D-I-TASSER P00390-D3

D-I-TASSER results for P00390-D3

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

Input Sequence in FASTA format

>P00390 (118 residues)
KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMK
MVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR
Prediction	CCCCCCCCSSSSCCCCCSCSSCCHHHHHHHCCCCCSSSSSSSCCCCHHHCCCCCCCSSSSSSSSCCCCSSSSSSSSCCCHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCHHHHHHCCC
Confidence	9985658779717997161217999999964998748999631651222128999728999996899939999997899689999999999909999999615557971788987079
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR
Prediction	8342721020001312301023206402763574614113031332330345655400000001375430000000036032112000102324022521350022111302143438
	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

CCCCCCCCSSSSCCCCCSCSSCCHHHHHHHCCCCCSSSSSSSCCCCHHHCCCCCCCSSSSSSSSCCCCSSSSSSSSCCCHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCHHHHHHCCC
KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR

3l8kA

0.18

5.79

1.50

DEthreader

YVDVKSIPVTIYTIPSLSYVGILPSKARKM-GI-EIVEAEYNMEEDVSAQIYGQKEGVLKLIFERGSMRLIGAWMIGVHSQYLINELGLAVAYGLNAKQLASFAEQHPSTNEIISYTA

1gerB2

0.70

0.69

19.75

3.00

SPARKS-K

-LDYSNIPTVVFSHPPIGTVGLTEPQAREQYGDDQVKVYKSSFTAMYTAVTTHRQPCRMKLVCVGSEEKIVGIHGIGFGMDEMLQGFAVALKMGATKKDFDNTVAIHPTAAEEFVTMR

2yquA1

0.30

0.29

8.75

0.76

MapAlign

-VDYQAIPSVVYTHPEIAAVGYTEEELKAQ-GI-PYKVGKFPYSASGRARAMGETEGFIKVLAHAKTDRILGVHGIGARVGDVLAEAALALFFKASAEDLGRAPHAHPSLSEILKEAA

2yquA

0.28

0.27

8.31

0.51

CEthreader

HVDYQAIPSVVYTHPEIAAVGYTEEELKAQGI--PYKVGKFPYSASGRARAMGETEGFIKVLAHAKTDRILGVHGIGARVGDVLAEAALALFFKASAEDLGRAPHAHPSLSEILKEAA

1grgA

1.00

28.00

1.96

MUSTER

KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR

2qaeA2

0.24

7.39

1.40

HHsearch

HVNYGVIPAVIYTMPEVASVGKSEDELKKEGV--AYKVGKFPFNANSRAKAVSTEDGFVKVLVDKATDRILGVHIVCTTAGELIGEACLAMEYGASSEDVGRTCHAHPTMSEALKEAC

1gerB2

0.70

0.69

19.75

2.22

FFAS-3D

-LDYSNIPTVVFSHPPIGTVGLTEPQAREQYGDDQVKVYKSSFTAMYTAVTTHRQPCRMKLVCVGSEEKIVGIHGIGFGMDEMLQGFAVALKMGATKKDFDNTVAIHPTAAEEFVTMR

1gerB2

0.70

0.69

19.75

1.02

EigenThreader

-LDYSNIPTVVFSHPPIGTVGLTEPQAREQYGDDQVKVYKSSFTAMYTAVTTHRQPCRMKLVCVGSEEKIVGIHGIGFGMDEMLQGFAVALKMGATKKDFDNTVAIHPTAAEEFVTMR

2aaqA

1.00

28.00

1.67

CNFpred

KLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR

3l8kA2

0.18

5.77

1.50

DEthreader

--DVKSIPVTIYTIPSLSYVGILPSKARKM-GI-EIVEAEYNMEEDVSAQIYGQKEGVLKLIFERGSMRLIGAWMIGVHSQYLINELGLAVAYGLNAKQLASFAEQHPSTNEIISYTA

(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	0.8945

(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	6bz0A	0.94	0.97	0.250	0.983	model1_6bz0A.pdb.gz
2	6uziA	0.93	0.98	0.267	0.983	model1_6uziA.pdb.gz
3	3l8kA	0.93	1.01	0.164	0.983	model1_3l8kA.pdb.gz
4	6aonA1	0.93	1.04	0.224	0.983	model1_6aonA1.pdb.gz
5	1zmcD	0.93	1.05	0.284	0.983	model1_1zmcD.pdb.gz
6	1v59A2	0.92	1.07	0.302	0.983	model1_1v59A2.pdb.gz
7	2yquA	0.92	1.08	0.276	0.983	model1_2yquA.pdb.gz
8	1lpfA	0.92	1.11	0.293	0.983	model1_1lpfA.pdb.gz
9	2qaeA	0.92	1.15	0.241	0.983	model1_2qaeA.pdb.gz
10	3ii4B	0.92	1.16	0.259	0.983	model1_3ii4B.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	0.96	catalytic activity
GO:0016491	0.94	oxidoreductase activity
GO:0016651	0.89	oxidoreductase activity, acting on NAD(P)H
GO:0016668	0.86	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0016209	0.64	antioxidant 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	0.81	single-organism process
GO:0009987	0.80	cellular process
GO:0008152	0.79	metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044763	0.60	single-organism cellular process
GO:0050896	0.58	response to stimulus
GO:0044710	0.54	single-organism metabolic process
GO:0006807	0.53	nitrogen compound metabolic 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	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0043226	0.80	organelle
GO:0043229	0.74	intracellular organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0044446	0.52	intracellular organelle part
GO:0005739	0.51	mitochondrion

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	0.297	1grtA	0.873	1.84	0.940	0.992	1.8.1.7	107,112
2	0.267	1gerB	0.867	1.96	0.658	0.992	1.8.1.7	107,112
3	0.226	1zdlA	0.876	1.70	0.410	0.992	1.8.1.9	107,112
4	0.224	1onfA	0.861	1.89	0.552	0.983	1.8.1.7	107,112
5	0.221	1feaA	0.850	1.91	0.374	0.975	1.8.1.12	107,112

	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	0.41	1grbA	0.873	1.86	0.940	0.992	0.14	FAD	complex1.pdb.gz	13,18,19,21,78,79,80,114
2	0.34	1bwcA	0.872	1.85	0.940	0.992	0.19	AJ3	complex2.pdb.gz	19,20,80
3	0.34	4grtA	0.873	1.87	0.940	0.992	0.10	FAD	complex3.pdb.gz	18,19,20,21,58,59,60
4	0.20	1zdlA	0.876	1.70	0.410	0.992	0.12	NDP	complex4.pdb.gz	18,19,20,80,81,82,83
5	0.19	2x99A	0.878	1.74	0.436	0.992	0.14	NDP	complex5.pdb.gz	4,19,20,41,42
6	0.18	2gh5B	0.868	1.90	0.940	0.992	0.17	ELI	complex6.pdb.gz	58,79,83
7	0.13	5grtA	0.874	1.85	0.940	0.992	0.20	TS4	complex7.pdb.gz	87,91,94
8	0.13	3grtA	0.874	1.84	0.940	0.992	0.15	TS2	complex8.pdb.gz	90,93,94
9	0.13	2aaqA	0.870	1.85	0.940	0.992	0.11	FAD	complex9.pdb.gz	11,21,22,27,30
10	0.13	1zy8C	0.926	1.06	0.284	0.983	0.12	FAD	complex10.pdb.gz	19,20,40,41,42

	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.