D-I-TASSER Q9NSA1-D1

D-I-TASSER results for Q9NSA1-D1

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

Input Sequence in FASTA format

>Q9NSA1 (209 residues)
MDSDETGFEHSGLWVSVLAGLLLGACQAHPIPDSSPLLQFGGQVRQRYLYTDDAQQTEAH
LEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEA
CSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPGLPPALPEPPGI
LAPQPPDVGSSDPLSMVGPSQGRSPSYAS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDSDETGFEHSGLWVSVLAGLLLGACQAHPIPDSSPLLQFGGQVRQRYLYTDDAQQTEAHLEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPGLPPALPEPPGILAPQPPDVGSSDPLSMVGPSQGRSPSYAS
Prediction	CCHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCSSSSSCCCCCSCCCCCCCCCCSSSSSSCCCCSSSSSSSCCCCSSSSCCCCCSSSCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCSSSSCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98134378533368999998766411565789887631247852147888547887626999949984714327997616899962588799985223754666787866501345677638999972698168986566817998579984778999863123125677656777743346788777888975446778788998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDSDETGFEHSGLWVSVLAGLLLGACQAHPIPDSSPLLQFGGQVRQRYLYTDDAQQTEAHLEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPGLPPALPEPPGILAPQPPDVGSSDPLSMVGPSQGRSPSYAS
Prediction	75344460422000000012011122444414444314435453121101033465220001025514141344734433131333633201021242421100255033314543446302020324642110010342310010245444554656442020031442475345446444644373446333533554554444468
	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

CCHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCSSSSSCCCCCSCCCCCCCCCCSSSSSSCCCCSSSSSSSCCCCSSSSCCCCCSSSCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCSSSSCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MDSDETGFEHSGLWVSVLAGLLLGACQAHPIPDSSPLLQFGGQVRQRYLYTDDAQQTEAHLEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPGLPPALPEPPGILAPQPPDVGSSDPLSMVGPSQGRSPSYAS

1dfcA

0.14

0.10

3.42

1.00

DEthreader

-----------------------------------------AVQIQFGLINC----GNKYLTAEAGFKVNASASSKKKQIWTLE---A-AVCLRSH-LGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHRRYFGGTEDRLSCFAQTVSPAEKWSVHIAMH------DRDTKKCAWTLTATGG-QSTASSKNASC----

2p23A

0.38

0.24

7.10

2.58

SPARKS-K

-----------------------------------------DPIRLRHLYTSGHGLSSCFLRIRADGVVDCARGQSAHSLLEIKAVALRTVAIKGVHSVRYLCMGADGKMQGLLQYSEEDCAFEEEIRPDGYNVYRSEKHRLPVSLSSAKQRQKNRGFLPLSHFLPMLPMVPEE-----------------------------------

3pubA

0.12

0.09

3.22

0.76

MapAlign

-------SEVITNVVNKLCMEYAYQLWLIVRDCFPVEFRLIFAENAIKLMYKR---DGLALTLSDGRLAFGDGDKSPKVSWKFIALWKVYFKILNTERNQYLVLGVDHMAFGVNSVDSFRAQWYLQPAKYNLFYIYNREYSKALTLNRMAWGYNGRVIPEHYAWGVKAF----------------------------------------

1qqlA

0.30

0.18

5.37

0.56

CEthreader

------------------------------------------DIRVRRLFCRT----QWYLRIDKRGKVKGTQEMNSYNIMEIRTVAVGIVAIKGVESEYYLAMNKEGKLYAKQTPN-EECLFLERLEENHYNTYISKKHAWFVGLKKNGSCKRGPRTQKAILFLPLPVSS--------------------------------------

2p39A

0.33

0.22

6.75

1.89

MUSTER

----------------------------------SPLLG-SSWGGLIHLYTATAR-NSYHLQIHKNGHVDGAPHQTIYSALMIRSEDAGFVVITGVMSRRYLCMDFRGNIFGSHYFDPENCRFQHQTLENGYDVYHSPQYHFLVSLGRAKRAFLPMNPPPYSQFLSRRNEIPLIHFN--------------------------------

3f1rA

0.31

0.22

6.51

3.40

HHsearch

-------------------------------PGAAQLAHLHGILRRRQLYCRT----GFHLQILPDGSVQGTRQDSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLT-SECIFREQFEENWYNTYSSNIYHYFVALNKDGTPRDGARHQKFTHFLPRPVDPERVPELYKDLL---------------------------

6m6eA

1.00

0.61

17.15

2.06

FFAS-3D

-----------------------------------------GQVRQRYLYTDDAQQTEAHLEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPG----------------------------------------

2ehiB

0.07

0.06

2.37

1.03

EigenThreader

------------------------------WIMSQTNANDLRNNEVFFISPSN--NTNKVLDKISQSEVKLL-SGANQKWRLIYDTNKQAYKIKVMDNTSLITWNAPLSSVKTDTNGDNQYWYLLQNYISRNVIIRNYMPNLVLQYN----IDDTTSSSNQFFKFSNCIYEALNNLNSDRLNSQIWFDSSRQKQNSNNYSTDSLIQYWN

