D-I-TASSER Q99828-D1

D-I-TASSER results for Q99828-D1

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

Input Sequence in FASTA format

>Q99828 (95 residues)
MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILS
LPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL
Prediction	CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSCHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCSSCHHHHHHHC
Confidence	99876628999999999972999999999999999968777776444752544899974165778884899999985057999925399998629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL
Prediction	86554251456205313723603461033004203712576455466436140326303614714443025200500263677440305302736
	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 AttentionPotential. 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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSCHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCSSCHHHHHHHC
MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

3cs1A

0.11

0.09

3.43

1.00

DEthreader

---GKKTSRVRDITKRAFDKSCYIYDFFELTVMFDEIDA-S-------GNMLVDEEEFKRAPKLEKVEDPAALFKELDKNG-TGSVTFDEFAAWA

1y1aA1

1.00

0.92

25.64

1.68

SPARKS-K

--------SKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

1y1aA

1.00

0.91

25.35

0.66

MapAlign

---------KELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

1y1aA

1.00

0.92

25.64

0.46

CEthreader

--------SKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

1y1aA1

1.00

0.92

25.64

1.60

MUSTER

--------SKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

1tuzA

0.13

4.35

0.83

HHsearch

MAKERGLISPSDFAQLQKYMEYSTKKVSDVLKLFED-GEMA----KYVQGDAIGYEGFQQFLKLVPRHLSLALFQSFET-GTKDVVCLNDVSCYF

1y1aA1

1.00

0.92

25.64

1.41

FFAS-3D

--------SKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

1y1aA1

0.99

0.91

25.36

0.88

EigenThreader

-------S-KELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

2l4hA

1.00

0.93

25.94

1.00

CNFpred

-------LSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

2lvvA

0.10

0.09

3.46

1.00

DEthreader

DGKTEFTTHLPDIVQRAFKALCYIYDIFELTVMFDTMDKD--G-----S-LLLELQEFKEAPKLKDITDATTVFNEIDTNGS-GVVTFDEFSCWA

(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	0.6498

(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 AttentionPotential, 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	1y1aA	0.90	0.48	1.000	0.916	model1_1y1aA.pdb.gz
2	1y1xA	0.66	3.06	0.128	0.863	model1_1y1xA.pdb.gz
3	6sl2A	0.65	2.75	0.085	0.863	model1_6sl2A.pdb.gz
4	1g8iB	0.64	2.26	0.203	0.810	model1_1g8iB.pdb.gz
5	1v1gA1	0.63	2.56	0.175	0.810	model1_1v1gA1.pdb.gz
6	2becA	0.63	2.42	0.195	0.810	model1_2becA.pdb.gz
7	5x9aA	0.63	2.32	0.158	0.800	model1_5x9aA.pdb.gz
8	4x3nA	0.62	3.16	0.080	0.874	model1_4x3nA.pdb.gz
9	1bjfA1	0.61	2.72	0.203	0.832	model1_1bjfA1.pdb.gz
10	5b8iB1	0.61	2.70	0.169	0.789	model1_5b8iB1.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:0046872	0.95	metal ion binding
GO:0005509	0.94	calcium ion binding
GO:0000287	0.52	magnesium ion 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	0.96	biological regulation
GO:0009987	0.93	cellular process
GO:0044699	0.91	single-organism process
GO:0050896	0.90	response to stimulus
GO:0044763	0.85	single-organism cellular process
GO:0071310	0.83	cellular response to organic substance
GO:0071495	0.79	cellular response to endogenous stimulus
GO:0050789	0.79	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0048518	0.67	positive regulation of biological process
GO:0044767	0.67	single-organism developmental process
GO:0048856	0.66	anatomical structure development
GO:0048522	0.66	positive regulation of cellular process
GO:0006355	0.66	regulation of transcription, DNA-templated
GO:0048523	0.65	negative regulation of cellular process
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0007165	0.65	signal transduction
GO:2000026	0.64	regulation of multicellular organismal development
GO:0051240	0.64	positive regulation of multicellular organismal process
GO:0051094	0.64	positive regulation of developmental process
GO:0045597	0.64	positive regulation of cell differentiation
GO:0030155	0.64	regulation of cell adhesion
GO:0002682	0.64	regulation of immune system process
