D-I-TASSER Q9NYL2-D4

D-I-TASSER results for Q9NYL2-D4

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

Input Sequence in FASTA format

>Q9NYL2 (174 residues)
ITPVNQSRSSSPTQYGLTKNFSSLHLNSRDSGFSSGNTDTSSERGRYSDRSRNKYGRGSI
SLNSSPRGRYSGKSQHSTPSRGRYPGKFYRVSQSALNPHQSPDFKRSPRDLHQPNTIPGM
PLHPETDSRASEEDSKVSEGGWTKVEYRKKPHRPSPAKTNKERARGDHRGWRNF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| ITPVNQSRSSSPTQYGLTKNFSSLHLNSRDSGFSSGNTDTSSERGRYSDRSRNKYGRGSISLNSSPRGRYSGKSQHSTPSRGRYPGKFYRVSQSALNPHQSPDFKRSPRDLHQPNTIPGMPLHPETDSRASEEDSKVSEGGWTKVEYRKKPHRPSPAKTNKERARGDHRGWRNF
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	987556777887401233102231014789987767678845234533456554457776557676566688888788887666776654467888898885346898777899999998678887544455666667887267654035788887656665667788876679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| ITPVNQSRSSSPTQYGLTKNFSSLHLNSRDSGFSSGNTDTSSERGRYSDRSRNKYGRGSISLNSSPRGRYSGKSQHSTPSRGRYPGKFYRVSQSALNPHQSPDFKRSPRDLHQPNTIPGMPLHPETDSRASEEDSKVSEGGWTKVEYRKKPHRPSPAKTNKERARGDHRGWRNF
Prediction	744445444443243323441230323466444444446445556444554445355444444444444444545444444643444334345444445445547444564644430201334445545457755544513123043454455544465455446554634556
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCC
ITPVNQSRSSSPTQYGLTKNFSSLHLNSRDSGFSSGNTDTSSERGRYSDRSRNKYGRGSISLNSSPRGRYSGKSQHSTPSRGRYPGKFYRVSQSALNPHQSPDFKRSPRDLHQPNTIPGMPLHPETDSRASEEDSKVSEGGWTKVEYRKKPHRPSPAKTNKERARGDHRGWRNF

4ifdI

0.05

2.40

0.54

CEthreader

TKLIQYEHNGRTLEAITATLVGTVRCEEEKKTRRTVKNILVSNDFANNLPKEGDIVLTQRANVEILAVEDKPAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKR

3craA

0.04

0.03

1.91

0.48

EigenThreader

VLDAIAREDFDDLRGELGDLLFQVVFYAQMAQEEGRFDFNDICAAISDKLERRLARWEQIKTEERAQKAQHSALDDIPRSLPALMRAQKIQKRCANVGFDWTTDKVYEEIDEVMYEARQAVVDQAKLEEEMGDLLFATVNLAR----HLGTKFERRFREVERIVTMEEVWQQVK

2ftcN

0.12

0.06

2.25

0.34

FFAS-3D

----------------------------------------------------------GDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEAG-ERVRVSTRSGRI--------------------

7jjvA

0.10

0.07

2.56

1.17

SPARKS-K

-----------------------------------MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAA----G-GAAGGAGT-----GGTGGNGGAGK-------PGGAPGAGGAGTPAGSAGSPGQT

6l7eA

0.05

0.03

1.69

0.67

DEthreader

-----------TVSSPAAYLTELYRLDTR-------RPDLKTLSLL-ARYYNLLFIIYRITRE------ISQPFEIGAAKDN--LLNGQYDWRKLDLFRLLYIKLLIHN-----LLTGLANTAF-VSAAI-KTTRIAE-AIAIQVNLENSYWMYNGRNYQFNALE-ID------

5lqwX

0.07

2.86

0.95

MapAlign

TMILQIDNTPDEATRSAFLSQDTTIHTCLMGSHSIIQVCTAELRHITGKSRYSNWVPPAGIRIVCAQLIISLSNYELVYFKIDVSSDLIELTTHPELDTMPSKVAIVHADLLAIADNEGMIKIMSLQFLTVISLQLVSEKISDMIMVRDLNLHVGLENGVYMKFHIGDVDGSFT

