D-I-TASSER P30519

D-I-TASSER results for P30519

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

Summary of the Protein

Uniprot ID: P30519
Protein Name: Heme oxygenase 2
Gene Name: HMOX2

Input Sequence in FASTA format

>P30519 (316 residues)
MSAEVETSEGVDESEKKNSGALEKENQMRMADLSELLKEGTKEAHDRAENTQFVKDFLKG
NIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGEN
WEEQVQCPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPST
GEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQA
GSTLARETLEDGFPVHDGKGDMRKCPFYAAEQDKGALEGSSCPFRTAMAVLRKPSLQFIL
AAGVALAAGLLAWYYM

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P30519-D1	1-316	316		MSAEVETSEGVDESEKKNSGALEKENQMRMADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQCPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGSTLARETLEDGFPVHDGKGDMRKCPFYAAEQDKGALEGSSCPFRTAMAVLRKPSLQFILAAGVALAAGLLAWYYM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.723

(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	1wowA	0.69	1.48	0.380	0.722	model1_1wowA.pdb.gz
2	1ni6C	0.68	1.41	0.525	0.706	model1_1ni6C.pdb.gz
3	1we1A	0.68	1.28	0.468	0.699	model1_1we1A.pdb.gz
4	2rgzB	0.68	1.07	0.982	0.693	model1_2rgzB.pdb.gz
5	1iw1A	0.64	1.45	0.338	0.665	model1_1iw1A.pdb.gz
6	4rajA	0.62	1.95	0.187	0.661	model1_4rajA.pdb.gz
7	5fj8A	0.31	7.03	0.055	0.567	model1_5fj8A.pdb.gz
8	1u2lA	0.30	6.59	0.038	0.500	model1_1u2lA.pdb.gz
9	3u44B	0.29	7.02	0.040	0.538	model1_3u44B.pdb.gz
10	4ci6B1	0.27	5.89	0.036	0.421	model1_4ci6B1.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	0.90	catalytic activity
GO:0016491	0.88	oxidoreductase activity
GO:0004392	0.87	heme oxygenase (decyclizing) 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:0050896	0.93	response to stimulus
GO:0009987	0.87	cellular process
GO:0006950	0.86	response to stress
GO:0044699	0.78	single-organism process
GO:0044763	0.73	single-organism cellular process
GO:0008152	0.73	metabolic process
GO:0065007	0.72	biological regulation
GO:0071704	0.70	organic substance metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044710	0.68	single-organism metabolic process
GO:0006807	0.68	nitrogen compound metabolic process
GO:1901360	0.67	organic cyclic compound metabolic process
GO:0046483	0.67	heterocycle metabolic process
GO:0009628	0.67	response to abiotic stimulus
GO:0006725	0.67	cellular aromatic compound metabolic process
GO:1901564	0.66	organonitrogen compound metabolic process
GO:0051186	0.65	cofactor metabolic process
GO:0042440	0.65	pigment metabolic process
GO:0033013	0.65	tetrapyrrole metabolic process
GO:0042168	0.63	heme metabolic process
GO:0050789	0.57	regulation of biological process
GO:0065008	0.56	regulation of biological quality
GO:0001666	0.56	response to hypoxia
GO:0050794	0.52	regulation of cellular process
GO:0034641	0.51	cellular 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	1.00	cell part
GO:0044424	0.88	intracellular part
GO:0044444	0.81	cytoplasmic part
GO:0016020	0.75	membrane
GO:0043226	0.61	organelle
GO:0043229	0.60	intracellular organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0005886	0.60	plasma membrane
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0044446	0.55	intracellular organelle part
GO:0044425	0.50	membrane 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	0.602	1ni6C	0.680	1.41	0.525	0.706	1.14.99.3	45,78,155,156,159,160,163,164
2	0.542	2rgzB	0.676	1.07	0.982	0.693	1.14.99.3	74,82,99,102,104,154,156,158,160,162,166,168,186,188,192,195
3	0.507	1wowA	0.695	1.48	0.380	0.722	1.14.99.3	45,78,155,156,159,160,163,164
4	0.501	1we1A	0.677	1.28	0.468	0.699	1.14.99.3	45,155,156,159,160,163,164
5	0.228	1iw1A	0.639	1.45	0.338	0.665	1.14.99.3	160,164

	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	0.94	2qppB	0.678	0.99	0.986	0.693	1.93	HEM	complex1.pdb.gz	45,54,58,154,155,156,158,159,162,199,203,227,230,234
2	0.74	2q32A	0.664	0.83	0.981	0.674	1.68	OXN	complex2.pdb.gz	48,49,54,57,74,134,155,156,167,187,226,227,230,234
3	0.56	1s8cA	0.657	1.26	0.547	0.677	1.51	BLA	complex3.pdb.gz	48,49,54,58,70,73,74,77,155,156,159,160,163,164,167,186,187,226,227,230,233,234,237
4	0.50	3hokB	0.647	1.81	0.549	0.677	1.49	Q80	complex4.pdb.gz	48,51,67,70,159,160,163,167,187,234,235
5	0.28	1twr0	0.660	1.17	0.547	0.677	1.39	III	complex5.pdb.gz	105,106,108,110,111,114,119,121,168,172,177,178,181,182,183,184,185,188,190,191,193
6	0.14	2q320	0.664	0.83	0.981	0.674	1.18	III	complex6.pdb.gz	47,51,52,228,231,232,235,238,239

	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.