D-I-TASSER Q86VF2-D3

D-I-TASSER results for Q86VF2-D3

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

Input Sequence in FASTA format

>Q86VF2 (94 residues)
INTISSLRHIRVTKDGNAKFDLELDLKDSQSKIYLYKDGEMIPYGFNNQTKHCLRRLGKR
YEFQIQDLRPEDSGIYQVKVEDAVVFSTELEASA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| INTISSLRHIRVTKDGNAKFDLELDLKDSQSKIYLYKDGEMIPYGFNNQTKHCLRRLGKRYEFQIQDLRPEDSGIYQVKVEDAVVFSTELEASA
Prediction	CCCCCCCCCSSSCCCCSSSSSSSSSCCCCCCCSSSSSCCSSSCCCCCCCCSSSSSSSCCSSSSSSCCCCCCCCSSSSSSSCCCSSSSSSSSSCC
Confidence	9533466226975994099999997479998369986999941568997317889969899999926992305389999848367757874179
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| INTISSLRHIRVTKDGNAKFDLELDLKDSQSKIYLYKDGEMIPYGFNNQTKHCLRRLGKRYEFQIQDLRPEDSGIYQVKVEDAVVFSTELEASA
Prediction	5642572551615773303040305374473413022445314353676432404533540303045254733230304155441233516368
	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

CCCCCCCCCSSSCCCCSSSSSSSSSCCCCCCCSSSSSCCSSSCCCCCCCCSSSSSSSCCSSSSSSCCCCCCCCSSSSSSSCCCSSSSSSSSSCC
INTISSLRHIRVTKDGNAKFDLELDLKDSQSKIYLYKDGEMIPYGFNNQTKHCLRRLGKRYEFQIQDLRPEDSGIYQVKVEDAVVFSTELEASA

