D-I-TASSER P09601

D-I-TASSER results for P09601

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

Summary of the Protein

Uniprot ID: P09601
Protein Name: Heme oxygenase 1
Gene Name: HMOX1

Input Sequence in FASTA format

>P09601 (288 residues)
MERPQPDSMPQDLSEALKEATKEVHTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVA
LEEEIERNKESPVFAPVYFPEELHRKAALEQDLAFWYGPRWQEVIPYTPAMQRYVKRLHE
VGRTEPELLVAHAYTRYLGDLSGGQVLKKIAQKALDLPSSGEGLAFFTFPNIASATKFKQ
LYRSRMNSLEMTPAVRQRVIEEAKTAFLLNIQLFEELQELLTHDTKDQSPSRAPGLRQRA
SNKVQDSAPVETPRGKPPLNTRSQAPLLRWVLTLSFLVATVAVGLYAM

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	P09601-D1	1-288	288		MERPQPDSMPQDLSEALKEATKEVHTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVALEEEIERNKESPVFAPVYFPEELHRKAALEQDLAFWYGPRWQEVIPYTPAMQRYVKRLHEVGRTEPELLVAHAYTRYLGDLSGGQVLKKIAQKALDLPSSGEGLAFFTFPNIASATKFKQLYRSRMNSLEMTPAVRQRVIEEAKTAFLLNIQLFEELQELLTHDTKDQSPSRAPGLRQRASNKVQDSAPVETPRGKPPLNTRSQAPLLRWVLTLSFLVATVAVGLYAM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7412

(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	0.76	1.73	0.399	0.799	model1_1wowA.pdb.gz
2	1ni6C	0.76	1.00	1.000	0.774	model1_1ni6C.pdb.gz
3	2rgzB	0.73	1.40	0.534	0.760	model1_2rgzB.pdb.gz
4	1we1A	0.72	1.71	0.432	0.753	model1_1we1A.pdb.gz
5	1iw1A	0.70	1.38	0.329	0.729	model1_1iw1A.pdb.gz
6	4rajA	0.68	1.91	0.215	0.726	model1_4rajA.pdb.gz
7	3u44B	0.32	6.33	0.054	0.538	model1_3u44B.pdb.gz
8	4mlzA	0.30	6.70	0.049	0.538	model1_4mlzA.pdb.gz
9	1u2lA	0.30	6.40	0.031	0.500	model1_1u2lA.pdb.gz
10	5fj8A	0.29	7.10	0.027	0.562	model1_5fj8A.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	0.83	catalytic activity
GO:0016491	0.81	oxidoreductase activity
GO:0004392	0.80	heme oxygenase (decyclizing) activity
GO:1901363	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0020037	0.53	heme 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:

[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	0.88	response to stimulus
GO:0009987	0.88	cellular process
GO:0065007	0.84	biological regulation
GO:0006950	0.82	response to stress
GO:0044699	0.79	single-organism process
GO:0050789	0.76	regulation of biological process
GO:0044763	0.75	single-organism cellular process
GO:0008152	0.75	metabolic process
GO:0065008	0.73	regulation of biological quality
GO:0050794	0.73	regulation of cellular process
GO:0071704	0.72	organic substance metabolic process
GO:0044237	0.72	cellular metabolic process
GO:0044710	0.71	single-organism metabolic process
GO:0006807	0.70	nitrogen compound metabolic process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0046483	0.69	heterocycle metabolic process
GO:0006725	0.69	cellular aromatic compound metabolic process
GO:1901564	0.68	organonitrogen compound metabolic process
GO:0051186	0.67	cofactor metabolic process
GO:0042440	0.67	pigment metabolic process
GO:0033013	0.67	tetrapyrrole metabolic process
GO:0042221	0.66	response to chemical
GO:0019222	0.66	regulation of metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0042168	0.65	heme metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0051716	0.64	cellular response to stimulus
GO:0048519	0.64	negative regulation of biological process
GO:0009628	0.64	response to abiotic stimulus
GO:0051171	0.63	regulation of nitrogen compound metabolic process
GO:0048523	0.63	negative regulation of cellular process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0010556	0.63	regulation of macromolecule biosynthetic process
GO:2001141	0.62	regulation of RNA biosynthetic process
GO:0070887	0.62	cellular response to chemical stimulus
GO:0034641	0.62	cellular nitrogen compound metabolic process
GO:0010468	0.62	regulation of gene expression
GO:0048518	0.57	positive regulation of biological process
GO:0042167	0.57	heme catabolic process
GO:0006979	0.57	response to oxidative stress
GO:0048583	0.51	regulation of response to stimulus
GO:0006355	0.51	regulation of transcription, DNA-templated
GO:0001666	0.50	response to hypoxia

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	0.94	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0043226	0.81	organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005783	0.73	endoplasmic reticulum
GO:0005634	0.72	nucleus
GO:0016020	0.67	membrane
GO:0044422	0.59	organelle part
GO:0044446	0.58	intracellular organelle part
GO:0048471	0.53	perinuclear region of cytoplasm
GO:0044425	0.53	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	0.616	2qppB	0.740	1.33	0.534	0.760	1.14.99.3	25,58,135,136,139,140,143,144
2	0.602	1iw1A	0.701	1.38	0.329	0.729	1.14.99.3	140,144
3	0.569	2rgzB	0.735	1.40	0.534	0.760	1.14.99.3	54,62,79,82,84,134,136,140,142,146,148,166,175
4	0.539	1wowA	0.759	1.73	0.399	0.799	1.14.99.3	25,58,135,136,139,140,143,144
5	0.259	1ni6C	0.759	1.00	1.000	0.774	1.14.99.3	25,58,135,136,139,140,143,144

	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	0.95	1n45A	0.730	0.90	1.000	0.743	1.94	HEM	complex1.pdb.gz	18,25,28,34,38,134,135,136,139,142,143,146,183,207,210,214
2	0.85	1s8cA	0.728	0.97	1.000	0.743	1.79	BLA	complex2.pdb.gz	28,29,34,38,50,53,54,57,135,136,139,140,143,144,147,166,167,206,207,210,213,214,217
3	0.53	2q32B	0.737	1.26	0.537	0.757	1.61	OXN	complex3.pdb.gz	33,34,37,54,114,135,136,139,140,143,147,206,207,210,213,214
4	0.48	1twr0	0.731	0.89	1.000	0.743	1.94	III	complex4.pdb.gz	85,86,88,90,91,94,99,101,148,152,157,158,162,163,164,165,168,170,171,173
5	0.47	3hokB	0.717	1.63	0.995	0.743	1.76	Q80	complex5.pdb.gz	28,31,47,50,139,140,143,147,167,214,215
6	0.46	2z68B	0.689	1.26	0.340	0.715	1.17	TIL	complex6.pdb.gz	25,28,29,134,135,138,139,183,207,210,214
7	0.09	2q320	0.724	1.03	0.549	0.740	1.03	III	complex7.pdb.gz	27,31,32,204,205,208,211,212

	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.