D-I-TASSER Q8N490-D1

D-I-TASSER results for Q8N490-D1

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

Input Sequence in FASTA format

>Q8N490 (104 residues)
MAAVVAATALKGRGARNARVLRGILAGATANKASHNRTRALQSHSSPEGKEEPEPLSPEL
EYIPRKRGKNPMKAVGLAWYSLYTRTWLGYLFYRQQLRRARNRY

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAAVVAATALKGRGARNARVLRGILAGATANKASHNRTRALQSHSSPEGKEEPEPLSPELEYIPRKRGKNPMKAVGLAWYSLYTRTWLGYLFYRQQLRRARNRY
Prediction	CCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
Confidence	93033302101368886145542324345413578864000146898777888889987665664447897424666678715347889888899998776419
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAAVVAATALKGRGARNARVLRGILAGATANKASHNRTRALQSHSSPEGKEEPEPLSPELEYIPRKRGKNPMKAVGLAWYSLYTRTWLGYLFYRQQLRRARNRY
Prediction	73342433324454264252243113223345345544454555455745667553577253135654643144222121343332200110134415554767
	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

CCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
MAAVVAATALKGRGARNARVLRGILAGATANKASHNRTRALQSHSSPEGKEEPEPLSPELEYIPRKRGKNPMKAVGLAWYSLYTRTWLGYLFYRQQLRRARNRY

2mouA

0.09

3.34

0.49

CEthreader

SDTFICHTITQSFSPRDFIDLVYIKRYEGNMNIISSKSVDFPEYPPSSNYIRGYNHPCGFVCSPMEENPAYSKLVMFVQTSPSIIEKTMPSNLVNFILNAKDGI

4w6vA1

0.08

3.08

0.53

EigenThreader

AVWYGSILIALGVFIVLGTGLFKTCISVMVGTLYKPGDAGGFSLFYMGINMGSFIAPLLSGWLLRTHGWHWGFGIGGIGMLVALLIFRGFAIPAMKRYDAEVGL

5y83A2

0.06

2.45

0.41

FFAS-3D

WAIMLFTLIVRLAQCLMLLIQLPIFMLLW---------SVIRYYVEEFAYSGSFLIWKDLSAGGFSYYTIIMSVIFPFLFVGLPSGLFLYYATNTLIQLAVT--

3iygQ2

0.11

0.10

3.47

0.82

SPARKS-K

EVSSLLHTSVMSKQYGNEVFLAKLIAQACVSDSGHFNVDNIRVCKILGSGVHSSSVLHGSTIVLRGSTDNLMDDIERAVDDGVNTFKVLTR-------------

4fyeA

0.15

0.05

1.62

0.53

CNFpred

----------------------------------------------------------------------DYKKLAIKAVTLINQEEVIQTLAQRQIDRMTNED

6p25A

0.04

0.03

1.57

1.00

DEthreader

LCIWRLWFMIGDLKSSSIFKVAFAKLAFLGVPFALYLVFFYIHFQSLTLLNNKI--S-YLHSHS-HNYPQQSTLLLHSNDDWVHAM------------------

5n6mA

0.06

2.56

0.68

MapAlign

LWRGWWYGFGAFGAGVAFFFALPAWLWARAALWLALELFRSWFLTGFPWLYAGYSQLQGPLAGLVPVGGVWLSSFVIALSAALLVNLSLLLGLVLLLGPWAAGL

6b3nA

0.11

3.82

0.54

MUSTER

MPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYF---MGSLNQDGLSNDNIQIGLQYIEHIERTLNHGSLTSREVTVLREI-

2pffB

0.16

0.14

4.80

0.47

HHsearch

TYHVLVGDLIK----FSAETLSELIRTTLDA--EKVFTQGLN---ILEWLENPSNTPD-KDYLLIPISCPLIGVIQLAHYLGFTPGELRSYVAIAETDSWESFF

4jq6A

0.06

2.50

0.43

CEthreader

VMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFLFNTIKWIVTVGWAIY------PIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDKET

