D-I-TASSER Q96PB7-D2

D-I-TASSER results for Q96PB7-D2

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

Input Sequence in FASTA format

>Q96PB7 (126 residues)
VQNMSQSIEVLNLRTQRDFQYVLKMETQMKGLKAKFRQIEDDRKTLMTKHFQELKEKMDE
LLPLIPVLEQYKTDAKLITQFKEEIRNLSAVLTGIQEEIGAYDYEELHQRVLSLETRLRD
CMKKLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VQNMSQSIEVLNLRTQRDFQYVLKMETQMKGLKAKFRQIEDDRKTLMTKHFQELKEKMDELLPLIPVLEQYKTDAKLITQFKEEIRNLSAVLTGIQEEIGAYDYEELHQRVLSLETRLRDCMKKLT
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHC
Confidence	960678999999997999999999999999899999999714676537789999999999836399998740119999999999999999999999970532699999999999999999998619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VQNMSQSIEVLNLRTQRDFQYVLKMETQMKGLKAKFRQIEDDRKTLMTKHFQELKEKMDELLPLIPVLEQYKTDAKLITQFKEEIRNLSAVLTGIQEEIGAYDYEELHQRVLSLETRLRDCMKKLT
Prediction	654345414313432453253045135305415441542464554243641640454055034014304635223410540453044134315403662444415403530350463045127638
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHC
VQNMSQSIEVLNLRTQRDFQYVLKMETQMKGLKAKFRQIEDDRKTLMTKHFQELKEKMDELLPLIPVLEQYKTDAKLITQFKEEIRNLSAVLTGIQEEIGAYDYEELHQRVLSLETRLRDCMKKLT

6z9lA

0.09

3.36

1.50

DEthreader

SKEELQQEIASNQEKLATAQQAESDAQQARSASQQALNTAKTTQATAEKELSVHKATLANLQAVATKSTTNYEEKVRQTATAEKSLQQTKDQLATINELIQNRAAVLEKAKTNVAEAQAIEQTSAK

5vr2A

0.08

0.03

1.25

1.22

HHsearch

------------RDLEAAYNNLLRDKSALEEE-----------KRQLEQENEDLARRLESSSEEVTRLRRGQC-----------------------------------------------------

2l10A

0.07

2.93

0.52

CEthreader

KRLLSDLLPPSTGTFQEAQSRLNEAAAGLNQAATELVQASRGTPQDLARASGRFGQDFSTFLEAGVEMAGQAPSQEDRAQVVSNLKGISMSSSKLLLAAKALSLAAAARAVTDSINQLITMCTQQA

3s84A

0.10

3.57

0.70

EigenThreader

EVSQKIGDNLRELQQRLEPYADQLRTQVNTQAEQLQASLRPHADELKAKIDQNVEELKGRLTPYADEFKLTFQMKKNAEELKARISASAEELRQRLAPLAEDVRGNQVEEFRRRVEPYGENFNKAL

5nenA1

0.17

5.46

0.88

FFAS-3D

---IALQTQLFASRRQALQSEIDGYKQSMDGIRFQLKGLQDSRGNK-QIQLSSLREQMNSMKQLARYLEVQRQFAEVIDETVGRIGQLQKQLLESQQRIDQRQLAQTQMDASEFRNKLQMADFDL-

7jrqA

0.13

0.12

4.16

0.77

SPARKS-K

---HHENLYFQSSEKEELFEKLKQTADEAVQLFQRLREIFDKDDDSFEQVLEELEEALQKHRQLADQGRKKGLTSEAAKQGDQFVQLFQRFREAWDKG----DKDSLEQILEELEQVAQKAVELGL

5xg2A

0.14

4.85

0.69

CNFpred

KERLKAEILTGEARLPGLRERAENLRRLVEEKRAEISELERRLSSIT-SQSFELRIKLSDLEKELELARKDLEVLAEERAVREEIEVAKRRINELDTLIERGELAKLRGRIERLERKRDKLKKALE

7kogB

0.07

2.93

1.50

DEthreader

FKKKLEQEVGGLKKDIEDLELSLQKSDQDKASKDHQIRNLNDEIAHQDELINKLNKEKKMQGEHTQKTAEELQASEDKVNHLTKVKAKLEQTLDELEDSLEREKKLRGDVEKAKRKVEGDLKLTQE

2x0cA2

0.05

2.29

0.79

MapAlign

PVQPINDMSYFGCLDSVMENSKVLGEAMTGISQNAKNGNLPEFGDAIATASKALCGFTEAAAQAAYLVGVSDEGRAAMEPIVISAKTMLESAGGLIQTARWSVLAGHSRTVSDSIKKLITSMRDKA