3qp3A

0.19

0.18

5.83

1.50

DEthreader

PRITLRMRSHRVPCGQNTRFILNVQSKP-TAEVKWYHNGVELQ-E-S--SKIHYTNTSGVLTLEILDCHTDDSGTYRAVCTGEASDYATLDVTG

7ahsA1

0.20

0.19

6.11

1.09

SPARKS-K

VTLIKDIENQTVLKDNDAVFEIDIKINYPEIKLSWYKGTEKL----EPSDKFEISIDGDRHTLRVKNCQLKDQGNYRLVCGP-HIASAKLTVI-

6on6A

0.13

4.44

0.39

MapAlign

PTIQPSMSSAVALLGQDVDFTCIVND-LGSHMVAFVKADRLLEKVFRRRNKYELKIGHNEWVLTIKNVQESDRGNYSCQINPITLSTGELDVKV

1g1cA

0.19

0.18

5.83

0.30

CEthreader

PKIFERIQSQTVGQGSDAHFRVRVVG-KPDPECEWYKNGVKIER----SDRIYWYWPDNVCELVIRDVTGEDSASIMVKAINETSSHAFLLVQA

5joeA

0.20

0.19

6.12

1.13

MUSTER

VTLIKDIENQTVLKDNDAVFEIDIKINYPEIKLSWYKGTEKL----EPSDKFEISIDGDRHTLRVKNCQLKDQGNYRLVCGP-HIASAKLTVIE

2jtdA

0.19

0.18

5.82

0.41

HHsearch

VPTKSELA-VEILEKGQVRFWMQAEKLSSNAKVSYIFNEKEIFE----GPKYKMHIDRGIIEMFMEKLQDEDEGTYTFQIQDGKA-TGTLVLIG

5joeA

0.21

0.19

6.10

1.66

FFAS-3D

-TLIKDIENQTVLKDNDAVFEIDIKINYPEIKLSWYKGTEKLEPSD----KFEISIDGDRHTLRVKNCQLKDQGNYRLVCGPHIA-SAKLTVI-

2edkA

0.19

0.18

5.85

0.32

EigenThreader

VLIVTPLEDQQVFVGDRVEMAVEVSEE--GAQVMWMKNGVELTREDSFKARYRFKKDGKRHILIFSDVVQEDRGRYQVITNGG-QCEAELIVEK

5joeA

0.20

0.19

6.12

1.56

CNFpred

VTLIKDIENQTVLKDNDAVFEIDIKINYPEIKLSWYKGTEKLEP----SDKFEISIDGDRHTLRVKNCQLKDQGNYRLVCGP-HIASAKLTVIE

3b43A

0.12

4.11

1.50

DEthreader

PFFDLKPVSVDLALGESGTFKCHVTG-TAPIKITWAKDNREIR-P-G--GNYKMTLVENTATLTVLKVTKGDAGQYTCYASGKDSCSAQLGVQE

(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	0.9117

(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	3qp3A	0.90	0.83	0.191	0.947	model1_3qp3A.pdb.gz
2	1tlkA	0.90	0.88	0.135	0.947	model1_1tlkA.pdb.gz
3	3b43A	0.89	0.94	0.124	0.947	model1_3b43A.pdb.gz
4	6fwxB2	0.89	1.35	0.176	0.968	model1_6fwxB2.pdb.gz
5	1ya5A	0.89	1.43	0.176	0.968	model1_1ya5A.pdb.gz
6	3pxjA1	0.88	1.15	0.189	0.957	model1_3pxjA1.pdb.gz
7	2wwkO	0.88	1.03	0.124	0.947	model1_2wwkO.pdb.gz
8	6on6A	0.88	1.60	0.129	0.989	model1_6on6A.pdb.gz
9	3pucA	0.88	1.02	0.247	0.947	model1_3pucA.pdb.gz
10	2nziA	0.88	1.18	0.189	0.957	model1_2nziA.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:0008307	0.91	structural constituent of muscle
GO:1901363	0.85	heterocyclic compound binding
GO:0097159	0.85	organic cyclic compound binding
GO:0035639	0.83	purine ribonucleoside triphosphate binding
GO:0032555	0.83	purine ribonucleotide binding
GO:0032550	0.83	purine ribonucleoside binding
GO:0005524	0.82	ATP binding
GO:0003824	0.82	catalytic activity
GO:0016740	0.80	transferase activity
GO:0005516	0.79	calmodulin binding
GO:0004674	0.79	protein serine/threonine kinase activity
GO:0008092	0.74	cytoskeletal protein binding
GO:0097493	0.72	structural molecule activity conferring elasticity
GO:0051371	0.72	muscle alpha-actinin binding
GO:0051015	0.72	actin filament binding
GO:0046872	0.65	metal ion binding
GO:0005509	0.60	calcium ion binding
GO:0019899	0.57	enzyme binding
GO:0042802	0.56	identical protein binding
GO:0031433	0.56	telethonin binding
GO:0019901	0.56	protein kinase binding
GO:0043621	0.55	protein self-association
GO:0004713	0.55	protein tyrosine kinase activity
GO:0002020	0.55	protease binding
GO:0098772	0.53	molecular function regulator
GO:0031432	0.52	titin binding
GO:0030506	0.52	ankyrin binding
GO:0005089	0.52	Rho guanyl-nucleotide exchange factor 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:0044699	0.98	single-organism process
GO:0009987	0.98	cellular process
GO:0044763	0.97	single-organism cellular process
GO:0016043	0.92	cellular component organization
GO:0006996	0.90	organelle organization
GO:0031032	0.89	actomyosin structure organization
GO:0045214	0.88	sarcomere organization
GO:0032502	0.87	developmental process
GO:0044767	0.85	single-organism developmental process
GO:0032501	0.80	multicellular organismal process
GO:0065007	0.79	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0006928	0.78	movement of cell or subcellular component
GO:0003008	0.78	system process
GO:0022607	0.77	cellular component assembly
GO:0048646	0.76	anatomical structure formation involved in morphogenesis
GO:0006936	0.76	muscle contraction
GO:0050794	0.75	regulation of cellular process
GO:0010927	0.74	cellular component assembly involved in morphogenesis