4k0mC

0.07

2.79

0.75

MUSTER

IDPRQNVRGTVSLPHGLGKQVRVLAI-AKGEKIKEAEEAGADYVGGEEIIQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----------AAAAAAAAAAAAAAAAAAAAAAA-

1n8pA1

0.14

0.05

1.78

0.50

HHsearch

-------------TLQESDKFAAIHAGEHV--------D------V--------------------------HGSVIE---P-----ISLSTT----------FKQSSPAN----PIGTYEYSRSQNPNRENLERAVLENA---------------------------------

3pquA

0.05

2.24

0.51

CEthreader

LSGFSDAGNGKNVAATSISDNVNRDHKVGEKLGDNEVKGVAHSSEFAVDFDNKKLTGSLYRNGYINRNKAQEVTKRYSIEADITGNRFRGKAKAEKAGDPIFTDSNYLENGETTTERIIDATKIDLTQFNAKELNNFGDASVLIIDGQKIDLAGVNFKNSKTVEINGKTMVAVA

3c9iB

0.06

2.70

0.48

EigenThreader

SILPRNVFSKSYLLYVIAQGTDVGAIAGKANEAGQGAYDAQVKNDEQDVELADHE--ARIKQLRIDVDDHESRITANTKAITALNVRVTTAEGEIASLQTNVSALDGRVTTAENNISALQADYVSKTAQSLASPLNVTTSYSKKVVGAATGTANKGVFDADLTFAVSDTYTQSE

(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	0.4095

(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	1cvmA	0.45	5.39	0.039	0.782	model1_1cvmA.pdb.gz
2	7cm1B	0.44	5.16	0.049	0.764	model1_7cm1B.pdb.gz
3	4zleA	0.44	4.89	0.063	0.730	model1_4zleA.pdb.gz
4	5yylA	0.44	5.67	0.019	0.816	model1_5yylA.pdb.gz
5	7c6oA	0.44	6.02	0.006	0.856	model1_7c6oA.pdb.gz
6	1urjB1	0.43	5.62	0.037	0.787	model1_1urjB1.pdb.gz
7	3nssA	0.43	5.26	0.039	0.764	model1_3nssA.pdb.gz
8	5n4aA	0.43	6.05	0.056	0.833	model1_5n4aA.pdb.gz
9	5aorA	0.43	5.28	0.045	0.747	model1_5aorA.pdb.gz
10	7e6qA	0.43	5.13	0.045	0.753	model1_7e6qA.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:0044822	1.00	poly(A) RNA binding
GO:0005524	1.00	ATP binding
GO:0004709	1.00	MAP kinase kinase kinase activity
GO:0000287	1.00	magnesium ion 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:0060173	1.00	limb development
GO:0043065	1.00	positive regulation of apoptotic process
GO:0042733	1.00	embryonic digit morphogenesis
GO:0035556	1.00	intracellular signal transduction
GO:0009314	1.00	response to radiation
GO:0007257	1.00	activation of JUN kinase activity
GO:0007050	1.00	cell cycle arrest
GO:0006468	1.00	protein phosphorylation
GO:0000077	1.00	DNA damage checkpoint
GO:0044763	0.61	single-organism cellular process
GO:0048869	0.57	cellular developmental process
GO:0030154	0.56	cell differentiation
GO:0008283	0.56	cell proliferation
GO:0008219	0.56	cell death
GO:0000186	0.56	activation of MAPKK 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 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:0005737	1.00	cytoplasm
GO:0043226	0.73	organelle
GO:0043229	0.72	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0005634	0.67	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	1fp4B	0.393	5.47	0.038	0.690	1.18.6.1	NA
2	0.060	1wgzA	0.405	5.45	0.055	0.718	3.4.24.66	NA
3	0.060	1ncaN	0.438	4.98	0.033	0.741	3.2.1.18	NA
4	0.060	3cmmC	0.416	5.60	0.033	0.759	6.3.2.19	20,43
5	0.060	2c6fA	0.403	5.96	0.054	0.782	3.4.15.1	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:

Click to view	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	1cvmA	0.445	5.39	0.039	0.782	0.43	CA	complex1.pdb.gz	119,137,139
	2	0.01	1b9tA	0.429	5.37	0.078	0.759	0.53	CA	complex2.pdb.gz	119,121,141

	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.