D-I-TASSER Q5T4D3-D2

D-I-TASSER results for Q5T4D3-D2

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

Input Sequence in FASTA format

>Q5T4D3 (136 residues)
KYVHAMNNLGNILKERNELQEAEELLSLAVQIQPDFAAAWMNLGIVQNSLKRFEAAEQSY
RTAIKHRRKYPDCYYNLGRLYADLNRHVDALNAWRNATVLKPEHSLAWNNMIILLDNTGN
LAQAEAVGREALELIP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KYVHAMNNLGNILKERNELQEAEELLSLAVQIQPDFAAAWMNLGIVQNSLKRFEAAEQSYRTAIKHRRKYPDCYYNLGRLYADLNRHVDALNAWRNATVLKPEHSLAWNNMIILLDNTGNLAQAEAVGREALELIP
Prediction	CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
Confidence	9668999999999990999999999999998199999999999999999099999999999999859999899988999999919999999999999983999999999999999990999999999999997396
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KYVHAMNNLGNILKERNELQEAEELLSLAVQIQPDFAAAWMNLGIVQNSLKRFEAAEQSYRTAIKHRRKYPDCYYNLGRLYADLNRHVDALNAWRNATVLKPEHSLAWNNMIILLDNTGNLAQAEAVGREALELIP
Prediction	8325012221301463642640161054006132720401201020144275264016205400623272140020112014527526401620540061327214001010200453652640261044006158
	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

CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
KYVHAMNNLGNILKERNELQEAEELLSLAVQIQPDFAAAWMNLGIVQNSLKRFEAAEQSYRTAIKHRRKYPDCYYNLGRLYADLNRHVDALNAWRNATVLKPEHSLAWNNMIILLDNTGNLAQAEAVGREALELIP

6b85J

0.32

9.54

1.67

DEthreader

VSALAYVMLGLLLSLLNRLSLAAEAYKKAIELDPNDALAWLLLGSVLEKLKRLDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAAEAYKKAIELDPEDAEAWKELGKVLEKLGRLDEAAEAYKKAIELDP

3pe3A1

0.30

9.14

1.76

SPARKS-K

THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP

3pe3A

0.30

0.29

8.93

0.47

MapAlign

THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-

3pe3A

0.30

9.14

0.31

CEthreader

THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP

6b85J

0.32

9.54

1.29

MUSTER

VSALAYVMLGLLLSLLNRLSLAAEAYKKAIELDPNDALAWLLLGSVLEKLKRLDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAAEAYKKAIELDPEDAEAWKELGKVLEKLGRLDEAAEAYKKAIELDP

3pe3A

0.30

9.14

0.63

HHsearch

THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP

3pe3A1

0.30

9.14

2.43

FFAS-3D

THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP

5gmkd

0.13

4.57

0.53

EigenThreader

LDMGQWIRYAQFEIEQHDMRRARSIFERALLVDSSFIPLWIRYIDAELKVKCINHARNLMNRAISTLPRVDKLWYKYLIVEESLNNVEIVRSLYTKWCSL-EPGVNAWNSFVDFEIRQKNWNGVREIYSKYVMAHP

5a01A

0.31

9.34

1.15

CNFpred

NHADSLNNLANIKREQGYIEEATRLYLKALEVFPDFAAAHSNLASVLQQQGKLKEALMHYKEAIRIQPTFADAYSNMGNTLKELQDVSGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIQSYRTALKLKP

