D-I-TASSER Q9Y219-D6

D-I-TASSER results for Q9Y219-D6

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

Input Sequence in FASTA format

>Q9Y219 (98 residues)
SCICDSGFTGTYCHENIDDCLGQPCRNGGTCIDEVDAFRCFCPSGWEGELCDTNPNDCLP
DPCHSRGRCCVNGGTCVGSGASFSCICRDGWEGRTCTH

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SCICDSGFTGTYCHENIDDCLGQPCRNGGTCIDEVDAFRCFCPSGWEGELCDTNPNDCLPDPCHSRGRCCVNGGTCVGSGASFSCICRDGWEGRTCTH
Prediction	CCCCCCCCSCCCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCCSCCCCCC
Confidence	96177986248662677588899888997887379948988589960487656665677887768886557897878279948978679950698889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SCICDSGFTGTYCHENIDDCLGQPCRNGGTCIDEVDAFRCFCPSGWEGELCDTNPNDCLPDPCHSRGRCCVNGGTCVGSGASFSCICRDGWEGRTCTH
Prediction	84435743547413441245353244151354345540424235414164054423404433065454413140203145541424347446474468
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCSCCCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCCSCCCCCC
SCICDSGFTGTYCHENIDDCLGQPCRNGGTCIDEVDAFRCFCPSGWEGELCDTNPNDCLPDPCHSRGRCCVNGGTCVGSGASFSCICRDGWEGRTCTH

