D-I-TASSER Q5VXM1-D2

D-I-TASSER results for Q5VXM1-D2

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

Input Sequence in FASTA format

>Q5VXM1 (111 residues)
VCGGVLTGLSGVLTSPEYPNNYPNSMECHWVIRAAGPAHVKLVFVDFQVEGNEECTYDYV
AVLGGPGPTRGHHYCGSTRPPTLVSLGHELQVVFKSDFNIGGRGFKAYYFS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VCGGVLTGLSGVLTSPEYPNNYPNSMECHWVIRAAGPAHVKLVFVDFQVEGNEECTYDYVAVLGGPGPTRGHHYCGSTRPPTLVSLGHELQVVFKSDFNIGGRGFKAYYFS
Prediction	CCCCSSSCCCSSSSCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSSSSSSCCCCCCCCSSSSSSCCCCCCCCSSSCCCCCCCCSSSCCCSSSSSSSSCCCCCCCCSSSSSSC
Confidence	979589588569979999857989982999999389968999997998258999887499998399996324765899998299819989999997998888857999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VCGGVLTGLSGVLTSPEYPNNYPNSMECHWVIRAAGPAHVKLVFVDFQVEGNEECTYDYVAVLGGPGPTRGHHYCGSTRPPTLVSLGHELQVVFKSDFNIGGRGFKAYYFS
Prediction	664441446514030132357245444030304047533030304304024465042020102216446332401244434413042443344531243354434404758
	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                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCSSSCCCSSSSCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSSSSSSCCCCCCCCSSSSSSCCCCCCCCSSSCCCCCCCCSSSCCCSSSSSSSSCCCCCCCCSSSSSSC
VCGGVLTGLSGVLTSPEYPNNYPNSMECHWVIRAAGPAHVKLVFVDFQVEGNEECTYDYVAVLGGPGPTRGHHYCGSTRPPTLVSLGHELQVVFKSDFNIGGRGFKAYYFS

3kq4B2

0.31

9.26

1.50

DEthreader

C-LQDYTDDLGTFTSPNFPNNYPNNWECIYRITVRTGQLIAVHFTNFSLEEAIGYYTDFLEIRDGGYSPLLGIFYGSNLPPTIISHSNKLWLKFKSDQIDTRSGFSAYWDG

2wnoA

0.32

9.51

2.21

SPARKS-K

ECGGVFTDPKQIFKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLEDDPGCLADYVEIYDSYDHGFVGRYCGDELPDDIISTGNVMTLKFLSDASVTAGGFQIKYVA

2qqmA

0.33

10.00

0.92

MapAlign

PCSQNYTTPSGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFDLEPDMFCRYDRLEIWDGDVGPHIGRYCGQKTPGRIRSSSGILSMVFYTDSAIAKEGFSANYSV

6v55A2

0.41

0.40

11.68

0.70

CEthreader

SCNVVLTDSQGSFTSPCYPNDYPPSQSCNWTIQAPAGFIVQITFLDFELEEAQGCIYDRVVVKTGT---SDAKFCGLTNGLTLNSTGNVMEVFFNSDFSVQKKGFHISYKQ

6fzvD1

0.37

10.97

2.11

MUSTER

LCGGDVKGESGYVASEGFPNLYPPNKECIWTITVPEGQTVSLSFRVFDLELHPACRYDALEVFAGSGTSRLGRFCGTFRPAPLVAPGNQVTLRMTTDEGTGGRGFLLWYSG

2qqmA

0.33

10.00

2.45

HHsearch

ECSQNYTTPSGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFDLEPDMFCRYDRLEIWDGFPDPHIGRYCGQKTPGRIRSSSGILSMVFYTDSAIAKEGFSANYSV

6fzvD1

0.36

10.73

1.89

FFAS-3D

LCGGDVKGESGYVASEGFPNLYPPNKECIWTITVPEGQTVSLSFRVFDLELHPACRYDALEVFAGSGTSGLGRFCGTFRPAPLVAPGNQVTLRMTTDEGTGGRGFLLWYSG

6fzvD2

0.37

10.97

0.98

EigenThreader

FCGGRLEKAQGTLTTPNWPSDYPPGISCSWHIIAPPDQVIALTFEKFDLEPDTYCRYDSVSVFNGAVSDRLGKFCGDAVPGSISSEGNELLVQFVSDLSVTADGFSASYKT

2wnoA

0.32

9.51

1.95

CNFpred

ECGGVFTDPKQIFKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLEDDPGCLADYVEIYDSYDHGFVGRYCGDELPDDIISTGNVMTLKFLSDASVTAGGFQIKYVA

2wnoA

0.32

9.51

1.50

DEthreader

ECGGVFTDPKQIFKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLEDDPGCLADYVEIYDSYDHGFVGRYCGDELPDDIISTGNVMTLKFLSDASVTAGGFQIKYVM