1w3bA

0.30

9.14

1.67

DEthreader

PLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQP

(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	0.8975

(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	1w3bA	0.95	1.03	0.279	1.000	model1_1w3bA.pdb.gz
2	5o09C	0.95	1.05	0.228	1.000	model1_5o09C.pdb.gz
3	5dseA	0.94	1.20	0.162	1.000	model1_5dseA.pdb.gz
4	3pe3A	0.94	1.19	0.301	1.000	model1_3pe3A.pdb.gz
5	5udiA	0.93	1.32	0.147	1.000	model1_5udiA.pdb.gz
6	6b85J	0.92	1.32	0.309	1.000	model1_6b85J.pdb.gz
7	5djsA	0.92	1.34	0.154	1.000	model1_5djsA.pdb.gz
8	3q15A	0.92	1.42	0.110	1.000	model1_3q15A.pdb.gz
9	2fi7A	0.91	1.53	0.213	1.000	model1_2fi7A.pdb.gz
10	2hyzA	0.91	1.28	0.284	0.985	model1_2hyzA.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:0003824	0.86	catalytic activity
GO:0016740	0.78	transferase activity
GO:0036094	0.73	small molecule binding
GO:0016757	0.73	transferase activity, transferring glycosyl groups
GO:0016758	0.72	transferase activity, transferring hexosyl groups
GO:0008194	0.72	UDP-glycosyltransferase activity
GO:0042277	0.71	peptide binding
GO:0016262	0.71	protein N-acetylglucosaminyltransferase activity
GO:0034212	0.70	peptide N-acetyltransferase activity
GO:0005543	0.70	phospholipid binding
GO:0030234	0.69	enzyme regulator activity
GO:0097363	0.68	protein O-GlcNAc transferase activity
GO:0046972	0.68	histone acetyltransferase activity (H4-K16 specific)
GO:0043996	0.68	histone acetyltransferase activity (H4-K8 specific)
GO:0043995	0.68	histone acetyltransferase activity (H4-K5 specific)
GO:0019904	0.68	protein domain specific binding
GO:0008047	0.68	enzyme activator activity
GO:0005547	0.68	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0048029	0.67	monosaccharide binding
GO:0008134	0.67	transcription factor binding
GO:1901363	0.50	heterocyclic compound binding
GO:0097159	0.50	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:0009987	0.97	cellular process
GO:0044699	0.89	single-organism process
GO:0044763	0.85	single-organism cellular process
GO:0008152	0.85	metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0065007	0.84	biological regulation
GO:0044238	0.84	primary metabolic process
GO:0050789	0.83	regulation of biological process
GO:0044237	0.83	cellular metabolic process
GO:0050794	0.82	regulation of cellular process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0016043	0.80	cellular component organization
GO:0043412	0.77	macromolecule modification
GO:0019538	0.77	protein metabolic process
GO:0044767	0.76	single-organism developmental process
GO:0044710	0.76	single-organism metabolic process
GO:0031323	0.76	regulation of cellular metabolic process
GO:0006464	0.76	cellular protein modification process
GO:0051171	0.75	regulation of nitrogen compound metabolic process
GO:0031326	0.75	regulation of cellular biosynthetic process
GO:0080090	0.74	regulation of primary metabolic process
GO:0051179	0.74	localization
GO:0048518	0.74	positive regulation of biological process
GO:0043933	0.74	macromolecular complex subunit organization
GO:0022607	0.74	cellular component assembly
GO:0010468	0.74	regulation of gene expression
GO:2000112	0.73	regulation of cellular macromolecule biosynthetic process
GO:0051641	0.73	cellular localization
GO:0050896	0.73	response to stimulus
GO:0048522	0.73	positive regulation of cellular process
GO:0009893	0.73	positive regulation of metabolic process
GO:0065003	0.72	macromolecular complex assembly
GO:0051173	0.72	positive regulation of nitrogen compound metabolic process
GO:0048856	0.72	anatomical structure development
GO:0048519	0.72	negative regulation of biological process
GO:0044707	0.72	single-multicellular organism process
GO:0033043	0.72	regulation of organelle organization
GO:0032268	0.72	regulation of cellular protein metabolic process
GO:0031328	0.72	positive regulation of cellular biosynthetic process
GO:0006996	0.72	organelle organization
GO:0006355	0.72	regulation of transcription, DNA-templated
GO:0005975	0.72	carbohydrate metabolic process
GO:0048523	0.71	negative regulation of cellular process
GO:0033044	0.71	regulation of chromosome organization
GO:0032259	0.71	methylation
GO:0018193	0.71	peptidyl-amino acid modification
GO:0010628	0.71	positive regulation of gene expression
GO:0009966	0.71	regulation of signal transduction
GO:0009892	0.71	negative regulation of metabolic process
GO:0007165	0.71	signal transduction
GO:0006493	0.71	protein O-linked glycosylation
GO:0051716	0.70	cellular response to stimulus
GO:0051254	0.70	positive regulation of RNA metabolic process
GO:0042221	0.70	response to chemical
GO:0031324	0.70	negative regulation of cellular metabolic process
GO:0031060	0.70	regulation of histone methylation
GO:0010605	0.70	negative regulation of macromolecule metabolic process
GO:0010557	0.70	positive regulation of macromolecule biosynthetic process
GO:0006357	0.70	regulation of transcription from RNA polymerase II promoter
GO:0006325	0.70	chromatin organization
GO:1903428	0.69	positive regulation of reactive oxygen species biosynthetic process
GO:1901135	0.69	carbohydrate derivative metabolic process
GO:0080134	0.69	regulation of response to stress
GO:0070887	0.69	cellular response to chemical stimulus
GO:0065008	0.69	regulation of biological quality
GO:0061085	0.69	regulation of histone H3-K27 methylation
GO:0051569	0.69	regulation of histone H3-K4 methylation
GO:0051568	0.69	histone H3-K4 methylation
GO:0051130	0.69	positive regulation of cellular component organization
GO:0045893	0.69	positive regulation of transcription, DNA-templated
GO:0032270	0.69	positive regulation of cellular protein metabolic process
GO:0031400	0.69	negative regulation of protein modification process
GO:0019220	0.69	regulation of phosphate metabolic process
GO:0010033	0.69	response to organic substance
GO:0009605	0.69	response to external stimulus
GO:0008219	0.69	cell death
GO:0006473	0.69	protein acetylation
GO:0006461	0.69	protein complex assembly
GO:0002682	0.69	regulation of immune system process
GO:2000026	0.68	regulation of multicellular organismal development
GO:1901701	0.68	cellular response to oxygen-containing compound
GO:0090526	0.68	regulation of gluconeogenesis involved in cellular glucose homeostasis
GO:0080182	0.68	histone H3-K4 trimethylation
GO:0071396	0.68	cellular response to lipid
GO:0061087	0.68	positive regulation of histone H3-K27 methylation
GO:0055082	0.68	cellular chemical homeostasis
GO:0051640	0.68	organelle localization
GO:0051240	0.68	positive regulation of multicellular organismal process
GO:0051129	0.68	negative regulation of cellular component organization
GO:0051094	0.68	positive regulation of developmental process
GO:0050790	0.68	regulation of catalytic activity
GO:0048585	0.68	negative regulation of response to stimulus
GO:0048015	0.68	phosphatidylinositol-mediated signaling
GO:0045944	0.68	positive regulation of transcription from RNA polymerase II promoter
GO:0045936	0.68	negative regulation of phosphate metabolic process
GO:0045862	0.68	positive regulation of proteolysis
GO:0045595	0.68	regulation of cell differentiation
GO:0044093	0.68	positive regulation of molecular function
GO:0043984	0.68	histone H4-K16 acetylation
GO:0043982	0.68	histone H4-K8 acetylation
GO:0043981	0.68	histone H4-K5 acetylation
GO:0043207	0.68	response to external biotic stimulus
GO:0032922	0.68	circadian regulation of gene expression
GO:0032879	0.68	regulation of localization
GO:0031397	0.68	negative regulation of protein ubiquitination
GO:0010941	0.68	regulation of cell death
GO:0006915	0.68	apoptotic process
GO:0006110	0.68	regulation of glycolytic process
GO:0006040	0.68	amino sugar metabolic process
GO:1900182	0.67	positive regulation of protein localization to nucleus
GO:1900038	0.67	negative regulation of cellular response to hypoxia
GO:0097237	0.67	cellular response to toxic substance
GO:0090315	0.67	negative regulation of protein targeting to membrane
GO:0071333	0.67	cellular response to glucose stimulus
GO:0071300	0.67	cellular response to retinoic acid
GO:0071222	0.67	cellular response to lipopolysaccharide
GO:0070208	0.67	protein heterotrimerization
GO:0070207	0.67	protein homotrimerization
GO:0060548	0.67	negative regulation of cell death
GO:0051571	0.67	positive regulation of histone H3-K4 methylation
GO:0048312	0.67	intracellular distribution of mitochondria
GO:0046626	0.67	regulation of insulin receptor signaling pathway
GO:0045793	0.67	positive regulation of cell size
GO:0043085	0.67	positive regulation of catalytic activity
GO:0035020	0.67	regulation of Rac protein signal transduction
GO:0033137	0.67	negative regulation of peptidyl-serine phosphorylation
GO:0030900	0.67	forebrain development
GO:0030854	0.67	positive regulation of granulocyte differentiation
GO:0016568	0.67	chromatin modification
GO:0010801	0.67	negative regulation of peptidyl-threonine phosphorylation
GO:0007584	0.67	response to nutrient
GO:0006041	0.67	glucosamine metabolic process
GO:0001934	0.67	positive regulation of protein phosphorylation

