199	0.65	activation of protein kinase A activity
GO:0010737	0.65	protein kinase A signaling
GO:0007507	0.65	heart development
GO:0001656	0.65	metanephros 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:0044464	0.89	cell part
GO:0044424	0.61	intracellular part
GO:0016020	0.57	membrane

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	1kv3A	0.351	4.99	0.071	0.740	2.3.2.13	NA
2	0.060	1apqA	0.385	2.59	0.354	0.500	3.4.21.41 3.4.21.42	92
3	0.060	1ylaA	0.438	4.72	0.085	0.885	6.3.2.19	73
4	0.060	1szbA	0.562	3.03	0.209	0.781	3.4.21.104	77
5	0.060	2ex2A	0.458	4.41	0.080	0.812	3.4.16.4	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.64	3p5bL	0.593	2.88	0.325	0.833	1.52	CA	complex1.pdb.gz	49,50,51,52,72,75
	2	0.38	1uzjA	0.511	3.24	0.273	0.771	1.72	CA	complex2.pdb.gz	49,50,52,71,72,74,75

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.