D-I-TASSER O60264-D2

D-I-TASSER results for O60264-D2

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

Input Sequence in FASTA format

>O60264 (138 residues)
KAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILFYRKTIGYKVPRNPELPNAAQAQKEEQ
LKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTP
EEVIEYSAVFWERCNELQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILFYRKTIGYKVPRNPELPNAAQAQKEEQLKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQ
Prediction	CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
Confidence	999999999999887656773899999999999999995877888865435899988887423455679999999999999928675689999999999999791389999998089999999999999999866429
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILFYRKTIGYKVPRNPELPNAAQAQKEEQLKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQ
Prediction	855744543443624523213620440153035214553625245575467555545555551763651466345335503751155033620430051035233621430064077243720451052016417538
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
KAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILFYRKTIGYKVPRNPELPNAAQAQKEEQLKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQ

1ofcX

0.70

0.64

18.13

1.17

DEthreader

-----APRPPQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVP-K----TK-VQREEQ-RKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTLIE

1ofcX1

0.77

0.74

20.91

2.04

SPARKS-K

EALKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKNT------KVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.77

0.72

20.51

1.32

MapAlign

--LKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVP------KNTKVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.77

0.74

20.91

1.34

CEthreader

EALKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKNT------KVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.77

0.74

20.91

1.73

MUSTER

EALKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKN------TKVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.77

0.74

20.91

4.57

HHsearch

EALKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKNT------KVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.78

0.73

20.70

2.13

FFAS-3D

---KAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKNT------KVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

1ofcX1

0.77

0.74

20.91

1.30

EigenThreader

EALKAPRPPKQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVPKNT------KVQREEQRKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ

2nogA

0.96

26.83

1.51

CNFpred

KVPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDLPNSAQVQKEEQLKIDEAEPLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQ

1ofcX1

0.70

0.64

18.13

1.17

DEthreader

-----APRPPQPIVQDFQFFPPRLFELLDQEIYYFRKTVGYKVP-K----TK-VQREEQ-RKIDEAEPLTEEEIQEKENLLSQGFTAWTKRDFNQFIKANEKYGRDDIDNIAKDVEGKTPEEVIEYNAVFWERCTLIE

(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	0.7793

(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 AttentionPotential, 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	1ofcX	0.93	1.16	0.765	0.957	model1_1ofcX.pdb.gz
2	2y9yA	0.70	3.20	0.218	0.927	model1_2y9yA.pdb.gz
3	6q7iB1	0.53	4.75	0.061	0.891	model1_6q7iB1.pdb.gz
4	4wnrA	0.53	4.68	0.092	0.906	model1_4wnrA.pdb.gz
5	5a7mA1	0.53	4.76	0.030	0.891	model1_5a7mA1.pdb.gz
6	4d0jA2	0.53	4.46	0.081	0.855	model1_4d0jA2.pdb.gz
7	4iibA	0.53	4.51	0.065	0.855	model1_4iibA.pdb.gz
8	3dpuA	0.52	4.77	0.045	0.884	model1_3dpuA.pdb.gz
9	4i3gA	0.52	4.79	0.071	0.870	model1_4i3gA.pdb.gz
10	3abzA	0.50	4.60	0.089	0.848	model1_3abzA.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:0016787	0.93	hydrolase activity
GO:1901363	0.92	heterocyclic compound binding
GO:0097159	0.92	organic cyclic compound binding
GO:0016887	0.92	ATPase activity
GO:0003676	0.82	nucleic acid binding
GO:0003677	0.57	DNA binding
GO:0035639	0.51	purine ribonucleoside triphosphate binding
GO:0032555	0.51	purine ribonucleotide binding
GO:0032550	0.51	purine ribonucleoside binding
GO:0005524	0.50	ATP 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	0.88	cellular process
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0065007	0.71	biological regulation
GO:0016043	0.71	cellular component organization
GO:0050794	0.70	regulation of cellular process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0044238	0.70	primary metabolic process
GO:0006325	0.69	chromatin organization
GO:0006807	0.68	nitrogen compound metabolic process
GO:0090304	0.67	nucleic acid metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0080090	0.66	regulation of primary metabolic process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0031326	0.65	regulation of cellular biosynthetic process
GO:0019219	0.65	regulation of nucleobase-containing compound metabolic process
GO:0016070	0.65	RNA metabolic process
GO:0010556	0.65	regulation of macromolecule biosynthetic process
GO:0010468	0.65	regulation of gene expression
GO:0044249	0.64	cellular biosynthetic process
GO:0009059	0.64	macromolecule biosynthetic process
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0032774	0.63	RNA biosynthetic process
GO:0032502	0.63	developmental process
GO:0048518	0.60	positive regulation of biological process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0006338	0.59	chromatin remodeling
GO:0044699	0.58	single-organism process
GO:0010628	0.58	positive regulation of gene expression
GO:0048856	0.57	anatomical structure development
GO:0044763	0.54	single-organism cellular process
GO:0048522	0.50	positive regulation of cellular 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:0044424	1.00	intracellular part
GO:0044446	0.96	intracellular organelle part
GO:0044428	0.95	nuclear part
GO:0032991	0.95	macromolecular complex
GO:0043234	0.88	protein complex
GO:0043229	0.85	intracellular organelle
GO:0031010	0.85	ISWI-type complex
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005634	0.81	nucleus
GO:0044427	0.70	chromosomal part
GO:0044454	0.68	nuclear chromosome part
GO:0016589	0.66	NURF 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	1ikpA	0.451	5.18	0.062	0.819	2.4.2.-	NA
2	0.060	1q16A	0.379	5.16	0.023	0.659	1.7.99.4	NA
3	0.060	1dj2A	0.448	4.96	0.022	0.775	6.3.4.4	NA
4	0.060	1mroB	0.466	4.67	0.109	0.790	2.8.4.1	108,110,115,124
5	0.060	1q16B	0.435	4.73	0.062	0.710	1.7.99.4	113

	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	0.01	1hbuB	0.466	4.69	0.107	0.797	0.35	TP7	complex1.pdb.gz	85,86,87,118
2	0.01	1hbmB	0.465	4.66	0.109	0.790	0.36	UUU	complex2.pdb.gz	84,86,87,88,116,117,118
3	0.01	1hbmE	0.464	4.66	0.109	0.790	0.32	UUU	complex3.pdb.gz	84,87,117,118,119
4	0.01	3sqgG	0.459	4.83	0.056	0.812	0.16	UUU	complex4.pdb.gz	104,113,114,115
5	0.01	1honA	0.421	5.17	0.081	0.804	0.14	GNH	complex5.pdb.gz	18,97,127,131
6	0.01	1jkw0	0.468	5.29	0.056	0.833	0.26	III	complex6.pdb.gz	99,100,103,104,118,123,126
7	0.01	1e6yA	0.455	4.88	0.041	0.797	0.11	F43	complex7.pdb.gz	17,18,85,86
8	0.01	3sqgD	0.465	5.13	0.063	0.833	0.37	M43	complex8.pdb.gz	85,88,117
9	0.01	1fiyA	0.467	5.25	0.068	0.906	0.23	ASP	complex9.pdb.gz	92,117,118
10	0.01	1cg1A	0.469	4.55	0.057	0.812	0.12	GDP	complex10.pdb.gz	88,89,128

	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.