D-I-TASSER O75072

D-I-TASSER results for O75072

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

Summary of the Protein

Uniprot ID: O75072
Protein Name: Fukutin
Gene Name: FKTN

Input Sequence in FASTA format

>O75072 (461 residues)
MSRINKNVVLALLTLTSSAFLLFQLYYYKHYLSTKNGAGLSKSKGSRIGFDSTQWRAVKK
FIMLTSNQNVPVFLIDPLILELINKNFEQVKNTSHGSTSQCKFFCVPRDFTAFALQYHLW
KNEEGWFRIAENMGFQCLKIESKDPRLDGIDSLSGTEIPLHYICKLATHAIHLVVFHERS
GNYLWHGHLRLKEHIDRKFVPFRKLQFGRYPGAFDRPELQQVTVDGLEVLIPKDPMHFVE
EVPHSRFIECRYKEARAFFQQYLDDNTVEAVAFRKSAKELLQLAAKTLNKLGVPFWLSSG
TCLGWYRQCNIIPYSKDVDLGIFIQDYKSDIILAFQDAGLPLKHKFGKVEDSLELSFQGK
DDVKLDVFFFYEETDHMWNGGTQAKTGKKFKYLFPKFTLCWTEFVDMKVHVPCETLEYIE
ANYGKTWKIPVKTWDWKRSPPNVQPNGIWPISEWDEVIQLY

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 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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	O75072-D1	1-248	248		MSRINKNVVLALLTLTSSAFLLFQLYYYKHYLSTKNGAGLSKSKGSRIGFDSTQWRAVKKFIMLTSNQNVPVFLIDPLILELINKNFEQVKNTSHGSTSQCKFFCVPRDFTAFALQYHLWKNEEGWFRIAENMGFQCLKIESKDPRLDGIDSLSGTEIPLHYICKLATHAIHLVVFHERSGNYLWHGHLRLKEHIDRKFVPFRKLQFGRYPGAFDRPELQQVTVDGLEVLIPKDPMHFVEEVPHSRFI
2	O75072-D2	249-461	213		ECRYKEARAFFQQYLDDNTVEAVAFRKSAKELLQLAAKTLNKLGVPFWLSSGTCLGWYRQCNIIPYSKDVDLGIFIQDYKSDIILAFQDAGLPLKHKFGKVEDSLELSFQGKDDVKLDVFFFYEETDHMWNGGTQAKTGKKFKYLFPKFTLCWTEFVDMKVHVPCETLEYIEANYGKTWKIPVKTWDWKRSPPNVQPNGIWPISEWDEVIQLY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.55

(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	5mz61	0.41	7.18	0.045	0.670	model1_5mz61.pdb.gz
2	3qmzA	0.39	7.28	0.048	0.640	model1_3qmzA.pdb.gz
3	1kc7A	0.38	7.24	0.039	0.636	model1_1kc7A.pdb.gz
4	3spaA	0.38	7.15	0.039	0.623	model1_3spaA.pdb.gz
5	2z86C	0.30	7.20	0.036	0.497	model1_2z86C.pdb.gz
6	1r6bX	0.30	7.75	0.045	0.531	model1_1r6bX.pdb.gz
7	2e28A	0.27	7.69	0.046	0.471	model1_2e28A.pdb.gz
8	4xdnA	0.25	7.86	0.038	0.429	model1_4xdnA.pdb.gz
9	1dp5A	0.24	7.32	0.040	0.406	model1_1dp5A.pdb.gz
10	2hwgA2	0.23	6.52	0.036	0.349	model1_2hwgA2.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:0008047	0.93	enzyme activator activity
GO:0003824	0.56	catalytic activity
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound binding
GO:0097367	0.50	carbohydrate derivative 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:0044763	1.00	single-organism cellular process
GO:0065007	0.82	biological regulation
GO:0050789	0.81	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0031323	0.79	regulation of cellular metabolic process
GO:2000112	0.78	regulation of cellular macromolecule biosynthetic process
GO:0032268	0.78	regulation of cellular protein metabolic process
GO:0060049	0.77	regulation of protein glycosylation
GO:0008152	0.74	metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044237	0.72	cellular metabolic process
GO:0043170	0.72	macromolecule metabolic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0044238	0.71	primary metabolic process
GO:0044710	0.68	single-organism metabolic process
GO:0006464	0.67	cellular protein modification process
GO:0006486	0.66	protein glycosylation
GO:0006493	0.64	protein O-linked glycosylation
GO:0035269	0.63	protein O-linked mannosylation
GO:0032502	0.63	developmental process
GO:0044767	0.62	single-organism developmental process
GO:0048856	0.61	anatomical structure development

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:0044444	1.00	cytoplasmic part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0005794	0.95	Golgi apparatus
GO:0005801	0.89	cis-Golgi network
GO:0005634	0.64	nucleus
GO:0005783	0.63	endoplasmic reticulum

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	0.060	2x0sA	0.360	7.13	0.026	0.594	2.7.9.1	NA
2	0.060	2uv8G	0.352	7.89	0.040	0.629	2.3.1.86	NA
3	0.060	3mosA	0.353	7.42	0.053	0.588	2.2.1.1	415
4	0.060	3eqlM	0.300	7.87	0.046	0.534	2.7.7.6	293
5	0.060	1g5aA	0.344	7.30	0.029	0.573	2.4.1.4	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:

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	3ahcA	0.363	7.68	0.043	0.627	0.21	TPP	complex1.pdb.gz	303,319,320,321,368,370
2	0.01	2qtcB	0.365	7.49	0.041	0.620	0.22	TDK	complex2.pdb.gz	251,307,415,416,426
3	0.01	3bg5C	0.357	7.19	0.062	0.592	0.18	PYR	complex3.pdb.gz	300,304,397
4	0.01	3lq2A	0.367	7.48	0.041	0.623	0.31	TDP	complex4.pdb.gz	299,302,320,398,399,400
5	0.01	1sqj0	0.366	7.29	0.036	0.612	0.19	III	complex5.pdb.gz	417,418,419,420
6	0.01	2g25B	0.368	7.53	0.056	0.631	0.17	TDK	complex6.pdb.gz	302,312,320,396,398,399
7	0.01	3bg5D	0.336	7.44	0.031	0.573	0.22	BTI	complex7.pdb.gz	281,284,285,289
8	0.01	3ho8C	0.346	7.33	0.044	0.584	0.15	COA	complex8.pdb.gz	292,294,358,365,410
9	0.01	3lplB	0.366	7.47	0.047	0.620	0.22	TDP	complex9.pdb.gz	299,322,392,394,396,442
10	0.01	3ho8C	0.346	7.33	0.044	0.584	0.31	BTI	complex10.pdb.gz	284,287,292,293

	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.