D-I-TASSER Q86VF2-D4

D-I-TASSER results for Q86VF2-D4

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

Input Sequence in FASTA format

>Q86VF2 (99 residues)
SPTIAPDVTEKLREPLVVKAGKPVIVKIPFQSHLPIQAAWRKDGAEVVGSSDREAQVDLG
DGYTRLCLPSAGRKDCGQYSVTLRSEGGSVQAELTLQVI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SPTIAPDVTEKLREPLVVKAGKPVIVKIPFQSHLPIQAAWRKDGAEVVGSSDREAQVDLGDGYTRLCLPSAGRKDCGQYSVTLRSEGGSVQAELTLQVI
Prediction	CCCCCCCCCCCCCCCSSSSCCCSSSSSSSSSSCCCCSSSSSSCCSSCCCCCCCSSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSCCCSSSSSSSSSSC
Confidence	997798755558997899479419999999943798899999999958889975999993995999988888122589999999799489999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SPTIAPDVTEKLREPLVVKAGKPVIVKIPFQSHLPIQAAWRKDGAEVVGSSDREAQVDLGDGYTRLCLPSAGRKDCGQYSVTLRSEGGSVQAELTLQVI
Prediction	746152713661575130434557526253544451534422464504567643140344753131335724462455645355463243405055458
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCSSSSCCCSSSSSSSSSSCCCCSSSSSSCCSSCCCCCCCSSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSCCCSSSSSSSSSSC
SPTIAPDVTEKLREPLVVKAGKPVIVKIPFQSHLPIQAAWRKDGAEVVGSSDREAQVDLGDGYTRLCLPSAGRKDCGQYSVTLRSEGGSVQAELTLQVI

