D-I-TASSER O76039-D5

D-I-TASSER results for O76039-D5

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

Input Sequence in FASTA format

>O76039 (92 residues)
LPEHMDSSHSHSLSAPHESFSYGLGYTSPFSSQQRPHRHSMYVTRDKVRAKGLDGSLSIG
QGMAARANSLQLLSPQPGEQLPPEMTVARSSV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| LPEHMDSSHSHSLSAPHESFSYGLGYTSPFSSQQRPHRHSMYVTRDKVRAKGLDGSLSIGQGMAARANSLQLLSPQPGEQLPPEMTVARSSV
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCC
Confidence	97544676566678998765556665788864568532204675110025776678554666200001120048898777997644467899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| LPEHMDSSHSHSLSAPHESFSYGLGYTSPFSSQQRPHRHSMYVTRDKVRAKGLDGSLSIGQGMAARANSLQLLSPQPGEQLPPEMTVARSSV
Prediction	75563665444515344642432332344155664444342314455344544744143344244435425114464466235625355578
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCC
LPEHMDSSHSHSLSAPHESFSYGLGYTSPFSSQQRPHRHSMYVTRDKVRAKGLDGSLSIGQGMAARANSLQLLSPQPGEQLPPEMTVARSSV

6vyvE3

0.09

3.35

0.67

CEthreader

SPVAIEKIRDEAPDGMLKQVSAQIGLDKAGTHAHTKIRYSLRVYTSAACSIHGTMGHFIVAHCPDYLKVSFEDADSHVKACKVQYKHDPLPV

2r3aA

0.07

2.75

0.57

EigenThreader

CTDCFFQKCCPAEAGVLLAYNKNQQIKTQYSKIKRMSFVME-YVGEVITSEEAERYLFDLEFTVDAGNVSHFVTINAGERTVCKCGAVTCRG

2ftcN

0.06

0.05

2.37

0.28

FFAS-3D

-------GDTVEILEGKDAGKQGK-VVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEAG-

