D-I-TASSER Q86YV6-D2

D-I-TASSER results for Q86YV6-D2

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

Input Sequence in FASTA format

>Q86YV6 (206 residues)
VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQ
IKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSP
FLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLS
DHKLHSRLNAQKKKNRGSDAQDFVTK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLNAQKKKNRGSDAQDFVTK
Prediction	CCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCSCCCCCHHHSSSCCCCCCCSSSSSCCCCSSSCCCCSSSSSCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence	97246799999819974999999999999999999998194446788355431589999758960587427149944775157902048556369999935657899999999714999999999899999999451237986556589899999999667995569689999719163889754212289999999999998609
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLNAQKKKNRGSDAQDFVTK
Prediction	87424001201657350305202400210030041017340000002010000324883400000000033156764031201112000000146662435020000000000100420043264354015204615151566406601640240044004432741220520061130465634652445344542550462268
	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                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCSCCCCCHHHSSSCCCCCCCSSSSSCCCCSSSCCCCSSSSSCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLNAQKKKNRGSDAQDFVTK

3hx4A

0.36

10.69

1.50

DEthreader

YTGGELFDEIIS-RKRFSEVDAARIIRQVLSGITYMHKNKIVHRDLKPENLLLESKSDANIRIIDFGLSTHFEASKKMKDKIGTAYYIAPEVLHGT-YDEKCDVWSTGVILYILLSGCPPFNGANEYDILKKVEKGKYTFELPQWKKVSESAKDLIRKMLTYVPSMRISARDALDHEWIQTYTKEQISVDQDTKELTAMDKTLLSR

2x4fA2

0.99

0.90

25.29

1.91

SPARKS-K

----ELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLSAQ---------------

3q5iA

0.35

0.34

10.16

0.42

MapAlign

YEGGELFEQIINR-HKFDECDAANIMKQILSGICYLHKHNIVHRDIKPENILLENKNSLNIKIVDFGLSSFFSKDYKLRDRLGTAYYIAPEVLKK-KYNEKCDVWSCGVIMYILLCGYPPFGGQNDQDIIKKVEKGKYYFDFNDWKNISDEAKELIKLMLTYDYNKRCTAEEALNSRWIKKYQKLAQAAILFIGSKLTTLEERK--

3q5iA

0.35

10.43

0.26

CEthreader

YEGGELFEQIINRH-KFDECDAANIMKQILSGICYLHKHNIVHRDIKPENILLENKNSLNIKIVDFGLSSFFSKDYKLRDRLGTAYYIAPEVLKK-KYNEKCDVWSCGVIMYILLCGYPPFGGQNDQDIIKKVEKGKYYFDFNDWKNISDEAKELIKLMLTYDYNKRCTAEEALNSRWIKKYANNINKSDQKTLCGALSNMRKFEG

2x4fA2

0.99

0.90

25.29

1.78

MUSTER

----ELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLSAQ---------------

6ygnA

0.39

0.38

11.20

0.73

HHsearch

ISGLDIFERINTSAFELNEREIVSYVHQVCEALQFLHSHNIGHFDIRPENIIYQTRRSSTIKIIEFGQARQLKPGDNFRLLFTAPEYYAPEVHQHDVVSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTFDEEAFKEISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQKIERVST----KVIRTLKHRRYYTL

2x4fA2

0.99

0.90

25.29

2.87

FFAS-3D

----ELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLSAQ---------------

3hx4A

0.36

0.35

10.56

0.63

EigenThreader

YTGGELFDEIIS-RKRFSEVDAARIIRQVLSGITYMHKNKIVHRDLKPENLLLESKSKDNIRIIDFGLSTHFEASKKMKDKIGTAYYIAPEVLHG-TYDEKCDVWSTGVILYILLSGCPPFNGANEYDILKKVEKGKYTFELPQWKKVSESAKDLIRKMLTYVPSMRISARDALDHEWIQTYTKEQNAILNIRQFQGTQKLAQAAL

2x4fA

0.99

0.92

25.83

2.46

CNFpred

VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLSAQ---------------

3lijA

0.34

10.17

1.50

DEthreader

YKGGELFDEIIHRM-KFNEVDAAVIIKQVLSGVTYLHKHNIVHRDLKPENLLLESKEDALIKIVDFGLSAVFENQKKMKERLGTAYYIAPEVLRKK-YDEKCDVWSIGVILFILLAGYPPFGGQTDQEILRKVEKGKYTFDSPEWKNVSEGAKDLIKQMLQFDSQRRISAQQALEHPWIKECSKKESLPSKELTDAMDRKSLLSKD

