D-I-TASSER Q8N5D0-D2

D-I-TASSER results for Q8N5D0-D2

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

Input Sequence in FASTA format

>Q8N5D0 (187 residues)
DLTEYCGQLVEAKCLTVNPQDNNCLAVGASGPFVRLYDIRMIHNHRKSMKQSPSAGVHTF
CDRQKPLPDGAAQYYVAGHLPVKLPDYNNRLRVLVATYVTFSPNGTELLVNMGGEQVYLF
DLTYKQRPYTFLLPRKCHSSGEVQNGKMSTNGVSNGVSNGLHLHSNGFRLPESRGHVSPQ
VELPPYL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| DLTEYCGQLVEAKCLTVNPQDNNCLAVGASGPFVRLYDIRMIHNHRKSMKQSPSAGVHTFCDRQKPLPDGAAQYYVAGHLPVKLPDYNNRLRVLVATYVTFSPNGTELLVNMGGEQVYLFDLTYKQRPYTFLLPRKCHSSGEVQNGKMSTNGVSNGVSNGLHLHSNGFRLPESRGHVSPQVELPPYL
Prediction	CCCCCCCCCSSSSSSSSCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCCCCSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCSSCCCCCCSCHCHHCCCCCCCCCCCCC
Confidence	9301378415689999779997359986289828999712245554444556765544456655566665312431531244555556555650378999889999899971798189996789987411125766667554458723267742332154031675301100111204223578899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| DLTEYCGQLVEAKCLTVNPQDNNCLAVGASGPFVRLYDIRMIHNHRKSMKQSPSAGVHTFCDRQKPLPDGAAQYYVAGHLPVKLPDYNNRLRVLVATYVTFSPNGTELLVNMGGEQVYLFDLTYKQRPYTFLLPRKCHSSGEVQNGKMSTNGVSNGVSNGLHLHSNGFRLPESRGHVSPQVELPPYL
Prediction	8345334430302000001441210000143210101021304444544444544434434454454244104210122043444544444432100000014414200001213000001034474444252455445456356464456545443546352447415445554544466735447
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSSSSSCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCCCCSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCSSCCCCCCSCHCHHCCCCCCCCCCCCC
DLTEYCGQLVEAKCLTVNPQDNNCLAVGASGPFVRLYDIRMIHNHRKSMKQSPSAGVHTFCDRQKPLPDGAAQYYVAGHLPVKLPDYNNRLRVLVATYVTFSPNGTELLVNMGGEQVYLFDLTYKQRPYTFLLPRKCHSSGEVQNGKMSTNGVSNGVSNGLHLHSNGFRLPESRGHVSPQVELPPYL

2pm9A

0.10

0.09

3.35

1.17

DEthreader

DPLTPGQMSDEVISLAWNQSLAHVFASAGSSNFASIWDLKAKKEVIHLS--Y---TSPNSG--IKQTGSPSILIWDLRNAN-TPLQTLNQGHQKGILSLDWCHDEHLLLSSGRDNTVLLWNPESAEQLSQFPARGNWCFKTKFAPEAPLFACASFNKIEVQT---LQ--------SKEKPSHLQAPY

4wjsA2

0.09

0.07

2.88

1.85

SPARKS-K

LAHRIPGHGQPILSCQFSPVSSSRLATGSGDNTARIWDTDSGTPKFTLKGHNHVQFSPDGTLIASAGWDNSTKLWNARD---GKFIKNLRGHVAPVYQCAWSADSRLVVTGSKDCTLKVWNVRTGKLAMDLPGHEDEVYAVDWAADGE---------LVASGGKDKAVRTWRN--------------

5yzvA

0.11

3.82

0.39

MapAlign

--VFE-GHTHYVLDIAFSP-DGSMVASGSRDGTARLWNVATGTEHAVLKGHTDYVYAVAFSPDGMVASGSRIRLWDVATGK---ERDVLQAPAENVVSLAFSPDGSMLVHGSDS-TVHLWDVASGEALHTFEGHTDWVRAVAFSPDGLLASGSDDRTIRLWDVAAQEEHTTLEGHTEPVHSVA----

