D-I-TASSER O60488-D3

D-I-TASSER results for O60488-D3

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

Input Sequence in FASTA format

>O60488 (139 residues)
DLVKLQAGEYVSLGKVEAALKNCPLIDNICAFAKSDQSYVISFVVPNQKRLTLLAQQKGV
EGTWVDICNNPAMEAEILKEIREAANAMKLERFEIPIKVRLSPEPWTPETGLVTDAFKLK
RKELRNHYLKDIERMYGGK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DLVKLQAGEYVSLGKVEAALKNCPLIDNICAFAKSDQSYVISFVVPNQKRLTLLAQQKGVEGTWVDICNNPAMEAEILKEIREAANAMKLERFEIPIKVRLSPEPWTPETGLVTDAFKLKRKELRNHYLKDIERMYGGK
Prediction	CSSSCCCCCSSCHHHHHHHHHHCCCCCSSSSSSCCCCCSSSSSSSSCHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCCCSCHHHHHCHHHHHHHHHHHHHHHHCCC
Confidence	9078689964357999999960987308999964999737999970999999999991999999999709999999999999999972999734575799958998887794264354418999999999999997259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DLVKLQAGEYVSLGKVEAALKNCPLIDNICAFAKSDQSYVISFVVPNQKRLTLLAQQKGVEGTWVDICNNPAMEAEILKEIREAANAMKLERFEIPIKVRLSPEPWTPETGLVTDAFKLKRKELRNHYLKDIERMYGGK
Prediction	8334327444121340153047141011000003563410000000337204500674727442530262650252026104610665705520303402024544236442023202320540363047205613678
	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

CSSSCCCCCSSCHHHHHHHHHHCCCCCSSSSSSCCCCCSSSSSSSSCHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCCCSCHHHHHCHHHHHHHHHHHHHHHHCCC
DLVKLQAGEYVSLGKVEAALKNCPLIDNICAFAKSDQSYVISFVVPNQKRLTLLAQQKGVEGTWVDICNNPAMEAEILKEIREAANAMKLERFEIPIKVRLSPEPWTPETGLVTDAFKLKRKELRNHYLKDIERMYGGK

6oz1A

0.33

0.29

8.87

1.33

DEthreader

NVLKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALE-RY----AD-----S--PDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD-

5mssA2

0.29

0.26

7.90

2.29

SPARKS-K

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTP----EALAKYG---------DGEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQL

5mssA2

0.29

0.26

7.90

0.87

MapAlign

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKY------------GDG-EAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQL

6oz1A

0.33

0.30

9.06

0.69

CEthreader

NVLKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALERYAD------------SPDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD-

5mssA2

0.29

0.26

7.90

1.93

MUSTER

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKYGD-------------GEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQL

6oz1A

0.33

0.29

8.87

1.43

HHsearch

NVLKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALERY------------ADSPDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD-

6oz1A5

0.34

0.30

9.04

2.30

FFAS-3D

--LKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALERYAD------------SPDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYA--

6oz1A

0.34

0.30

9.06

1.10

EigenThreader

VL-KLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALERYA---DSPDALKPL---------IQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD-

5mscA

0.29

0.26

7.89

1.36

CNFpred

NVLKLSQGEFVTVAHLEAVFASSPLIRQIFIYGSSERSYLLAVIVPTDDALRGR--------------DTATLKSALAESIQRIAKDANLQPYEIPRDFLIETEPFTIANGLLSGIAKLLRPNLKERYGAQLEQMYTDL

6oz1A5

0.33

0.29

8.86

1.17

DEthreader

--LKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALE-RYA---D------S--PDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD-

(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	0.8375

(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	6oz1A	0.85	1.25	0.325	0.906	model1_6oz1A.pdb.gz
2	5mscA	0.85	1.17	0.288	0.899	model1_5mscA.pdb.gz
3	5mssA	0.84	1.26	0.286	0.906	model1_5mssA.pdb.gz
4	6eqoA	0.65	2.38	0.145	0.791	model1_6eqoA.pdb.gz
5	3e7xA2	0.65	2.35	0.159	0.770	model1_3e7xA2.pdb.gz
6	5gxdA2	0.63	2.66	0.173	0.791	model1_5gxdA2.pdb.gz
7	4wv3A2	0.63	2.27	0.171	0.755	model1_4wv3A2.pdb.gz
8	1ultA2	0.63	2.00	0.255	0.727	model1_1ultA2.pdb.gz
9	5wmmA	0.63	3.45	0.143	0.849	model1_5wmmA.pdb.gz
10	5ifiA2	0.62	2.83	0.225	0.791	model1_5ifiA2.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:0003824	0.99	catalytic activity
GO:0004467	0.85	long-chain fatty acid-CoA ligase 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:0044699	0.98	single-organism process
GO:0009987	0.95	cellular process
GO:0008152	0.92	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0044763	0.86	single-organism cellular process
GO:0044238	0.86	primary metabolic process
GO:0044710	0.85	single-organism metabolic process
GO:0006629	0.80	lipid metabolic process
GO:0044281	0.74	small molecule metabolic process
GO:0044255	0.73	cellular lipid metabolic process
GO:0019752	0.70	carboxylic acid metabolic process
GO:0006631	0.69	fatty acid metabolic process
GO:0065007	0.52	biological regulation
GO:0050789	0.50	regulation of biological 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:0044464	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.87	cytoplasmic part
GO:0043229	0.79	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0016020	0.67	membrane
GO:0044422	0.57	organelle part
GO:0044446	0.53	intracellular organelle part

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	1ps9A	0.454	4.79	0.033	0.770	1.3.1.34	NA
2	0.060	3dlpX	0.594	2.20	0.172	0.712	6.2.1.33	NA
3	0.060	2z8gB	0.442	4.76	0.048	0.748	3.2.1.57	NA
4	0.060	1ry2A	0.580	2.68	0.218	0.727	6.2.1.1	NA
5	0.060	1qmgA	0.447	4.52	0.043	0.727	1.1.1.86	83

	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	0.05	2qvyX	0.590	2.17	0.194	0.705	0.14	34Z	complex1.pdb.gz	1,2,32,33
2	0.05	3lgxC	0.620	2.30	0.183	0.748	0.12	ATP	complex2.pdb.gz	13,14,128
3	0.05	3gpcB	0.616	2.21	0.223	0.741	0.11	COA	complex3.pdb.gz	33,41,42,43,44,110
4	0.04	3cw8X	0.580	2.50	0.153	0.705	0.12	00A	complex4.pdb.gz	3,16,31,32,41
5	0.04	2d1sA	0.582	2.65	0.158	0.727	0.13	SLU	complex5.pdb.gz	31,32,33,34,35,36,38,39
6	0.04	1pg3A	0.618	2.49	0.168	0.755	0.13	PRX	complex6.pdb.gz	30,107,128
7	0.04	1amuB	0.575	2.40	0.175	0.698	0.16	PHE	complex7.pdb.gz	31,111,113,119,120
8	0.03	3gpcA	0.616	2.22	0.214	0.741	0.15	COA	complex8.pdb.gz	42,43,112
9	0.02	3e7xA	0.645	2.35	0.159	0.770	0.12	AMP	complex9.pdb.gz	20,28,29,30,31,32
10	0.02	2d1rA	0.583	2.65	0.158	0.727	0.25	OLU	complex10.pdb.gz	8,9,11,12,13

	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.