6f1tg2

0.08

3.02

0.91

SPARKS-K

WSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSATFAKFHPNLVVGGTYSGQI---VLWDNRSNKRTPVQRTPLSAAA

2jfoA

0.12

0.04

1.53

0.37

CNFpred

--------------------------------------RLIYLGDTARCPYGPR---PAEQVVQFTWEMADFLL------------------

6at7B

0.07

2.67

0.83

DEthreader

--GAALSHEVATVMYD-A-NV---AVLSEVLIFMSPLGQEVAASIEVSVNNFQGTPIVSMDNARLAIANIGKLMFAQSEMASCS-EYLNPIV

6vyvE3

0.06

0.05

2.30

0.76

MapAlign

----IEKIRDEAPDGMLKIQAHTKIRYMAGHDVQESKRDSLRVYTSAACSIHGTMGHFIVAHCPPGDYLKVSFEDADSHVK-----------

6b3nA

0.14

4.80

0.49

MUSTER

MPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQGELMVSIRPMQVNGYFMGSLNQDDNIQIGLQYIEHIERTLGSLTSREVTVLREI-

3f93C3

0.17

0.16

5.37

0.67

HHsearch

LPIKAS--SRILVAGKGANINMAGGWSVSWQGNDFPNATSIFITLSEEYTSKPDVAIVIGEEPGDIEHALALLK-QLKANIPVTVFLGRPLW

1ee8A1

0.03

1.84

0.56

CEthreader

LGQTLRQVVHRDPARYRNTALAEGRRILELLFALEGGVELVAHLGMTGGFRLEPTPHTRAAFHDPRRFGRLFGVRRGDYREIPLLLRL----

(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	0.5187

(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	5b2oA	0.45	4.49	0.048	0.870	model1_5b2oA.pdb.gz
2	3b1bA	0.45	3.52	0.014	0.739	model1_3b1bA.pdb.gz
3	6zqqA	0.45	4.56	0.012	0.880	model1_6zqqA.pdb.gz
4	1xzzA	0.45	4.09	0.076	0.793	model1_1xzzA.pdb.gz
5	3t8sA1	0.45	4.15	0.076	0.793	model1_3t8sA1.pdb.gz
6	2xoaA	0.43	4.26	0.035	0.804	model1_2xoaA.pdb.gz
7	3im5B	0.42	4.07	0.096	0.772	model1_3im5B.pdb.gz
8	3javA	0.41	4.27	0.087	0.783	model1_3javA.pdb.gz
9	1y7wA	0.35	4.85	0.054	0.750	model1_1y7wA.pdb.gz
10	1yfiA	0.35	3.85	0.079	0.620	model1_1yfiA.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:1901363	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0032553	0.73	ribonucleotide binding
GO:0035639	0.72	purine ribonucleoside triphosphate binding
GO:0032555	0.72	purine ribonucleotide binding
GO:0032550	0.72	purine ribonucleoside binding
GO:0003824	0.72	catalytic activity
GO:0005524	0.71	ATP binding
GO:0016740	0.70	transferase activity
GO:0019899	0.68	enzyme binding
GO:0016301	0.68	kinase activity
GO:0048365	0.67	Rac GTPase binding
GO:0004672	0.67	protein kinase 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:0009987	0.86	cellular process
GO:0065007	0.83	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0048518	0.78	positive regulation of biological process
GO:0048522	0.77	positive regulation of cellular process
GO:2000026	0.76	regulation of multicellular organismal development
GO:0051128	0.76	regulation of cellular component organization
GO:0050775	0.75	positive regulation of dendrite morphogenesis
GO:0044699	0.71	single-organism process
GO:0044763	0.65	single-organism cellular process
GO:0008152	0.63	metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0044238	0.59	primary metabolic process
GO:0043170	0.57	macromolecule metabolic process
GO:0044260	0.56	cellular macromolecule metabolic process
GO:0006464	0.53	cellular protein modification process
GO:0065009	0.52	regulation of molecular function
GO:0006468	0.52	protein phosphorylation
GO:0046777	0.51	protein autophosphorylation
GO:0043087	0.51	regulation of GTPase activity
GO:0006928	0.51	movement of cell or subcellular component
GO:0045773	0.50	positive regulation of axon extension
GO:0043547	0.50	positive regulation of GTPase activity
GO:0001764	0.50	neuron migration

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:0005737	1.00	cytoplasm
GO:0044444	0.76	cytoplasmic part
GO:0043226	0.75	organelle
GO:0044446	0.74	intracellular organelle part
GO:0043229	0.74	intracellular organelle
GO:0016020	0.74	membrane
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005634	0.71	nucleus
GO:0044428	0.69	nuclear part
GO:0044425	0.69	membrane part
GO:0097458	0.68	neuron part
GO:0044459	0.68	plasma membrane part
GO:0044294	0.67	dendritic growth cone
GO:0032839	0.67	dendrite cytoplasm
GO:0032587	0.67	ruffle membrane
GO:0005654	0.67	nucleoplasm

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	1jbwA	0.423	4.42	0.073	0.826	6.3.2.17	NA
2	0.060	1op0A	0.407	4.62	0.066	0.815	3.4.21.-	NA
3	0.060	2aipA	0.416	4.51	0.067	0.804	3.4.21.74	NA
4	0.060	2zchP	0.408	4.65	0.078	0.815	3.4.21.77	NA
5	0.060	1kdqB	0.244	4.59	0.087	0.489	3.4.21.1	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	2bdiC	0.413	4.67	0.115	0.837	0.44	PBZ	complex1.pdb.gz	20,21,22,38,60,61
2	0.01	2bdiF	0.412	4.66	0.090	0.837	0.45	PBZ	complex2.pdb.gz	20,21,23,24,62,63
3	0.01	2bdiG	0.411	4.67	0.090	0.837	0.46	PBZ	complex3.pdb.gz	6,7,10,23,24,38
4	0.01	2bdiO	0.412	4.66	0.090	0.837	0.45	PBZ	complex4.pdb.gz	10,11,22,23,59
5	0.01	3ddrA	0.414	3.93	0.075	0.739	0.40	HEM	complex5.pdb.gz	21,23,62
6	0.01	2bdiL	0.411	4.66	0.090	0.837	0.42	PBZ	complex6.pdb.gz	21,43,45,59

	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.