D-I-TASSER Q7Z736-D3

D-I-TASSER results for Q7Z736-D3

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

Input Sequence in FASTA format

>Q7Z736 (113 residues)
RELVPSLAEISALSQRQELLCTVHCPGAGACAVAIDSHTTAGEVARELVGRLGLARSRNA
FALYEQRGAQERALAGGTLVADVLTRFENLAAEEAGLEDSPDSGWRLCLRLHG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| RELVPSLAEISALSQRQELLCTVHCPGAGACAVAIDSHTTAGEVARELVGRLGLARSRNAFALYEQRGAQERALAGGTLVADVLTRFENLAAEEAGLEDSPDSGWRLCLRLHG
Prediction	CCCCCCHHHHHHHHCCCCSSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSSSCCSSSSCCCCCSSSHHHHHHHHHHHHHCCCCCCCCCCSSSSSSSCC
Confidence	99999899999998099547999966998799996586419999999999829976886489999909999984899664228999999998522444467875699999559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| RELVPSLAEISALSQRQELLCTVHCPGAGACAVAIDSHTTAGEVARELVGRLGLARSRNAFALYEQRGAQERALAGGTLVADVLTRFENLAAEEAGLEDSPDSGWRLCLRLHG
Prediction	87432143003003654503020203244334140333220430053027526146344000001336633430465310000013035145655565765543010103348
	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

CCCCCCHHHHHHHHCCCCSSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSSSCCSSSSCCCCCSSSHHHHHHHHHHHHHCCCCCCCCCCSSSSSSSCC
RELVPSLAEISALSQRQELLCTVHCPGAGACAVAIDSHTTAGEVARELVGRLGLARSRNAFALYEQRGAQERALAGGTLVADVLTRFENLAAEEAGLEDSPDSGWRLCLRLHG

5ejqA

0.22

0.21

6.71

1.33

DEthreader

LKQVPSVTELESIKENRPIFVRITATDGSLKGLHIDSATTCQESSNDLSQRSRMRVNSKGFTIIESFNGIERDIAPTDKLCDVLSKVENLQAT-LSSKIQ--VNFKFVFKKKF

5xbfA3

0.14

0.13

4.53

2.92

SPARKS-K

RKQPPHQVEVEAAEQNVRICHKIYFPNDTSEMLEVVANTRVRDVCDSIATRLQ-LASWEGCSLFIKISDKVISQKEGDFFFDSLREVSDWVKKNKV-----TLPYQVYFMRKL

3pvlA

0.26

0.25

7.65

0.74

MapAlign

-TQPPSWLELQATKSKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISL-KDRFGFSLYIALFDKVSSLGSSDHVMDAISQCEQYAKEQGAQERN--APWRLFFRKEV

3pvlA3

0.27

8.14

0.52

CEthreader

RTQPPSWLELQATKSKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISLKD-RFGFSLYIALFDKVSSLGSGDHVMDAISQCEQYAKEQGAQERN--APWRLFFRKEV

3pzdA

0.48

0.46

13.39

1.75

MUSTER

REFVPSRDEIEALIHRQEMTSTVYCHGGGSCKITINSHTTAGEVVEKLIRGLAMEDSRNMFALFEYNGHVDKAIESRTVVADVLAKFEKLAATSE----VGDLPWKFYFKLYC

5xbfA3

0.15

0.14

4.77

2.14

HHsearch

RKQPPHQVEVEAAEQNVSICHKIYFPNDTSEMLEVVANTRVRDVCDSIATRLQLAS-WEGCSLFIKISDKVISQKEGDFFFDSLREVSDWVKKNK-----VTLPYQVYFMRKL

5xbfA3

0.16

0.15

4.98

1.83

FFAS-3D

RKQPPHQVEVEAAEQNVSICHKIYFPNDTSEMLEVVANTRVRDVCDSIATRLQLA-SWEGCSLFIKISDKVISQKEGDFFFDSLREVSDWVKKN-----KVTLPYQVYFM---

5ejqA

0.24

0.23

7.19

0.87

EigenThreader

RKQVPSVTELESIKENRPIFVRITATDGSLKGLHIDSATTCQESSNDLSQRSRMRVNSNGFTIIESFNGIERDIAPTDKLCDVLSKVENLQATLS---SKIQVNFKFVFKKKL

3au4A

0.47

0.45

13.15

1.76

CNFpred

REFVPSRDEIEALIHRQEMTSTVYCHGGGSCKITINSHTTAGEVVEKLIRGLAMEDSRNMFALFEYNGHVDKAIESRTVVADVLAKFEKLAATSEVGD----LPWKFYFKLYC

3pvlA

0.26

0.25

7.65

1.33

DEthreader

ITQPPSWLELQATKSKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISLK-DRFGFSLYIALFDKVSSLGGSDHVMDAISQCEQYAKE-Q--GAQ-NAPWRLFFRKEF

