D-I-TASSER P53667

D-I-TASSER results for P53667

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

Summary of the Protein

Uniprot ID: P53667
Protein Name: LIM domain kinase 1
Gene Name: LIMK1

Input Sequence in FASTA format

>P53667 (647 residues)
MRLTLLCCTWREERMGEEGSELPVCASCGQRIYDGQYLQALNADWHADCFRCCDCSASLS
HQYYEKDGQLFCKKDYWARYGESCHGCSEQITKGLVMVAGELKYHPECFICLTCGTFIGD
GDTYTLVEHSKLYCGHCYYQTVVTPVIEQILPDSPGSHLPHTVTLVSIPASSHGKRGLSV
SIDPPHGPPGCGTEHSHTVRVQGVDPGCMSPDVKNSIHVGDRILEINGTPIRNVPLDEID
LLIQETSRLLQLTLEHDPHDTLGHGLGPETSPLSSPAYTPSGEAGSSARQKPVLRSCSID
RSPGAGSLGSPASQRKDLGRSESLRVVCRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRE
TGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGT
LRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVRENKNVVVADFG
LARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLC
EIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKL
EHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGESGLPAHPEVPD

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	P53667-D1	1-141,262-309	189		MRLTLLCCTWREERMGEEGSELPVCASCGQRIYDGQYLQALNADWHADCFRCCDCSASLSHQYYEKDGQLFCKKDYWARYGESCHGCSEQITKGLVMVAGELKYHPECFICLTCGTFIGDGDTYTLVEHSKLYCGHCYYQTLGHGLGPETSPLSSPAYTPSGEAGSSARQKPVLRSCSIDRSPGAGSLG
2	P53667-D2	142-261	120		VVTPVIEQILPDSPGSHLPHTVTLVSIPASSHGKRGLSVSIDPPHGPPGCGTEHSHTVRVQGVDPGCMSPDVKNSIHVGDRILEINGTPIRNVPLDEIDLLIQETSRLLQLTLEHDPHDT
3	P53667-D3	310-647	338		SPASQRKDLGRSESLRVVCRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGESGLPAHPEVPD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.45

(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	4fl2A	0.54	5.29	0.152	0.666	model1_4fl2A.pdb.gz
2	2ozoA	0.49	5.15	0.145	0.597	model1_2ozoA.pdb.gz
3	7lhtA	0.45	5.29	0.119	0.553	model1_7lhtA.pdb.gz
4	3s95A	0.45	0.65	0.993	0.448	model1_3s95A.pdb.gz
5	2fo0A	0.44	4.80	0.187	0.530	model1_2fo0A.pdb.gz
6	6pjxA	0.42	4.29	0.126	0.479	model1_6pjxA.pdb.gz
7	4myiA	0.42	5.30	0.135	0.508	model1_4myiA.pdb.gz
8	3c4wB	0.42	4.05	0.151	0.471	model1_3c4wB.pdb.gz
9	4yhjA	0.41	4.29	0.131	0.476	model1_4yhjA.pdb.gz
10	1qcfA	0.41	4.80	0.199	0.488	model1_1qcfA.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	0.96	catalytic activity
GO:0004672	0.93	protein kinase activity
GO:0004674	0.79	protein serine/threonine kinase 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:0009987	0.92	cellular process
GO:0008152	0.84	metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0044238	0.82	primary metabolic process
GO:0065007	0.81	biological regulation
GO:0043170	0.81	macromolecule metabolic process
GO:0050789	0.80	regulation of biological process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0050794	0.78	regulation of cellular process
GO:0006796	0.72	phosphate-containing compound metabolic process
GO:0006464	0.70	cellular protein modification process
GO:0006468	0.69	protein phosphorylation
GO:0007165	0.62	signal transduction
GO:0044699	0.53	single-organism 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	0.92	intracellular part
GO:0043226	0.66	organelle
GO:0043229	0.64	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0005634	0.55	nucleus

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	2ecdA	0.097	4.90	0.045	0.121	2.7.10.2	NA
2	0.060	1cmkE	0.395	3.60	0.180	0.441	2.7.11.11 2.7.1.37	NA
3	0.060	1qcfA	0.410	4.73	0.191	0.487	2.7.10.2	NA
4	0.060	3kulB	0.383	2.49	0.266	0.406	2.7.10.1	353
5	0.060	2ivtA	0.383	2.62	0.287	0.408	2.7.10.1	353

	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	0.91	3s95A	0.446	0.65	0.993	0.448	1.89	STU	complex1.pdb.gz	345,346,353,366,368,384,397,413,414,415,416,419,420,464,465,467
2	0.43	1fpuB	0.358	3.02	0.268	0.388	1.09	PRC	complex2.pdb.gz	345,353,367,369,384,388,397,411,413,415,416,419,467,477,478
3	0.41	2g2fB	0.374	2.36	0.266	0.396	1.10	ATG	complex3.pdb.gz	345,353,366,414,415,416,418,419,464
4	0.23	2g2iB	0.373	2.52	0.284	0.397	1.22	ADP	complex4.pdb.gz	347,348,352,367,413,414,415,416,419,420,467
5	0.20	2xynB	0.373	2.43	0.289	0.396	1.33	VX6	complex5.pdb.gz	345,366,388,413,414,415,416,417,418,419,467,478
6	0.20	3qrkA	0.352	3.04	0.268	0.383	0.95	9DP	complex6.pdb.gz	366,367,368,384,388,397,411,413,458,477,478
7	0.18	3kfaA	0.366	2.91	0.254	0.394	1.05	B91	complex7.pdb.gz	345,353,366,367,368,380,384,387,388,391,396,397,411,413,414,415,416,417,419,456,458,467,477,478
8	0.17	3hmiA	0.372	2.82	0.281	0.402	1.24	DKI	complex8.pdb.gz	345,346,352,414,415,416,419,465,467,477,479

	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.