D-I-TASSER A6NM62-D1

D-I-TASSER results for A6NM62-D1

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

Input Sequence in FASTA format

>A6NM62 (112 residues)
MLRLVAACPESCVVCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFNLA
LLSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MLRLVAACPESCVVCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFNLALLSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVL
Prediction	CCCCCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCSSSCCCCCCCSSCCCCCCCCCCCCSSSCCCCSCCSSCCCCCCCCCCCCSSSCCCCCCCCCSCCCCCCCCCCCCCSC
Confidence	9874667898754759983543898888889997419983688287328272438878879879899087418261248888989787799887753481414587445719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MLRLVAACPESCVVCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFNLALLSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVL
Prediction	7342345325424145543321552533453344134435742404514652354045544535542444414640344454544544542404353046412564656668
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCSSSCCCCCCCSSCCCCCCCCCCCCSSSCCCCSCCSSCCCCCCCCCCCCSSSCCCCCCCCCSCCCCCCCCCCCCCSC
MLRLVAACPESCVVCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFNLALLSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVL

3m18A1

0.25

0.23

7.21

1.50

DEthreader

-T--CETVTG-C-TCNEKEVDCKSLDSVPSIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLAS--LPLGVFDHLTQLDKY

3e6jA1

0.29

0.27

8.16

2.31

SPARKS-K

-----AACPSQC-SCSGTTVDCRSHASVPAIPTNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTV--LPSAVFDRLVHLKEL

5z8xA

0.30

0.28

8.38

0.42

MapAlign

-------CPPKCRCE-KLLFYCDGFHSVPNALKGSLGLSLRHNHITELERDQFASFSQLTWLHLDHNQISTVKEDAFQGLYKLKELILSSNKIF--YLPNTTFTQLINLQNL

3zyiA1

0.28

0.26

7.93

0.33

CEthreader

-----QNCPSVCSCSNQSKVVCTGLSEVPQIPSNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLT--VIPSGAFEYLSKLREL

2o6qA1

0.29

0.28

8.43

1.99

MUSTER

---NEALCGGVCSCNNKNSVDCKKLTAIPNIPADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKL--QALPIGVFDQLVNLAEL

5y31B

0.28

0.26

7.91

0.86

HHsearch

------KCPAVCT-CTKDNALCENARSIPRVPPDVISLSFVRSGFTEISEGSFLGLPHLEYLFIENNNIKSISRHTFRGLKSLIHLSLANNNLQ--TLPKDIFKGLDSLTNV

3e6jA1

0.27

0.25

7.68

1.24

FFAS-3D

-----AACPSQCSC-SGTTVDCKRHASVPGIPTNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQL--TVLPSAVFDRLVHLKEL

2o6qA1

0.27

8.21

0.58

EigenThreader

NEALCKKDGGVCSCNNKNSVDCKKLTAIPNIPADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKLQ--ALPIGVFDQLVNLAEL

5y31B

0.31

0.29

8.62

4.33

CNFpred

-------CPAVCTCT-KDNALCENARSIPRVPPDVISLSFVRSGFTEISEGSFLFTPSLQLLLFTSNSFDVISDDAFIGLPHLEYLFIENNNIKS--ISRHTFRGLKSLIHL

3m18A

0.25

0.23

7.21

1.50

DEthreader

-T--CETVTG-C-TCNEKEVDCKSLDSVPSIPADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLAS--LPLGVFDHLTQLDKY

(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	0.8321

(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	3e6jA	0.89	0.87	0.269	0.929	model1_3e6jA.pdb.gz
2	5wk4D	0.89	0.91	0.260	0.929	model1_5wk4D.pdb.gz
3	4k5uB	0.89	0.82	0.320	0.920	model1_4k5uB.pdb.gz
4	5a5cA1	0.88	0.98	0.308	0.929	model1_5a5cA1.pdb.gz
5	3g3bA	0.88	0.87	0.301	0.920	model1_3g3bA.pdb.gz
6	3m18A1	0.88	1.11	0.248	0.938	model1_3m18A1.pdb.gz
7	2v9tB	0.88	1.05	0.311	0.929	model1_2v9tB.pdb.gz
8	3wo9A1	0.87	1.93	0.259	0.964	model1_3wo9A1.pdb.gz