(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	0.837

(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	3pvlA	0.91	1.21	0.273	0.974	model1_3pvlA.pdb.gz
2	5f3yA	0.89	1.32	0.218	0.974	model1_5f3yA.pdb.gz
3	5ejqA	0.86	1.76	0.227	0.956	model1_5ejqA.pdb.gz
4	5mv9A	0.81	1.73	0.170	0.938	model1_5mv9A.pdb.gz
5	3pzdA	0.81	2.14	0.468	0.938	model1_3pzdA.pdb.gz
6	5ejrA	0.79	1.81	0.192	0.920	model1_5ejrA.pdb.gz
7	5xbfA	0.78	2.13	0.140	0.929	model1_5xbfA.pdb.gz
8	6cb0A	0.69	1.94	0.169	0.788	model1_6cb0A.pdb.gz
9	3ddcB	0.68	2.83	0.184	0.858	model1_3ddcB.pdb.gz
10	2kmaA	0.61	2.81	0.125	0.788	model1_2kmaA.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:0003824	0.87	catalytic activity
GO:0017111	0.86	nucleoside-triphosphatase activity
GO:0016887	0.84	ATPase activity
GO:0003774	0.78	motor activity
GO:0008092	0.75	cytoskeletal protein binding
GO:0042623	0.73	ATPase activity, coupled
GO:0003779	0.73	actin binding
GO:0032403	0.70	protein complex binding
GO:0030898	0.70	actin-dependent ATPase activity
GO:1901363	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0051015	0.67	actin filament binding
GO:0000146	0.61	microfilament motor activity
GO:0035091	0.58	phosphatidylinositol binding
GO:0060002	0.57	plus-end directed microfilament motor activity
GO:0005547	0.57	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0032559	0.54	adenyl ribonucleotide binding
GO:0032550	0.54	purine ribonucleoside binding
GO:0005524	0.53	ATP binding
GO:0030507	0.51	spectrin 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:0009987	0.87	cellular process
GO:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0044699	0.74	single-organism process
GO:0050794	0.73	regulation of cellular process
GO:0044763	0.72	single-organism cellular process
GO:0051179	0.71	localization
GO:0006810	0.68	transport
GO:0051641	0.65	cellular localization
GO:0051649	0.61	establishment of localization in cell
GO:0051128	0.60	regulation of cellular component organization
GO:0046907	0.60	intracellular transport
GO:0065008	0.59	regulation of biological quality
GO:0051489	0.57	regulation of filopodium assembly
GO:0030705	0.57	cytoskeleton-dependent intracellular transport
GO:0008360	0.57	regulation of cell shape
GO:0016043	0.56	cellular component organization
GO:0032502	0.52	developmental process
GO:0006928	0.52	movement of cell or subcellular component
GO:0044767	0.51	single-organism developmental process
GO:0048518	0.50	positive regulation of biological 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	0.88	cell part
GO:0044424	0.78	intracellular part
GO:0043226	0.60	organelle
GO:0043229	0.55	intracellular organelle
GO:0044446	0.52	intracellular organelle part
GO:0044421	0.50	extracellular region 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	0.067	2jrhA	0.530	2.86	0.098	0.726	2.7.11.25	44,74,84,106
2	0.066	2o2vA	0.526	3.19	0.118	0.752	2.7.12.2	85
3	0.060	1sowB	0.453	4.12	0.104	0.761	1.1.1.27	NA
4	0.060	1s76D	0.424	4.57	0.058	0.743	2.7.7.6	NA
5	0.060	3no9A	0.476	3.74	0.054	0.735	4.2.1.2	40

	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	0.10	3ml9A	0.579	2.96	0.099	0.788	0.19	ML9	complex1.pdb.gz	23,25,31,32,40
2	0.03	1e8zA	0.598	2.93	0.098	0.805	0.28	STU	complex2.pdb.gz	21,23,24,33,35,79,80
3	0.03	2wxkA	0.599	2.88	0.101	0.779	0.12	RW4	complex3.pdb.gz	27,71,72,73,75,84
4	0.03	2j0kB	0.655	1.80	0.153	0.752	0.21	4ST	complex4.pdb.gz	22,30,32
5	0.02	2x38A	0.580	3.03	0.101	0.761	0.15	IC8	complex5.pdb.gz	70,71,73,75,76
6	0.02	3dbsA	0.592	2.90	0.097	0.814	0.17	GD9	complex6.pdb.gz	22,24,25,45,49,54
7	0.02	3apfA	0.588	3.16	0.094	0.832	0.14	BMW	complex7.pdb.gz	26,71,72,73,74
8	0.02	3l17A	0.598	2.95	0.097	0.814	0.22	JZY	complex8.pdb.gz	22,24,25,45,49,54,56
9	0.02	2wxfA	0.585	3.14	0.101	0.770	0.19	039	complex9.pdb.gz	24,25,26,49,76
10	0.01	2wxjA	0.583	3.17	0.101	0.770	0.13	RW3	complex10.pdb.gz	25,26,45,56

	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.