D-I-TASSER Q8N0Z9-D1

D-I-TASSER results for Q8N0Z9-D1

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

Input Sequence in FASTA format

>Q8N0Z9 (121 residues)
MAAGGSAPEPRVLVCLGALLAGWVAVGLEAVVIGEVHENVTLHCGNISGLRGQVTWYRNN
SEPVFLLSSNSSLRPAEPRFSLVDATSLHIESLSLGDEGIYTCQEILNVTQWFQVWLQVA
S

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAAGGSAPEPRVLVCLGALLAGWVAVGLEAVVIGEVHENVTLHCGNISGLRGQVTWYRNNSEPVFLLSSNSSLRPAEPRFSLVDATSLHIESLSLGDEGIYTCQEILNVTQWFQVWLQVAS
Prediction	CCCCCCCCCHHHHHHHHHHCCCSSSSCCCCSSSSCCCCCSSSSSSCCCCCCCCSSSSCCCCCCSSSSSCCCCCCCCCCCSCCCCCCCSSSCCCCHHHCSSSSSSSSCCCCCSSSSSSSSCC
Confidence	9877667766999999973331345424856885289729999866799988725663599983688638908999986217997426884789356577778756599962566899449
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAAGGSAPEPRVLVCLGALLAGWVAVGLEAVVIGEVHENVTLHCGNISGLRGQVTWYRNNSEPVFLLSSNSSLRPAEPRFSLVDATSLHIESLSLGDEGIYTCQEILNVTQWFQVWLQVAS
Prediction	6444443333101201131334333444323130434440304031434444301021444413100242452444211023344220304414451403020113344442131133248
	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

CCCCCCCCCHHHHHHHHHHCCCSSSSCCCCSSSSCCCCCSSSSSSCCCCCCCCSSSSCCCCCCSSSSSCCCCCCCCCCCSCCCCCCCSSSCCCCHHHCSSSSSSSSCCCCCSSSSSSSSCC
MAAGGSAPEPRVLVCLGALLAGWVAVGLEAVVIGEVHENVTLHCGNISGLRGQVTWYRNNSEPVFLLSSNSSLRPAEPRFSLVDATSLHIESLSLGDEGIYTCQEILNVTQWFQVWLQVAS

2fboJ

0.18

0.17

5.64

1.33

DEthreader

DTQEG-G--AAPWCVVLKPSNNVHV-STAEVVQVDEGNDITMTCPCTDCANANVTWYTGPTTYQPLANKNGITWFIAGRASFSGARNLVIRAAKITDAGRVWCELATGDADRSSTILKV--

6on9A

0.16

0.15

4.93

1.08

SPARKS-K

--------ASEEVMACLRQERSRVENPSQTIVNVVAENPAYLHCSVPPDAEHEIAWTRVSDGAL--LTAGNRTFTRDPRWQVSKIWVLNLRRAEQQDSGCYLCEINDKHNTVYAVYLKVLE

3rbgA

0.17

0.13

4.36

1.51

FFAS-3D

-------------------------TNHTETITVEEGQTLTLKCVTSLRKNSSLQWLTPSGFTIFLNYPVLKNSKYQLLHHSANQLSITVPNVTLQDEGVYKCLHYSDSVSTKEVKVIVLA

3rbgA

0.19

0.14

4.53

1.29

CNFpred

-----------------------------ETITVEEGQTLTLKCVTSLRKNSSLQWLTPS---GFTIFLNEYPVLKNSKYQLLHQLSITVPNVTLQDEGVYKCLHYSDSVSTKEVKVIVLA

5whzL

0.21

0.20

6.31

1.17

DEthreader

TYYCMGGTKVDIKDKTH--A--SELT-QDPAVSVALKQTVTITCRGDSLRSHYASWYQKKQAPVLLFYGKN-NRPIPDRFSGSASASLTITGAQAEDEADYYCSSRSRLSVFGGTKLTVLD

6nrqA

0.18

0.16

5.09

1.04

SPARKS-K

----------------GSWNEPYFDLTMPRNITSLVGKSAYLGCRVKHLGNKTVAWIRHRDL--HILTVGTYTYTTDQRFQTSYEWTLQIKWAQQRDAGVYECQISTQPVRSYSVNLNIVH

2fboJ

0.19

0.16

5.06

0.45

MapAlign

----------------------IMTVRTHTEVEVHAGGTVELPCSYQLTQPPVISWLKGADRSTKVFKGNSYKESFLGRASVANLPTLRLTHVHPQDGGRYWCQVAWFGLDAKSVVLKVTH

7k0xD

0.22

0.18

5.74

0.34

CEthreader

--------------------TGVALEQRPISITRNAKQSASLNCKILNPVSDYVHWYRSQEGPERLLVYSRSSVPDADKVRAYDTCRLIVSDLQVSDSGVYHCASWDGRVKVFGTRLIVTE

6eg1A1

0.19

0.16

5.07

0.99

MUSTER

------------------YPPPVFDFGMPRNITTRTGHTAAINCRVDNLGDKSVSWIRKRDL--HILTAGILTYTSDERFKVVRTWTLHVKYAQPRDSGIYECQVNTEPKISMAFRLNVI-

6iaaA2

0.20

0.17

5.27

0.38

HHsearch

--------------------APPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLL---FPNQPQQPNSRCSVSPTGDLTITNIQRSDAGYYICQALTVAGSIAKAQLEVTD

