D-I-TASSER Q00839-D5

D-I-TASSER results for Q00839-D5

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

Input Sequence in FASTA format

>Q00839 (146 residues)
EKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGAPGNRGGYNRRGNMPQR
GGGGGGSGGIGYPYPRAPVFPGRGSYSNRGNYNRGGMPNRGNYNQNFRGRGNNRGYKNQS
QGYNQWQQGQFWGQKPWSQHYHQGYY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGAPGNRGGYNRRGNMPQRGGGGGGSGGIGYPYPRAPVFPGRGSYSNRGNYNRGGMPNRGNYNQNFRGRGNNRGYKNQSQGYNQWQQGQFWGQKPWSQHYHQGYY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	96557787666778888776467888888898788898767887789887678888887788777878888987889988887876777887778888888856677787787787542222232235653567855446677889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGAPGNRGGYNRRGNMPQRGGGGGGSGGIGYPYPRAPVFPGRGSYSNRGNYNRGGMPNRGNYNQNFRGRGNNRGYKNQSQGYNQWQQGQFWGQKPWSQHYHQGYY
Prediction	86566555645464554544444533556442374544523332445623244744455434444444345343443433445423454443443336542424551544454443544543354445441354641455346538
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
EKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGAPGNRGGYNRRGNMPQRGGGGGGSGGIGYPYPRAPVFPGRGSYSNRGNYNRGGMPNRGNYNQNFRGRGNNRGYKNQSQGYNQWQQGQFWGQKPWSQHYHQGYY

5c0pA

0.05

2.48

0.54

CEthreader

VSSLRLRDPFILVDKKTSYYLHFNNNLKIRVYKSKDLSTWKDEGYSFIAKSDFWGQQDFWAPDVYEYEGRYYLFTTFSNAGVKRGTTPSGWCLDGSLYIDKEGNPWLLFCREWLETIDGEIYAQRLAKDLKTTEGDPYLLFKASEA

6frku

0.03

1.90

0.48

EigenThreader

YCSRRQRRLRKTLNFRYLLLVLMDAERAWSYAMQLKQEARLRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIGDQK---PLFFDL

6cd2C

0.27

0.24

7.36

0.57

FFAS-3D

DKKSEAGYVLPGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGLPPSRWDDGIPGLMLDYNLNGTVSRNYQ----------------

7jjvA

0.19

0.16

5.29

1.96

SPARKS-K

-----MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTTVL----------------

6wu9M

0.32

0.07

2.06

0.31

CNFpred

ELKPAEGSRQ-VRNRVGRGTSSGNGKTAGRGQ------------------------------------------------------------------------------------------------------------------

5zqzA

0.06

0.05

2.12

0.83

DEthreader

NTLSDNMLAACKTLVTQSQAQVGGLTPEALPGGTQRLPAMLTGAPKESKLMGYGQVL-CKKN---APQ-KDVKHLAI---LM--GIAQVSVLKTIADMVIFASIAARPEEKTSKDTSASAVAVGLKQGKV----------------

4fspA

0.07

2.82

0.76

MapAlign

----RRFAGAAQADRFDLAGLDYRIAPDWTGSYHYGQHFLGLKGRIGIAADSLESDLRLALSRDTGGARGGRIDNRSFYRLRNGQAFGLGYQRMSGDHGFPYLEGTDPYLVNFGQYNDFAEAGESSWQLRYDCDFAPLGVPGLSLM

2pffA1

0.26

8.03

0.85

MUSTER

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3qz0A

0.19

0.03

1.10

0.45

HHsearch

DKKPGTSIAQGTKAAALRKRFIPKK----I--------------------------------------------------------------------------------------------------------------------

6chgD

0.08

3.03

0.52

CEthreader

HTLEVPVAAVCVKFSPRGDYLAVGCSNGAIIIYDMDSLKPIAMLGTHSGAHTRSVQSVCWSNDGRYLWSSGRDWYAKLWDMTQPTKCFQQYKFDGPLWSCHVVRWNVCIVTVVEEPTAYVLTLTDRQNAFHCFPLLEQDQDISGHG

