D-I-TASSER Q9NVE5-D6

D-I-TASSER results for Q9NVE5-D6

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

Input Sequence in FASTA format

>Q9NVE5 (94 residues)
ATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTV
ERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQK

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| ATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQK
Prediction	CCCCCCCCCCCCCCCSSSSSSSSSSCCCCCHHHHHHHHHHCHHHHHCCCCCHHHHHHHHHHCCCCCCSCCCCHHHHHHHHCCCCCSSSSSSCCC
Confidence	9988999988788611577643674354719999999984534441488984565644453578542205886889985156762322223479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| ATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQK
Prediction	8565664655445513032114141455141550343024134247341433320202225564414124456540452414541410143268
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCSSSSSSSSSSCCCCCHHHHHHHHHHCHHHHHCCCCCHHHHHHHHHHCCCCCCSCCCCHHHHHHHHCCCCCSSSSSSCCC
ATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQK

3ppaA2

0.11

0.10

3.48

1.32

SPARKS-K

YLTELKLCENGNMNNVV----TRRFSKADTIDTIEKEIRKIF-----SIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQQ-VLVIEQKNE

4a3pA

0.10

0.07

2.79

1.04

CNFpred

----------------MNNVVTRRFSKADTIDTIEKEIRKIFSIPDE-----KETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNE

3kuzA

0.12

0.10

3.37

1.00

DEthreader

-----------------VVFNISVVLDCDTIGQAKEKIFQFLNGSPYG-LQLNEIGLELQMGTRQKELLDIDLNTIGHYEISNGSTIKVFKK--

4b6wA

0.15

0.13

4.32

1.23

SPARKS-K

-----SVVKVSLTHSASRRVPEKRYGLAQTIESIKENVFT-----HFATPPEYQL-QLIDDRGITIEKN-ANDKQLGYYQCRDEFVIHVVDLQP

1t0yA

0.09

0.07

2.80

0.74

MapAlign

--------------DLEITTNATKYPAGMSLNDLKKKLELV--V----GTTVDSMRIQLFDDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG

1t0yA

0.09

3.20

0.51

CEthreader

---MTEVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGT------TVDSMRIQLFGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG

2kanA

0.17

0.15

4.88

0.91

MUSTER

HHHHHSHAAVRKIHVTVKFPSKVEVDRTETVSSLKDKIHIV------NTP-IKRMQLYY------GIELADDYRNLNEYGITEFSEIVVFLKSI

1x1mA

0.21

0.18

5.74

0.77

HHsearch

-GSSG-SSGMSLSDWHLKLKSILQLPETESISFLKQLIAG-----KLQVPDPELIDLIY-----CGRKLKDDQ-TLDFYGIQPGSTVHVLRKSW

4melA2

0.16

0.12

3.87

0.65

FFAS-3D

----------------------VQFSHTDSIGLVLRTA-----RERFLVEPQEDTRLWAKNSEGSLDRLYDTHITVLDAALETGQLIIMETRKK

5fwiC2

0.12

4.11

0.78

EigenThreader

SGATLPKFDKDHKTRSLNYCGHIYTPISCKIRDLLPVMC---DRAGFIQDTS--LILYEEVKPNLTERIQDYDVSLDKALLMDGDIIVFQKDDP

(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	0.6485

(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	1t0yA	0.63	2.07	0.085	0.766	model1_1t0yA.pdb.gz
2	1v6eA	0.63	2.29	0.128	0.777	model1_1v6eA.pdb.gz
3	3ig3A	0.62	2.54	0.075	0.798	model1_3ig3A.pdb.gz
4	5v6rA	0.62	2.78	0.097	0.798	model1_5v6rA.pdb.gz
5	3kuzA	0.62	2.61	0.059	0.808	model1_3kuzA.pdb.gz
6	3hm6X1	0.62	2.78	0.125	0.808	model1_3hm6X1.pdb.gz
7	5e6pA1	0.61	2.66	0.090	0.787	model1_5e6pA1.pdb.gz
8	1v5oA	0.60	2.44	0.145	0.745	model1_1v5oA.pdb.gz
9	1wx8A	0.58	2.13	0.098	0.713	model1_1wx8A.pdb.gz
10	4e71A	0.58	2.41	0.090	0.723	model1_4e71A.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	0.39	catalytic activity
GO:0005198	0.36	structural molecule 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:0009987	0.85	cellular process
GO:0008152	0.79	metabolic process
GO:0044238	0.77	primary metabolic process
GO:0043170	0.77	macromolecule metabolic process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0019538	0.74	protein metabolic process
GO:0044267	0.69	cellular protein metabolic process
GO:0006464	0.68	cellular protein modification process
GO:0044699	0.67	single-organism process
GO:0006508	0.67	proteolysis
GO:0065007	0.66	biological regulation
GO:0050794	0.65	regulation of cellular process
GO:0044763	0.63	single-organism cellular process
GO:0006511	0.62	ubiquitin-dependent protein catabolic process
GO:0034641	0.60	cellular nitrogen compound metabolic process
GO:0016043	0.60	cellular component organization
GO:0006810	0.60	transport
GO:1902578	0.59	single-organism localization
GO:0090304	0.59	nucleic acid metabolic process
GO:0080090	0.59	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0048523	0.59	negative regulation of cellular process
GO:0048522	0.59	positive regulation of cellular process
GO:0044710	0.59	single-organism metabolic process
GO:0034654	0.59	nucleobase-containing compound biosynthetic process
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0007165	0.59	signal transduction
GO:1903047	0.58	mitotic cell cycle process
GO:1902531	0.58	regulation of intracellular signal transduction
GO:0055085	0.58	transmembrane transport
GO:0051726	0.58	regulation of cell cycle
GO:0048585	0.58	negative regulation of response to stimulus
GO:0046907	0.58	intracellular transport
GO:0045935	0.58	positive regulation of nucleobase-containing compound metabolic process
GO:0044707	0.58	single-multicellular organism process
GO:0043933	0.58	macromolecular complex subunit organization
GO:0043069	0.58	negative regulation of programmed cell death
GO:0042221	0.58	response to chemical
GO:0035556	0.58	intracellular signal transduction
GO:0033554	0.58	cellular response to stress
GO:0032269	0.58	negative regulation of cellular protein metabolic process
GO:0023056	0.58	positive regulation of signaling
GO:0022607	0.58	cellular component assembly
GO:0019221	0.58	cytokine-mediated signaling pathway
GO:0016032	0.58	viral process
GO:0010647	0.58	positive regulation of cell communication
GO:0010604	0.58	positive regulation of macromolecule metabolic process
GO:0008219	0.58	cell death
GO:0006996	0.58	organelle organization
GO:0006355	0.58	regulation of transcription, DNA-templated
GO:0002224	0.58	toll-like receptor signaling pathway
GO:2000060	0.57	positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:1904668	0.57	positive regulation of ubiquitin protein ligase activity
GO:1904667	0.57	negative regulation of ubiquitin protein ligase activity
GO:1903845	0.57	negative regulation of cellular response to transforming growth factor beta stimulus
GO:1902583	0.57	multi-organism intracellular transport
GO:1901186	0.57	positive regulation of ERBB signaling pathway
GO:1901185	0.57	negative regulation of ERBB signaling pathway
GO:0090305	0.57	nucleic acid phosphodiester bond hydrolysis
GO:0090175	0.57	regulation of establishment of planar polarity
GO:0090101	0.57	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0072431	0.57	signal transduction involved in mitotic G1 DNA damage checkpoint
GO:0071456	0.57	cellular response to hypoxia
GO:0071158	0.57	positive regulation of cell cycle arrest
GO:0070265	0.57	necrotic cell death
GO:0065004	0.57	protein-DNA complex assembly
GO:0060828	0.57	regulation of canonical Wnt signaling pathway
GO:0051606	0.57	detection of stimulus
GO:0051439	0.57	regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
GO:0051403	0.57	stress-activated MAPK cascade
GO:0051091	0.57	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0050851	0.57	antigen receptor-mediated signaling pathway
GO:0046794	0.57	transport of virus
GO:0045893	0.57	positive regulation of transcription, DNA-templated
GO:0045892	0.57	negative regulation of transcription, DNA-templated
GO:0044839	0.57	cell cycle G2/M phase transition
GO:0044344	0.57	cellular response to fibroblast growth factor stimulus
GO:0043618	0.57	regulation of transcription from RNA polymerase II promoter in response to stress
GO:0043487	0.57	regulation of RNA stability
GO:0043406	0.57	positive regulation of MAP kinase activity
GO:0043161	0.57	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043122	0.57	regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043068	0.57	positive regulation of programmed cell death
GO:0042981	0.57	regulation of apoptotic process
GO:0042058	0.57	regulation of epidermal growth factor receptor signaling pathway
GO:0038093	0.57	Fc receptor signaling pathway
GO:0035872	0.57	nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
GO:0035567	0.57	non-canonical Wnt signaling pathway
GO:0033209	0.57	tumor necrosis factor-mediated signaling pathway
GO:0032606	0.57	type I interferon production
GO:0032508	0.57	DNA duplex unwinding
GO:0032147	0.57	activation of protein kinase activity
GO:0030330	0.57	DNA damage response, signal transduction by p53 class mediator
GO:0030178	0.57	negative regulation of Wnt signaling pathway
GO:0030177	0.57	positive regulation of Wnt signaling pathway
GO:0017015	0.57	regulation of transforming growth factor beta receptor signaling pathway
GO:0009250	0.57	glucan biosynthetic process
GO:0007034	0.57	vacuolar transport
GO:0006914	0.57	autophagy
GO:0006811	0.57	ion transport
GO:0006301	0.57	postreplication repair
GO:0006289	0.57	nucleotide-excision repair
GO:0005977	0.57	glycogen metabolic process
GO:0002756	0.57	MyD88-independent toll-like receptor signaling pathway
GO:0002753	0.57	cytoplasmic pattern recognition receptor signaling pathway
GO:0002220	0.57	innate immune response activating cell surface receptor signaling pathway
GO:0001959	0.57	regulation of cytokine-mediated signaling pathway
GO:0001818	0.57	negative regulation of cytokine production
GO:0000731	0.57	DNA synthesis involved in DNA repair

