D-I-TASSER Q96DN2-D1

D-I-TASSER results for Q96DN2-D1

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

Input Sequence in FASTA format

>Q96DN2 (123 residues)
MWAGLLLRAACVALLLPGAPARGYTGRKPPGHFAAERRRLGPHVCLSGFGSGCCPGWAPS
MGGGHCTLPLCSFGCGSGICIAPNVCSCQDGEQGATCPETHGPCGEYGCDLTCNHGGCQE
VAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MWAGLLLRAACVALLLPGAPARGYTGRKPPGHFAAERRRLGPHVCLSGFGSGCCPGWAPSMGGGHCTLPLCSFGCGSGICIAPNVCSCQDGEQGATCPETHGPCGEYGCDLTCNHGGCQEVAR
Prediction	CCCCCCCCCCSCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCSSSCCCCCCCCCCCCCCCCCSCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCC
Confidence	975421035223420146789997666798740478888888603799937728986258899981654257999996261799589369965788997888555688877667982056889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MWAGLLLRAACVALLLPGAPARGYTGRKPPGHFAAERRRLGPHVCLSGFGSGCCPGWAPSMGGGHCTLPLCSFGCGSGICIAPNVCSCQDGEQGATCPETHGPCGEYGCDLTCNHGGCQEVAR
Prediction	533333233403320012224632425446441425652503120334441331421344452640331235750541402442404257414064164245514766154304416446538
	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                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCSSSCCCCCCCCCCCCCCCCCSCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCC
MWAGLLLRAACVALLLPGAPARGYTGRKPPGHFAAERRRLGPHVCLSGFGSGCCPGWAPSMGGGHCTLPLCSFGCGSGICIAPNVCSCQDGEQGATCPETHGPCGEYGCDLTCNHGGCQEVAR

2vj2B

0.20

0.19

5.99

2.63

SPARKS-K

RPRDDFFGHYACDQNGNKTCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQG----LYCDKCIPHPGCVHGICNEPWQCLCETNWGGQLCDKDLNYCGTHPCL---NGGTCSNTGP

4xbmB

0.19

0.18

5.77

1.80

MUSTER

RPRDDAFGHFTCGERGEKVCNPGWKGPYCTEPICLPGCDEQHGFCDKPGECKCRVGWQG----RYCDECIRYPGCLHGTCQQPWQCNCQEGWGGLFCNQDLNYCTHKPCK---NGATCTNTGQ

5mvxA

0.25

0.24

7.29

1.43

HHsearch

AWHAPGDEALPPDALISLSCLPGWTGEYCQQPICLSGCHEQNGYCSKPAECLCRPGWQ----GRLCN--ECIPGCRHGTCSTPWQCTCDEGWGGLFCDQDLNYCTHSPCK---NGATCSNSGR

2m74A

0.36

0.24

7.02

1.69

CNFpred

--------------------------------------LKGPNVCGSRYNAYCCPGWKTLPGGNQCIVPICRHSCGDGFCSRPNMCTCPSGQIAPSCGSRSI----QHCNIRCMGGSCSDDHC

6govA

0.02

1.29

0.83

DEthreader

TQTAKQVIVQKVREAERAMVVDQFEHGEII-TGVVKKVNRDNISLDLPGDRVRGVLYS--GA--FVTRSKPEKAA---ARDPG-RAKI----VDIVLWFVINVASI--VVD--MDIAVEAGN-

2m74A

0.34

0.26

7.80

2.47

SPARKS-K

----------------------------SARGGGGHDALKGPNVCGSRYNAYCCPGWKTLPGGNQCIVPICRHSCGDGFCSRPNMCTCPSGQIAPSCGSRSTHCGQPVCESGCLNGRCVAPNR

6pogB2

0.28

0.18

5.48

0.55

MapAlign

------------------------------------HNCDENALCFNTHNCVCKPGYTG---NGTCK-AFCKDGCRNGACIAANVCACPQGFTGPSCETDIDECSDGFVQ-CDSRANCINL--

2vj2B

0.20

0.19

6.00

0.52

CEthreader

RPRDDFFGHYACDQNGNKTCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQG----LYCDKCIPHPGCVHGICNEPWQCLCETNWGGQLCDKDLNYCGTHQPCL--NGGTCSNTGP

2vj2B

0.20

0.19

5.99

1.76

MUSTER

RPRDDFFGHYACDQNGNKTCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQGLY----CDKCIPHPGCVHGICNEPWQCLCETNWGGQLCDKDLNYCGTQPCL---NGGTCSNTGP

4cbzA

0.23

0.21

6.63

1.35

HHsearch

QWQTLKQNTGVAHFNGNKTCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQ----GLYCD--KCIPPCVHGICNEPWQCLCETNWGGQLCDKDLNYCGTQPCL---NGGTCSNTPD