6m6fA

0.93

0.57

15.99

2.45

CNFpred

-----------------------------------------GQVRQRYLYTSGPHLSSCHLEIREDGTVGCAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPG----------------------------------------

2vseA

0.06

0.04

1.72

1.00

DEthreader

---------------------NGQPQNNQKWYLRHLNSSNN-FTGYFNISSKK--NFNKIITMNSNKQAVIFDNIGINQSWKLKYNDKNAYQIHIL--DNFLYFQGGHNVATMRNVTDLRSYWYVEYNFNDGFIIRNAFDSYVLDVGNTPIITY-QNYLNDNLWNFIP-SL-G------------------------------------

(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	0.6754

(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	2ehiB	0.65	3.66	0.069	0.813	model1_2ehiB.pdb.gz
2	2vseA	0.63	3.69	0.074	0.785	model1_2vseA.pdb.gz
3	1dfcA	0.63	4.16	0.080	0.837	model1_1dfcA.pdb.gz
4	3phzA	0.61	3.49	0.083	0.751	model1_3phzA.pdb.gz
5	2ihoA	0.61	3.46	0.057	0.751	model1_2ihoA.pdb.gz
6	1ybiA1	0.55	2.08	0.085	0.612	model1_1ybiA1.pdb.gz
7	3vsfA	0.54	1.87	0.120	0.598	model1_3vsfA.pdb.gz
8	3pg0A	0.54	1.93	0.114	0.589	model1_3pg0A.pdb.gz
9	4g9mA	0.54	1.93	0.129	0.593	model1_4g9mA.pdb.gz
10	4ionA	0.53	2.01	0.040	0.593	model1_4ionA.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:0005102	0.94	receptor binding
GO:0008083	0.88	growth factor activity
GO:0003824	0.78	catalytic activity
GO:0098772	0.77	molecular function regulator
GO:0016740	0.77	transferase activity
GO:0016773	0.75	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.75	kinase activity
GO:0097367	0.74	carbohydrate derivative binding
GO:0005104	0.74	fibroblast growth factor receptor binding
GO:0046934	0.73	phosphatidylinositol-4,5-bisphosphate 3-kinase activity
GO:0016303	0.73	1-phosphatidylinositol-3-kinase activity
GO:0005088	0.73	Ras guanyl-nucleotide exchange factor activity
GO:0008201	0.72	heparin binding
GO:0004672	0.66	protein kinase activity
GO:0004713	0.64	protein tyrosine kinase 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:0065007	0.89	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0044699	0.88	single-organism process
GO:0050794	0.87	regulation of cellular process
GO:0009987	0.76	cellular process
GO:0048518	0.72	positive regulation of biological process
GO:0044763	0.67	single-organism cellular process
GO:0032502	0.66	developmental process
GO:0048522	0.64	positive regulation of cellular process
GO:0007165	0.64	signal transduction
GO:0044767	0.59	single-organism developmental process
GO:0048856	0.56	anatomical structure development
GO:0048583	0.55	regulation of response to stimulus
GO:0019222	0.55	regulation of metabolic process
GO:0080090	0.54	regulation of primary metabolic process
GO:0051239	0.54	regulation of multicellular organismal process
GO:0031323	0.54	regulation of cellular metabolic process
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:0042127	0.52	regulation of cell proliferation
GO:0009893	0.51	positive regulation of metabolic process
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0009966	0.50	regulation of signal transduction

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	0.84	cell part
GO:0044424	0.78	intracellular part
GO:0044421	0.68	extracellular region part
GO:0005615	0.64	extracellular space
GO:0005576	0.52	extracellular region
GO:0043226	0.51	organelle
GO:0043227	0.50	membrane-bounded organelle

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	0.247	1nunA	0.580	1.71	0.262	0.622	2.7.10.1	132,165
2	0.237	1ry7A	0.570	2.19	0.298	0.627	2.7.10.1	110,127,133,166
3	0.060	1cgtA	0.389	5.87	0.028	0.703	2.4.1.19	125
4	0.060	2vuaA	0.572	3.84	0.053	0.751	3.4.24.69	100
5	0.060	1cdgA	0.395	5.81	0.068	0.708	2.4.1.19	66

	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	0.05	1iil0	0.582	1.56	0.295	0.617	1.23	III	complex1.pdb.gz	50,52,54,60,73,83,84,85,86,87,88,91,92,101,116,125,127,128,130,131,132,133,165,167
2	0.05	1ihk0	0.601	2.14	0.280	0.655	1.10	III	complex2.pdb.gz	47,50,52,60,74,130,131,165,166,167,168,169,172
3	0.05	1fq9A	0.563	1.41	0.306	0.593	0.84	UUU	complex3.pdb.gz	105,106,110,119,120
4	0.03	3aj5A	0.646	3.34	0.094	0.789	0.83	NGA	complex4.pdb.gz	62,63,64,69,71,76,78
5	0.03	2fdb0	0.570	1.64	0.140	0.608	1.03	III	complex5.pdb.gz	43,44,45,50,52,58,60,83,85,87,88,89,91,125,127,128,132,133,148,165,166,167
6	0.02	1w3aA	0.569	2.49	0.098	0.646	0.80	LBT	complex6.pdb.gz	103,105,107,113,117,120,121

	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.