(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	0.4628

(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	3ahcA2	0.47	5.01	0.037	0.877	model1_3ahcA2.pdb.gz
2	5xjjA	0.47	4.70	0.051	0.781	model1_5xjjA.pdb.gz
3	1zvwA	0.47	4.90	0.061	0.815	model1_1zvwA.pdb.gz
4	6lxvA	0.47	5.16	0.022	0.877	model1_6lxvA.pdb.gz
5	3s99A	0.46	4.58	0.068	0.774	model1_3s99A.pdb.gz
6	5y50A	0.46	5.00	0.044	0.808	model1_5y50A.pdb.gz
7	6tjvF	0.46	5.16	0.048	0.794	model1_6tjvF.pdb.gz
8	4d4gA	0.46	5.24	0.074	0.856	model1_4d4gA.pdb.gz
9	4z3nA	0.46	4.97	0.045	0.788	model1_4z3nA.pdb.gz
10	1pg3B	0.44	5.11	0.042	0.794	model1_1pg3B.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:0044822	1.00	poly(A) RNA binding
GO:0001047	1.00	core promoter binding
GO:0070034	0.52	telomerase RNA binding
GO:0044877	0.50	macromolecular complex 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:0010468	1.00	regulation of gene expression
GO:0009987	1.00	cellular process
GO:0008152	0.64	metabolic process
GO:0043170	0.62	macromolecule metabolic process
GO:0050794	0.61	regulation of cellular process
GO:0044237	0.61	cellular metabolic process
GO:0044238	0.60	primary metabolic process
GO:0044699	0.59	single-organism process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:0034641	0.58	cellular nitrogen compound metabolic process
GO:0080090	0.57	regulation of primary metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0044763	0.56	single-organism cellular process
GO:2000112	0.55	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.55	regulation of nitrogen compound metabolic process
GO:0048523	0.54	negative regulation of cellular process
GO:0019219	0.54	regulation of nucleobase-containing compound metabolic process
GO:0006139	0.54	nucleobase-containing compound metabolic process
GO:0065008	0.53	regulation of biological quality
GO:0048869	0.53	cellular developmental process
GO:0048518	0.53	positive regulation of biological process
GO:0044707	0.53	single-multicellular organism process
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0016070	0.53	RNA metabolic process
GO:0010608	0.53	posttranscriptional regulation of gene expression
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:0070934	0.52	CRD-mediated mRNA stabilization
GO:0032922	0.52	circadian regulation of gene expression
GO:0032211	0.52	negative regulation of telomere maintenance via telomerase
GO:0001649	0.52	osteoblast differentiation
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0050896	0.50	response to stimulus
GO:0010628	0.50	positive regulation of gene expression

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:0044424	1.00	intracellular part
GO:0032991	0.87	macromolecular complex
GO:0030529	0.85	intracellular ribonucleoprotein complex
GO:0043229	0.84	intracellular organelle
GO:0043231	0.83	intracellular membrane-bounded organelle
GO:0005634	0.82	nucleus
GO:0044446	0.80	intracellular organelle part
GO:0044428	0.76	nuclear part
GO:0005654	0.65	nucleoplasm
GO:0044444	0.55	cytoplasmic part
GO:0005681	0.51	spliceosomal complex

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	3l4uA	0.439	5.25	0.035	0.822	3.2.1.20 3.2.1.3	44
2	0.060	1fgjA	0.452	5.12	0.023	0.788	1.7.3.4	NA
3	0.060	1k8eD	0.435	4.82	0.040	0.753	2.4.2.18	32,90
4	0.060	1vhdA	0.393	4.87	0.063	0.699	1.1.1.-	NA
5	0.060	1h54B	0.426	5.34	0.070	0.801	2.4.1.8	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:

Click to view	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	1okcA	0.418	4.98	0.058	0.733	1.07	CDL	complex1.pdb.gz	97,123,124,127,128
	2	0.01	1azs1	0.253	4.95	0.043	0.431	0.43	III	complex2.pdb.gz	88,89,91,99,126,129,130,131

	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.