D-I-TASSER Q96Q11-D3

D-I-TASSER results for Q96Q11-D3

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

Input Sequence in FASTA format

>Q96Q11 (201 residues)
SGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPV
TLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDS
REPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLRE
QWKKSGYQMEKDELLSYIKKT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKKT
Prediction	CCHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHC
Confidence	811899999999819998999999999097042189865567999999999858993799999997499246999998608898999999999998632202444157899999999962378999999999843698999999981888889979899998189876699999999999999479999999999998629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKKT
Prediction	865413410330021630440041036140042031343340630340052057040420102004133474244015425145411510220053244225345444113302410043234402420330152542440152057263461214052026341640440150053026202757152425402630578
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHC
SGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKKT

1mivA

0.11

0.10

3.74

1.17

DEthreader

ISVERT-E-EKLLGGPFAARALPLLAETGLNAYLGLAGKEQLRLAAAY--RWP-WLAAREERWALLCHGVQESRPFLRAWKLPNKVVDEAGAILTALADIP-R-----PEAWTNEQLFSAG-LERALSVETVRAGAPPGPWHEKLRRRFALPIKGELAVNGKDVIE--GP-VKALDAIWRAVV-NGEVENEERIYAWLERN

6q52A

0.12

0.11

3.87

1.21

SPARKS-K

AVERLKSEIDKIFVNPSMQKSMAYLKDSVLTRFL-PVGGLFEVDWITY-----HTDGNPTYGWLYLLHQQKRQFTDIKDYRFSNEEKRLIEKSLELTA------LNTWD-----QWTFYKYTLKQLEMASRVTKKKDLAAIKRQLPIQSRSELAVDGWDLIEWSAKSGPWLKVWIEKIERLIVYGILKNDKELIKDWFEDE

1mivA

0.11

0.10

3.76

1.39

MapAlign

-VE-RTE--EKLLGGPFAARALPLLAETGLNAYLPGLAGK-EKQLRLAAYRWP-WLAAREERWALLCHALGVSRPFLRAWKLPNKVVDEAGAILTALADIPRP--EAWTNEQLFSAGLE-----RALSVETVRAAFPPGPWHEKLRRRFPIELAVNGKDVIEWGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLERN

1ou5A

1.00

0.75

20.90

1.07

CEthreader

SGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSI---------------------------------------------------

6q52A

0.12

0.11

3.87

1.09

MUSTER

AVERLKSEIDKIFVNPSMQKSMAYLKDSVLTRFLPV-----GGLFEVDWITY-HTDGNPTYGWLYLLHQQKRQFTDIKDYRFSNEEKRLIEKSLELTAL-----------NTWDQWTFYKYTLKQLEMASRVTGKKDLAAIKRQLPIQSRSELAVDGWDLIEW-AKSGPWLKVWIEKIERLIVYGILKNDKELIKDWFEDE

3h37B

0.17

5.54

3.22

HHsearch

TGPRLRQELEKILEEKNPLKSIRR-AQFDVIKHLF-PKTYYTPSKENLFRNIPGEVDRFYAVLHVFLEFYDSWKEVRDRYSLRRNLINEIRHVEKSAPALLELSE-RVPASFVYPL-VKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEINGEYLIRKGITSGKIIGEVLEKIL-KKLDGDTRDEE-EILEEVLAS

6q52A

0.14

0.12

4.27

1.26

FFAS-3D

AVERLKSEIDKIFVNPSMQKSMAYLKDSVLTRFLPV------GGLFEVDWITYHTDGNPTYGWLYLLHQQKRQFTDIKDYRFSNEEKRLIEKSLELT----------ALNTWDQWTFYKYTLKQLEMASRVTGKKKDLAAIKRQLPIQSRSELAVDGWDLIESGAKSGPWLKVWIEKIERLIVYGILKNDKELIKDWFED-

1mivA

0.09

3.38

1.23

EigenThreader

IVQNAPLLAHILLGGPFAARALPLLAETGLN-AYLPGLAGKEKQLRLAAAYRWPWLAAREERWALLCHASRPFLRAWK---LPNKVVDEAGAILTALADI---PRPEAWTNEQLFSAGLERALSVETVRAAFTGAPPGPWHEKLRRRFASLPIVNGKDVIEWVGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLERN

3h37A

0.16

0.15

5.14

1.17

CNFpred

TGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKT-EKMENLFRNIPWVEEN-DRFYAVLHVFLEFYESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKG-VSNETICHFLAYLSGEKEGLFKSYLLKIKNKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTR-DEEEILEEVLAS

3h37B

0.14

0.13

4.57

1.00

DEthreader

TGPRLRQELEKILEEKNPLKSIRR-AQFDVIKHLFPKT-YYTPSD-EKENLFRNIPVRFYAVLHVFLEFYDDSWKVRDRYSLRRNLINEIRHVEKSAPALL-EL--SERVPASFVYPLVKGVSNETICHFLAYLSGEKGLFKSYLLKIKKLEKINGEYLIRKGIT----SG-KIIGEVLEKILKKLGRDEEILEVLSGKLA

