D-I-TASSER Q99741-D2

D-I-TASSER results for Q99741-D2

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

Input Sequence in FASTA format

>Q99741 (118 residues)
GNRMTLSQEGAQDSFPLQQKILVCSLMLLIRQLKIKEVTLGKLYEAYSKVCRKQQVAAVD
QSECLSLSGLLEARGILGLKRNKETRLTKVFFKIEEKEIEHALKDKALIGNILATGLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GNRMTLSQEGAQDSFPLQQKILVCSLMLLIRQLKIKEVTLGKLYEAYSKVCRKQQVAAVDQSECLSLSGLLEARGILGLKRNKETRLTKVFFKIEEKEIEHALKDKALIGNILATGLP
Prediction	CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCSSSSCCCCCCSSSSSSCCCHHHHHHHHCCHHHHHHHHHHCCC
Confidence	9876678631010261889999999999995168532538999999999974728998998999999999996387354136664315787159999999998221899999980699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GNRMTLSQEGAQDSFPLQQKILVCSLMLLIRQLKIKEVTLGKLYEAYSKVCRKQQVAAVDQSECLSLSGLLEARGILGLKRNKETRLTKVFFKIEEKEIEHALKDKALIGNILATGLP
Prediction	8543456655446413312111010002114645445131240252035104547164243420330043044311020355444223403051547203300463410240276628
	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

CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCSSSSCCCCCCSSSSSSCCCHHHHHHHHCCHHHHHHHHHHCCC
GNRMTLSQEGAQDSFPLQQKILVCSLMLLIRQLKIKEVTLGKLYEAYSKVCRKQQVAAVDQSECLSLSGLLEARGILGLKRNKETRLTKVFFKIEEKEIEHALKDKALIGNILATGLP

2v1uA2

0.18

0.17

5.52

1.33

DEthreader

YARIEDRVSEVVRTLPLHAKLVLLSIMMLED--GGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGKTREVSLDADRLAVENALSEDPFVARLL-----

7jgrG2

0.43

0.38

11.18

2.05

SPARKS-K

--------------FPLQQKLMLCTLVLMLRNERNKDISMGRLHEVYRRVCAKRNILALDQAEFTGTVDLVETRGILRIMRKKEPRLHKVLLQWDEEEVHAALSDKQLIASILSDTAC

7jgrG

0.41

0.38

11.24

0.79

MapAlign

-----VAAVLNKVYFPLQQKLMLCTLVLMLRNERNKDISMGRLHEVYRRVCAKRNILALDQAEFTGTVDLVETRGILRIMRKKEPRLHKVLLQWDEEEVHAALSDKQLIASILSDT--

7jgrG2

0.43

0.38

11.18

0.54

CEthreader

--------------FPLQQKLMLCTLVLMLRNERNKDISMGRLHEVYRRVCAKRNILALDQAEFTGTVDLVETRGILRIMRKKEPRLHKVLLQWDEEEVHAALSDKQLIASILSDTAC

2v1uA2

0.17

0.16

5.29

1.51

MUSTER

AEIERDRVSEVVRTLPLHAKLVLLSIMMLED--GGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVRYGKTREVSLDADRLAVENALSEDPFVARLL-----

7jgrG2

0.43

0.38

11.18

2.07

HHsearch

--------------FPLQQKLMLCTLVLMLRNERNKDISMGRLHEVYRRVCAKRNILALDQAEFTGTVDLVETRGILRIMRKKEPRLHKVLLQWDEEEVHAALSDKQLIASILSDTAC

7jgrG2

0.45

0.38

11.15

1.80

FFAS-3D

--------------FPLQQKLMLCTLVLMLRNERNKDISMGRLHEVYRRVCAKRNILALDQAEFTGTVDLVETRGILRIMRKKEPRLHKVLLQWDEEEVHAALSDKQLIASILSD---

4xgcD2

0.09

0.08

3.23

0.82

EigenThreader

-----DDKIELLCGLSVLELCLIIAIKHHSQIYDRDSFNFEIIYARFSKFAKVSTTMQVERSIVLKAFEHLRIAELIMPLTKVQKEFEMHKLALTYSQIHHCMQRYQEVAQWAQSS--

2v1uA

0.19

0.16

5.21

1.08

CNFpred

---------EVVRTLPLHAKLVLLSIMMLEDG--GRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGKTREVSLDADRLAVENALSEDPFVARLL-----

