D-I-TASSER Q2V2M9-D2

D-I-TASSER results for Q2V2M9-D2

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

Input Sequence in FASTA format

>Q2V2M9 (116 residues)
GSKFRLVVKTALKLLLVFVEKKTIRLFWNEVRPFDWPCKNNRRCREFLWSKLEPIKVDTS
RLEHLFESKSKELSVSKKTAADGKRQEIDQLENNKTLGFILSTLLAIGNFLNGTNA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GSKFRLVVKTALKLLLVFVEKKTIRLFWNEVRPFDWPCKNNRRCREFLWSKLEPIKVDTSRLEHLFESKSKELSVSKKTAADGKRQEIDQLENNKTLGFILSTLLAIGNFLNGTNA
Prediction	CCCSSSSHHHHHHHCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHCCCCSSSSCCCCCSSSSSSSCCCCCCCCCCCCCC
Confidence	98423314567653021246506874101222457875555567774122477764388999999997524365303333316773367525874565765315430110257789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GSKFRLVVKTALKLLLVFVEKKTIRLFWNEVRPFDWPCKNNRRCREFLWSKLEPIKVDTSRLEHLFESKSKELSVSKKTAADGKRQEIDQLENNKTLGFILSTLLAIGNFLNGTNA
Prediction	85413310430452233445431030103304547344455544451016516517233730441244336635355554577355304214453202000332333242254568
	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

CCCSSSSHHHHHHHCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHCCCCSSSSCCCCCSSSSSSSCCCCCCCCCCCCCC
GSKFRLVVKTALKLLLVFVEKKTIRLFWNEVRPFDWPCKNNRRCREFLWSKLEPIKVDTSRLEHLFESKSKELSVSKKTAADGKRQEIDQLENNKTLGFILSTLLAIGNFLNGTNA

3pqsA1

0.09

3.33

0.48

CEthreader

VYYKGVHPSKELPKGNIIVYQGEWDFTSNADLDAKRPNYNPEFNGYGAGQRVGVTSADAKERTYISKFNIDNGQLLTKTKENQEKLRYTVEANISGNRFRGKATATDKTDPILGKD

6yacA1

0.07

2.86

0.53

EigenThreader

TWIWNLHADAHEISRKVFSAHFGQLSIYFHGARFSNYEAWLNDPSAQLYCTAIGALVFAALMLFAGWFHYHKLVWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAG