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:0005634	1.00	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	0.066	2nptD	0.509	2.58	0.141	0.681	2.7.11.25	NA
2	0.060	2pi8B	0.488	3.77	0.059	0.862	4.2.2.-	60
3	0.060	1pov0	0.489	4.39	0.044	0.872	3.4.22.29	37
4	0.060	3eqlD	0.511	3.32	0.068	0.777	2.7.7.6	NA
5	0.060	2j0mA	0.504	3.48	0.049	0.766	2.7.10.2	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	0.04	2hd51	0.575	2.06	0.167	0.702	0.92	III	complex1.pdb.gz	19,21,41,56,59,66,68,70,80,82,83,84,85,86,88,89,90,91
2	0.03	1q0wB	0.556	2.28	0.178	0.713	0.85	III	complex2.pdb.gz	18,56,58,59,66,68,82,88,89,90,91
3	0.03	2ayo1	0.576	2.17	0.149	0.713	0.84	III	complex3.pdb.gz	54,56,58,66,67,68,84,88,90,91,92,93,94
4	0.03	2bkr1	0.572	2.18	0.149	0.713	0.79	III	complex4.pdb.gz	18,56,58,59,66,67,68,70,71,72,74,79,88,90,91,92,93
5	0.03	2c7n1	0.574	2.28	0.139	0.713	0.77	III	complex5.pdb.gz	18,56,58,59,66,68,83,84,86,88,90

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.