D-I-TASSER Q8N9C0-D6

D-I-TASSER results for Q8N9C0-D6

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

Input Sequence in FASTA format

>Q8N9C0 (97 residues)
PPTIDPSVLEALAAHAITVKVGHTAHIKVPFRGKPLPKVTWYKDGMEVTEEERVSMERGE
DQALLTISNCVREDSGLILLKLKNDHGSATATLHLSV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PPTIDPSVLEALAAHAITVKVGHTAHIKVPFRGKPLPKVTWYKDGMEVTEEERVSMERGEDQALLTISNCVREDSGLILLKLKNDHGSATATLHLSV
Prediction	CCCCCCCCCCCCCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSCCCSSSSSSSSSC
Confidence	9977985234579976899489419999999840798899998999958899689999399899999686612167999999979958999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PPTIDPSVLEALAAHAITVKVGHTAHIKVPFRGKPLPKVTWYKDGMEVTEEERVSMERGEDQALLTISNCVREDSGLILLKLKNDHGSATATLHLSV
Prediction	7461416125615755140534561456250415455403021575505776414034576423433650446157464440405324341416758
	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

CCCCCCCCCCCCCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSCCCSSSSSSSSSC
PPTIDPSVLEALAAHAITVKVGHTAHIKVPFRGKPLPKVTWYKDGMEVTEEERVSMERGEDQALLTISNCVREDSGLILLKLKNDHGSATATLHLSV