2v1uA

0.18

0.17

5.52

1.33

DEthreader

YARIEDRVSEVVRTLPLHAKLVLLSIMMLED--GGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGKTREVSLDADRLAVENALSEDPFVARLL-----

(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	0.799

(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	7jgrG2	0.80	1.54	0.433	0.881	model1_7jgrG2.pdb.gz
2	2v1uA2	0.78	2.09	0.178	0.898	model1_2v1uA2.pdb.gz
3	5uj7A	0.77	1.75	0.157	0.856	model1_5uj7A.pdb.gz
4	4xgcA	0.73	2.14	0.129	0.848	model1_4xgcA.pdb.gz
5	4xgcD	0.73	2.56	0.090	0.932	model1_4xgcD.pdb.gz
6	2qbyA2	0.72	1.97	0.219	0.814	model1_2qbyA2.pdb.gz
7	1fnnA	0.71	2.52	0.171	0.864	model1_1fnnA.pdb.gz
8	1lj9A	0.54	3.36	0.130	0.729	model1_1lj9A.pdb.gz
9	3onqA	0.44	3.54	0.063	0.652	model1_3onqA.pdb.gz
10	2ix8A4	0.41	5.22	0.045	0.831	model1_2ix8A4.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:0019900	0.80	kinase binding
GO:1901363	0.66	heterocyclic compound binding
GO:0097159	0.66	organic cyclic compound binding
GO:0000166	0.54	nucleotide 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:0050794	0.94	regulation of cellular process
GO:0045787	0.92	positive regulation of cell cycle
GO:0009987	0.89	cellular process
GO:0080090	0.68	regulation of primary metabolic process
GO:0060255	0.68	regulation of macromolecule metabolic process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0050790	0.65	regulation of catalytic activity
GO:0031399	0.65	regulation of protein modification process
GO:0019220	0.65	regulation of phosphate metabolic process
GO:0042127	0.64	regulation of cell proliferation
GO:0010564	0.64	regulation of cell cycle process
GO:0007346	0.64	regulation of mitotic cell cycle
GO:0000079	0.64	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0032467	0.63	positive regulation of cytokinesis
GO:0030071	0.63	regulation of mitotic metaphase/anaphase transition
GO:0051984	0.62	positive regulation of chromosome segregation
GO:0008152	0.60	metabolic process
GO:0071704	0.59	organic substance metabolic process
GO:0044238	0.59	primary metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0044260	0.57	cellular macromolecule metabolic process
GO:1901360	0.54	organic cyclic compound metabolic process
GO:0034641	0.54	cellular nitrogen compound metabolic process
GO:0090304	0.53	nucleic acid metabolic process
GO:1901576	0.50	organic substance biosynthetic process
GO:0044249	0.50	cellular biosynthetic 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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044446	0.91	intracellular organelle part
GO:0044444	0.90	cytoplasmic part
GO:0044428	0.90	nuclear part
GO:0005794	0.88	Golgi apparatus
GO:0005737	0.88	cytoplasm
GO:0005654	0.88	nucleoplasm
GO:0005634	0.77	nucleus
GO:0044430	0.58	cytoskeletal part
GO:0051233	0.57	spindle midzone
GO:0000922	0.56	spindle pole

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	1kyzE	0.553	3.67	0.082	0.805	2.1.1.68	NA
2	0.060	3ilwA	0.599	3.46	0.055	0.831	5.99.1.3	NA
3	0.060	3fofA	0.590	3.25	0.072	0.814	5.99.1.-	NA
4	0.060	2rgrA	0.592	3.17	0.108	0.814	5.99.1.3	NA
5	0.060	3k9fA	0.604	3.08	0.080	0.805	5.99.1.-	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	0.04	1fnnA	0.712	2.52	0.171	0.864	0.16	ADP	complex1.pdb.gz	24,70,71,72,76,77
2	0.01	1ab40	0.609	3.37	0.082	0.831	0.12	III	complex2.pdb.gz	23,26,27,29,39,40,65,67,68,69,70,72,73,74
3	0.01	3ksbB	0.601	3.10	0.080	0.805	0.17	QNA	complex3.pdb.gz	61,64,71
4	0.01	3foeB	0.584	3.32	0.062	0.814	0.39	QNA	complex4.pdb.gz	64,67,74
5	0.01	2nov0	0.602	3.20	0.075	0.814	0.13	III	complex5.pdb.gz	26,27,64,65,66
6	0.01	1zaoA	0.604	2.92	0.041	0.754	0.12	ATP	complex6.pdb.gz	39,41,91,92

	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.