D-I-TASSER Q8N2U0-D1

D-I-TASSER results for Q8N2U0-D1

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

Input Sequence in FASTA format

>Q8N2U0 (113 residues)
MAGPAAAFRRLGALSGAAALGFASYGAHGAQFPDAYGKELFDKANKHHFLHSLALLGVPH
CRKPLWAGLLLASGTTLFCTSFYYQALSGDPSIQTLAPAGGTLLLLGWLALAL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAGPAAAFRRLGALSGAAALGFASYGAHGAQFPDAYGKELFDKANKHHFLHSLALLGVPHCRKPLWAGLLLASGTTLFCTSFYYQALSGDPSIQTLAPAGGTLLLLGWLALAL
Prediction	CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
Confidence	99876569999999999999999999813666797899999999999999999999999851127999999999999979999999829960000363779999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAGPAAAFRRLGALSGAAALGFASYGAHGAQFPDAYGKELFDKANKHHFLHSLALLGVPHCRKPLWAGLLLASGTTLFCTSFYYQALSGDPSIQTLAPAGGTLLLLGWLALAL
Prediction	74444330111113311300130020112244346733430420031033113102302324434131112332133103211210134343223213331332233233334
	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

CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
MAGPAAAFRRLGALSGAAALGFASYGAHGAQFPDAYGKELFDKANKHHFLHSLALLGVPHCRKPLWAGLLLASGTTLFCTSFYYQALSGDPSIQTLAPAGGTLLLLGWLALAL

6xkwn

0.14

0.13

4.57

1.33

DEthreader

RTDPVIRMMVVSIGFYGMSTFEGPMMSIAVNSLSHYT--DWTIGHVHSGALWNGMITFGMYLLVSWHFWLATIGIVLYASSMWVSGIMEAKPMNVVRGVGGVLYLTGGLIMAY

6i0dL

0.15

0.14

4.79

0.85

SPARKS-K

LYSVLPDVSYAIAVVGLLTAAYGALSAFGQTD----IKKIVAYSTISQLGYMFLAAGVYWVALFHVFTHAFFKALLFLASGSVIHALGGEQDVRKMLPQTRWHALIGALALGG

4o9uB1

0.18

0.17

5.50

0.79

MapAlign

---PQMVAIYNGMGGGAAATIAAVELLKGA-FENTGLMALAILGGLIGSVAFTGSLIAFAKLQIMPVAISFYNAFTGMAVGFEGFAVGNPALMVAGTLVGAAGTLLTVLMAR-

6xkwn

0.13

4.58

0.61

CEthreader

RTDPVIRMMVVSIGFYGMSTFEGPMMSIKAVNSLSHYT-DWTIGHVHSGALGWNGMITFGMKLVSWHFWLATIGIVLYASSMWVSGIMEGLMMNVVRGVGGVLYLTGGLIMAY

4xydA1

0.07

2.91

0.72

MUSTER

MKYQSQVYFAVALGLFAIQVSGGLLLGWIYVSPNIVWLLLGFMGAAYFVIPEESEREIHSPLLAYLQLAIMVLGTLGVVVTYLFNLFEGNWLLGKQPVWVKMGIVVAALIFMY

4xydA1

0.11

3.85

0.87

HHsearch

MKYIALVYFAVALGLFAIQVSGGLLLGWIYVSPNF--LSEILPFNIVRMLHTNSFMGAAYPLLAYLQLAIMVLGTLGVVVTYLFNLFEGGREFLEQPVWVKMGIVVAALIFMY

6m9tA

0.16

5.30

0.60

FFAS-3D

VSVAFPITMLLTGFVGNALAMLLVSRSYRRRESKRKKSFLLCIGWLALTDLVGQLLTTPVVSGRLCTFFGLTMTVFGLSSLFIASAMAVERALAIRAPHWYAVLLGVWLAVLA

4xydA1

0.08

3.15

0.75

EigenThreader

MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWLPFNIVRMLHTNSLIVWLLLAAYFVIPEEIHSPLLAYLQLAIMVLGTLGVVVTYLFNLFEPVWVKMGIVVAALIFMYNISM

