D-I-TASSER Q5T2N8-D2

D-I-TASSER results for Q5T2N8-D2

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

Input Sequence in FASTA format

>Q5T2N8 (195 residues)
GKPSLVRETSRITVLEALRHPIQQVSRRLLSRPQDVLEGVVLSPSLEARVRDIAIMTRNI
KKNRGLYRHILLYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDW
ANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLILASCHPEQ
FDWAINACIDVMVHF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GKPSLVRETSRITVLEALRHPIQQVSRRLLSRPQDVLEGVVLSPSLEARVRDIAIMTRNIKKNRGLYRHILLYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLILASCHPEQFDWAINACIDVMVHF
Prediction	CCCCCSSSCCCCCCCHHHCCCHHHHHHHHHHCCCCCHCHCCCCHHHHHHHHHHHHHHHCHHHCCCCCCCSSSSCCCCCCHHHHHHHHHHHCCCCSSSSSCCCHHHHHCHHHHHHHHHHHHHHHHCCCSSSSSSCHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCHHHHHHHHCSCCC
Confidence	998612543677752011053578887643166643210379888999999999998593534877897388799998788999999715099869975650033312689999999999997189949998456664024688999389999999999985898896799994699420248999851300249
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GKPSLVRETSRITVLEALRHPIQQVSRRLLSRPQDVLEGVVLSPSLEARVRDIAIMTRNIKKNRGLYRHILLYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLILASCHPEQFDWAINACIDVMVHF
Prediction	853533111253443522442354045334743533052003376045204400510432744451221000101333212110320044170200103332004234400420251053047434200000010000035366643363223002201431464443000000012263014002211244267
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSCCCCCCCHHHCCCHHHHHHHHHHCCCCCHCHCCCCHHHHHHHHHHHHHHHCHHHCCCCCCCSSSSCCCCCCHHHHHHHHHHHCCCCSSSSSCCCHHHHHCHHHHHHHHHHHHHHHHCCCSSSSSSCHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCHHHHHHHHCSCCC
GKPSLVRETSRITVLEALRHPIQQVSRRLLSRPQDVLEGVVLSPSLEARVRDIAIMTRNIKKNRGLYRHILLYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLILASCHPEQFDWAINACIDVMVHF

5e7pA

0.20

0.19

6.06

1.33

DEthreader

VARAPVCDRE----L--G--LS-LPDTARADPG--TLDDVGDMVETKRALTEALWPLQHPDTFSDPPRGVLLYGPPGCGKTFVVRALASSGRLSVHAVKGSELMDWVGSSEKAVRELFARARDS-APSLVFLDEIDALAPRRGQNFDSGVTDKVVASLLTELDGIELDVVVLGATNRPDLIDPALLRRLERLVFV

6nyyA

0.22

0.19

6.14

1.56

SPARKS-K

------------------FSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYAKIPKGAILTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEFVGVGPARVRDLFALARKNA-PCILFIDQIDAVGRKRGQS----EQENTLNQLLVEMDNTTTNVVILAGTNRPDILDPALLRRFDRQIFI

3h4mA

0.25

0.22

6.82

0.61

MapAlign

-------------------------AMEVDERPNVRYEDIGGLEKQMQEIREVELPLKFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKFIGEGASLVKDIFKLAKEK-APSIIFIDEIDAIAAKRTDALTDREVQRTLMQLLAEMDGFDGDVKIIGATNRPDILDPAILGRFDRIIEV

3h4mA

0.25

0.22

6.68

0.44

CEthreader

-------------------------AMEVDERPNVRYEDIGGLEKQMQEIREVELPLKHPELFIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKFIGEGASLVKDIFKLAKEKA-PSIIFIDEIDAIAAKRTDALTGREVQRTLMQLLAEMDDARGDVKIIGATNRPDILDPAILRRFDRIIEV

2dhrA

0.24

0.21

6.55

1.36

MUSTER

------------------------RARVLTEAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMVGVGAARVRDLFETAKRH-APCIVFIDEIDAVGRKRGSGGGNDEREQTLNQLLVEMDGFEKAIVVMAATNRPDILDPALLRRFDRQIAI

5e7pA

0.19

6.12

1.12

HHsearch

RGVPSDPVLRHADLEGALTVIRPLSRSAEVSVGSVTLDDVGDMVETKRALTEAVLWPLQHRLGIDPPRGVLLYGPPGCGKTFVVRALASSGRLSVHAVKGSELMDKWGSSEKAVRELFARARD-SAPSLVFLDEIDALAPRRGQNFDSGVTDKVVASLLTELDEPLRDVVVLGATNRPDLIDPALLRRLERLVFV