(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	0.7962

(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	1ou5A2	0.72	0.93	0.933	0.741	model1_1ou5A2.pdb.gz
2	1mivA	0.72	3.22	0.141	0.920	model1_1mivA.pdb.gz
3	6q52A	0.68	3.20	0.124	0.886	model1_6q52A.pdb.gz
4	3h37B	0.66	3.57	0.166	0.900	model1_3h37B.pdb.gz
5	3aqkA	0.50	3.97	0.122	0.672	model1_3aqkA.pdb.gz
6	1gkuB	0.40	5.86	0.036	0.707	model1_1gkuB.pdb.gz
7	3ke9B	0.33	5.62	0.050	0.567	model1_3ke9B.pdb.gz
8	3wfoA1	0.32	5.61	0.077	0.557	model1_3wfoA1.pdb.gz
9	3g17G1	0.28	4.72	0.060	0.433	model1_3g17G1.pdb.gz
10	2y92A	0.26	5.29	0.075	0.423	model1_2y92A.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:0004810	1.00	tRNA adenylyltransferase activity
GO:0000049	1.00	tRNA binding
GO:0000166	0.64	nucleotide binding
GO:0097367	0.63	carbohydrate derivative binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032555	0.62	purine ribonucleotide binding
GO:0032550	0.62	purine ribonucleoside binding
GO:0030554	0.62	adenyl nucleotide binding
GO:0005524	0.61	ATP binding
GO:0034062	0.53	RNA polymerase activity

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	1.00	cellular process
GO:0008152	0.94	metabolic process
GO:0071704	0.93	organic substance metabolic process
GO:0044237	0.93	cellular metabolic process
GO:0044238	0.92	primary metabolic process
GO:0043170	0.92	macromolecule metabolic process
GO:0034641	0.92	cellular nitrogen compound metabolic process
GO:0016070	0.91	RNA metabolic process
GO:0034660	0.89	ncRNA metabolic process
GO:0006396	0.89	RNA processing
GO:0008033	0.88	tRNA processing
GO:0044699	0.75	single-organism process
GO:0032501	0.63	multicellular organismal process
GO:0050896	0.52	response to stimulus
GO:0048856	0.51	anatomical structure development
GO:0044767	0.51	single-organism developmental process
GO:0044708	0.50	single-organism behavior
GO:0044707	0.50	single-multicellular organism process
GO:0001654	0.50	eye development

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:0005739	1.00	mitochondrion
GO:0005622	1.00	intracellular
GO:0044422	0.69	organelle part
GO:0044446	0.68	intracellular organelle part
GO:0044428	0.59	nuclear part
GO:0044429	0.57	mitochondrial part
GO:0005759	0.54	mitochondrial matrix
GO:0005654	0.53	nucleoplasm

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	1w9xA	0.450	5.19	0.046	0.731	3.2.1.1	159
2	0.060	1ahpA	0.450	4.55	0.084	0.672	2.4.1.1	NA
3	0.060	2fhbA	0.437	5.55	0.041	0.751	3.2.1.41	NA
4	0.060	2dieA	0.446	5.45	0.028	0.736	3.2.1.1	164,197
5	0.060	2elcD	0.429	5.34	0.074	0.721	2.4.2.18	88

	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	0.03	3h39A	0.672	3.47	0.147	0.910	0.25	ATP	complex1.pdb.gz	83,86,87,90,93,94,97
2	0.01	1tf2A	0.427	6.07	0.058	0.796	0.26	ADP	complex2.pdb.gz	165,166,171,174
3	0.01	2d3lA	0.454	5.07	0.029	0.726	0.16	GLC	complex3.pdb.gz	164,170,171,174
4	0.01	3dinA	0.460	5.56	0.069	0.811	0.13	UUU	complex4.pdb.gz	165,166,167
5	0.01	1vfgA	0.524	3.53	0.090	0.697	0.19	APC	complex5.pdb.gz	170,173,176,179,183
6	0.01	1ximA	0.456	5.22	0.056	0.746	0.18	XYL	complex6.pdb.gz	6,8,35,65
7	0.01	2xinA	0.452	5.26	0.055	0.746	0.13	SOR	complex7.pdb.gz	49,52,58
8	0.01	5xinC	0.435	5.44	0.049	0.756	0.17	XLS	complex8.pdb.gz	63,66,93
9	0.01	1sijA	0.364	6.17	0.044	0.702	0.37	FES	complex9.pdb.gz	159,160,166,171
10	0.01	2yajA	0.449	5.28	0.048	0.736	0.17	4HP	complex10.pdb.gz	61,86,92,125

	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.