D-I-TASSER O00300-D2

D-I-TASSER results for O00300-D2

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

Input Sequence in FASTA format

>O00300 (153 residues)
EGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSV
FGLLLTQKGNATHDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLP
GTKVNAESVERIKRQHSSQEQTFQLLKLWKHQN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLPGTKVNAESVERIKRQHSSQEQTFQLLKLWKHQN
Prediction	CCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSCCCCCCCCCSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence	972357884234787999924864687999982146998942288999986636751489996998289876566236899887678887532665225423665578613556666457878874566778763151478999999987519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLPGTKVNAESVERIKRQHSSQEQTFQLLKLWKHQN
Prediction	833135373445166154344135514664334146146231124642454144125145544233441354311203443643554424243045021412233513453152026405765164642651375455464024105304758
	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

CCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSCCCCCCCCCSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHCC
EGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLPGTKVNAESVERIKRQHSSQEQTFQLLKLWKHQN

2hevR

0.23

0.16

4.91

0.83

DEthreader

DTYPSN--D-RCCHECRPGNGMVSRCSRSQNTVCRPCGPGFYNDVVS-SKPCKPCTWCNRSGSERKQLCTATQDTVCRCRAGTQPCPGHFSPGDN-QACKP-WT-N-----------------------------TLA-K-------------

2hevR

0.25

0.21

6.48

3.44

SPARKS-K

GDTYPSNDR--CCHECRPGNGMVSRCSRSQNTVCRPCGPGFYNDVVSSKP-CKPCTWCNLSGSERKQLCTATQDTVCRCRAGTQPLDSVDCAPCPPGHFSPGDNQACTNCTLAGKHTLQPASNSSDAICED----------------------

3ij2X

0.17

0.16

5.16

0.84

MapAlign

STGLYTHSGEC-CKACNLGEGVAQPCGA-DQTVCEPCLDVTFSDVVSATEPCKPCTEC-LGLQSMSAPCVEADDAVCRCAYGYYCEVGSGLVFSCKQNTVCEECPEGTYSDEANHVDPCLPCTVCEDTERQLRECTPWADAECEH--------

3ij2X

0.18

5.74

0.62

CEthreader

TGLYTHSGE--CCKACNLGEGVAQPCG-ADQTVCEPCLDSTFSDVVSATEPCKPCTECLG-LQSMSAPCVEADDAVCRCAYGYYQDEEEACSVCEVGSGLVFSCQDKQNTVCEECPEGTYSDEANHVDPCLPCTVCEDTERQLRECTPWADAE

3urfZ2

0.96

0.51

14.29

2.18

MUSTER

EGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSHHH------------------------------------------------------------------------

4mxwR

0.22

0.18

5.58

1.50

HHsearch

EKEYYEHRIC--CSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPCDP-V--EIAPCTSKRKTQCRCCPPGTEAVGNHCVPCKAGHFQNTSSQPHTRCENQGLVEAAPGTAQSDTTCK-----------------------

3qo4A2

0.33

0.17

5.10

1.01

FFAS-3D

PGMFQSNATCAPHTVCPVGWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQNLVVIKPGTKETDNVCG---------------------------------------------------------------------------

1extA

0.11

0.08

2.85

0.98

EigenThreader

GKYIHPQSICCTK--CHKGTYLYNDCPGPGQDDCRECESGSFTASENHLRHCLSSKCRKEMGQVEISSCTVDRDTVCGCRKNCQEKQAGFFLRE---NEVSCSN---------------CKKSLEC---------------------TKLCLP

2hevR

0.26

0.22

6.66

2.82

CNFpred

GDTYPSN--DRCCHECRPGNGMVSRCSRSQNTVCRPCGPGFYNDVVSS-KPCKPCTWCNLSGSERKQLCTATQDTVCRCRAGTQPLPGVDCAPCPPGHFSPGACKPWTNCTLAGKHTLQPASNSSDAICED----------------------

5dmjA

0.23

0.16

5.14

0.83

DEthreader

QYLINS----QCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDNLGLRVQQKGTSETDTICTCEEG-W------HCTSEA-VHRS---------CSP-FG-------CEPCPVGFFSD--SAFEKC-----------

