D-I-TASSER Q9NVR5-D4

D-I-TASSER results for Q9NVR5-D4

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

Input Sequence in FASTA format

>Q9NVR5 (113 residues)
VTCFQQESLDVSQMILGKSQQPESKMQSEFIKEKSATCSNEEKDNLNESVITEEKETDGD
HLSSLLNKTTVHNIPGFDSIKETNMQDGSVQVIKDHVTNCAFSFQNSLLYDLD

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VTCFQQESLDVSQMILGKSQQPESKMQSEFIKEKSATCSNEEKDNLNESVITEEKETDGDHLSSLLNKTTVHNIPGFDSIKETNMQDGSVQVIKDHVTNCAFSFQNSLLYDLD
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHCHCCCCCCCCCCHHHCCCCCCCSSSSSCCCCCCCSSSCCCCSSSCC
Confidence	96534578986543468778862113624420356665531011024664112224688777531110001478874101002478872798622321242675141103069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VTCFQQESLDVSQMILGKSQQPESKMQSEFIKEKSATCSNEEKDNLNESVITEEKETDGDHLSSLLNKTTVHNIPGFDSIKETNMQDGSVQVIKDHVTNCAFSFQNSLLYDLD
Prediction	64234443472544244545546553455135664443556547425542345557156742553354443563542540454446523142045234413241434233538
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHCHCCCCCCCCCCHHHCCCCCCCSSSSSCCCCCCCSSSCCCCSSSCC
VTCFQQESLDVSQMILGKSQQPESKMQSEFIKEKSATCSNEEKDNLNESVITEEKETDGDHLSSLLNKTTVHNIPGFDSIKETNMQDGSVQVIKDHVTNCAFSFQNSLLYDLD

1hr6A

0.07

2.91

0.59

CEthreader

TKKVAQYTGGESCIPPAPVFGNLPELFHIQIGFEGLPIDHPDIYALATLQTLLGGGGKGMYSRLYTHVLNQYYFVENCVAFNHSYSDSGIFGISLSCIPAAPQAVEVIAQQMY

5oqj1

0.06

0.05

2.31

0.52

EigenThreader

GGGGGGGGGGGGGGGGGGGEVKSTLPIDLLESCRMLHTTCCEFLKHFYIHFQSGEQKQASTVKKLYNHLKDCIEKLNELF--------------QDVLNGDGESMSNTCTAYL

1q6uA

0.07

0.06

2.52

0.25

FFAS-3D

----------VQDAFADKSKLSDQEIEQTLQAFEARV--KSSAQAKMEKDAADNEAKGKEYREKFAKEKGVKTSSTGLVYQVVEAGKGEADTVVVNYK---GTLIDGKEFD--

7abiE

0.08

3.12

0.91

SPARKS-K

RKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGELAAE---MAAAFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNT

3s2kA

0.23

0.07

2.22

0.64

CNFpred

------------------------------------------------------------------------------LIESSNMLGLNREVIADDPHPFGLTQYQDYIYWTD

5odcA

0.09

0.08

3.02

0.83

DEthreader

LKNVVLNRLNPLEFIK-VGVTRALVIGGVGGRMQLDKTF-TNDCSCILAMAVPAKYTAIDDQEPEI-----------IGYDASVCMYASVMVPTKS--VILIFCQGPKDIPSV

3amjB2

0.03

1.49

0.84

MapAlign

------------------------ATQAHIAIGMPTLKRGDPDFFPLVVGNYALGGGGFESRL-MKEIRDKRGLSYGAYSYFSPQKSMGLFQIGFETRAEKADEAVQVANDT-

6fmlG

0.14

0.13

4.56

0.62

MUSTER

LGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMRKALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPS---MARFVTDSGLAKLDELLRELK