5xg2A

0.12

4.21

0.72

MUSTER

VEEKRAEISELERRLSSITSQSFELRIKLSDLEKELELARKD-LEKVLAEERAVREEIEVAKRRINELDTLIERERELAKLRGRIERLERKRDKLKKALENPEARELTEKIRAVEKEIAALREELS

(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	0.5576

(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	6y07A	0.73	2.50	0.111	0.929	model1_6y07A.pdb.gz
2	1sziA	0.73	2.86	0.049	0.976	model1_1sziA.pdb.gz
3	6egcA	0.73	2.33	0.108	0.881	model1_6egcA.pdb.gz
4	2x0cA	0.73	2.59	0.085	0.929	model1_2x0cA.pdb.gz
5	6bfiA2	0.72	2.89	0.064	0.992	model1_6bfiA2.pdb.gz
6	2b0hA	0.72	3.12	0.065	0.968	model1_2b0hA.pdb.gz
7	1st6A	0.72	2.90	0.066	0.968	model1_1st6A.pdb.gz
8	5h5mA	0.71	2.89	0.072	0.992	model1_5h5mA.pdb.gz
9	3t6gB	0.71	2.69	0.094	0.913	model1_3t6gB.pdb.gz
10	5ic0A3	0.66	2.61	0.055	0.865	model1_5ic0A3.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	0.27	heterocyclic compound binding
GO:0097159	0.27	organic cyclic compound binding
GO:0022836	0.25	gated channel activity
GO:0005216	0.25	ion channel activity
GO:0003676	0.21	nucleic acid binding
GO:0003723	0.19	RNA binding
GO:0004872	0.18	receptor activity
GO:0099600	0.16	transmembrane receptor activity
GO:0051015	0.15	actin filament binding
GO:0017166	0.15	vinculin binding
GO:0001540	0.15	beta-amyloid binding
GO:0043167	0.14	ion binding
GO:0005230	0.14	extracellular ligand-gated ion channel activity
GO:0046872	0.13	metal ion binding
GO:0005198	0.12	structural molecule activity
GO:0045296	0.11	cadherin binding
GO:0008013	0.11	beta-catenin binding
GO:0005244	0.11	voltage-gated ion channel 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:0044763	0.98	single-organism cellular process
GO:0032502	0.92	developmental process
GO:0048869	0.91	cellular developmental process
GO:0044767	0.91	single-organism developmental process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0048518	0.82	positive regulation of biological process
GO:0051094	0.81	positive regulation of developmental process
GO:0048522	0.78	positive regulation of cellular process
GO:0016043	0.78	cellular component organization
GO:0045597	0.77	positive regulation of cell differentiation
GO:0032989	0.76	cellular component morphogenesis
GO:2000026	0.71	regulation of multicellular organismal development
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0051240	0.70	positive regulation of multicellular organismal process
GO:0048519	0.70	negative regulation of biological process
GO:0060284	0.69	regulation of cell development
GO:0010468	0.69	regulation of gene expression
GO:0010770	0.68	positive regulation of cell morphogenesis involved in differentiation
GO:0010628	0.68	positive regulation of gene expression
GO:0010605	0.68	negative regulation of macromolecule metabolic process
GO:0060317	0.67	cardiac epithelial to mesenchymal transition
GO:0010718	0.67	positive regulation of epithelial to mesenchymal transition
GO:0010629	0.67	negative regulation of gene expression
GO:0003190	0.67	atrioventricular valve formation

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:0005623	0.77	cell
GO:0044464	0.76	cell part
GO:0044424	0.57	intracellular 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	0.073	1q0mD	0.616	2.71	0.075	0.818	1.15.1.1	NA
2	0.066	2kk1A	0.613	2.74	0.099	0.770	2.7.10.2	NA
3	0.066	2npuA	0.537	3.31	0.051	0.762	2.7.11.1	NA
4	0.066	3eziA	0.517	3.57	0.069	0.794	2.7.13.3	NA
5	0.066	1i5nD	0.568	3.13	0.069	0.794	2.7.13.3	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	1g5z0	0.682	3.15	0.115	0.968	0.47	III	complex1.pdb.gz	10,18,21,22,29,34,52,53,54,55,56,58,63,89,94,96
	2	0.02	1f1m0	0.681	3.24	0.106	0.976	0.50	III	complex2.pdb.gz	4,8,16,23,24,27,28,31,34,35,43,47,48,49,51,52,53,56,99

	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.