9	2o6qA1	0.87	1.49	0.267	0.938	model1_2o6qA1.pdb.gz
10	2o6sA	0.87	0.89	0.294	0.911	model1_2o6sA.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:0030234	0.74	enzyme regulator activity
GO:0019887	0.73	protein kinase regulator activity
GO:0004857	0.73	enzyme inhibitor activity
GO:0004860	0.72	protein kinase inhibitor activity
GO:0097367	0.63	carbohydrate derivative binding
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound 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:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0007165	0.83	signal transduction
GO:0009987	0.82	cellular process
GO:0044699	0.77	single-organism process
GO:0048583	0.74	regulation of response to stimulus
GO:0044763	0.73	single-organism cellular process
GO:0019222	0.73	regulation of metabolic process
GO:0007166	0.73	cell surface receptor signaling pathway
GO:0080090	0.72	regulation of primary metabolic process
GO:0048523	0.72	negative regulation of cellular process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0023051	0.71	regulation of signaling
GO:0010646	0.71	regulation of cell communication
GO:0051246	0.70	regulation of protein metabolic process
GO:0050790	0.70	regulation of catalytic activity
GO:0019220	0.70	regulation of phosphate metabolic process
GO:0009966	0.70	regulation of signal transduction
GO:1902531	0.69	regulation of intracellular signal transduction
GO:0048585	0.69	negative regulation of response to stimulus
GO:0031324	0.69	negative regulation of cellular metabolic process
GO:0001932	0.69	regulation of protein phosphorylation
GO:1902532	0.68	negative regulation of intracellular signal transduction
GO:0045859	0.68	regulation of protein kinase activity
GO:0043086	0.68	negative regulation of catalytic activity
GO:0001933	0.68	negative regulation of protein phosphorylation
GO:0046426	0.67	negative regulation of JAK-STAT cascade
GO:0019221	0.67	cytokine-mediated signaling pathway
GO:0006469	0.67	negative regulation of protein kinase activity
GO:0032502	0.66	developmental process
GO:0044767	0.65	single-organism developmental process
GO:0016043	0.59	cellular component organization
GO:0048869	0.56	cellular developmental process
GO:0009653	0.55	anatomical structure morphogenesis

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	0.99	cell part
GO:0016020	0.93	membrane
GO:0044424	0.88	intracellular part
GO:0044425	0.78	membrane part
GO:0031224	0.76	intrinsic component of membrane
GO:0016021	0.73	integral component of membrane
GO:0005886	0.65	plasma membrane
GO:0005737	0.56	cytoplasm
GO:0044459	0.54	plasma membrane 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	3dsxA	0.429	4.38	0.035	0.750	2.5.1.60	NA
2	0.060	1qjvA	0.560	3.85	0.047	0.893	3.1.1.11	NA
3	0.060	1k5cA	0.582	3.95	0.056	0.920	3.2.1.15	41,42,90
4	0.060	1idjA	0.591	3.74	0.019	0.938	4.2.2.10	NA
5	0.060	1wmrA	0.562	4.38	0.063	0.973	3.2.1.57	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.32	2id5A	0.862	1.19	0.260	0.929	0.68	UUU	complex1.pdb.gz	41,43,63,67,88
2	0.24	3rg1J	0.784	1.61	0.270	0.893	0.62	UUU	complex2.pdb.gz	42,43,65,86,88,91,112
3	0.24	3rg1I	0.788	1.56	0.260	0.893	0.67	UUU	complex3.pdb.gz	43,65,67,87,89
4	0.04	3cigA	0.781	2.94	0.209	0.955	0.70	UUU	complex4.pdb.gz	56,58,79

	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.