D-I-TASSER Q9NRU3-D3

D-I-TASSER results for Q9NRU3-D3

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

Input Sequence in FASTA format

>Q9NRU3 (212 residues)
TREKLLETLRAADPYSDLVKEELNIIQGALELRTKVVEEVLTPLGDCFMLRSDAVLDFAT
VSEILRSGYTRIPVYEGDQRHNIVDILFVKDLAFVDPDDCTPLLTVTRFYNRPLHCVFND
TRLDTVLEEFKKGKSHLAIVQRVNNEGEGDPFYEVMGIVTLEDIIEEIIKSEILDETDLY
TDNRKKQRVPQRERKRHDFSLFKLSDTEMRVK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| TREKLLETLRAADPYSDLVKEELNIIQGALELRTKVVEEVLTPLGDCFMLRSDAVLDFATVSEILRSGYTRIPVYEGDQRHNIVDILFVKDLAFVDPDDCTPLLTVTRFYNRPLHCVFNDTRLDTVLEEFKKGKSHLAIVQRVNNEGEGDPFYEVMGIVTLEDIIEEIIKSEILDETDLYTDNRKKQRVPQRERKRHDFSLFKLSDTEMRVK
Prediction	CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCSSSSSCCCCCCSSSSSCCCCHHHHHHHHHHHCCCCSSSSSCCCCCCSSSSSSSHHHHHHHHHCCCCCCCHHHHHHCCCCCSCCCCCSHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCCCSSSSSSHHHHHHHHHCCCCCCCCCCCCCCHHHSSCCCCSSSCCCCCCCCCCCCCCCCC
Confidence	88999999999877199798999999986134995898852240118999689986399999999719985465539997606787658998865122697510289997389836279880999999999539579999964788889998866555307888899846834578887653311012365324306610123674201579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| TREKLLETLRAADPYSDLVKEELNIIQGALELRTKVVEEVLTPLGDCFMLRSDAVLDFATVSEILRSGYTRIPVYEGDQRHNIVDILFVKDLAFVDPDDCTPLLTVTRFYNRPLHCVFNDTRLDTVLEEFKKGKSHLAIVQRVNNEGEGDPFYEVMGIVTLEDIIEEIIKSEILDETDLYTDNRKKQRVPQRERKRHDFSLFKLSDTEMRVK
Prediction	84620340053047544037513510410040562405404031410110337351344005202735204020245744631000000120030136564633411530433030024414055046334752130001023455544011010111131331101015430410325436544444356544355514046055543628
	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                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCSSSSSCCCCCCSSSSSCCCCHHHHHHHHHHHCCCCSSSSSCCCCCCSSSSSSSHHHHHHHHHCCCCCCCHHHHHHCCCCCSCCCCCSHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCCCSSSSSSHHHHHHHHHCCCCCCCCCCCCCCHHHSSCCCCSSSCCCCCCCCCCCCCCCCC
TREKLLETLRAADPYSDLVKEELNIIQGALELRTKVVEEVLTPLGDCFMLRSDAVLDFATVSEILRSGYTRIPVYEGDQRHNIVDILFVKDLAFVDPDDCTPLLTVTRFYNRPLHCVFNDTRLDTVLEEFKKGKSHLAIVQRVNNEGEGDPFYEVMGIVTLEDIIEEIIKSEILDETDLYTDNRKKQRVPQRERKRHDFSLFKLSDTEMRVK

7cfhA

0.29

0.23

6.88

1.17

DEthreader

VSEELKLILAGAEESGAIQPQEEEMIHSILELEETPVREIMTPRVEMVAIEDEATLE-DLLALYREHRASRVPVYR-ESVDHIVGVAYAKDLLDYYCEEDLKGRTVASIT-HPPYFVPENMDAWSLLKELRRRKVHMAIVVDEF--------GGTAGLVTLEDVIEEIV-GEIYD-------------------------------------

7cfhA

0.29

0.22

6.75

1.38

SPARKS-K

SEEELKLILAGAEESGAIQPQEEEMIHSILELEETPVREIMTPRVEMVAIEDEATL-EDLLALYREHRASRVPVYRESVDH-IVGVAYAKDLLDYYCEEDLKGRTVASITHPPYF-VPENMDAWSLLKELRRRKVHMAIVVD--------EFGGTAGLVTLEDVIEEIVGEIYD--------------------------------------

7cfhA

0.30

0.23

6.87

0.66

MapAlign

-EEELKLILAGAEESGAIQPQEEEMIHSILELEETPVREIMTPRVEMVAIEDEATL-EDLLALYREHRASRVPVYR-ESVDHIVGVAYAKDLLDYYCEEDLKGRTVASIT-HPPYFVPENMDAWSLLKELRRRKVHMAIVVDE--------FGGTAGLVTLEDVIEEIV-GEI---------------------------------------

7cfhA

0.30

0.23

7.01

0.43

CEthreader

SEEELKLILAGAEESGAIQPQEEEMIHSILELEETPVREIMTPRVEMVAIEDEATL-EDLLALYREHRASRVPVYRES-VDHIVGVAYAKDLLDYYCEEDLKGRTVASIT-HPPYFVPENMDAWSLLKELRRRKVHMAIVVD--------EFGGTAGLVTLEDVIEEIVG-EIYD-------------------------------------

6n7eA

0.80

0.63

17.73

1.36

MUSTER

---------------------ELNIIQGALELRTKTVEDVMTPLRDCFMITGEAILDFNTMSEIMESGYTRIPVFEG-ERSNIVDLLFVKDLAFVDPDDCTPLKTITKFYNHPLHFVFNDTKLDAMLEEFKKGKSHLAIVQ-----------YEVLGIVTLEDVIEEIIKSEILDETDLYTDN------------RTKFSAFKQTDSEMKVK