(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	0.5023

(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	5b4sA	0.52	4.51	0.089	0.952	model1_5b4sA.pdb.gz
2	1wvuB	0.50	4.51	0.093	0.923	model1_1wvuB.pdb.gz
3	2d05A	0.49	4.53	0.084	0.913	model1_2d05A.pdb.gz
4	2jssA	0.49	4.70	0.081	0.904	model1_2jssA.pdb.gz
5	2dkvA	0.49	4.46	0.103	0.923	model1_2dkvA.pdb.gz
6	2z38A	0.48	4.40	0.091	0.913	model1_2z38A.pdb.gz
7	4ok7A	0.48	4.55	0.083	0.885	model1_4ok7A.pdb.gz
8	4mckA	0.47	4.50	0.063	0.875	model1_4mckA.pdb.gz
9	3wh1A	0.45	4.58	0.052	0.865	model1_3wh1A.pdb.gz
10	3hbhA	0.44	4.98	0.052	0.865	model1_3hbhA.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	0.42	catalytic activity
GO:1901363	0.41	heterocyclic compound binding
GO:0097159	0.41	organic cyclic compound binding
GO:0016787	0.38	hydrolase activity
GO:0004553	0.37	hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0003676	0.37	nucleic acid binding
GO:0043167	0.35	ion binding
GO:0046872	0.34	metal ion binding
GO:0003677	0.34	DNA 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:0050884	1.00	neuromuscular process controlling posture
GO:0046929	1.00	negative regulation of neurotransmitter secretion
GO:0042053	1.00	regulation of dopamine metabolic process
GO:0032225	1.00	regulation of synaptic transmission, dopaminergic
GO:0009987	0.74	cellular process
GO:0008152	0.67	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044237	0.64	cellular metabolic process
GO:0044238	0.63	primary metabolic process
GO:0044260	0.61	cellular macromolecule metabolic process
GO:0006807	0.61	nitrogen compound metabolic process
GO:0034641	0.60	cellular nitrogen compound metabolic process
GO:0009058	0.59	biosynthetic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:1901576	0.58	organic substance biosynthetic process
GO:0090304	0.58	nucleic acid metabolic process
GO:0044249	0.58	cellular biosynthetic process
GO:1901362	0.57	organic cyclic compound biosynthetic process
GO:0044271	0.57	cellular nitrogen compound biosynthetic process
GO:0034645	0.57	cellular macromolecule biosynthetic process
GO:0016070	0.57	RNA metabolic process
GO:0006351	0.56	transcription, DNA-templated

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:0005739	1.00	mitochondrion
GO:0016020	0.68	membrane
GO:0005634	0.68	nucleus

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	2pffD	0.434	5.05	0.097	0.846	2.3.1.86	88
2	0.060	1d0kA	0.444	4.65	0.095	0.875	4.2.2.-	34
3	0.060	1cleA	0.435	4.87	0.064	0.846	3.1.1.3	NA
4	0.060	1b37B	0.451	4.68	0.033	0.837	1.5.3.15 1.5.3.14	NA
5	0.060	1crlA	0.437	4.80	0.053	0.846	3.1.1.3	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	0.01	1f8sB	0.433	4.55	0.065	0.817	0.40	BE2	complex1.pdb.gz	78,88,89
2	0.01	2ch6B	0.455	4.75	0.051	0.856	0.26	ADP	complex2.pdb.gz	4,21,22,61,74,75
3	0.01	1v8bA	0.445	4.90	0.051	0.885	0.16	ADN	complex3.pdb.gz	75,76,80,92
4	0.01	2ch6A	0.442	4.71	0.081	0.846	0.24	ADP	complex4.pdb.gz	23,24,26,75,79
5	0.01	2vhxC	0.421	5.01	0.032	0.837	0.15	PYR	complex5.pdb.gz	76,85,88
6	0.01	3cqlA	0.479	4.61	0.082	0.904	0.12	NDG	complex6.pdb.gz	28,60,76
7	0.01	2avw0	0.446	4.71	0.078	0.827	0.12	III	complex7.pdb.gz	46,47,83,85,89
8	0.01	2x2iA	0.453	4.81	0.061	0.856	0.18	QPS	complex8.pdb.gz	55,75,78,79,84,85
9	0.01	2x2iC	0.457	4.79	0.061	0.856	0.24	QPS	complex9.pdb.gz	76,77,84,86,88,89
10	0.01	2ch6D	0.440	4.56	0.030	0.817	0.30	ADP	complex10.pdb.gz	2,24,25,69,73,74

	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.