2pffB

0.17

0.15

4.94

0.82

HHsearch

EHVLL-V-PTASFFIASQLQEQFNKPTEGFAADDEPTTPAEAPSGLDQPFSERKLKFSNRFLPVASPFHSHLLVPASDL------------INKDLVKNVSFNAKDIQIPVYD

3amiA

0.09

3.39

0.54

CEthreader

PARKQQGEPQQAGVRRVTVKAPAELPYLALAWHVPAIVDLDKSRDAYALEILAAVLDGYDGARMTRQLVRGNKHAVSAGAGYDSLSRGQQGLFILEGVPSKGVTIAQLETDLR

(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	0.5077

(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	4z80A1	0.46	4.52	0.062	0.788	model1_4z80A1.pdb.gz
2	6g1yA1	0.43	4.40	0.094	0.743	model1_6g1yA1.pdb.gz
3	1jq3A2	0.43	4.01	0.075	0.681	model1_1jq3A2.pdb.gz
4	5a22A	0.43	4.50	0.071	0.735	model1_5a22A.pdb.gz
5	4r70A1	0.43	4.31	0.053	0.743	model1_4r70A1.pdb.gz
6	6ptqA1	0.42	4.37	0.032	0.761	model1_6ptqA1.pdb.gz
7	2oolA	0.42	4.36	0.054	0.743	model1_2oolA.pdb.gz
8	6ui4A	0.42	4.34	0.083	0.735	model1_6ui4A.pdb.gz
9	6j27A	0.42	4.11	0.062	0.673	model1_6j27A.pdb.gz
10	4p7hA1	0.42	4.34	0.119	0.743	model1_4p7hA1.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:1901363	0.51	heterocyclic compound binding
GO:0097159	0.51	organic cyclic 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:0070286	1.00	axonemal dynein complex assembly
GO:0006928	0.82	movement of cell or subcellular component
GO:0060285	0.79	cilium-dependent cell motility
GO:0065007	0.63	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0050794	0.62	regulation of cellular process
GO:0006996	0.58	organelle organization
GO:1902589	0.57	single-organism organelle organization
GO:0048583	0.56	regulation of response to stimulus
GO:0098792	0.55	xenophagy
GO:0098779	0.55	mitophagy in response to mitochondrial depolarization
GO:0071973	0.55	bacterial-type flagellum-dependent cell motility
GO:0002230	0.55	positive regulation of defense response to virus by host

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

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	1dj2B	0.389	4.75	0.056	0.699	6.3.4.4	NA
2	0.060	3cbgA	0.415	4.38	0.021	0.681	2.1.1.-	54
3	0.060	1dxhA	0.394	4.69	0.039	0.717	2.1.3.3	NA
4	0.060	2z26A	0.351	4.87	0.029	0.646	3.5.2.3	78
5	0.060	3c6kD	0.402	4.46	0.052	0.708	2.5.1.22	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	2o06B	0.412	4.40	0.021	0.699	0.19	MTA	complex1.pdb.gz	32,33,34,35,58,59
2	0.01	2o05B	0.410	4.39	0.032	0.690	0.14	MTA	complex2.pdb.gz	48,49,50,93,94,98
3	0.01	2o05A	0.366	4.90	0.011	0.699	0.16	MTA	complex3.pdb.gz	4,77,78,79,93
4	0.01	1ecgA	0.420	4.28	0.050	0.708	0.21	ONL	complex4.pdb.gz	58,59,63
5	0.01	3nweA	0.393	4.87	0.041	0.717	0.12	662	complex5.pdb.gz	58,59,81,82,106
6	0.01	1jq3A	0.421	3.91	0.042	0.681	0.10	AAT	complex6.pdb.gz	35,81,82,83,89,90
7	0.01	3bwyA	0.410	4.15	0.043	0.664	0.18	SAM	complex7.pdb.gz	35,36,37,93,94,95
8	0.01	1jr4A	0.397	4.59	0.042	0.681	0.12	CL4	complex8.pdb.gz	59,60,82,83,89
9	0.01	3rw9A	0.369	4.95	0.011	0.726	0.11	DSH	complex9.pdb.gz	42,60,63

	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.