(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	0.8968

(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	3hx4A	0.87	1.25	0.353	0.898	model1_3hx4A.pdb.gz
2	3lijA	0.87	1.54	0.338	0.908	model1_3lijA.pdb.gz
3	3q5iA	0.87	1.14	0.343	0.893	model1_3q5iA.pdb.gz
4	2owbA	0.85	1.94	0.278	0.922	model1_2owbA.pdb.gz
5	2acxA	0.84	1.93	0.283	0.913	model1_2acxA.pdb.gz
6	4b6lA	0.84	2.01	0.289	0.922	model1_4b6lA.pdb.gz
7	4tnbA1	0.84	1.90	0.277	0.913	model1_4tnbA1.pdb.gz
8	4yhjA	0.84	2.52	0.279	0.942	model1_4yhjA.pdb.gz
9	3comB	0.84	2.21	0.238	0.937	model1_3comB.pdb.gz
10	1yhwA	0.84	2.16	0.259	0.927	model1_1yhwA.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	0.98	catalytic activity
GO:0004672	0.97	protein kinase activity
GO:0004674	0.90	protein serine/threonine kinase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0035639	0.72	purine ribonucleoside triphosphate binding
GO:0032555	0.72	purine ribonucleotide binding
GO:0032550	0.72	purine ribonucleoside binding
GO:0005524	0.71	ATP binding
GO:0005516	0.69	calmodulin binding
GO:0042802	0.60	identical protein binding
GO:0005525	0.59	GTP binding
GO:0017075	0.58	syntaxin-1 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	0.98	cellular process
GO:0044260	0.95	cellular macromolecule metabolic process
GO:0044238	0.95	primary metabolic process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0006468	0.90	protein phosphorylation
GO:0007165	0.84	signal transduction
GO:0035556	0.79	intracellular signal transduction
GO:0050896	0.69	response to stimulus
GO:0048518	0.69	positive regulation of biological process
GO:0046777	0.68	protein autophosphorylation
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0048522	0.67	positive regulation of cellular process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0048583	0.65	regulation of response to stimulus
GO:2000112	0.64	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.64	regulation of nitrogen compound metabolic process
GO:0048523	0.64	negative regulation of cellular process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0010646	0.64	regulation of cell communication
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0010468	0.64	regulation of gene expression
GO:0009966	0.63	regulation of signal transduction
GO:0065009	0.62	regulation of molecular function
GO:0051716	0.62	cellular response to stimulus
GO:0042981	0.62	regulation of apoptotic process
GO:0042221	0.62	response to chemical
GO:0032879	0.62	regulation of localization
GO:0032268	0.62	regulation of cellular protein metabolic process
GO:0051049	0.61	regulation of transport
GO:0050790	0.61	regulation of catalytic activity
GO:0044093	0.61	positive regulation of molecular function
GO:0032270	0.61	positive regulation of cellular protein metabolic process
GO:0010033	0.61	response to organic substance
GO:0071310	0.60	cellular response to organic substance
GO:0043085	0.60	positive regulation of catalytic activity
GO:0043066	0.60	negative regulation of apoptotic process
GO:0043065	0.60	positive regulation of apoptotic process
GO:0031324	0.60	negative regulation of cellular metabolic process
GO:0010605	0.60	negative regulation of macromolecule metabolic process
GO:0009968	0.60	negative regulation of signal transduction
GO:2001233	0.59	regulation of apoptotic signaling pathway
GO:2000113	0.59	negative regulation of cellular macromolecule biosynthetic process
GO:0071345	0.59	cellular response to cytokine stimulus
GO:0052547	0.59	regulation of peptidase activity
GO:0051345	0.59	positive regulation of hydrolase activity
GO:0051172	0.59	negative regulation of nitrogen compound metabolic process
GO:0045862	0.59	positive regulation of proteolysis
GO:0032412	0.59	regulation of ion transmembrane transporter activity
GO:0032269	0.59	negative regulation of cellular protein metabolic process
GO:0010629	0.59	negative regulation of gene expression
GO:0010506	0.59	regulation of autophagy
GO:0006417	0.59	regulation of translation
GO:2000310	0.58	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1902042	0.58	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:0071346	0.58	cellular response to interferon-gamma
GO:0043280	0.58	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0017148	0.58	negative regulation of translation
GO:0044699	0.55	single-organism process
GO:1901576	0.53	organic substance biosynthetic process
GO:0034645	0.52	cellular macromolecule biosynthetic 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	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0043226	0.77	organelle
GO:0043229	0.76	intracellular organelle
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005634	0.70	nucleus
GO:0005737	0.59	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	0.406	3is5F	0.770	2.15	0.353	0.830	2.7.11.17	45,47,49,50,84
2	0.388	3d5uA	0.847	2.01	0.277	0.922	2.7.11.21	45,47,50
3	0.385	2biyA	0.829	1.77	0.274	0.893	2.7.11.1	45,47,49,50,84
4	0.380	3a62A	0.777	2.37	0.320	0.864	2.7.11.1	45,47,49,50,84
5	0.339	2iwiB	0.753	1.55	0.287	0.811	2.7.11.1	45,47,49,50

	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	0.30	2phkA	0.826	1.28	0.369	0.864	1.01	III	complex1.pdb.gz	5,7,47,68,80,81,82,83,84,85,86
2	0.30	3hx4A	0.872	1.25	0.353	0.898	0.92	CA	complex2.pdb.gz	45,65,67,83
3	0.28	2phkA	0.826	1.28	0.369	0.864	0.72	ATP	complex3.pdb.gz	2,5,47,49,50,52,65
4	0.08	2q0nA	0.840	2.09	0.229	0.922	1.09	III	complex4.pdb.gz	7,45,47,48,49,68,80,81,82,83,84,86,87,88,113,118,122,124,125,126,130

	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.