D-I-TASSER O95782-D6

D-I-TASSER results for O95782-D6

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

Input Sequence in FASTA format

>O95782 (113 residues)
FQPTEMAAQDFFQRWKQLSLPQQEAQKIFKANHPMDAEVTKAKLLGFGSALLDNVDPNPE
NFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEPVSRHLCELLAQQF

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| FQPTEMAAQDFFQRWKQLSLPQQEAQKIFKANHPMDAEVTKAKLLGFGSALLDNVDPNPENFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEPVSRHLCELLAQQF
Prediction	CCCCCCCHHHHHHHHHHCCCCCCSSSSSSCCCCCCCHHHHHHHHHHCCSSSCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCCHHHHHHHHHHHHC
Confidence	98723898999999996257886468997489876889999999703908647999997828999999818964889999844888877999999699727899999999759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| FQPTEMAAQDFFQRWKQLSLPQQEAQKIFKANHPMDAEVTKAKLLGFGSALLDNVDPNPENFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEPVSRHLCELLAQQF
Prediction	85547154740252045265674423431426452437404411542413216632443411000011315734100001032357442020002044550152015105748
	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

CCCCCCCHHHHHHHHHHCCCCCCSSSSSSCCCCCCCHHHHHHHHHHCCSSSCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCCHHHHHHHHHHHHC
FQPTEMAAQDFFQRWKQLSLPQQEAQKIFKANHPMDAEVTKAKLLGFGSALLDNVDPNPENFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEPVSRHLCELLAQQF

1qtpA

0.78

0.76

21.52

1.50

DEthreader

FQPTE-ASQDFFQRWKQLSNPQQEVQNIFKAKH-PDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.79

0.77

21.76

2.69

SPARKS-K

FQPTE-ASQDFFQRWKQLSNPQQEVQNIFKAKHP-DTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA

0.76

0.74

21.04

1.29

MapAlign

FQPT-EASQDFFQRWKQLSNPQQEVQNIFKA-KHPDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.78

0.76

21.52

1.18

CEthreader

FQPT-EASQDFFQRWKQLSNPQQEVQNIFKAKHP-DTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.79

0.77

21.76

2.20

MUSTER

FQPTE-ASQDFFQRWKQLSNPQQEVQNIFKAKHP-DTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.79

0.77

21.76

3.44

HHsearch

FQPTE-ASQDFFQRWKQLSNPQQEVQNIFKAKHP-DTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.78

0.76

21.52

1.74

FFAS-3D

FQPTEA-SQDFFQRWKQLSNPQQEVQNIFKAKHP-DTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.70

0.69

19.62

1.22

EigenThreader

NKFFTEASQDFFQRWKQLSNPQQEVQNIFKAKHPD-TEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPN-LQAQYRLTLRTSKDTVSQRLCELLSEQF

1ky6A

0.80

22.50

1.95

CNFpred

FQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF

1qtpA2

0.78

0.76

21.52

1.50

DEthreader

FQPTE-ASQDFFQRWKQLSNPQQEVQNIFKAKH-PDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQ-YRLTLRTSKDTVSQRLCELLSEQF

(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	0.8709

(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	1qtpA	0.95	0.62	0.791	0.974	model1_1qtpA.pdb.gz
2	2mj7A	0.77	2.36	0.103	0.929	model1_2mj7A.pdb.gz
3	2iv9A	0.77	2.13	0.179	0.938	model1_2iv9A.pdb.gz
4	1pzdA2	0.75	2.44	0.154	0.911	model1_1pzdA2.pdb.gz
5	5a1uE2	0.73	2.53	0.163	0.903	model1_5a1uE2.pdb.gz
6	2refA	0.47	3.41	0.059	0.664	model1_2refA.pdb.gz
7	1qgnA2	0.40	4.09	0.025	0.681	model1_1qgnA2.pdb.gz
8	4q3pA	0.39	4.65	0.048	0.735	model1_4q3pA.pdb.gz
9	5b0uA	0.39	4.73	0.030	0.637	model1_5b0uA.pdb.gz
10	4l4wA	0.38	4.73	0.069	0.664	model1_4l4wA.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:0019899	0.39	enzyme binding
GO:0019901	0.37	protein kinase binding
GO:1901363	0.31	heterocyclic compound binding
GO:0097159	0.31	organic cyclic compound 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:0006810	0.73	transport
GO:0044699	0.71	single-organism process
GO:0016192	0.66	vesicle-mediated transport
GO:0065007	0.65	biological regulation
GO:0050789	0.62	regulation of biological process
GO:0008104	0.60	protein localization
GO:0009987	0.57	cellular process
GO:0015031	0.55	protein transport
GO:0051649	0.53	establishment of localization in cell
GO:0050794	0.52	regulation of cellular 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	0.88	intracellular part
GO:0044425	0.86	membrane part
GO:0016020	0.85	membrane
GO:0044444	0.82	cytoplasmic part
GO:0043234	0.70	protein complex
GO:0005886	0.63	plasma membrane
GO:0098796	0.60	membrane protein complex
GO:0043226	0.59	organelle
GO:0043227	0.58	membrane-bounded organelle
GO:0043229	0.57	intracellular organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0044459	0.54	plasma membrane part
GO:0044446	0.52	intracellular organelle 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	3en1A	0.559	3.39	0.062	0.814	1.14.12.11	NA
2	0.060	2ihwA	0.558	3.87	0.048	0.832	2.3.1.168	NA
3	0.060	2debA	0.521	3.91	0.009	0.761	2.3.1.21	NA
4	0.060	1wqlA	0.547	3.50	0.082	0.814	1.14.12.-	NA
5	0.060	1mhmA	0.550	3.95	0.082	0.867	4.1.1.50	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	0.59	1ky7A	0.969	0.75	0.796	1.000	1.88	III	complex1.pdb.gz	8,11,12,15,16,28,55,56,57,63,80,82,83,84,91
2	0.39	1kydA	0.969	0.78	0.796	1.000	0.86	III	complex2.pdb.gz	11,12,15,16,63
3	0.02	2zylA	0.652	3.15	0.056	0.894	0.79	FES	complex3.pdb.gz	48,49,64,66,78,80
4	0.02	3c0vC	0.604	2.84	0.056	0.788	0.79	TBR	complex4.pdb.gz	5,52,64,77

	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.