D-I-TASSER Q9UIU6-D5

D-I-TASSER results for Q9UIU6-D5

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

Input Sequence in FASTA format

>Q9UIU6 (78 residues)
VFSQLMPVNQNAQVNANLSSENISGSGLHPLASSLVNVSPTHNFSLSPSTLLNPTELNRD
IADSQPMSAPVASKSTVT

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VFSQLMPVNQNAQVNANLSSENISGSGLHPLASSLVNVSPTHNFSLSPSTLLNPTELNRDIADSQPMSAPVASKSTVT
Prediction	CCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	976543467664255105834577753231205430456677877798334784225877544675566643333349
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VFSQLMPVNQNAQVNANLSSENISGSGLHPLASSLVNVSPTHNFSLSPSTLLNPTELNRDIADSQPMSAPVASKSTVT
Prediction	744532424563524351447515453134224322423445715143433244452457157644253424555648
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
VFSQLMPVNQNAQVNANLSSENISGSGLHPLASSLVNVSPTHNFSLSPSTLLNPTELNRDIADSQPMSAPVASKSTVT

6hbeA3

0.08

3.08

0.62

CEthreader

YVDEPIPVRPGDYLRIYFLNVGPNLTSTLHTALAGPSDSWVIEWRVPPVEGDYTLVTHVFGTAIKGALGILRAKKDAP

6t58A1

0.03

1.65

0.57

EigenThreader

CPLEKALD---VMVSTFHKYSGKLNKSELKELLTRELPEVDPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELPSF

3kitJ

0.16

0.14

4.71

0.26

FFAS-3D

LLATLKENLERAQGSFFLVNQGLPAKETHALRQALKQNG--ARLFVAKNTLIRLALKELGLPELDGLQGPSA------

6vqwA

0.14

0.13

4.38

0.94

SPARKS-K

--TMSTAIIFNSSVAAVVDTEIANGANVT-FSTVTVKEEINANRDF---NLVNAQNGKISEASKCEYFGREINPTEFF

4hy3A

0.10

0.03

0.96

0.56

CNFpred

---------------------------------AFILLS--------RADVVDFDALMAAVS----------------

5cdiA

0.09

0.08

2.97

0.83

DEthreader

-TGVVFVEG----KILIMAEEKAPGFRYLEDILT-AITITTV-VGDGS-TAADVAARVKQIRNLQLERRLGGVAIIQV

2z0sA1

0.06

0.05

2.19

0.84

MapAlign

----IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLGDYIKAKVVAFDKTRSPLLTVQGEGLGRI-----------

3ixxD

0.15

0.14

4.77

0.55

MUSTER

NFKVMMTVNATD-VTDVITIPTAAGKNLCIVRAMDVGYMCDDTITYECPVLSAGNDPEDIDCWCTKSAVYVRGRCT--

2pffB

0.23

0.22

6.85

0.65

HHsearch

VPSPMLSISNLTQVQVNKTNS--HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLEKLKFSNRF-LPVASPFHSHLLVP

1oczB

0.12

4.12

0.61

CEthreader

EVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKY

(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	0.5819

(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	3ebgA1	0.46	3.75	0.090	0.744	model1_3ebgA1.pdb.gz
2	6vwoA2	0.46	3.77	0.093	0.795	model1_6vwoA2.pdb.gz
3	7c1xA2	0.45	3.70	0.069	0.769	model1_7c1xA2.pdb.gz
4	4opeA1	0.45	4.03	0.095	0.833	model1_4opeA1.pdb.gz
5	6dtkA	0.45	4.36	0.067	0.846	model1_6dtkA.pdb.gz
6	2hs3A	0.45	4.61	0.067	0.885	model1_2hs3A.pdb.gz
7	5elpC1	0.44	4.05	0.070	0.833	model1_5elpC1.pdb.gz
8	6qspA	0.44	4.04	0.105	0.821	model1_6qspA.pdb.gz
9	2qb6A2	0.44	3.76	0.044	0.744	model1_2qb6A2.pdb.gz
10	2z1fA	0.41	4.48	0.028	0.782	model1_2z1fA.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:0001077	1.00	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000978	1.00	RNA polymerase II core promoter proximal region sequence-specific DNA 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:1902725	1.00	negative regulation of satellite cell differentiation
GO:0098528	1.00	skeletal muscle fiber differentiation
GO:0090190	1.00	positive regulation of branching involved in ureteric bud morphogenesis
GO:0072107	1.00	positive regulation of ureteric bud formation
GO:0072095	1.00	regulation of branch elongation involved in ureteric bud branching
GO:0072075	1.00	metanephric mesenchyme development
GO:0061551	1.00	trigeminal ganglion development
GO:0061197	1.00	fungiform papilla morphogenesis
GO:0061055	1.00	myotome development
GO:0060037	1.00	pharyngeal system development
GO:0050678	1.00	regulation of epithelial cell proliferation
GO:0048699	1.00	generation of neurons
GO:0046661	1.00	male sex differentiation
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0045892	1.00	negative regulation of transcription, DNA-templated
GO:0045214	1.00	sarcomere organization
GO:0043586	1.00	tongue development
GO:0043524	1.00	negative regulation of neuron apoptotic process
GO:0034504	1.00	protein localization to nucleus
GO:0030910	1.00	olfactory placode formation
GO:0030238	1.00	male sex determination
GO:0008584	1.00	male gonad development
GO:0007519	1.00	skeletal muscle tissue 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:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus

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	3dqwA	0.375	4.17	0.048	0.718	2.7.10.2	NA
2	0.060	1xsoA	0.429	4.32	0.056	0.795	1.15.1.1	34
3	0.060	3gseA	0.423	4.14	0.110	0.808	5.4.4.2	NA
4	0.060	1g83A	0.354	3.63	0.054	0.628	2.7.10.2	NA
5	0.060	1yi6A	0.367	3.95	0.032	0.705	2.7.10.2	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	0.01	1v0yA	0.333	4.93	0.117	0.833	0.20	HI5	complex1.pdb.gz	26,28,37,42
	2	0.01	1v0rA	0.395	4.40	0.054	0.782	0.20	WO5	complex2.pdb.gz	27,29,44

	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.