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	0.99	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0043226	0.84	organelle
GO:0044422	0.81	organelle part
GO:0044446	0.80	intracellular organelle part
GO:0043229	0.79	intracellular organelle
GO:0032991	0.77	macromolecular complex
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005737	0.73	cytoplasm
GO:0043234	0.71	protein complex
GO:0016020	0.63	membrane
GO:0005634	0.58	nucleus
GO:0044428	0.53	nuclear part
GO:0005829	0.50	cytosol

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	0.230	1tjcA	0.579	2.03	0.170	0.647	1.14.11.2	43
2	0.168	2fbnA	0.765	1.95	0.171	0.882	5.2.1.8	65,75,77
3	0.066	1klxA	0.553	3.54	0.117	0.787	3.5.2.6	NA
4	0.060	1kt1A	0.805	1.67	0.118	0.882	5.2.1.8	NA
5	0.060	1j0mA	0.606	4.09	0.104	0.978	4.2.2.12	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	0.54	3kd7C	0.721	0.77	0.248	0.743	1.08	III	complex1.pdb.gz	38,42,45,49
2	0.49	1na0B	0.787	1.60	0.261	0.875	0.83	IPT	complex2.pdb.gz	10,42,45,46,76
3	0.33	3fp2A	0.837	2.02	0.209	0.985	1.15	III	complex3.pdb.gz	41,45,48,60,72,76,106
4	0.32	3cv0A	0.834	2.05	0.213	0.941	0.95	III	complex4.pdb.gz	14,41,42,45,48,49,60,72,75,76,79,83
5	0.31	3q4aB	0.807	1.71	0.159	0.882	1.15	III	complex5.pdb.gz	7,11,14,26,38,42,45,72,75
6	0.19	3cvqA	0.843	1.98	0.200	0.956	0.89	III	complex6.pdb.gz	41,42,45,48,49,72,75,76,79,83,110,113

	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.