2vj3A

0.34

0.32

9.47

2.78

SPARKS-K

ECQCLQGYTGPRCEIDVNECVSNPCQNDATCLDQIGEFQCICMPGYEGVHCEVNTDEC-------ASSPCLHNGRCLDKINEFQCECPTGFTGHLCQV

5mwbA

0.37

0.35

10.30

2.15

MUSTER

HCECLKGYAGPRCEMDINECHSDPCQNDATCLDKIGGFTCLCMPGFKGVHCELEINECQSNP-------CVNNGQCVDKVNRFQCLCPPGFTGPVCQI

4xbmB

0.40

0.37

10.85

1.92

HHsearch

TCSCRPGYTGATCELGIDECDPSPCKNGGSCTDLENSYSCTCPPGFYGKICELSAMTCADGP-------CFNGGRCSDSPDGYSCRCPVGYSGFNCEK

5uk5A

0.36

0.34

10.02

3.68

CNFpred

ICTCPSGYTGPACSQDVDECAANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISN-------PCQNDATCLDQIGEFQCICMPGYEGVYCES

5mwbA

0.33

0.29

8.59

1.00

DEthreader

HCECLKGYAGPRCEMDINECHSDPCQNDATCLDKIGGFTCLCMPGFKGVHCELEINECQSNPC----NGQ----CVDKVN-RFQCLC---FTGPVCQD

5mwbA

0.37

0.35

10.30

2.69

SPARKS-K

HCECLKGYAGPRCEMDINECHSDPCQNDATCLDKIGGFTCLCMPGFKGVHCELEINECQSNPC-------VNNGQCVDKVNRFQCLCPPGFTGPVCQI

5fmaA

0.34

0.32

9.46

0.68

MapAlign

-CHCPPSFHGPTCRQDVNECGPGLCRHGGTCHNEVGSYRCVCRATHTGPNCERPYVPC-------SPSPCQNGGTCRPTDVTHECACLPGFTGQNCEE

5mwbA

0.36

0.34

10.02

0.62

CEthreader

HCECLKGYAGPRCEMDINECHSDPCQNDATCLDKIGGFTCLCMPGFKGVHCELEINECQSN-------PCVNNGQCVDKVNRFQCLCPPGFTGPVCQI

5fmaA2

0.38

0.29

8.47

2.15

MUSTER

-----------------VPCSPSPCQNGGTCRPTGVTHECACLPGFTGQNCEENIDDCPGNN-------CKNGGACVDGVNTYNCRCPPEWTGQYCTE

4xbmB

0.35

0.33

9.74

1.76

HHsearch

QCNCQEGWGGLFCNQDLNYCTHKPCKNGATCTNTQGSYTCSCRPGYTGATCELGIDECDPSPC-------KNGGSCTDLENSYSCTCPPGFYGKICEL

(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	0.5677

(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	5mwbA	0.87	0.97	0.363	0.929	model1_5mwbA.pdb.gz
2	2vj3A	0.80	1.67	0.352	0.929	model1_2vj3A.pdb.gz
3	5uk5A	0.80	1.67	0.385	0.929	model1_5uk5A.pdb.gz
4	4xbmB	0.76	1.38	0.325	0.847	model1_4xbmB.pdb.gz
5	4d90A	0.71	2.47	0.330	0.837	model1_4d90A.pdb.gz
6	5fmaA1	0.60	2.07	0.360	0.765	model1_5fmaA1.pdb.gz
7	4c16A	0.55	3.79	0.172	0.857	model1_4c16A.pdb.gz
8	6pogB2	0.55	2.85	0.225	0.775	model1_6pogB2.pdb.gz
9	1lmjA	0.54	2.80	0.247	0.786	model1_1lmjA.pdb.gz
10	1w0yL	0.54	3.33	0.213	0.796	model1_1w0yL.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	0.83	metal ion binding
GO:0005509	0.81	calcium ion binding
GO:0005102	0.78	receptor binding
GO:0005112	0.67	Notch binding
GO:0097159	0.62	organic cyclic compound binding
GO:1901363	0.61	heterocyclic compound binding
GO:0044877	0.58	macromolecular complex binding
GO:0003676	0.58	nucleic acid binding
GO:0004872	0.57	receptor activity
GO:0046983	0.56	protein dimerization activity
GO:0019899	0.56	enzyme binding
GO:0003700	0.56	transcription factor activity, sequence-specific DNA binding
GO:0003677	0.56	DNA binding
GO:0030234	0.55	enzyme regulator activity
GO:0003682	0.55	chromatin binding
GO:0046982	0.54	protein heterodimerization activity
GO:0044212	0.54	transcription regulatory region DNA binding
GO:0043565	0.54	sequence-specific DNA binding
GO:0004857	0.54	enzyme inhibitor activity
GO:0001047	0.53	core promoter binding
GO:0000989	0.53	transcription factor activity, transcription factor binding
GO:0031490	0.52	chromatin DNA binding
GO:0001190	0.52	transcriptional activator activity, RNA polymerase II transcription factor binding
GO:0097367	0.50	carbohydrate derivative 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:0044699	0.92	single-organism process
GO:0065007	0.91	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0032502	0.88	developmental process
GO:0009987	0.87	cellular process
GO:0044767	0.82	single-organism developmental process
GO:0044763	0.82	single-organism cellular process
GO:0048856	0.78	anatomical structure development
GO:0009653	0.74	anatomical structure morphogenesis
GO:0048583	0.73	regulation of response to stimulus
GO:0048518	0.73	positive regulation of biological process
GO:0051239	0.72	regulation of multicellular organismal process
GO:0048519	0.72	negative regulation of biological process
GO:2000026	0.71	regulation of multicellular organismal development
GO:0048523	0.71	negative regulation of cellular process
GO:0048522	0.71	positive regulation of cellular process
GO:0032501	0.71	multicellular organismal process
GO:0045595	0.70	regulation of cell differentiation
GO:0044707	0.69	single-multicellular organism process
GO:0009966	0.69	regulation of signal transduction
GO:0022603	0.68	regulation of anatomical structure morphogenesis
GO:0060284	0.67	regulation of cell development
GO:0051960	0.67	regulation of nervous system development
GO:0048513	0.66	animal organ development
GO:0045664	0.66	regulation of neuron differentiation
GO:0007165	0.66	signal transduction
GO:0051241	0.65	negative regulation of multicellular organismal process
GO:0048584	0.65	positive regulation of response to stimulus
GO:0051093	0.64	negative regulation of developmental process
GO:0048869	0.64	cellular developmental process
GO:0009967	0.64	positive regulation of signal transduction
GO:0008593	0.64	regulation of Notch signaling pathway
GO:0051961	0.63	negative regulation of nervous system development
GO:0045596	0.63	negative regulation of cell differentiation
GO:0016043	0.63	cellular component organization
GO:0007389	0.63	pattern specification process
GO:0007166	0.63	cell surface receptor signaling pathway
GO:0050768	0.62	negative regulation of neurogenesis
GO:0048598	0.62	embryonic morphogenesis
GO:0009952	0.62	anterior/posterior pattern specification
GO:0002009	0.62	morphogenesis of an epithelium
GO:0045747	0.61	positive regulation of Notch signaling pathway
GO:0045665	0.61	negative regulation of neuron differentiation
GO:0035239	0.61	tube morphogenesis
GO:0097150	0.60	neuronal stem cell population maintenance