3rkoB

0.10

3.63

0.95

CNFpred

AGPTPVSALIHAATMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMFLALGVQAWDAAIFHLMTHAFFKALLFLASGSVILAC

3mk7A

0.14

4.81

1.33

DEthreader

RSDPILRFLVVSLAFYGMSTFEGPMMAITVNALSHYT--DWTIGHVHAGALWVAMVSIGAYMLINTHFWLATIGTVLYIASMWVNGIAQASPGFVVRMIGGAIFFAGMLVMAT

(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	0.6984

(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	6xkwn	0.83	2.10	0.135	0.982	model1_6xkwn.pdb.gz
2	1m56A3	0.79	2.11	0.073	0.965	model1_1m56A3.pdb.gz
3	4xydA3	0.79	2.36	0.135	0.982	model1_4xydA3.pdb.gz
4	2yevA1	0.79	2.24	0.136	0.974	model1_2yevA1.pdb.gz
5	6t15a1	0.78	2.52	0.142	0.991	model1_6t15a1.pdb.gz
6	6elhA	0.78	2.51	0.117	0.982	model1_6elhA.pdb.gz
7	7jroa2	0.78	2.34	0.118	0.974	model1_7jroa2.pdb.gz
8	1fftA2	0.78	2.32	0.155	0.974	model1_1fftA2.pdb.gz
9	3o0rB3	0.77	2.40	0.117	0.982	model1_3o0rB3.pdb.gz
10	1xmeA	0.77	2.52	0.153	0.982	model1_1xmeA.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:0022892	0.83	substrate-specific transporter activity
GO:0016491	0.75	oxidoreductase activity
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0015075	0.62	ion transmembrane transporter activity
GO:0046872	0.61	metal ion binding
GO:0009055	0.60	electron carrier activity
GO:0015078	0.59	hydrogen ion transmembrane transporter activity
GO:0020037	0.58	heme binding
GO:0005506	0.58	iron ion binding
GO:0004129	0.58	cytochrome-c oxidase activity
GO:0017128	0.55	phospholipid scramblase activity

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	0.92	cellular process
GO:0008152	0.92	metabolic process
GO:0044699	0.90	single-organism process
GO:0044237	0.88	cellular metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0044238	0.83	primary metabolic process
GO:0016310	0.82	phosphorylation
GO:0044710	0.76	single-organism metabolic process
GO:0044763	0.75	single-organism cellular process
GO:0044281	0.68	small molecule metabolic process
GO:0055114	0.66	oxidation-reduction process
GO:0006091	0.66	generation of precursor metabolites and energy
GO:0009060	0.63	aerobic respiration
GO:0006810	0.62	transport
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0055086	0.58	nucleobase-containing small molecule metabolic process
GO:0046835	0.57	carbohydrate phosphorylation
GO:0006119	0.57	oxidative 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	0.87	cell part
GO:0044424	0.79	intracellular part
GO:0044444	0.73	cytoplasmic part
GO:0043226	0.67	organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0044446	0.63	intracellular organelle part
GO:0016020	0.60	membrane
GO:0044425	0.58	membrane part
GO:0070062	0.52	extracellular exosome
GO:0044429	0.50	mitochondrial 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	0.220	2h8aA	0.673	2.78	0.058	0.911	2.5.1.18	14,23,44,56,80
2	0.159	3dwwA	0.737	2.70	0.082	0.974	5.3.99.3	42
3	0.060	1jkuA	0.603	2.33	0.072	0.770	1.11.1.6	NA
4	0.060	1o9iA	0.600	2.34	0.081	0.770	1.11.1.6	54
5	0.060	2pfmA	0.610	3.40	0.027	0.867	4.3.2.2	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:

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	3s8gA	0.767	2.52	0.135	0.982	0.94	OLC	complex1.pdb.gz	12,16,52,53,54
2	0.03	3eh3A	0.762	2.30	0.145	0.965	0.44	HEM	complex2.pdb.gz	49,50,53,54,57,67,71,74,78,108
3	0.03	3ag4N	0.730	2.80	0.088	0.982	0.57	CDL	complex3.pdb.gz	69,70,73,95,99,102,106

	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.