(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	0.5208

(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	6eomA	0.54	4.51	0.068	0.915	model1_6eomA.pdb.gz
2	5dmjA	0.53	3.19	0.191	0.686	model1_5dmjA.pdb.gz
3	3me2R	0.53	3.24	0.136	0.640	model1_3me2R.pdb.gz
4	3cskA	0.52	4.93	0.092	0.922	model1_3cskA.pdb.gz
5	3ij2X	0.52	2.72	0.161	0.621	model1_3ij2X.pdb.gz
6	2hevR	0.52	2.77	0.185	0.627	model1_2hevR.pdb.gz
7	3alqR	0.52	3.58	0.142	0.667	model1_3alqR.pdb.gz
8	3urfZ	0.51	4.42	0.169	0.765	model1_3urfZ.pdb.gz
9	3qd6R	0.51	2.65	0.200	0.608	model1_3qd6R.pdb.gz
10	1extA	0.50	3.15	0.079	0.634	model1_1extA.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:0005031	0.98	tumor necrosis factor-activated receptor 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:0050794	0.98	regulation of cellular process
GO:0009605	0.96	response to external stimulus
GO:0043207	0.95	response to external biotic stimulus
GO:0006952	0.95	defense response
GO:1901700	0.94	response to oxygen-containing compound
GO:0042981	0.94	regulation of apoptotic process
GO:0042127	0.94	regulation of cell proliferation
GO:0033993	0.94	response to lipid
GO:0007165	0.94	signal transduction
GO:0097190	0.93	apoptotic signaling pathway
GO:0032496	0.93	response to lipopolysaccharide
GO:0006954	0.93	inflammatory response
GO:0002376	0.93	immune system process
GO:0006955	0.91	immune response
GO:0044699	0.89	single-organism process
GO:0048518	0.88	positive regulation of biological process
GO:0048522	0.86	positive regulation of cellular process
GO:0080090	0.85	regulation of primary metabolic process
GO:0060255	0.85	regulation of macromolecule metabolic process
GO:0051246	0.84	regulation of protein metabolic process
GO:0048584	0.84	positive regulation of response to stimulus
GO:0031323	0.84	regulation of cellular metabolic process
GO:0009893	0.84	positive regulation of metabolic process
GO:0032502	0.83	developmental process
GO:0032268	0.83	regulation of cellular protein metabolic process
GO:0031325	0.83	positive regulation of cellular metabolic process
GO:0010604	0.83	positive regulation of macromolecule metabolic process
GO:0048856	0.82	anatomical structure development
GO:0001934	0.82	positive regulation of protein phosphorylation
GO:0009966	0.81	regulation of signal transduction
GO:1902533	0.80	positive regulation of intracellular signal transduction
GO:0044767	0.79	single-organism developmental process
GO:0043410	0.79	positive regulation of MAPK cascade
GO:0044707	0.76	single-multicellular organism process
GO:0007275	0.75	multicellular organism development

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:0044459	0.99	plasma membrane part
GO:0005887	0.96	integral component of plasma 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	1qksB	0.356	5.64	0.055	0.673	1.7.2.1	NA
2	0.060	3bfjT	0.432	4.79	0.041	0.706	1.1.1.202	NA
3	0.060	3k2iA	0.433	4.61	0.047	0.712	3.1.2.2	24
4	0.060	2ze4A	0.388	4.93	0.048	0.667	3.1.4.4	NA
5	0.060	2pmzQ	0.422	4.97	0.088	0.732	2.7.7.6	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	0.08	3me2R	0.526	3.24	0.136	0.640	1.39	NA	complex1.pdb.gz	16,17,18,20,43,45,47
2	0.03	2aw21	0.466	2.79	0.183	0.569	0.95	III	complex2.pdb.gz	14,15,17,20,23,27,28,29,30,31,32,33,34,46
3	0.01	2bgrB	0.418	5.05	0.035	0.739	0.87	UUU	complex3.pdb.gz	19,40,42,43,44
4	0.01	1u8eA	0.417	5.26	0.028	0.758	0.82	UUU	complex4.pdb.gz	19,37,40,42,43,44

	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.