GO:0070986	0.60	left/right axis specification
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0051128	0.60	regulation of cellular component organization
GO:0045662	0.60	negative regulation of myoblast differentiation
GO:0045605	0.60	negative regulation of epidermal cell differentiation
GO:0031099	0.60	regeneration
GO:0014807	0.60	regulation of somitogenesis
GO:0007386	0.60	compartment pattern specification
GO:0001947	0.60	heart looping
GO:0080090	0.59	regulation of primary metabolic process
GO:0045608	0.59	negative regulation of auditory receptor cell differentiation
GO:0031323	0.59	regulation of cellular metabolic process
GO:0031100	0.58	organ regeneration
GO:0006928	0.58	movement of cell or subcellular component
GO:0050896	0.57	response to stimulus
GO:0048589	0.56	developmental growth
GO:0030154	0.56	cell differentiation
GO:0010468	0.56	regulation of gene expression
GO:0009893	0.56	positive regulation of metabolic process
GO:0051179	0.55	localization
GO:0048646	0.55	anatomical structure formation involved in morphogenesis
GO:0048585	0.55	negative regulation of response to stimulus
GO:0040011	0.55	locomotion
GO:0031325	0.55	positive regulation of cellular metabolic process
GO:0010769	0.55	regulation of cell morphogenesis involved in differentiation
GO:0010604	0.55	positive regulation of macromolecule metabolic process
GO:0006355	0.55	regulation of transcription, DNA-templated
GO:0090287	0.54	regulation of cellular response to growth factor stimulus
GO:0030030	0.54	cell projection organization
GO:0016477	0.54	cell migration
GO:0009968	0.54	negative regulation of signal transduction
GO:0060560	0.53	developmental growth involved in morphogenesis
GO:0051240	0.53	positive regulation of multicellular organismal process
GO:0042221	0.53	response to chemical
GO:0042127	0.53	regulation of cell proliferation
GO:0032989	0.53	cellular component morphogenesis
GO:0032879	0.53	regulation of localization
GO:0009888	0.53	tissue development
GO:0006810	0.53	transport
GO:0065009	0.52	regulation of molecular function
GO:0051716	0.52	cellular response to stimulus
GO:0051130	0.52	positive regulation of cellular component organization
GO:0051094	0.52	positive regulation of developmental process
GO:0048812	0.52	neuron projection morphogenesis
GO:0048468	0.52	cell development
GO:0045893	0.52	positive regulation of transcription, DNA-templated
GO:0045597	0.52	positive regulation of cell differentiation
GO:0040008	0.52	regulation of growth
GO:0010605	0.52	negative regulation of macromolecule metabolic process
GO:0010033	0.52	response to organic substance
GO:0007219	0.52	Notch signaling pathway
GO:0002376	0.52	immune system process
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0071310	0.51	cellular response to organic substance
GO:0050790	0.51	regulation of catalytic activity
GO:0048732	0.51	gland development
GO:0044765	0.51	single-organism transport
GO:0040012	0.51	regulation of locomotion
GO:0031324	0.51	negative regulation of cellular metabolic process
GO:0022414	0.51	reproductive process
GO:0008104	0.51	protein localization
GO:0007409	0.51	axonogenesis
GO:0006950	0.51	response to stress
GO:0006357	0.51	regulation of transcription from RNA polymerase II promoter
GO:0002682	0.51	regulation of immune system process
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:1901700	0.50	response to oxygen-containing compound
GO:0090092	0.50	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0071702	0.50	organic substance transport
GO:0060627	0.50	regulation of vesicle-mediated transport
GO:0060429	0.50	epithelium development
GO:0048638	0.50	regulation of developmental growth
GO:0045892	0.50	negative regulation of transcription, DNA-templated
GO:0045765	0.50	regulation of angiogenesis
GO:0045184	0.50	establishment of protein localization
GO:0045165	0.50	cell fate commitment
GO:0044702	0.50	single organism reproductive process
GO:0044092	0.50	negative regulation of molecular function
GO:0044087	0.50	regulation of cellular component biogenesis
GO:0042981	0.50	regulation of apoptotic process
GO:0032101	0.50	regulation of response to external stimulus
GO:0030855	0.50	epithelial cell differentiation
GO:0030334	0.50	regulation of cell migration
GO:0021515	0.50	cell differentiation in spinal cord
GO:0010720	0.50	positive regulation of cell development
GO:0009719	0.50	response to endogenous stimulus
GO:0009605	0.50	response to external stimulus
GO:0008285	0.50	negative regulation of cell proliferation
GO:0008284	0.50	positive regulation of cell proliferation
GO:0007275	0.50	multicellular organism development
GO:0002064	0.50	epithelial cell 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:0044464	0.94	cell part
GO:0044424	0.76	intracellular part
GO:0044421	0.68	extracellular region part
GO:0043226	0.65	organelle
GO:0016020	0.63	membrane
GO:0043227	0.61	membrane-bounded organelle
GO:0005886	0.54	plasma membrane
GO:0005576	0.54	extracellular region
GO:0044425	0.53	membrane part
GO:0031012	0.50	extracellular matrix

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	2q28A	0.414	4.27	0.082	0.745	4.1.1.8	NA
2	0.060	3ictA	0.422	4.45	0.060	0.806	1.8.1.14	NA
3	0.060	3bcbA	0.427	4.36	0.038	0.775	2.9.1.2	NA
4	0.060	2vgkD	0.440	4.76	0.101	0.847	3.4.16.4	44,54
5	0.060	3b8eA	0.383	4.17	0.034	0.673	3.6.3.9	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	0.22	2rqzA	0.324	1.83	0.368	0.388	1.05	UUU	complex1.pdb.gz	28,29,30,41,42
	2	0.01	1elvA	0.453	4.27	0.068	0.796	0.85	UUU	complex2.pdb.gz	75,77,84,93,94

	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.