D-I-TASSER Q8N118

D-I-TASSER results for Q8N118

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

Summary of the Protein

Uniprot ID: Q8N118
Protein Name: Cytochrome P450 4X1
Gene Name: CYP4X1

Input Sequence in FASTA format

>Q8N118 (509 residues)
MEFSWLETRWARPFYLAFVFCLALGLLQAIKLYLRRQRLLRDLRPFPAPPTHWFLGHQKF
IQDDNMEKLEEIIEKYPRAFPFWIGPFQAFFCIYDPDYAKTLLSRTDPKSQYLQKFSPPL
LGKGLAALDGPKWFQHRRLLTPGFHFNILKAYIEVMAHSVKMMLDKWEKICSTQDTSVEV
YEHINSMSLDIIMKCAFSKETNCQTNSTHDPYAKAIFELSKIIFHRLYSLLYHSDIIFKL
SPQGYRFQKLSRVLNQYTDTIIQERKKSLQAGVKQDNTPKRKYQDFLDIVLSAKDESGSS
FSDIDVHSEVSTFLLAGHDTLAASISWILYCLALNPEHQERCREEVRGILGDGSSITWDQ
LGEMSYTTMCIKETCRLIPAVPSISRDLSKPLTFPDGCTLPAGITVVLSIWGLHHNPAVW
KNPKVFDPLRFSQENSDQRHPYAYLPFSAGSRNCIGQEFAMIELKVTIALILLHFRVTPD
PTRPLTFPNHFILKPKNGMYLHLKKLSEC

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	Q8N118-D1	1-188,316-509	382		MEFSWLETRWARPFYLAFVFCLALGLLQAIKLYLRRQRLLRDLRPFPAPPTHWFLGHQKFIQDDNMEKLEEIIEKYPRAFPFWIGPFQAFFCIYDPDYAKTLLSRTDPKSQYLQKFSPPLLGKGLAALDGPKWFQHRRLLTPGFHFNILKAYIEVMAHSVKMMLDKWEKICSTQDTSVEVYEHINSMSAGHDTLAASISWILYCLALNPEHQERCREEVRGILGDGSSITWDQLGEMSYTTMCIKETCRLIPAVPSISRDLSKPLTFPDGCTLPAGITVVLSIWGLHHNPAVWKNPKVFDPLRFSQENSDQRHPYAYLPFSAGSRNCIGQEFAMIELKVTIALILLHFRVTPDPTRPLTFPNHFILKPKNGMYLHLKKLSEC
2	Q8N118-D2	189-315	127		LDIIMKCAFSKETNCQTNSTHDPYAKAIFELSKIIFHRLYSLLYHSDIIFKLSPQGYRFQKLSRVLNQYTDTIIQERKKSLQAGVKQDNTPKRKYQDFLDIVLSAKDESGSSFSDIDVHSEVSTFLL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.89

(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	5t6qA	0.89	1.64	0.493	0.925	model1_5t6qA.pdb.gz
2	6l8hA	0.84	2.33	0.222	0.894	model1_6l8hA.pdb.gz
3	1tqnA	0.82	2.94	0.241	0.902	model1_1tqnA.pdb.gz
4	7cb9A	0.81	2.77	0.186	0.888	model1_7cb9A.pdb.gz
5	1zo4B	0.81	2.58	0.248	0.876	model1_1zo4B.pdb.gz
6	3k9vA	0.80	2.60	0.213	0.874	model1_3k9vA.pdb.gz
7	3na0A	0.80	2.91	0.181	0.890	model1_3na0A.pdb.gz
8	6vbyA	0.80	2.94	0.195	0.886	model1_6vbyA.pdb.gz
9	6j94A	0.79	2.59	0.235	0.855	model1_6j94A.pdb.gz
10	4k0fA	0.79	3.39	0.166	0.894	model1_4k0fA.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:0016491	0.99	oxidoreductase activity
GO:0004497	0.96	monooxygenase activity
GO:0016705	0.83	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0046872	0.81	metal ion binding
GO:0005506	0.79	iron ion binding
GO:0020037	0.78	heme binding
GO:0016709	0.69	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:0019825	0.59	oxygen binding
GO:0016712	0.59	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
GO:0008395	0.58	steroid hydroxylase activity
GO:0070330	0.57	aromatase 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	1.00	metabolic process
GO:0044710	0.99	single-organism metabolic process
GO:0009058	0.86	biosynthetic process
GO:0044711	0.85	single-organism biosynthetic process
GO:0071704	0.82	organic substance metabolic process
GO:0009987	0.81	cellular process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.76	cellular metabolic process
GO:0044763	0.74	single-organism cellular process
GO:0006629	0.74	lipid metabolic process
GO:0044281	0.73	small molecule metabolic process
GO:1901360	0.67	organic cyclic compound metabolic process
GO:0044255	0.62	cellular lipid metabolic process
GO:1901576	0.61	organic substance biosynthetic process
GO:0008202	0.60	steroid metabolic process
GO:0019748	0.58	secondary metabolic process
GO:1901362	0.57	organic cyclic compound biosynthetic process
GO:0008610	0.57	lipid biosynthetic process
GO:1901615	0.56	organic hydroxy compound metabolic process
GO:0044249	0.55	cellular biosynthetic process
GO:0044550	0.54	secondary metabolite biosynthetic process
GO:0006694	0.54	steroid biosynthetic process
GO:0006807	0.53	nitrogen compound metabolic process
GO:1901617	0.52	organic hydroxy compound biosynthetic process
GO:0034641	0.51	cellular nitrogen compound metabolic process
GO:1901564	0.50	organonitrogen compound metabolic process
GO:0055114	0.50	oxidation-reduction process
GO:0044283	0.50	small molecule biosynthetic 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	0.97	cell part
GO:0016020	0.97	membrane
GO:0044424	0.91	intracellular part
GO:0044444	0.81	cytoplasmic part
GO:0044422	0.67	organelle part
GO:0044446	0.66	intracellular organelle part
GO:0043229	0.65	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044425	0.60	membrane part
GO:0005789	0.50	endoplasmic reticulum 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	0.325	3c6gB	0.777	3.00	0.208	0.870	1.14.13.15	125,137,144,317,320,384,447,460
2	0.179	1jpzB	0.809	2.61	0.248	0.876	1.14.14.1 1.6.2.4	NA
3	0.178	1w0eA	0.784	3.01	0.236	0.870	1.14.13.67 1.14.14.1	NA
4	0.177	2q9fA	0.776	2.53	0.232	0.835	1.14.13.98	NA
5	0.176	3hf2A	0.772	2.30	0.255	0.825	1.14.14.1 1.6.2.4	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.72	2x7yA	0.784	2.39	0.259	0.841	1.11	HEM	complex1.pdb.gz	114,125,126,133,144,313,316,317,320,321,324,381,384,446,447,448,452,454,455,456,459,460
	2	0.41	2v0mA	0.802	2.77	0.252	0.874	1.03	UUU	complex2.pdb.gz	110,125,126,133,137,144,219,312,315,316,320,324,380,381,382,383,384,385,386,446,447,448,452,453,454,455,459,460,464,490,492

	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.