D-I-TASSER Q12791-D4

D-I-TASSER results for Q12791-D4

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

Input Sequence in FASTA format

>Q12791 (57 residues)
HNAGQSRASLSHSSHSSQSSSKKSSSVHSIPSTANRQNRPKSRESRDKQKYVQEERL

Predicted Secondary Structure

Sequence	20 40 \| \| HNAGQSRASLSHSSHSSQSSSKKSSSVHSIPSTANRQNRPKSRESRDKQKYVQEERL
Prediction	CCCCCCHHHHCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCHHHHHHHHHHHHHCC
Confidence	963100010112466654455555542205775577887510355777777877409
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| HNAGQSRASLSHSSHSSQSSSKKSSSVHSIPSTANRQNRPKSRESRDKQKYVQEERL
Prediction	874645444244454554446554543443354464764554564555654554668
	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

                   |                   |

SS
Seq

CCCCCCHHHHCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCHHHHHHHHHHHHHCC
HNAGQSRASLSHSSHSSQSSSKKSSSVHSIPSTANRQNRPKSRESRDKQKYVQEERL

2fknB1

0.05

2.42

0.46

CEthreader

VNTAAGASWVSFHHGGGVGMGYSLHAGMVAVADGSELADERLARVLTSDPGMGIIRH

5de0A

0.07

2.89

0.58

EigenThreader

QTAILLTVSVAFSKGFWSPPELIVDVLIHCHARHDLLFYTLRKGISDIAAQEKVIGR

2d46A

0.33

0.26

7.91

0.24

FFAS-3D

HGIEDSEAGSADSYTSRPSDSDVS----------LEEDREAIRQEREQQAAIQLER-

6ypuv

0.14

0.12

4.21

0.92

SPARKS-K

LKEGEPVDVAIRRFKRSCEKAGVLA------DVRKREFYEKPTQERKRKKAAAVKRY

5mqfC

0.42

0.09

2.58

0.36

CNFpred

---------------------------------------------AQKEKEKHEEKL

6kg7A

0.11

3.81

1.00

DEthreader

LLSGSAVFFLT--ALSLRYAMISSPFVANLVYIWSFPLKILFITFWLLLRQHLTEQK

4plcA2

0.13

0.12

4.23

0.71

MapAlign

-----KRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIEPEEKELFDKSVEEVR

2xkxA

0.18

5.74

0.61

MUSTER

DSYAPPDITTSYSQEISHSSYLGTDYPTAMTPTSPRRYSPVAKDLLGEEDIPREPRR

6li9A

0.19

0.18

5.68

0.38

HHsearch

LNFGES-TLLNLHNMISDKGSKVDTSGIFLDKEGKNLLHRQT--AFRDRCFVSNSVL

2fknB

0.05

2.42

0.46

CEthreader

VNTAAGASWVSFHHGGGVGMGYSLHAGMVAVADGSELADERLARVLTSDPGMGIIRH

(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	0.5729

(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	6vwoA	0.54	3.58	0.053	0.983	model1_6vwoA.pdb.gz
2	1d0kA	0.51	3.03	0.059	0.877	model1_1d0kA.pdb.gz
3	4bjpA	0.51	3.33	0.039	0.842	model1_4bjpA.pdb.gz
4	1gxsA	0.51	3.41	0.148	0.912	model1_1gxsA.pdb.gz
5	1whtA1	0.50	3.53	0.132	0.912	model1_1whtA1.pdb.gz
6	1ivyA1	0.50	3.92	0.089	0.947	model1_1ivyA1.pdb.gz
7	1wpxA	0.49	3.81	0.056	0.930	model1_1wpxA.pdb.gz
8	1ac5A	0.48	3.88	0.070	0.912	model1_1ac5A.pdb.gz
9	3ue3A	0.44	4.21	0.077	0.895	model1_3ue3A.pdb.gz
10	3oc2A3	0.43	4.06	0.078	0.842	model1_3oc2A3.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:0015079	0.95	potassium ion transmembrane transporter activity
GO:0005261	0.95	cation channel activity
GO:0005244	0.95	voltage-gated ion channel activity
GO:0060072	0.94	large conductance calcium-activated potassium channel activity
GO:0005249	0.94	voltage-gated potassium 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:0065007	0.87	biological regulation
GO:0050896	0.87	response to stimulus
GO:0050789	0.86	regulation of biological process
GO:0009628	0.86	response to abiotic stimulus
GO:0065008	0.81	regulation of biological quality
GO:0048518	0.81	positive regulation of biological process
GO:0032501	0.80	multicellular organismal process
GO:0044699	0.79	single-organism process
GO:0009987	0.79	cellular process
GO:0003008	0.79	system process
GO:0050794	0.74	regulation of cellular process
GO:0051239	0.67	regulation of multicellular organismal process
GO:0048522	0.67	positive regulation of cellular process
GO:0048519	0.67	negative regulation of biological process
GO:0042391	0.67	regulation of membrane potential
GO:0016043	0.67	cellular component organization
GO:0003012	0.67	muscle system process
GO:0044057	0.66	regulation of system process
GO:0010033	0.66	response to organic substance
GO:0006950	0.66	response to stress
GO:0090066	0.65	regulation of anatomical structure size
GO:0051592	0.65	response to calcium ion
GO:0045986	0.65	negative regulation of smooth muscle contraction
GO:0043065	0.65	positive regulation of apoptotic process
GO:0001666	0.65	response to hypoxia
GO:0044763	0.64	single-organism cellular process
GO:0009605	0.60	response to external stimulus
GO:0006810	0.58	transport
GO:0006811	0.55	ion transport
GO:0042592	0.54	homeostatic process
GO:0032502	0.54	developmental process
GO:0030001	0.54	metal ion transport
GO:0060087	0.53	relaxation of vascular smooth muscle
GO:0060083	0.53	smooth muscle contraction involved in micturition
GO:0060073	0.53	micturition
GO:0045794	0.53	negative regulation of cell volume
GO:0044767	0.53	single-organism developmental process
GO:0034465	0.53	response to carbon monoxide
GO:0030007	0.53	cellular potassium ion homeostasis
GO:0006970	0.53	response to osmotic stress
GO:0006813	0.53	potassium ion transport
GO:0051260	0.52	protein homooligomerization
GO:0050880	0.51	regulation of blood vessel size

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:0008076	1.00	voltage-gated potassium channel complex
GO:0016020	0.84	membrane
GO:0016324	0.76	apical plasma membrane
GO:0044424	0.59	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	0.060	1qwoA	0.470	3.22	0.067	0.754	3.1.3.8	NA
2	0.060	1skaA	0.473	3.29	0.068	0.754	3.1.3.8	NA
3	0.060	3b9xA	0.482	3.81	0.036	0.947	3.2.2.8	NA
4	0.060	3hfaV	0.471	3.47	0.056	0.860	3.4.25.1	NA
5	0.060	2f6dA	0.469	3.50	0.041	0.789	3.2.1.3	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:

No Binding sites was predicted

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

	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.