5ubvA1

0.28

0.23

6.91

2.28

FFAS-3D

---------------------------------NARFSDVHGCDEAKEELQELVEFLRNPEKFGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYMSGSEFDEIVGVGAKRVRELFNAAKA-KAPSIVFIDELDAIGGRRNS-RDATYVRQTLNQLLTEMDGFNSGVIILGATNFPESLDKALTRRFDRHVHV

5l4gH

0.17

5.57

0.72

EigenThreader

GIKESDTGLAPPALWDLAADKQTLQMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGGDNEVQRTMLELINQLDGPRGNIKVLMATNRPDTLDPALMRRLDRKIEF

3eihA

0.23

0.19

6.09

1.31

CNFpred

--------------------------------PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKMGESEKLVKQLFAMAREN-KPSIIFIDQVDALTGTRGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYI

6matA

0.23

0.21

6.59

1.33

DEthreader

-------HGPSGCYVGDL-YV-RVS------IPDTTWSHVGALEDVRKKLEMSIIGPIKNPEFTKPAAGILLWGPPGCGKTLVAKAVANESKANFISIKGPELLNKVGESERAVRQLFSRAKSS-APCILFFDQMDALVPRRDDSL-SDASARVVNTLLTELDGVGDSIYVIGATNRPDMIDEAIRRRLGTSIYV

(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	0.8141

(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	2dhrA1	0.81	1.58	0.241	0.872	model1_2dhrA1.pdb.gz
2	5mpbM	0.80	2.05	0.181	0.892	model1_5mpbM.pdb.gz
3	3h4mA1	0.80	1.64	0.254	0.867	model1_3h4mA1.pdb.gz
4	5e7pA	0.80	2.97	0.198	0.959	model1_5e7pA.pdb.gz
5	3d8bA1	0.80	2.17	0.215	0.882	model1_3d8bA1.pdb.gz
6	4b4tK	0.79	2.56	0.194	0.897	model1_4b4tK.pdb.gz
7	4b4tH	0.79	2.06	0.213	0.877	model1_4b4tH.pdb.gz
8	4b4tI	0.79	2.39	0.193	0.892	model1_4b4tI.pdb.gz
9	6nyyA	0.79	2.24	0.233	0.882	model1_6nyyA.pdb.gz
10	6he8H	0.78	2.30	0.193	0.887	model1_6he8H.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:0016887	0.99	ATPase activity
GO:0042623	0.94	ATPase activity, coupled
GO:1901363	0.91	heterocyclic compound binding
GO:0097159	0.91	organic cyclic compound binding
GO:0035639	0.81	purine ribonucleoside triphosphate binding
GO:0032555	0.81	purine ribonucleotide binding
GO:0032550	0.81	purine ribonucleoside binding
GO:0005524	0.79	ATP binding
GO:0036402	0.65	proteasome-activating ATPase activity
GO:0017025	0.65	TBP-class protein 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	0.95	cellular process
GO:0008152	0.78	metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.74	primary metabolic process
GO:0043170	0.73	macromolecule metabolic process
GO:0044699	0.67	single-organism process
GO:0044237	0.66	cellular metabolic process
GO:0071840	0.65	cellular component organization or biogenesis
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0016043	0.63	cellular component organization
GO:0044763	0.62	single-organism cellular process
GO:0019538	0.62	protein metabolic process
GO:0065007	0.59	biological regulation
GO:0006508	0.59	proteolysis
GO:0050789	0.57	regulation of biological process
GO:0050794	0.56	regulation of cellular process
GO:0006996	0.55	organelle organization

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:0043226	0.79	organelle
GO:0044444	0.78	cytoplasmic part
GO:0043229	0.78	intracellular organelle
GO:0044446	0.77	intracellular organelle part
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle

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	0.226	3b9pA	0.773	2.24	0.172	0.867	3.6.4.3	76,79,81,133
2	0.067	1nsfA	0.671	3.48	0.179	0.846	3.6.4.6	NA
3	0.060	3f9vA	0.591	3.87	0.123	0.790	3.-.-.-	NA
4	0.060	3kx2B	0.528	4.33	0.084	0.754	3.6.4.13	77,81
5	0.060	2hldK	0.593	4.12	0.105	0.821	3.6.3.14	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	0.65	3h4mA	0.802	1.64	0.254	0.867	0.89	ADP	complex1.pdb.gz	39,40,41,76,77,78,79,80,81,82
	2	0.20	1ofhC	0.678	2.86	0.124	0.821	1.65	PO4	complex2.pdb.gz	75,76,77,80

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.