3qp3A

0.21

0.20

6.42

1.50

DEthreader

FTDHAPRITLRM-RSHRVPCGQNTRFILNVQSKPTAEVKWYHNGVELQES--SKIHYTNTSGVLTLEILDCHTDDSGTYRAVCTNYKGEASDYATLDVT

2wwmD

0.21

6.72

1.23

SPARKS-K

SRGIPPKIE-ALPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIR

2wwmD

0.21

0.20

6.42

0.53

MapAlign

--GIPPKIEA-LPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIR

2wwmD

0.21

6.72

0.39

CEthreader

SRGIPPKIEA-LPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIR

2wwmD

0.21

6.72

1.19

MUSTER

SRGIPPKIEA-LPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIR

3b43A

0.17

0.16

5.32

0.40

HHsearch

-AMEPPYFIEP-LEHVEAAIGEPITLQCKVDGTPEIRIAWYKEHTKLRSAP--AYKMQFKNNVASLVINKVDHSDVGEYTCKAENSVGAVASSAVLVIK

1ya5A1

0.24

0.23

7.25

1.80

FFAS-3D

MTTQAPTFTQPL-QSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTSTLPGVQISFSDGRAKLTIPAVTKANSGRYSLKATNGSGQATSTAELLV-

2dm2A

0.20

0.19

6.16

0.33

EigenThreader

GSSGAPFFE-MKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKS-DHYTIQRDDGTCSLHTTASTLDDDGNYTIMAANPQGRISCTGRLMVQ

2nziA

0.23

0.22

6.96

1.63

CNFpred

---MAPHFKE-ELRNLNVRYQSNATLVCKVTGHPKPIVKWYRQGKEIIADGLKYRIQEFKGGYHQLIIASVTDDDATVYQVRATNQGGSVSGTASLEVE

3b43A

0.20

0.19

6.16

1.50

DEthreader

DVQEPPRFIKKLEPSRIVKQDEHTRYECKIGGSPEIKVLWYKDETEIQES--SKFRMSFVESVAVLEMYNLSVEDSGDYTCEAHNAAGSASSSTSLKVK

(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	0.9318

(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	2wwmD	0.94	0.83	0.214	0.990	model1_2wwmD.pdb.gz
2	3qp3A	0.93	0.83	0.219	0.970	model1_3qp3A.pdb.gz
3	1tlkA	0.92	0.94	0.208	0.970	model1_1tlkA.pdb.gz
4	6fwxB	0.91	1.11	0.240	0.970	model1_6fwxB.pdb.gz
5	3pucA	0.91	1.01	0.188	0.970	model1_3pucA.pdb.gz
6	1ya5A1	0.90	1.30	0.235	0.970	model1_1ya5A1.pdb.gz
7	3b43A4	0.90	0.93	0.202	0.950	model1_3b43A4.pdb.gz
8	2nziA	0.89	1.07	0.253	0.960	model1_2nziA.pdb.gz
9	3lcyA	0.89	1.25	0.186	0.980	model1_3lcyA.pdb.gz
10	2wwkO	0.89	1.07	0.221	0.960	model1_2wwkO.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:0005198	0.90	structural molecule activity
GO:0008307	0.87	structural constituent of muscle
GO:0008092	0.87	cytoskeletal protein binding
GO:0051371	0.83	muscle alpha-actinin binding
GO:1901363	0.78	heterocyclic compound binding
GO:0097159	0.78	organic cyclic compound binding
GO:0035639	0.76	purine ribonucleoside triphosphate binding
GO:0032555	0.76	purine ribonucleotide binding
GO:0032550	0.76	purine ribonucleoside binding
GO:0032403	0.75	protein complex binding
GO:0097493	0.74	structural molecule activity conferring elasticity
GO:0051015	0.74	actin filament binding
GO:0005524	0.74	ATP binding
GO:0003824	0.68	catalytic activity
GO:0043167	0.66	ion binding
GO:0046872	0.65	metal ion binding
GO:0016740	0.64	transferase activity
GO:0004674	0.63	protein serine/threonine kinase activity
GO:0005509	0.61	calcium ion binding
GO:0019899	0.59	enzyme binding
GO:0031433	0.57	telethonin binding
GO:0019901	0.57	protein kinase binding
GO:0043621	0.56	protein self-association
GO:0005516	0.56	calmodulin binding
GO:0002020	0.56	protease 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	0.95	cellular process
GO:0044699	0.93	single-organism process
GO:0044763	0.89	single-organism cellular process
GO:0032502	0.83	developmental process
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0008152	0.81	metabolic process
GO:0071704	0.80	organic substance metabolic process
GO:0044767	0.80	single-organism developmental process
GO:0044237	0.80	cellular metabolic process
GO:0044238	0.79	primary metabolic process
GO:0043170	0.78	macromolecule metabolic process
GO:0050794	0.77	regulation of cellular process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0016043	0.77	cellular component organization
GO:0006464	0.75	cellular protein modification process
GO:0006796	0.74	phosphate-containing compound metabolic process
GO:0048869	0.73	cellular developmental process
GO:0048856	0.73	anatomical structure development
GO:0006468	0.73	protein phosphorylation
GO:0032501	0.71	multicellular organismal process
GO:0018108	0.70	peptidyl-tyrosine phosphorylation
GO:0003008	0.68	system process
GO:0030029	0.67	actin filament-based process
GO:0007010	0.67	cytoskeleton organization
GO:0030036	0.66	actin cytoskeleton organization
GO:0050896	0.65	response to stimulus
GO:0048646	0.65	anatomical structure formation involved in morphogenesis
GO:0048468	0.65	cell development
GO:0022607	0.65	cellular component assembly
GO:0006928	0.65	movement of cell or subcellular component
GO:0003012	0.65	muscle system process
GO:0045214	0.64	sarcomere organization
GO:0006936	0.64	muscle contraction
GO:0006941	0.63	striated muscle contraction
GO:0019222	0.62	regulation of metabolic process
GO:0010927	0.62	cellular component assembly involved in morphogenesis
GO:0007015	0.62	actin filament organization
GO:0006461	0.62	protein complex assembly
GO:0080090	0.61	regulation of primary metabolic process
GO:0048739	0.61	cardiac muscle fiber development
GO:0031323	0.61	regulation of cellular metabolic process
GO:0031034	0.61	myosin filament assembly
GO:0030239	0.61	myofibril assembly
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0055003	0.60	cardiac myofibril assembly
GO:0042221	0.60	response to chemical
GO:0030241	0.60	skeletal muscle myosin thick filament assembly
GO:0030240	0.60	skeletal muscle thin filament assembly
GO:0051246	0.59	regulation of protein metabolic process
GO:0050790	0.59	regulation of catalytic activity
GO:0019220	0.59	regulation of phosphate metabolic process
GO:0009653	0.59	anatomical structure morphogenesis
GO:0006810	0.59	transport
GO:1902578	0.58	single-organism localization
GO:0001932	0.58	regulation of protein phosphorylation
GO:0045859	0.57	regulation of protein kinase activity
GO:0044765	0.57	single-organism transport
GO:0016192	0.57	vesicle-mediated transport
GO:0010035	0.57	response to inorganic substance
GO:0009628	0.57	response to abiotic stimulus
GO:0009605	0.57	response to external stimulus
GO:0060048	0.56	cardiac muscle contraction
GO:0050982	0.56	detection of mechanical stimulus
GO:0030049	0.56	muscle filament sliding
GO:0051592	0.55	response to calcium ion
GO:0048769	0.55	sarcomerogenesis
GO:0035995	0.55	detection of muscle stretch
GO:0007076	0.55	mitotic chromosome condensation
GO:0003300	0.55	cardiac muscle hypertrophy
GO:0002576	0.55	platelet degranulation
GO:0051239	0.50	regulation of multicellular organismal 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	0.90	intracellular part
GO:0044444	0.76	cytoplasmic part
GO:0044422	0.72	organelle part
GO:0044449	0.62	contractile fiber part
GO:0044446	0.50	intracellular organelle part
GO:0032991	0.48	macromolecular complex
GO:0043234	0.47	protein complex
GO:0030018	0.45	Z disc
GO:0044430	0.44	cytoskeletal part
GO:0043226	0.43	organelle
GO:0043229	0.38	intracellular organelle
GO:0005623	0.36	cell
GO:0016459	0.35	myosin complex
GO:0043227	0.33	membrane-bounded organelle
GO:0005859	0.32	muscle myosin complex
GO:0036379	0.31	myofilament

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	0.247	2bk8A	0.838	1.32	0.174	0.929	2.7.11.1	NA
2	0.242	2eo1A	0.784	2.22	0.217	0.919	2.7.11.1	43,80
3	0.209	2dm7A	0.773	1.80	0.144	0.909	2.7.11.1	80,95
4	0.171	2rq8A	0.651	2.75	0.161	0.879	2.7.11.1	18,80,96
5	0.094	1zvhA	0.741	2.64	0.140	0.929	3.2.1.17	12,97

	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	0.06	2j8o0	0.900	1.01	0.253	0.960	0.66	III	complex1.pdb.gz	13,18,19,22,23,27,60,61,63,65
2	0.05	1tlk0	0.924	0.94	0.208	0.970	0.93	III	complex2.pdb.gz	4,7,31,33,35,37,38,39,57,59,61
3	0.04	1epf0	0.792	2.41	0.191	0.939	0.51	III	complex3.pdb.gz	80,84,87,88,89,91
4	0.04	1p6a1	0.801	1.82	0.141	0.919	0.67	III	complex4.pdb.gz	37,39,45,82,84,85,86,87
5	0.03	2e7lC	0.750	2.69	0.140	0.929	0.52	III	complex5.pdb.gz	34,35,36,86,87

	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.