D-I-TASSER O95759-D2

D-I-TASSER results for O95759-D2

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

Input Sequence in FASTA format

>O95759 (149 residues)
AVLDSNARVAPFRILLQVPGSQVYSPIACGATLEEINQHWDWLEQNLLHTLSVFDNKDDI
ASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEARFNFPEAEKLVTYYSCCCWKG
RVPRQGWLYLSINHLCFYSFFLGKELKLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AVLDSNARVAPFRILLQVPGSQVYSPIACGATLEEINQHWDWLEQNLLHTLSVFDNKDDIASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEARFNFPEAEKLVTYYSCCCWKGRVPRQGWLYLSINHLCFYSFFLGKELKLV
Prediction	CCCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCSSSSSSSCSSCCCCCCCCSSSSSCCSSSSSSCCCCCSSSSC
Confidence	94578999998379852699853788630588899999899999644455431367344444321115666523666655434456356899999999971999976224536520122862223179976776899734577035639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AVLDSNARVAPFRILLQVPGSQVYSPIACGATLEEINQHWDWLEQNLLHTLSVFDNKDDIASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEARFNFPEAEKLVTYYSCCCWKGRVPRQGWLYLSINHLCFYSFFLGKELKLV
Prediction	74435664333020004157451222113334373046315303641153045165774346234441543244567654456764476155225504630723673411521201124540242010102432000202134452436
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCSSSSSSSCSSCCCCCCCCSSSSSCCSSSSSSCCCCCSSSSC
AVLDSNARVAPFRILLQVPGSQVYSPIACGATLEEINQHWDWLEQNLLHTLSVFDNKDDIASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEARFNFPEAEKLVTYYSCCCWKGRVPRQGWLYLSINHLCFYSFFLGKELKLV

6fsfA

0.07

2.99

0.61

CEthreader

TLYRDNEDDLSILIAIIDRKSGKEMFKFSKSIHKVRELDVYMKSHVPDLPLPTLPDRQLFQTLSPTKVDTRKNILNQYYTSIFSVPEFPKNVGLKIAQFISTDTVMTPVKDGSLLLRRPNSTWRVRYGILRDDVLQLFDKNQLTETIKL

4xhjA

0.06

0.04

1.81

0.62

EigenThreader

TGFDEENDRKHVFLVIVKTTHEGDVGLVIFPKY-------------------------------------LPYLTTFGVSLLHFATWDALARAIITPLF--GSVWPIRYWATGSVLLTS--DSGRVEVNIGVGFMSSLISLSSGPIELI

4tyzA

0.23

0.09

2.74

0.74

FFAS-3D

-------------------------------------------------------------------------------------------NIEGVFRKSFPDLAGETLLDSFNCAWVEGSALKQGYLFITPHWLCFQSTLAAAHFSI-

6rreB

0.09

0.07

2.83

0.68

SPARKS-K

SLF-VHHKDSDDKIVIGYKDGMAFQIVVDGFYGCERQAVFSFIDNYVLP---------LIDNFSLDLTRY-------------PDSKKVTESLIHTIYSLRSAPLAE-FTMSLCVTYQKDEQLFCAGFGIGDTGIAIKRNEGTIEQLVC

5yqrA

0.29

0.19

5.93

0.67

CNFpred

--------------------------------LRMLQQRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAY---------------SEANKKFRQMFKLAPNTRLITDYFCYFHRE-FPYQGRIYLSNTHLCFNSTVLNWMAKLQ

6g9fA

0.06

0.05

2.30

0.83

DEthreader

IYD-RNG------ALVIGYGKLGIY--TLDL-K-LQQYIETLLAGSATPSYDPNTPL--VN-RATQTPIQMSKALMILNGDIHSYWELAKDGMYGVANRHFSAP-YKIA--AKSGTAQ--LRDHKLMTAFAQVAVAMIL-G--AVGTLQ

3hizA

0.10

0.09

3.52

0.66

MapAlign

-YNKLDKGQIIVVIWVIVSPNNDKQKYLKINHPEQVIAEAIRKPEQAMELLCNYPDPMVRGFAVRCLLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTLSPLNPAHQLGNLRCRIMSS-AKRPLWLNWENPDQNNEIIFKNVGLIEVV