7lj7A

0.28

0.21

6.36

1.68

HHsearch

TEEEIKEWIDVGEEEGTIEEEERDMLYSVLRFGDTTAREVMTPRVDVVMIEDTATLE-SALAIFNETGFSRIPVYHER-IDNIVGLLNVKDVFSAQTS-----ATIRDL-MYEPYFIPESKKIDELLKELQVKKQHMAVVL--------DEYGSFAGIVTVEDMLEELVLEHHHHH------------------------------------

6n7eA1

0.78

0.57

16.00

2.22

FFAS-3D

---------------------ELNIIQGALELRTKTVEDVMTPLRDCFMITGEAILDFNTMSEIMESGYTRIPVF-EGERSNIVDLLFVKDLAFVDPDDCTPLKTITKFYNHPLHFVFNDTKLDAMLEEFKKGKSHLAIVQYEVL-----------GIVTLEDVIEEIIKSEILDETDLYTDNRTK--------------------------

6n7eA

0.63

0.53

15.11

1.18

EigenThreader

------------------EL---NIIQGALELRTKTVEDVMTPLRDCFMITGEAILDFNTMSEIMESGYTRIPVFE-GERSNIVDLLFVKDLAFVDPDDCTPLKTITKFYNHPLHFVFNDTKLDAMLEEFKKGKSHLAIVQ-----------YEVLGIVTLEDVIEEIIKSEIDSEMKVKISPQLLLAMHRFLATEVEAFSELKYDEKNKKA

4iy0A

0.82

0.59

16.64

1.58

CNFpred

-------------------KEELNIIQGALELRTKTVEDVMTPLRDCFMITGEAILDFNTMSEIMESGYTRIPVFEG-ERSNIVDLLFVKDLAFVDPDDCTPLKTITKFYNHPLHFVFNDTKLDAMLEEFKKGKSHLAIVQRVNNEGEGDPFYEVLGIVTLEDVIEEIIKSE----------------------------------------

7lj7A

0.27

0.20

6.08

1.00

DEthreader

VTEEIKEWIDVGEEEGTIEEEERDMLYSVLRFGDTTAREVMTPRVDVVMIEDTATLE-SALAIFNETGFSRIPVYH-ERIDNIVGLLNVKDVFSA---QT--SATIRDLM-YEPYFIPESKKIDELLKELQVKKQHMAVVLDEY--------GSFAGIVTVEDMLEELVLEH----------------------------------------

(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	0.7113

(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	7cfhA	0.73	1.41	0.288	0.769	model1_7cfhA.pdb.gz
2	6n7eA1	0.67	1.74	0.810	0.722	model1_6n7eA1.pdb.gz
3	7lj7A	0.64	2.47	0.258	0.731	model1_7lj7A.pdb.gz
4	3oi8A	0.63	2.02	0.235	0.703	model1_3oi8A.pdb.gz
5	3ocmA	0.60	2.27	0.212	0.689	model1_3ocmA.pdb.gz
6	4hg0A	0.59	3.09	0.231	0.689	model1_4hg0A.pdb.gz
7	2ooxE	0.58	4.08	0.078	0.774	model1_2ooxE.pdb.gz
8	6mn6A	0.57	2.42	0.543	0.637	model1_6mn6A.pdb.gz
9	2qlvC	0.56	4.43	0.105	0.769	model1_2qlvC.pdb.gz
10	2v9jE	0.56	3.41	0.178	0.670	model1_2v9jE.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:0022891	0.74	substrate-specific transmembrane transporter activity
GO:0008324	0.73	cation transmembrane transporter activity
GO:0046873	0.72	metal ion transmembrane transporter activity
GO:0015095	0.71	magnesium ion transmembrane transporter activity
GO:0097159	0.54	organic cyclic compound binding
GO:1901363	0.53	heterocyclic compound 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	0.87	biological regulation
GO:0065008	0.84	regulation of biological quality
GO:0050801	0.78	ion homeostasis
GO:0044699	0.78	single-organism process
GO:0055065	0.72	metal ion homeostasis
GO:0009987	0.69	cellular process
GO:0010960	0.68	magnesium ion homeostasis
GO:0048856	0.64	anatomical structure 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	0.97	cell part
GO:0016020	0.87	membrane
GO:0044424	0.69	intracellular 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	0.060	1gkrA	0.401	5.43	0.076	0.656	3.5.2.2	NA
2	0.060	2g3mF	0.405	5.70	0.042	0.703	3.2.1.20	NA
3	0.060	3edyA	0.396	5.65	0.062	0.679	3.4.14.9	NA
4	0.060	1ea9C	0.393	6.01	0.056	0.712	3.2.1.54	NA
5	0.060	1a5lC	0.442	5.07	0.083	0.703	3.5.1.5	163

	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	0.14	3jtfB	0.524	2.11	0.304	0.576	1.32	AMP	complex1.pdb.gz	46,47,48,68,69,70,71,158,160
2	0.08	3kpdD	0.489	2.17	0.193	0.552	0.90	MTA	complex2.pdb.gz	42,68,69,71,73,158,160,162,163
3	0.03	1yav0	0.532	2.13	0.125	0.599	0.85	III	complex3.pdb.gz	33,62,64,65,66,68,70,96,100,123,127,130,131,161,162,164,165,168,169
4	0.03	2nyc0	0.487	2.89	0.141	0.590	0.85	III	complex4.pdb.gz	32,57,69,71,87,88,127,128,130,131,133,134,135,136,161,165,166,168,169
5	0.03	2j9l3	0.517	2.83	0.165	0.613	0.87	III	complex5.pdb.gz	82,83,84,115,118,121,129,132,133,153

	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.