3j65q

0.11

4.02

0.30

CEthreader

SSSAIAGHGSTILCSAFAPHTSSRMVTGAGDNTARIWDCDTQTPMHTLKGHYNVSWSPDGEVIATGSMDNTIRLWDPKSGQ--CLGDALRGHSKWITSLSWEPSKPRLASSSKDGTIKIWDTVSRVCQYTMSGHTNSVSCVKWGGQGLLYSGSHDRTVRVWDINSQGRCINILKSHAHWVNHLSLSM

4yvdA

0.12

0.11

4.01

1.20

MUSTER

LYRVISGHLGWVRCIAVEP-GNQWFVTGSADRTIKIWDLASGKLKLSLTGHISTVRGVRSPYLFSCGEDKQVKCWD---LEYNKVIRHYHGHLSAVYGLDLHPTIDVLVTCSRDSTARIWDVRTKASVHTLSGHTNAVATVRCQAAEPQITGSHDTTIRLWDLVA-GKTRVTLTNHKKSVRAVHPRH

3dm0A

0.13

4.44

0.65

HHsearch

AQRRLTGHSHFVEDVVLSS-DGQFALSGSWDGELRLWDLAAGVSTRRFVGHLSVAFSLDNRQIVSASRDRTIKLW---NTL-GECKYTIEGHRDWVSCVRFSPNTLTIVSASWDKTVKVWNLSNCKLRSTLAGHTGYVSTVAVSPDGSLASGGKDGVLLWDLAEEHGIKIWDLESKSITSLNWSADG

5i2tA3

0.08

0.07

2.75

1.61

FFAS-3D

-----EEHTSSVTAVQFAK-RGQVMFSSSLDGTVRAWDLIRYRNFRTFTGTER-----IQFNCLAVDPSGEVVCAGSLDVQTGQLLDALSGHEGPVSCLSFSQENSVLASASWDKTIRIWSIFGRSQQVEIEVYSDVLALSMRPDGKEVAVSTLKGQISIFNI-EDAKQVGNIDCR-----------

6t9iD2

0.09

3.44

0.52

EigenThreader

TCKTLVGHSGTVYSTSFSPD-NKYLLSGSEDKTVRLWSMDTHTALVSYKGHNHDVSFSPLGFATASHLNDVDCVSFHPNGCDKSTGDFLG-HTAPVISIAVCPDGRWLSTGSEDGIINVWDIGTGKRLKQMRHGKNAIYSLSYSKEGNVLISADHTVRVWDLKKATTEPSAEPDEGDVTASINQDIK

5cvoA

0.11

0.10

3.48

2.45

CNFpred

TTSSLSGNKDSIYSLAMNQL-GTIIVSGSTEKVLRVWDPRTCAKLMKLKG-KALLLNRDGTQCLSGSSDGTIRLWSLGQ---QRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTDLRNPDIRVLICEEKAPVLKMELDRSA-------PPPAIWVATTKSTVNKWTLKGI-----------

4bzjA

0.10

0.09

3.35

1.17

DEthreader

DPLTPGQMSDEVISLAWNQSLAHVFASAGSSNFASIWDLKAKKEVIHLS--Y---TSPNSG--IKQTGSPSILIWDLRNAN-TPLQTLNQGHQKGILSLDWCHDEHLLLSSGRDNTVLLWNPESAEQLSQFPARGNWCFKTKFAPEAPLFACASFNKIEVQT---LQ--------SKEKPSVHLQYG

