D-I-TASSER O43678-D1

D-I-TASSER results for O43678-D1

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

Input Sequence in FASTA format

>O43678 (99 residues)
MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSD
VQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA
Prediction	CCCHHHHCCCCCCCCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCSSSSSSCCCCSSSSSCCCCCHHHHHHHHHHHHHCCC
Confidence	952155511001234379999985999743789999999899999989996499997799996899998179579997799999999999999996169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA
Prediction	744233432234434044010300742630520141046404510762471302034277440302020434553413076254740251045027668
	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

                   |                   |                   |                   |

SS
Seq

CCCHHHHCCCCCCCCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCSSSSSSCCCCSSSSSCCCCCHHHHHHHHHHHHHCCC
MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA

4v1ag

0.17

0.16

5.32

1.33

DEthreader

--LHNGLGR--YVQQLQRLSFSLSRDAPSSRGAREFVEREVTDFARRNPGVVIYVNPRPCCVPRVVAEYLNGAVREESIHCKSVEEIAALVQKLADQSV

7a23Q

0.48

0.44

12.93

2.69

SPARKS-K

-------WRGSISKSMKELRILLCQSSPASAPTRTFVEKNYKDLKSLNPKLPILIRECSGVQPQMWARYDMGVERCVNLDGLTEPQILKALENLVKSGA

1vw44

0.21

0.19

6.09

0.87

MapAlign

------NGVGAFVFPCRKITLQFCNWGGSSEGMRKFLTSRLDKWGQEFPWIQFEVMRK-SGHPLLRAEYTNGREKVICVRNLNIDNVENKLKLLKDS--

1vw44

0.24

7.54

0.75

CEthreader

ARNSIGRNGVGAFVFCRKITLQFCNWGGSSEGMRKFLTSRLDKWGQEFPWIQFEVMRKS-GHPLLRAEYTNGREKVICVRNLNIDNVENKLKLLKDSDG

1s3aA

1.00

0.86

24.04

2.28

MUSTER

--------------GLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA

4v1ag

0.18

5.91

2.56

HHsearch

FLTSVLHNGLGRYVQLQRLSFSLSRDAPSSRGAREFVEREVTDFARRNPGVVIYVNPRPCCVPRVVAEYLNGAVREESIHCKSVEEIAALVQKLADQSG

1s3aA

1.00

0.86

24.04

1.74

FFAS-3D

--------------GLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA

4v1ag

0.16

5.36

0.75

EigenThreader

LTSVLHNGLGRYVQQLQRLSFSLSRDAPSSRGAREFVEREVTDFARRNPGVVIYVNPRPCCVPRVVAEYLNGAVREESIHCKSVEEIAALVQKLADQSG

1s3aA

1.00

0.86

24.04

1.59

CNFpred

--------------GLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA

1vw44

0.21

0.20

6.40

1.33

DEthreader

SIGRNGV----FVFPCRKITLQFCNWGGSSEGMRKFLTSRLDKWGQEFPWIQFEVMRKS-GHPLLRAEYTNGREKVICVRNLNIDNVENKLKLLKDSDD

(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	0.8396

(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	4v1ag	0.85	1.36	0.172	0.909	model1_4v1ag.pdb.gz
2	1vw44	0.82	1.51	0.194	0.889	model1_1vw44.pdb.gz
3	7arcS	0.81	1.92	0.409	0.929	model1_7arcS.pdb.gz
4	7a23Q	0.80	2.05	0.478	0.929	model1_7a23Q.pdb.gz
5	5aj3c	0.80	1.96	0.130	0.899	model1_5aj3c.pdb.gz
6	7zm7f	0.79	1.60	0.341	0.889	model1_7zm7f.pdb.gz
7	6y79f	0.73	1.30	0.338	0.808	model1_6y79f.pdb.gz
8	4v1ap	0.68	2.66	0.110	0.919	model1_4v1ap.pdb.gz
9	6qt8A	0.67	3.70	0.051	0.970	model1_6qt8A.pdb.gz
10	1s3aA	0.65	2.43	1.000	0.859	model1_1s3aA.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:0003735	0.70	structural constituent of ribosome
GO:0003824	0.62	catalytic activity
GO:0016491	0.55	oxidoreductase 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:0008152	0.93	metabolic process
GO:0044699	0.87	single-organism process
GO:0044710	0.84	single-organism metabolic process
GO:0009987	0.82	cellular process
GO:0044237	0.79	cellular metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0055114	0.63	oxidation-reduction process
GO:0006091	0.63	generation of precursor metabolites and energy
GO:0022904	0.62	respiratory electron transport chain
GO:0071822	0.60	protein complex subunit organization
GO:0034622	0.60	cellular macromolecular complex assembly
GO:0032981	0.59	mitochondrial respiratory chain complex I assembly
GO:0006120	0.59	mitochondrial electron transport, NADH to ubiquinone

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:0044429	1.00	mitochondrial part
GO:0032991	1.00	macromolecular complex
GO:0044425	0.67	membrane part
GO:0044455	0.62	mitochondrial membrane part
GO:0043234	0.62	protein complex
GO:1902494	0.61	catalytic complex
GO:0098800	0.61	inner mitochondrial membrane protein complex
GO:1990204	0.60	oxidoreductase complex
GO:0098803	0.60	respiratory chain complex
GO:0005747	0.59	mitochondrial respiratory chain complex I
GO:0030529	0.54	intracellular ribonucleoprotein complex
GO:0044391	0.53	ribosomal subunit
GO:0005762	0.52	mitochondrial large ribosomal subunit
GO:0016020	0.50	membrane

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	0.067	2vimA	0.599	2.74	0.079	0.758	1.8.4.8	NA
2	0.067	1dbyA	0.574	3.11	0.056	0.778	1.8.4.10	NA
3	0.067	1v98A	0.584	2.90	0.130	0.778	1.8.1.9	NA
4	0.066	1cqgA	0.579	3.00	0.045	0.758	1.8.4.10	NA
5	0.066	1syrA	0.566	2.78	0.067	0.737	1.8.1.8	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:

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	2pvo2	0.591	2.85	0.090	0.768	0.98	III	complex1.pdb.gz	24,25,26,27,28,29,32,58,62
2	0.02	1mdkA	0.578	2.82	0.045	0.748	0.68	III	complex2.pdb.gz	25,26,27,29,32,33,57,58,59,63,78,79,80
3	0.01	3qfaD	0.582	2.86	0.045	0.758	0.84	GOL	complex3.pdb.gz	24,26,30,31,34

	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.