3lcyA

0.26

0.25

7.65

1.50

DEthreader

TPQFHPGY--PL-KEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSENITIENTEHYTHLVMKNVQRTHAGKYKVQLSNVFGTVDAILDVEI

3lcyA2

0.24

7.37

1.26

SPARKS-K

TPQFHP---GYPLKEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSENITIENTEHYTHLVMKNVQRTHAGKYKVQLSNVFGTVDAILDVEI

3lcyA2

0.26

0.25

7.65

0.39

MapAlign

TPQFHPGY--PLK-EKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSENITIENTEHYTHLVMKNVQRTHAGKYKVQLSNVFGTVDAILDVEI

3lcyA

0.23

7.09

0.34

CEthreader

TPQFHPGYP---LKEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSENITIENTEHYTHLVMKNVRKTHAGKYKVQLSNVFGTVDAILDVEI

1ya5A

0.31

0.30

9.05

1.00

MUSTER

AETAPPNFVQRL--QSMTVRQGSQVRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGDLYSLLIAEAYPEDSGTYSVNATNSVGRATSTAELLV

5i99A

0.29

0.28

8.47

0.42

HHsearch

-PGSAPDFSRNPMKKMVQVQVGSLVILDCKPRASPRALSFWKKGDMMVREQARVSFLN---DGGLKIMNVTKADAGTYTCTAENQFGKANGTTHLVV

3pucA

0.27

8.22

1.73

FFAS-3D

PISSKPVIVTGL--QDTTVSSDSVAKFAVKATGEPRPTAIWTKDGKAITQGGKYKLSEDKGGFFLEIHKTDTSDSGLYTCTVKNSAGSVSSSCKLTI

2kdgA

0.23

0.22

6.78

0.32

EigenThreader

MGPPI------QVPENMSIDEGRFCRMDFKVSGLPAPDVSWYLNGRTVQSDDLHKMIVSKGLHSLIFEVVRASDAGAYACVAKNRAGEATFTVQLDV

2wp3T

0.32

0.30

9.01

1.77

CNFpred

PPKIEA------LPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHI

3lcyA2

0.26

0.25

7.65

1.50

DEthreader

TPQFHPGY--PL-KEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSENITIENTEHYTHLVMKNVQRTHAGKYKVQLSNVFGTVDAILDVEI

(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	0.9528

(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	3lcyA2	0.91	1.06	0.255	0.969	model1_3lcyA2.pdb.gz
2	2wwmD	0.90	0.91	0.308	0.938	model1_2wwmD.pdb.gz
3	2nziA2	0.89	1.42	0.274	0.979	model1_2nziA2.pdb.gz
4	1tlkA	0.89	0.99	0.297	0.938	model1_1tlkA.pdb.gz
5	3qp3A	0.88	1.01	0.253	0.938	model1_3qp3A.pdb.gz
6	3b43A6	0.88	1.03	0.209	0.938	model1_3b43A6.pdb.gz
7	3pucA	0.88	0.97	0.286	0.938	model1_3pucA.pdb.gz
8	2wwkO	0.87	1.14	0.264	0.938	model1_2wwkO.pdb.gz
9	1u2hA	0.87	1.17	0.286	0.938	model1_1u2hA.pdb.gz
10	6fwxB2	0.87	1.17	0.330	0.938	model1_6fwxB2.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:0097159	0.78	organic cyclic compound binding
GO:1901363	0.77	heterocyclic compound binding
GO:0097367	0.76	carbohydrate derivative binding
GO:0035639	0.75	purine ribonucleoside triphosphate binding
GO:0032555	0.75	purine ribonucleotide binding
GO:0032550	0.75	purine ribonucleoside binding
GO:0005524	0.74	ATP binding
GO:0005516	0.58	calmodulin binding
GO:0004872	0.55	receptor activity
GO:0042802	0.54	identical protein binding
GO:0003824	0.52	catalytic activity
GO:0046983	0.51	protein dimerization activity
GO:0046872	0.51	metal ion binding
GO:0004888	0.51	transmembrane signaling receptor activity
GO:0042803	0.50	protein homodimerization activity
GO:0005198	0.50	structural molecule 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:0044699	0.94	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.91	single-organism cellular process
GO:0032502	0.85	developmental process
GO:0065007	0.82	biological regulation
GO:0044767	0.82	single-organism developmental process
GO:0050789	0.81	regulation of biological process
GO:0050794	0.77	regulation of cellular process
GO:0016043	0.75	cellular component organization
GO:0071704	0.70	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.69	cellular metabolic process
GO:0044260	0.67	cellular macromolecule metabolic process
GO:0048869	0.66	cellular developmental process
GO:0048856	0.65	anatomical structure development
GO:0006996	0.65	organelle organization
GO:0006796	0.65	phosphate-containing compound metabolic process
GO:0006464	0.65	cellular protein modification process
GO:1902589	0.64	single-organism organelle organization
GO:0048646	0.64	anatomical structure formation involved in morphogenesis
GO:0030029	0.64	actin filament-based process
GO:0022607	0.64	cellular component assembly
GO:0007010	0.64	cytoskeleton organization
GO:0006468	0.64	protein phosphorylation
GO:0031032	0.63	actomyosin structure organization
GO:0030239	0.61	myofibril assembly
GO:0009653	0.61	anatomical structure morphogenesis
GO:0055003	0.60	cardiac myofibril assembly
GO:0018108	0.59	peptidyl-tyrosine phosphorylation
GO:0006928	0.58	movement of cell or subcellular component
GO:0051239	0.55	regulation of multicellular organismal process
GO:0032501	0.55	multicellular organismal process
GO:0048518	0.54	positive regulation of biological process
GO:0050896	0.53	response to stimulus
GO:0019222	0.53	regulation of metabolic process
GO:0051179	0.52	localization
GO:0031323	0.52	regulation of cellular metabolic process
GO:0080090	0.51	regulation of primary metabolic process
GO:0048468	0.51	cell development
GO:0007165	0.51	signal transduction
GO:0006810	0.51	transport
GO:0051128	0.50	regulation of cellular component organization
GO:0050793	0.50	regulation of developmental process
GO:0048522	0.50	positive regulation of cellular 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:0044424	0.93	intracellular part
GO:0044444	0.79	cytoplasmic part
GO:0043226	0.79	organelle
GO:0044422	0.75	organelle part
GO:0043229	0.67	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0044425	0.61	membrane part
GO:0016020	0.59	membrane
GO:0031224	0.57	intrinsic component of membrane
GO:0044449	0.56	contractile fiber part
GO:0044446	0.56	intracellular organelle part
GO:0016021	0.55	integral component of membrane
GO:0005886	0.52	plasma membrane
GO:0005737	0.51	cytoplasm
GO:0032991	0.50	macromolecular complex

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	0.378	2wwmD	0.895	0.91	0.308	0.938	2.7.11.1	40,77,92
2	0.305	2eo1A	0.819	1.52	0.180	0.917	2.7.11.1	40,42,44,54
3	0.284	2edwA	0.767	1.51	0.176	0.876	2.7.11.1	74
4	0.176	2edrA	0.746	1.67	0.176	0.876	2.7.11.1	53
5	0.114	1rv6Y	0.698	2.80	0.121	0.928	2.7.10.1	40

	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	0.07	2pyeD	0.801	1.94	0.143	0.938	0.92	III	complex1.pdb.gz	44,77,78,79,80,91,93
2	0.07	1tlk0	0.886	0.99	0.297	0.938	1.10	III	complex2.pdb.gz	3,32,34,36,38,39,40,48,56,58,59,60
3	0.05	2iep0	0.837	1.35	0.225	0.917	0.66	III	complex3.pdb.gz	5,28,30,32,64
4	0.04	3hujG	0.798	2.02	0.156	0.928	0.73	AGH	complex4.pdb.gz	36,37,84,85

	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.