(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	0.4006

(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	4cbzA	0.82	2.01	0.190	0.927	model1_4cbzA.pdb.gz
2	2vj2B	0.79	2.28	0.188	0.927	model1_2vj2B.pdb.gz
3	4xbmB	0.76	2.48	0.172	0.919	model1_4xbmB.pdb.gz
4	5mw5A	0.69	1.68	0.186	0.772	model1_5mw5A.pdb.gz
5	3ho4B	0.50	3.01	0.198	0.667	model1_3ho4B.pdb.gz
6	2m74A2	0.39	2.54	0.303	0.496	model1_2m74A2.pdb.gz
7	1emnA	0.35	3.35	0.109	0.504	model1_1emnA.pdb.gz
8	1lmjA	0.34	4.12	0.072	0.561	model1_1lmjA.pdb.gz
9	1pfxL	0.33	4.69	0.151	0.577	model1_1pfxL.pdb.gz
10	1g1qA	0.32	3.65	0.083	0.488	model1_1g1qA.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	0.70	metal ion binding
GO:0005102	0.68	receptor binding
GO:0005198	0.66	structural molecule activity
GO:0005509	0.65	calcium ion binding
GO:0005201	0.65	extracellular matrix structural constituent
GO:0005112	0.55	Notch 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	0.91	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0044699	0.87	single-organism process
GO:0032502	0.86	developmental process
GO:0009987	0.82	cellular process
GO:0044763	0.77	single-organism cellular process
GO:0048583	0.76	regulation of response to stimulus
GO:0044767	0.71	single-organism developmental process
GO:0009653	0.70	anatomical structure morphogenesis
GO:0048518	0.69	positive regulation of biological process
GO:0048856	0.67	anatomical structure development
GO:0048522	0.67	positive regulation of cellular process
GO:0009966	0.63	regulation of signal transduction
GO:0090287	0.60	regulation of cellular response to growth factor stimulus
GO:0016043	0.60	cellular component organization
GO:0048519	0.59	negative regulation of biological process
GO:0007165	0.59	signal transduction
GO:0048584	0.58	positive regulation of response to stimulus
GO:0048523	0.58	negative regulation of cellular process
GO:0080090	0.57	regulation of primary metabolic process
GO:0060255	0.57	regulation of macromolecule metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0009967	0.57	positive regulation of signal transduction
GO:0008593	0.56	regulation of Notch signaling pathway
GO:0051239	0.55	regulation of multicellular organismal process
GO:0048869	0.55	cellular developmental process
GO:0008152	0.55	metabolic process
GO:0045747	0.54	positive regulation of Notch signaling pathway
GO:0032501	0.54	multicellular organismal process
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0071704	0.53	organic substance metabolic process
GO:0051179	0.53	localization
GO:0044707	0.53	single-multicellular organism process
GO:0044238	0.53	primary metabolic process
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.53	regulation of gene expression
GO:0050896	0.52	response to stimulus
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0006355	0.52	regulation of transcription, DNA-templated
GO:0065008	0.51	regulation of biological quality
GO:0048585	0.51	negative regulation of response to stimulus
GO:0023057	0.51	negative regulation of signaling
GO:0010648	0.51	negative regulation of cell communication
GO:0007155	0.51	cell adhesion
GO:0044237	0.50	cellular metabolic process
GO:0009968	0.50	negative regulation of signal transduction
GO:0001932	0.50	regulation of 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:0044464	0.92	cell part
GO:0044424	0.81	intracellular part
GO:0005576	0.77	extracellular region
GO:0044421	0.70	extracellular region part
GO:0016020	0.66	membrane
GO:0044425	0.63	membrane part
GO:0043226	0.62	organelle
GO:0005886	0.60	plasma membrane
GO:0043227	0.57	membrane-bounded organelle
GO:0016021	0.54	integral component of membrane
GO:0044444	0.50	cytoplasmic part
GO:0044422	0.50	organelle part

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	2q6bA	0.393	4.93	0.041	0.740	1.1.1.34	NA
2	0.060	2ebsB	0.391	4.94	0.033	0.756	3.2.1.150	NA
3	0.060	2gv9B	0.418	5.10	0.046	0.772	2.7.7.7	37,39
4	0.060	1ffyA	0.395	4.95	0.083	0.740	6.1.1.5	NA
5	0.060	1f13A	0.416	4.96	0.016	0.805	2.3.2.13	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	0.02	2wfxB	0.431	4.65	0.137	0.748	1.25	NA	complex1.pdb.gz	85,86,88,94,95
	2	0.01	3akgA	0.461	4.37	0.042	0.829	0.49	AHR	complex2.pdb.gz	88,89,90,91,94

	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.