(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	0.9664

(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	2wnoA	0.96	0.82	0.315	1.000	model1_2wnoA.pdb.gz
2	6fzvD	0.96	0.86	0.369	1.000	model1_6fzvD.pdb.gz
3	3kq4B	0.94	1.15	0.315	1.000	model1_3kq4B.pdb.gz
4	6gh8A	0.94	1.00	0.345	0.991	model1_6gh8A.pdb.gz
5	2qqmA	0.94	1.22	0.333	1.000	model1_2qqmA.pdb.gz
6	4gzaH	0.93	1.18	0.364	0.991	model1_4gzaH.pdb.gz
7	2qqoA	0.93	1.07	0.294	0.982	model1_2qqoA.pdb.gz
8	3demA2	0.92	1.12	0.330	0.982	model1_3demA2.pdb.gz
9	4losA1	0.91	1.31	0.284	0.982	model1_4losA1.pdb.gz
10	4lmfA1	0.87	1.30	0.340	0.928	model1_4lmfA1.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	0.77	catalytic activity
GO:0016787	0.71	hydrolase activity
GO:0008233	0.70	peptidase activity
GO:0070011	0.69	peptidase activity, acting on L-amino acid peptides
GO:0043169	0.63	cation binding
GO:0046872	0.61	metal ion binding
GO:0008236	0.61	serine-type peptidase activity
GO:0004872	0.61	receptor activity
GO:0004175	0.61	endopeptidase activity
GO:0004888	0.60	transmembrane signaling receptor activity
GO:0004252	0.60	serine-type endopeptidase activity
GO:0016740	0.57	transferase activity
GO:0097367	0.56	carbohydrate derivative binding
GO:1901681	0.55	sulfur compound binding
GO:0005509	0.55	calcium ion binding
GO:0017154	0.54	semaphorin receptor activity
GO:0008201	0.54	heparin binding
GO:0005021	0.54	vascular endothelial growth factor-activated receptor activity
GO:1901363	0.50	heterocyclic compound binding
GO:0097159	0.50	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:0009987	0.96	cellular process
GO:0044699	0.92	single-organism process
GO:0044238	0.90	primary metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:0065007	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.82	regulation of cellular process
GO:0044763	0.80	single-organism cellular process
GO:0019538	0.77	protein metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0032502	0.70	developmental process
GO:0044767	0.69	single-organism developmental process
GO:0007165	0.69	signal transduction
GO:0006508	0.67	proteolysis
GO:0007166	0.66	cell surface receptor signaling pathway
GO:0048856	0.65	anatomical structure development
GO:0007167	0.64	enzyme linked receptor protein signaling pathway
GO:0048518	0.63	positive regulation of biological process
GO:0048583	0.62	regulation of response to stimulus
GO:0006928	0.60	movement of cell or subcellular component
GO:0048522	0.59	positive regulation of cellular process
GO:0007169	0.59	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0007155	0.58	cell adhesion
GO:0097485	0.56	neuron projection guidance
GO:0060255	0.56	regulation of macromolecule metabolic process
GO:0048513	0.56	animal organ development
GO:0009888	0.55	tissue development
GO:0080090	0.54	regulation of primary metabolic process
GO:0048589	0.54	developmental growth
GO:0031323	0.54	regulation of cellular metabolic process
GO:0097491	0.53	sympathetic neuron projection guidance
GO:0097490	0.53	sympathetic neuron projection extension
GO:0061549	0.53	sympathetic ganglion development
GO:0048584	0.53	positive regulation of response to stimulus
GO:0048010	0.53	vascular endothelial growth factor receptor signaling pathway
GO:0023051	0.53	regulation of signaling
GO:0010646	0.53	regulation of cell communication
GO:0009966	0.52	regulation of signal transduction
GO:0031325	0.51	positive regulation of cellular metabolic process

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	0.94	cell part
GO:0044424	0.81	intracellular part
GO:0043227	0.73	membrane-bounded organelle
GO:0005576	0.71	extracellular region
GO:0044421	0.68	extracellular region part
GO:0043229	0.59	intracellular organelle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0016020	0.56	membrane
GO:0005615	0.52	extracellular space

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	2i74A	0.660	3.55	0.057	0.955	3.5.1.52	NA
2	0.060	1pov0	0.569	3.49	0.069	0.856	3.4.22.29	72
3	0.060	1nt0A	0.865	1.31	0.356	0.937	3.4.21.104	16,18,58,75
4	0.060	2jenA	0.576	3.66	0.019	0.892	3.2.1.4	NA
5	0.060	1nlrA	0.576	3.56	0.038	0.892	3.2.1.4	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	0.12	3kq4B	0.940	1.15	0.315	1.000	0.73	CA	complex1.pdb.gz	58,100,101,102,103
2	0.12	1nziA	0.840	1.37	0.327	0.910	0.98	MG	complex2.pdb.gz	50,58,97
3	0.07	3pobA	0.909	1.25	0.330	0.982	0.68	III	complex3.pdb.gz	50,52,57
4	0.06	1nzi0	0.840	1.37	0.327	0.910	0.74	III	complex4.pdb.gz	9,10,18,19,38,43,46,108
5	0.04	1spp1	0.779	2.00	0.149	0.910	0.89	III	complex5.pdb.gz	41,42,43,45,82,104,105,106,108

	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.