(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	0.662

(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	6f3tA2	0.86	1.83	0.143	0.925	model1_6f3tA2.pdb.gz
2	2h9lA	0.86	1.60	0.082	0.914	model1_2h9lA.pdb.gz
3	3j80g	0.85	1.60	0.082	0.909	model1_3j80g.pdb.gz
4	5wjcA	0.85	1.93	0.171	0.936	model1_5wjcA.pdb.gz
5	5oa3g	0.85	1.49	0.127	0.904	model1_5oa3g.pdb.gz
6	3dm0A	0.85	1.67	0.138	0.909	model1_3dm0A.pdb.gz
7	3fm0A	0.85	1.63	0.076	0.920	model1_3fm0A.pdb.gz
8	5datSR	0.85	1.73	0.094	0.909	model1_5datSR.pdb.gz
9	3cfvB	0.85	1.85	0.140	0.930	model1_3cfvB.pdb.gz
10	4xyhA	0.85	1.92	0.139	0.936	model1_4xyhA.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:1901363	0.49	heterocyclic compound binding
GO:0097159	0.49	organic cyclic compound binding
GO:0030234	0.47	enzyme regulator activity
GO:0019899	0.46	enzyme binding
GO:0097367	0.45	carbohydrate derivative binding
GO:0042393	0.45	histone binding
GO:0004857	0.45	enzyme inhibitor activity
GO:0042826	0.44	histone deacetylase binding
GO:0000166	0.44	nucleotide binding
GO:0035639	0.43	purine ribonucleoside triphosphate binding
GO:0032555	0.43	purine ribonucleotide binding
GO:0032550	0.43	purine ribonucleoside binding
GO:0005524	0.36	ATP 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:0071704	0.99	organic substance metabolic process
GO:0044699	0.99	single-organism process
GO:0044238	0.99	primary metabolic process
GO:0065007	0.98	biological regulation
GO:0050896	0.97	response to stimulus
GO:0050789	0.97	regulation of biological process
GO:0044710	0.97	single-organism metabolic process
GO:1901700	0.96	response to oxygen-containing compound
GO:0065008	0.96	regulation of biological quality
GO:0048519	0.96	negative regulation of biological process
GO:0005975	0.96	carbohydrate metabolic process
GO:0009987	0.94	cellular process
GO:0044763	0.88	single-organism cellular process
GO:0044281	0.82	small molecule metabolic process
GO:0050794	0.81	regulation of cellular process
GO:0044723	0.79	single-organism carbohydrate metabolic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0051716	0.78	cellular response to stimulus
GO:0048523	0.78	negative regulation of cellular process
GO:0044707	0.78	single-multicellular organism process
GO:0019725	0.78	cellular homeostasis
GO:0016043	0.78	cellular component organization
GO:0055082	0.77	cellular chemical homeostasis
GO:0048856	0.77	anatomical structure development
GO:0045892	0.77	negative regulation of transcription, DNA-templated
GO:0044767	0.77	single-organism developmental process
GO:0006357	0.77	regulation of transcription from RNA polymerase II promoter
GO:0006006	0.77	glucose metabolic process
GO:0045717	0.76	negative regulation of fatty acid biosynthetic process
GO:0035264	0.76	multicellular organism growth
GO:0032869	0.76	cellular response to insulin stimulus
GO:0008361	0.76	regulation of cell size
GO:0001701	0.76	in utero embryonic development
GO:0000122	0.76	negative regulation of transcription from RNA polymerase II promoter

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:0044444	0.98	cytoplasmic part
GO:0043229	0.98	intracellular organelle
GO:0043227	0.98	membrane-bounded organelle
GO:0005634	0.97	nucleus
GO:0005829	0.96	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	3dr2A	0.719	2.89	0.045	0.888	3.1.1.17	45
2	0.075	1ri6A	0.809	2.08	0.104	0.909	3.1.1.31	NA
3	0.072	2fpcA	0.769	2.77	0.066	0.909	4.3.3.2	NA
4	0.066	1v04A	0.746	2.72	0.083	0.898	3.1.1.2 3.1.8.1	NA
5	0.066	2iwaA	0.628	3.75	0.095	0.834	2.3.2.5	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	0.04	2h6kB	0.861	1.54	0.082	0.914	0.67	III	complex1.pdb.gz	13,30,68,69,94,95,113,140
2	0.04	1got3	0.836	1.83	0.082	0.914	0.67	III	complex2.pdb.gz	9,11,30,33,43,44,45,46,52,54,68,70,93,94,95,113,114,137,139,154
3	0.03	1omw3	0.834	1.85	0.082	0.914	0.64	III	complex3.pdb.gz	9,11,13,31,34,48,49,50,52,53,68,95,139
4	0.03	3sbpA	0.825	1.98	0.077	0.914	0.72	CUA	complex4.pdb.gz	101,103,108
5	0.03	2bcj5	0.833	1.84	0.082	0.914	0.61	III	complex5.pdb.gz	9,11,13,30,31,32,49,51,52,54,68,95,97,140
6	0.03	1a0rB	0.832	1.80	0.077	0.909	0.62	FAR	complex6.pdb.gz	90,94,110,112,114,116,118,120

	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.