2z6eB

0.13

0.09

2.97

0.50

FFAS-3D

-----------KKKSIPQPTNALKSFNWSKLP--------ENKLEGTVWTEIDDTKLDLEDLERTFSAYQRQ--------QDFFVKELSVIDGRRAQNCNIL--------------

2z6eB

0.14

0.11

3.84

0.92

SPARKS-K

------MGLALKKKSIPQPTNALKSFNW--------SKLPENKLEGTVWTEIDDTILDLEDLERTFSAYQRQQ--------DFFVKELSVIDGRRACNILLSRLLSNDEIKREQED

2z6eA

0.13

0.08

2.69

0.73

CNFpred

---------------IPQPTNALKSFNWSKLPEN--------KLEGTVWTEIDDTKLDLEDLERTFSAYQRQ-----------KVKELSVIDGRRAQNCNILL-------------

3o8oB

0.05

0.04

2.00

0.83

DEthreader

IAVMTSGCGGGSIDAALRIAIDSRGGSITGASLLERARESYPAFRI--MV---------------DTALN-ALMEYCDVKFAKPAYPGVQQGGLPSDR-RATRMAKAVGFINTAAV

1vt4I3

0.04

2.16

0.76

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3hgfC

0.15

0.11

3.77

0.67

MUSTER

--------------------KKIENI----VTKIDKKKYIYKKLLNEI-AEIEKDKTSLEEVKNINMSYGKSLNKLFLEKIKKKSENMI-----KSMEKYIKDLDEIKEQSPKAEM

2z6eB

0.13

0.10

3.60

3.00

HHsearch

------MGLALKKKSIPQPTNALKSFNWSKLPENK--------LEGTVWTEIDDTILDLEDLERTFSAYQRQQD--------FFVKELSVIDGRRAQNILLSRLKSNDAILTMDED

1vt4I3

0.04

2.16

0.46

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

(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	0.513

(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	1o70A2	0.49	4.37	0.094	0.819	model1_1o70A2.pdb.gz
2	5tpwB	0.47	4.58	0.019	0.819	model1_5tpwB.pdb.gz
3	5mrwB	0.46	4.39	0.043	0.793	model1_5mrwB.pdb.gz
4	5oklA	0.46	4.39	0.029	0.776	model1_5oklA.pdb.gz
5	3jpwA	0.46	4.64	0.000	0.802	model1_3jpwA.pdb.gz
6	5koeA	0.45	4.77	0.035	0.828	model1_5koeA.pdb.gz
7	3e2tA	0.45	4.45	0.042	0.784	model1_3e2tA.pdb.gz
8	2phmA	0.45	4.79	0.052	0.802	model1_2phmA.pdb.gz
9	3q41A	0.45	4.78	0.101	0.793	model1_3q41A.pdb.gz
10	2tohA	0.44	4.79	0.032	0.819	model1_2tohA.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:0003779	0.74	actin 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:0044763	0.89	single-organism cellular process
GO:0044087	0.79	regulation of cellular component biogenesis
GO:0032956	0.79	regulation of actin cytoskeleton organization
GO:0044767	0.74	single-organism developmental process
GO:0065008	0.73	regulation of biological quality
GO:0051495	0.66	positive regulation of cytoskeleton organization
GO:0044089	0.66	positive regulation of cellular component biogenesis
GO:0051496	0.65	positive regulation of stress fiber assembly
GO:0048869	0.61	cellular developmental process
GO:0048870	0.60	cell motility
GO:0009653	0.60	anatomical structure morphogenesis
GO:1900026	0.59	positive regulation of substrate adhesion-dependent cell spreading
GO:0060439	0.59	trachea morphogenesis
GO:0046716	0.59	muscle cell cellular homeostasis
GO:0044319	0.59	wound healing, spreading of cells
GO:0035070	0.59	salivary gland histolysis
GO:0030335	0.59	positive regulation of cell migration
GO:0019233	0.59	sensory perception of pain
GO:0010623	0.59	programmed cell death involved in cell development
GO:0007476	0.59	imaginal disc-derived wing morphogenesis
GO:0003012	0.59	muscle system 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	0.94	intracellular part
GO:0044444	0.84	cytoplasmic part
GO:0043226	0.74	organelle
GO:0043229	0.72	intracellular organelle
GO:0005737	0.66	cytoplasm
GO:0043227	0.63	membrane-bounded organelle
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0005634	0.61	nucleus
GO:0048471	0.55	perinuclear region of cytoplasm
GO:0016020	0.51	membrane

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	0.060	1iduA	0.436	4.98	0.053	0.853	1.11.1.10	69
2	0.060	1cnsA	0.427	4.44	0.058	0.759	3.2.1.14	NA
3	0.060	1m56A	0.426	4.50	0.020	0.741	1.9.3.1	NA
4	0.060	1phzA	0.447	4.76	0.042	0.802	1.14.16.1	102
5	0.060	3b8cB	0.430	5.01	0.107	0.819	3.6.3.6	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	0.01	2ydfB	0.405	4.95	0.028	0.793	0.16	IO3	complex1.pdb.gz	19,66,71
2	0.01	2xvvA	0.392	4.65	0.035	0.672	0.12	9DN	complex2.pdb.gz	69,94,98
3	0.01	2bxqA	0.358	4.48	0.038	0.629	0.18	P1Z	complex3.pdb.gz	62,65,69,98,99
4	0.01	2vufB	0.443	4.84	0.037	0.810	0.29	FUA	complex4.pdb.gz	60,63,64,72
5	0.01	1mmtA	0.440	4.44	0.074	0.776	0.13	NLE	complex5.pdb.gz	52,106,107
6	0.01	2xw1B	0.405	4.94	0.028	0.793	0.21	9NV	complex6.pdb.gz	64,65,68,69,93,98
7	0.01	2vueB	0.403	4.99	0.028	0.784	0.22	BLA	complex7.pdb.gz	61,65,69,99
8	0.01	2xvqA	0.438	4.85	0.036	0.802	0.21	9DS	complex8.pdb.gz	65,66,69,70,86,91,98
9	0.01	3hf8A	0.452	4.72	0.063	0.810	0.19	ML0	complex9.pdb.gz	31,49,98,111,112
10	0.01	2bxfA	0.441	4.27	0.010	0.767	0.19	DZP	complex10.pdb.gz	62,63,66,67

	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.