4tyzA

0.22

0.09

2.74

0.68

MUSTER

-------------------------------------------------------------------------------------------NIEGVFRKSFPDLAGETLLDSFNCAWVEGSALKQGYLFITPHWLCFQSTLAAAHFSIE

4tyzA

0.23

0.09

2.73

2.80

HHsearch

-------------------------------------------------------------------------------------------NIEGVFRKSFPDLAGETLLDSFNCAWVEGSALKQGYLFITPHWLCFQSTLAA--AHFS

4kxrC

0.10

3.72

0.56

CEthreader

RMKVLAAPDLEVVALLSRGKLNEFRVVLARRGQHWVVSDSASIAALVMDGLESIHHADNVPMEEMLEATKSWQESGFNVFSGGDLRRMGISAATVAALGQALSDPAAEVAVYARQYRDDAKGPSASVLSLKDGRIALYQQAREAWLAIC

(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	0.5939

(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	7kisA	0.54	4.65	0.036	0.886	model1_7kisA.pdb.gz
2	3lo7A	0.54	4.66	0.041	0.893	model1_3lo7A.pdb.gz
3	6bsqA	0.54	4.65	0.058	0.866	model1_6bsqA.pdb.gz
4	5lp4A	0.54	4.62	0.023	0.866	model1_5lp4A.pdb.gz
5	6c84A	0.53	4.76	0.043	0.873	model1_6c84A.pdb.gz
6	6synA	0.53	5.14	0.068	0.926	model1_6synA.pdb.gz
7	4bjpA	0.52	4.83	0.042	0.873	model1_4bjpA.pdb.gz
8	3ue3A	0.52	5.09	0.028	0.913	model1_3ue3A.pdb.gz
9	1mwrB2	0.52	4.84	0.052	0.866	model1_1mwrB2.pdb.gz
10	6eu6A	0.52	4.52	0.045	0.839	model1_6eu6A.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:0017016	0.98	Ras GTPase binding
GO:0005096	0.98	GTPase activator activity
GO:0017137	0.97	Rab GTPase binding
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0032555	0.51	purine ribonucleotide binding
GO:0032550	0.51	purine ribonucleoside 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:0050794	0.99	regulation of cellular process
GO:0051234	0.98	establishment of localization
GO:0043087	0.98	regulation of GTPase activity
GO:0090630	0.97	activation of GTPase activity
GO:0031338	0.97	regulation of vesicle fusion
GO:0006886	0.97	intracellular protein transport

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:0012505	0.98	endomembrane system
GO:0005622	0.98	intracellular
GO:0044424	0.59	intracellular part

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	2w68C	0.293	5.53	0.106	0.550	3.2.1.18	138
2	0.060	3cmmC	0.443	5.41	0.085	0.846	6.3.2.19	99
3	0.060	1yrlA	0.452	4.99	0.082	0.772	1.1.1.86	NA
4	0.060	2jguA	0.411	4.59	0.031	0.638	2.7.7.7	98
5	0.060	1iduA	0.447	5.42	0.049	0.812	1.11.1.10	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	2y2iA	0.498	5.05	0.036	0.873	0.11	ZA3	complex1.pdb.gz	126,143,144
2	0.01	2xd5A	0.483	5.14	0.050	0.859	0.20	S2D	complex2.pdb.gz	100,101,136
3	0.01	3pbqA	0.529	4.99	0.068	0.919	0.10	IM2	complex3.pdb.gz	96,97,138,144
4	0.01	2y2pA	0.493	5.18	0.064	0.873	0.20	Z10	complex4.pdb.gz	123,124,125,126,139
5	0.01	3ocnA	0.525	4.93	0.061	0.906	0.15	CTJ	complex5.pdb.gz	118,119,123
6	0.01	1qmfA	0.530	4.87	0.041	0.893	0.17	KEF	complex6.pdb.gz	126,128,142
7	0.01	2zc4B	0.460	4.79	0.048	0.792	0.18	TEB	complex7.pdb.gz	139,140,141
8	0.01	2je50	0.496	5.13	0.037	0.859	0.16	III	complex8.pdb.gz	121,124,126,128
9	0.01	2olvA	0.500	5.18	0.062	0.886	0.11	M0E	complex9.pdb.gz	92,144,145,146

	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.