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DMFold results for DMF179954460

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

Input Sequence in FASTA format

DMF179954460 (318 residues)
>protein-A
MKAFTYERVNTPAEAALSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGLGLDKIE
VTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRTRCP
YFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVETIT
PEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASYAFA
LVSVAAIIQPDGSGRVALGGVAHKPWRIEAADAQLSQGAQAVYDTLFASAHPTAENTFKL
LLAKRTLASVLAEARAQA

Multiple Sequence Alignments

Alignment depth: Nf=297.473, number of sequences=6879

Download multiple sequence alignment in aln format.

Download multiple sequence alignment in a3m format.

Predicted Contact and Distance Map

Contact Map

Distance Map

Top 5 final models from DMFold

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Click to view	Rank	Download PDB	pLDDT
	1	model1.pdb.gz	0.98
	2	model2.pdb.gz	0.98
	3	model3.pdb.gz	0.98
	4	model4.pdb.gz	0.98
	5	model5.pdb.gz	0.98

(a)	DMFold generates a large set of structural models by different MSAs as inputs. These models are ranked by predicted TM-score (pTM-score for multimer) or predicted LDDT (pLDDT for monomer) and top 5 models are selected with the highest predicted scores.

Proteins with similar structure

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5g5gB	0.98	0.67	1.00	0.99	Download
2	5y6qB	0.95	1.57	0.41	0.99	Download
3	1rm6B	0.87	2.24	0.27	0.95	Download
4	1zxiC	0.79	1.84	0.26	0.84	Download
5	1ffuC	0.78	1.96	0.27	0.84	Download
6	7dqxB	0.78	2.09	0.26	0.84	Download
7	1t3qC	0.78	2.03	0.26	0.84	Download
8	3hrdG	0.77	2.53	0.24	0.85	Download
9	4zohB	0.75	2.13	0.22	0.82	Download
10	1wygA	0.75	2.57	0.16	0.85	Download

(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

DMF179954460-model1-A/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0016491	1.00	oxidoreductase activity
GO:0016903	0.79	oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0000166	0.76	nucleotide binding
GO:0050660	0.75	flavin adenine dinucleotide 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:

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[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

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[0.9,1.0]

DMF179954460-model1-A/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	1.00	cellular process
GO:0008152	1.00	metabolic process
GO:0044699	0.99	single-organism process
GO:0044237	0.99	cellular metabolic process
GO:0044710	0.98	single-organism metabolic process
GO:0044763	0.97	single-organism cellular process
GO:0071704	0.96	organic substance metabolic process
GO:0044281	0.96	small molecule metabolic process
GO:1901360	0.95	organic cyclic compound metabolic process
GO:0046483	0.95	heterocycle metabolic process
GO:0044238	0.95	primary metabolic process
GO:0006807	0.95	nitrogen compound metabolic process
GO:1901564	0.94	organonitrogen compound metabolic process
GO:0006139	0.94	nucleobase-containing compound metabolic process
GO:0055086	0.93	nucleobase-containing small molecule metabolic process
GO:0072521	0.92	purine-containing compound metabolic process
GO:0044248	0.92	cellular catabolic process
GO:1901565	0.90	organonitrogen compound catabolic process
GO:1901361	0.90	organic cyclic compound catabolic process
GO:0046700	0.90	heterocycle catabolic process
GO:0044712	0.90	single-organism catabolic process
GO:0044270	0.90	cellular nitrogen compound catabolic process
GO:0006144	0.90	purine nucleobase metabolic process
GO:0072523	0.89	purine-containing compound catabolic process
GO:0006145	0.88	purine nucleobase catabolic process
GO:0009115	0.77	xanthine catabolic process
GO:0055114	0.56	oxidation-reduction 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:

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[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

DMF179954460-model1-A/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0042597	0.75	periplasmic space
GO:0016020	0.51	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

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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	0.180	1zxiC	0.788	1.84	0.258	0.840	1.2.99.2	NA
2	0.173	1ffuC	0.782	1.96	0.270	0.840	1.2.99.2	NA
3	0.070	1jroA	0.743	2.57	0.234	0.830	1.1.1.204	NA
4	0.060	2zxcA	0.415	6.24	0.066	0.682	3.5.1.23	NA
5	0.060	3hkzJ	0.383	5.79	0.053	0.601	2.7.7.6	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

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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	0.54	1rm6B	0.869	2.24	0.272	0.947	1.35	FAD	Download	227,29,30,31,32,33,34,51,75,98,99,107,108,111,112,114,115,163,164,207,212,213,230,237,238,239
2	0.18	1ffv4	0.781	1.97	0.266	0.840	1.32	III	Download	11,3,4,6,28,31,32,35,39,40,50,77,100,101,102,105,106,236
3	0.14	1n5wC	0.790	1.82	0.258	0.840	1.10	FAD	Download	332,98,99,103,112,163,164,230,237,238,239
4	0.06	1rm6B	0.869	2.24	0.272	0.947	1.15	SF4	Download	1119,122,123,129,131,138,139,140,157,158,159
5	0.05	1ffv6	0.781	1.97	0.266	0.840	0.86	III	Download	441,231,234,236,239,297,298,301,302,305,309

	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, Quancheng Liu, Qiqige Wuyun, P. Lydia Freddolino, Yang Zhang. DMFold: A deep learning platform for protein complex structure and function predictions based on DeepMSA2. In preparation.
2.	Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, P Lydia Freddolino, Yang Zhang. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods, in press (2023).
3.	Wei Zheng, Qiqige Wuyun, Peter L Freddolino, Yang Zhang. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. 1-20. doi:10.1002/prot.26585. Proteins. (2023).