GO:0007015	0.73	actin filament organization
GO:0006941	0.73	striated muscle contraction
GO:0006461	0.73	protein complex assembly
GO:0071688	0.72	striated muscle myosin thick filament assembly
GO:0048856	0.71	anatomical structure development
GO:0008152	0.71	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0030049	0.70	muscle filament sliding
GO:0044238	0.68	primary metabolic process
GO:0048869	0.66	cellular developmental process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0009653	0.64	anatomical structure morphogenesis
GO:0050896	0.63	response to stimulus
GO:0048518	0.63	positive regulation of biological process
GO:0048468	0.63	cell development
GO:0055002	0.62	striated muscle cell development
GO:0048522	0.62	positive regulation of cellular process
GO:0006464	0.62	cellular protein modification process
GO:0048747	0.61	muscle fiber development
GO:0048729	0.61	tissue morphogenesis
GO:0030239	0.61	myofibril assembly
GO:0019222	0.61	regulation of metabolic process
GO:0006796	0.61	phosphate-containing compound metabolic process
GO:0080090	0.60	regulation of primary metabolic process
GO:0055008	0.60	cardiac muscle tissue morphogenesis
GO:0048739	0.60	cardiac muscle fiber development
GO:0042221	0.60	response to chemical
GO:0031323	0.60	regulation of cellular metabolic process
GO:0006468	0.60	protein phosphorylation
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0055003	0.59	cardiac myofibril assembly
GO:0051179	0.59	localization
GO:0048583	0.59	regulation of response to stimulus
GO:0030241	0.59	skeletal muscle myosin thick filament assembly
GO:0030240	0.59	skeletal muscle thin filament assembly
GO:0050790	0.58	regulation of catalytic activity
GO:1902578	0.57	single-organism localization
GO:0060048	0.57	cardiac muscle contraction
GO:0010035	0.57	response to inorganic substance
GO:0006810	0.57	transport
GO:0001932	0.57	regulation of protein phosphorylation
GO:0051592	0.56	response to calcium ion
GO:0048769	0.56	sarcomerogenesis
GO:0045859	0.56	regulation of protein kinase activity
GO:0044765	0.56	single-organism transport
GO:0035995	0.56	detection of muscle stretch
GO:0018193	0.56	peptidyl-amino acid modification
GO:0016192	0.56	vesicle-mediated transport
GO:0009966	0.56	regulation of signal transduction
GO:0007076	0.56	mitotic chromosome condensation
GO:0003300	0.56	cardiac muscle hypertrophy
GO:0018108	0.55	peptidyl-tyrosine phosphorylation
GO:0002576	0.55	platelet degranulation
GO:1902531	0.54	regulation of intracellular signal transduction
GO:0051641	0.54	cellular localization
GO:0043085	0.54	positive regulation of catalytic activity
GO:0022411	0.54	cellular component disassembly
GO:0010941	0.54	regulation of cell death
GO:0008104	0.54	protein localization
GO:0098779	0.53	mitophagy in response to mitochondrial depolarization
GO:0051345	0.53	positive regulation of hydrolase activity
GO:0042981	0.53	regulation of apoptotic process
GO:0035023	0.53	regulation of Rho protein signal transduction
GO:0034613	0.53	cellular protein localization
GO:0043547	0.52	positive regulation of GTPase activity
GO:0043065	0.52	positive regulation of apoptotic process
GO:0036309	0.52	protein localization to M-band

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:0030018	1.00	Z disc
GO:0043226	0.82	organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005634	0.78	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	0.345	2bk8A	0.847	1.40	0.157	0.947	2.7.11.1	36,39,79,89
2	0.273	2edtA	0.802	1.47	0.256	0.915	2.7.11.1	40,80,87
3	0.273	2edwA	0.822	1.30	0.221	0.915	2.7.11.1	40,62,64,72,87
4	0.255	2eo1A	0.816	1.63	0.172	0.925	2.7.11.1	36,38,87
5	0.240	2edhA	0.839	1.18	0.291	0.915	2.7.11.1	52,62,87

	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	2j8o0	0.880	1.18	0.189	0.957	0.45	III	complex1.pdb.gz	8,12,13,16,17,21,60,62
2	0.04	1ktrH	0.833	1.88	0.151	0.989	0.79	III	complex2.pdb.gz	36,38,75,78,87
3	0.04	3hujG	0.841	1.70	0.144	0.957	0.46	AGH	complex3.pdb.gz	24,59,60,61
4	0.03	1zeaH	0.830	1.96	0.129	0.989	0.40	III	complex4.pdb.gz	35,36,37,74,76,77

	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.