(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	0.811

(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	6on9A	0.78	1.81	0.187	0.884	model1_6on9A.pdb.gz
2	7deuB	0.76	2.31	0.175	0.893	model1_7deuB.pdb.gz
3	2fboJ	0.76	2.59	0.188	0.926	model1_2fboJ.pdb.gz
4	5whzL	0.76	2.40	0.207	0.909	model1_5whzL.pdb.gz
5	3uzeA	0.76	2.52	0.167	0.901	model1_3uzeA.pdb.gz
6	5whzH	0.76	2.82	0.119	0.934	model1_5whzH.pdb.gz
7	5yd5A	0.76	2.52	0.174	0.901	model1_5yd5A.pdb.gz
8	7k78K	0.75	2.56	0.183	0.893	model1_7k78K.pdb.gz
9	7deoA	0.75	2.29	0.151	0.893	model1_7deoA.pdb.gz
10	6ehwB	0.75	2.50	0.183	0.893	model1_6ehwB.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	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0005198	0.66	structural molecule activity
GO:0042802	0.59	identical protein binding
GO:0003723	0.52	RNA binding
GO:0046983	0.51	protein dimerization activity
GO:0042803	0.50	protein homodimerization activity

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	1.00	regulation of cellular process
GO:0048518	1.00	positive regulation of biological process
GO:0044699	0.75	single-organism process
GO:0048583	0.74	regulation of response to stimulus
GO:0009987	0.74	cellular process
GO:0044763	0.72	single-organism cellular process
GO:0048522	0.71	positive regulation of cellular process
GO:0032502	0.70	developmental process
GO:0007165	0.68	signal transduction
GO:0048584	0.66	positive regulation of response to stimulus
GO:0032268	0.66	regulation of cellular protein metabolic process
GO:0050776	0.65	regulation of immune response
GO:0032270	0.65	positive regulation of cellular protein metabolic process
GO:0002684	0.65	positive regulation of immune system process
GO:2000112	0.64	regulation of cellular macromolecule biosynthetic process
GO:0051173	0.64	positive regulation of nitrogen compound metabolic process
GO:0050778	0.64	positive regulation of immune response
GO:0031328	0.64	positive regulation of cellular biosynthetic process
GO:0010628	0.64	positive regulation of gene expression
GO:0010557	0.64	positive regulation of macromolecule biosynthetic process
GO:0002376	0.63	immune system process
GO:0031347	0.62	regulation of defense response
GO:0045089	0.61	positive regulation of innate immune response
GO:0044767	0.58	single-organism developmental process
GO:0016043	0.57	cellular component organization
GO:0007155	0.57	cell adhesion
GO:0098609	0.56	cell-cell adhesion
GO:0098742	0.54	cell-cell adhesion via plasma-membrane adhesion molecules
GO:0048856	0.54	anatomical structure development
GO:0007156	0.53	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0051239	0.52	regulation of multicellular organismal process
GO:0045727	0.52	positive regulation of translation
GO:0002757	0.52	immune response-activating signal transduction
GO:0048869	0.51	cellular developmental 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:0044464	1.00	cell part
GO:0043226	0.90	organelle
GO:0044424	0.85	intracellular part
GO:0043229	0.79	intracellular organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0016020	0.69	membrane
GO:0044421	0.68	extracellular region part
GO:0005886	0.68	plasma membrane
GO:0043231	0.65	intracellular membrane-bounded organelle
GO:0044444	0.64	cytoplasmic part
GO:0005634	0.58	nucleus
GO:0005737	0.53	cytoplasm
GO:0044422	0.51	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	0.222	2gqhA	0.600	1.93	0.200	0.694	2.7.11.1	41,58,67,82
2	0.200	2wwmD	0.662	2.14	0.179	0.760	2.7.11.1	55,102
3	0.184	1zvyA	0.682	2.15	0.175	0.802	3.2.1.17	29,100
4	0.180	1ri8A	0.676	2.19	0.184	0.802	3.2.1.17	29,101,118
5	0.166	2edwA	0.605	1.91	0.187	0.694	2.7.11.1	44,66,97

	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	0.08	1mjjL	0.740	1.71	0.210	0.826	0.55	HAL	complex1.pdb.gz	117,119,120
2	0.07	1dbbL	0.719	1.91	0.190	0.826	0.65	STR	complex2.pdb.gz	34,97,99,100
3	0.07	1cbvL	0.724	1.85	0.180	0.826	0.60	QNA	complex3.pdb.gz	37,94,97,98
4	0.07	1mpaL	0.729	1.77	0.170	0.826	0.52	III	complex4.pdb.gz	31,97,99
5	0.06	2dqtL	0.729	1.82	0.150	0.826	0.62	CPD	complex5.pdb.gz	41,42,97,100
6	0.05	3cfbA	0.719	1.81	0.202	0.818	0.56	SPB	complex6.pdb.gz	93,94,95,99
7	0.04	1mf21	0.732	1.80	0.200	0.826	0.90	III	complex7.pdb.gz	79,94,96
8	0.04	1wcbA	0.714	1.74	0.224	0.810	0.54	PE1	complex8.pdb.gz	41,43,98,100
9	0.04	1rivL	0.737	1.72	0.200	0.826	0.54	OBE	complex9.pdb.gz	27,28,43,45
10	0.03	1yekL	0.728	1.78	0.160	0.826	0.55	NPO	complex10.pdb.gz	26,28,45

	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.