GO:0045652	0.63	regulation of megakaryocyte differentiation
GO:0033628	0.63	regulation of cell adhesion mediated by integrin
GO:0008285	0.63	negative regulation of cell proliferation
GO:0016043	0.61	cellular component organization
GO:0044093	0.60	positive regulation of molecular function
GO:0032879	0.60	regulation of localization
GO:0030154	0.60	cell differentiation
GO:0051050	0.59	positive regulation of transport
GO:0048468	0.59	cell development
GO:0044702	0.59	single organism reproductive process
GO:0030099	0.59	myeloid cell differentiation
GO:0003006	0.59	developmental process involved in reproduction
GO:0048583	0.57	regulation of response to stimulus
GO:0051128	0.56	regulation of cellular component organization
GO:0050790	0.56	regulation of catalytic activity
GO:0048584	0.56	positive regulation of response to stimulus
GO:0031324	0.56	negative regulation of cellular metabolic process
GO:0010605	0.56	negative regulation of macromolecule metabolic process
GO:0009966	0.56	regulation of signal transduction
GO:0006996	0.56	organelle organization
GO:0001932	0.56	regulation of protein phosphorylation
GO:2000256	0.55	positive regulation of male germ cell proliferation
GO:1990090	0.55	cellular response to nerve growth factor stimulus
GO:1900026	0.55	positive regulation of substrate adhesion-dependent cell spreading
GO:0090314	0.55	positive regulation of protein targeting to membrane
GO:0090050	0.55	positive regulation of cell migration involved in sprouting angiogenesis
GO:0071902	0.55	positive regulation of protein serine/threonine kinase activity
GO:0071356	0.55	cellular response to tumor necrosis factor
GO:0070374	0.55	positive regulation of ERK1 and ERK2 cascade
GO:0051898	0.55	negative regulation of protein kinase B signaling
GO:0051302	0.55	regulation of cell division
GO:0051092	0.55	positive regulation of NF-kappaB transcription factor activity
GO:0045653	0.55	negative regulation of megakaryocyte differentiation
GO:0043066	0.55	negative regulation of apoptotic process
GO:0038163	0.55	thrombopoietin-mediated signaling pathway
GO:0033630	0.55	positive regulation of cell adhesion mediated by integrin
GO:0031122	0.55	cytoplasmic microtubule organization
GO:0030307	0.55	positive regulation of cell growth
GO:0030220	0.55	platelet formation
GO:0010977	0.55	negative regulation of neuron projection development
GO:0008152	0.55	metabolic process
GO:0007286	0.55	spermatid development
GO:0007113	0.55	endomitotic cell cycle
GO:0007026	0.55	negative regulation of microtubule depolymerization
GO:0002931	0.55	response to ischemia
GO:0001954	0.55	positive regulation of cell-matrix adhesion
GO:0001933	0.55	negative regulation of protein phosphorylation
GO:0071704	0.54	organic substance metabolic process
GO:0044238	0.54	primary metabolic process
GO:0043170	0.53	macromolecule metabolic process
GO:0044237	0.51	cellular metabolic process
GO:0044260	0.50	cellular macromolecule metabolic process

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:0044424	1.00	intracellular part
GO:0043226	0.97	organelle
GO:0042995	0.89	cell projection
GO:0043229	0.86	intracellular organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0005737	0.85	cytoplasm
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0044422	0.83	organelle part
GO:0005634	0.81	nucleus
GO:0097458	0.80	neuron part
GO:0016020	0.74	membrane
GO:0005886	0.72	plasma membrane
GO:0044444	0.68	cytoplasmic part
GO:0030027	0.65	lamellipodium
GO:0044446	0.62	intracellular organelle part
GO:0044430	0.58	cytoskeletal part
GO:0043232	0.57	intracellular non-membrane-bounded organelle
GO:0071944	0.56	cell periphery
GO:0048471	0.56	perinuclear region of cytoplasm
GO:0043025	0.56	neuronal cell body
GO:0043005	0.56	neuron projection
GO:0032433	0.56	filopodium tip
GO:0030426	0.56	growth cone
GO:0005813	0.56	centrosome

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	2oi3A	0.207	4.38	0.075	0.390	2.7.10.2	40
2	0.060	1kfxL	0.604	2.75	0.106	0.800	3.4.22.53	NA
3	0.060	3jzlA	0.479	4.59	0.078	0.926	4.4.1.8	93
4	0.060	1fbvA	0.486	2.71	0.099	0.684	6.3.2.19	NA
5	0.060	1bljA	0.298	4.65	0.095	0.590	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:

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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.