D-I-TASSER Q00532

D-I-TASSER results for Q00532

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

Summary of the Protein

Uniprot ID: Q00532
Protein Name: Cyclin-dependent kinase-like 1
Gene Name: CDKL1

Input Sequence in FASTA format

>Q00532 (358 residues)
MMEKYEKIGKIGEGSYGVVFKCRNRDTGQIVAIKKFLESEDDPVIKKIALREIRMLKQLK
HPNLVNLLEVFRRKRRLHLVFEYCDHTVLHELDRYQRGVPEHLVKSITWQTLQAVNFCHK
HNCIHRDVKPENILITKHSVIKLCDFGFARLLAGPSDYYTDYVATRWYRSPELLVGDTQY
GPPVDVWAIGCVFAELLSGVPLWPGKSDVDQLYLIRKTLGDLIPRHQQVFSTNQYFSGVK
IPDPEDMEPLELKFPNISYPALGLLKGCLHMDPTQRLTCEQLLHHPYFENIREIEDLAKE
HNKPTRKTLRKSRKHHCFTETSKLQYLPQLTGSSILPALDNKKYYCDTKKLNYRFPNI

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	Q00532-D1	1-84	84		MMEKYEKIGKIGEGSYGVVFKCRNRDTGQIVAIKKFLESEDDPVIKKIALREIRMLKQLKHPNLVNLLEVFRRKRRLHLVFEYC
2	Q00532-D2	85-358	274		DHTVLHELDRYQRGVPEHLVKSITWQTLQAVNFCHKHNCIHRDVKPENILITKHSVIKLCDFGFARLLAGPSDYYTDYVATRWYRSPELLVGDTQYGPPVDVWAIGCVFAELLSGVPLWPGKSDVDQLYLIRKTLGDLIPRHQQVFSTNQYFSGVKIPDPEDMEPLELKFPNISYPALGLLKGCLHMDPTQRLTCEQLLHHPYFENIREIEDLAKEHNKPTRKTLRKSRKHHCFTETSKLQYLPQLTGSSILPALDNKKYYCDTKKLNYRFPNI

Top 1 final models from D-I-TASSER

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q00532/model1.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(model1.pdb.gz): 3192 ms

reading 5932 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

5932 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4e7wA	0.84	2.58	0.318	0.922	model1_4e7wA.pdb.gz
2	3i4bA	0.84	2.18	0.335	0.899	model1_3i4bA.pdb.gz
3	3eb0A	0.79	2.15	0.289	0.852	model1_3eb0A.pdb.gz
4	3e3pA	0.79	2.41	0.269	0.860	model1_3e3pA.pdb.gz
5	5z33A	0.77	2.45	0.288	0.844	model1_5z33A.pdb.gz
6	6gubA	0.77	1.89	0.392	0.813	model1_6gubA.pdb.gz
7	7kpvA	0.77	2.74	0.321	0.849	model1_7kpvA.pdb.gz
8	1unlA	0.76	1.93	0.390	0.810	model1_1unlA.pdb.gz
9	7nxjA	0.76	2.37	0.334	0.827	model1_7nxjA.pdb.gz
10	4qnyA	0.76	2.18	0.274	0.810	model1_4qnyA.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	0.97	catalytic activity
GO:0004672	0.96	protein kinase activity
GO:0004674	0.86	protein serine/threonine kinase activity
GO:1901363	0.51	heterocyclic compound binding
GO:0097159	0.51	organic cyclic compound 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:0009987	0.92	cellular process
GO:0008152	0.85	metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0044238	0.82	primary metabolic process
GO:0050794	0.81	regulation of cellular process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0019538	0.76	protein metabolic process
GO:0006796	0.75	phosphate-containing compound metabolic process
GO:0006464	0.75	cellular protein modification process
GO:0006468	0.74	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	0.59	organelle
GO:0043229	0.58	intracellular organelle
GO:0043231	0.55	intracellular membrane-bounded organelle
GO:0005737	0.53	cytoplasm

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

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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	0.433	3mtlA	0.718	2.81	0.321	0.793	2.7.11.22	12,14,16,19,126,146,169
2	0.283	3lm0A	0.666	2.34	0.269	0.718	2.7.11.1	52
3	0.186	1unlA	0.763	1.93	0.390	0.810	2.7.11.22	NA
4	0.174	2i6lA	0.719	2.19	0.322	0.768	2.7.11.24	NA
5	0.161	2pk9A	0.742	1.89	0.349	0.785	2.7.11.22	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

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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	0.71	1q3dA	0.816	2.28	0.339	0.883	1.49	STU	complex1.pdb.gz	11,12,19,32,81,82,83,84,131,134,144,145
2	0.68	3i4bB	0.831	2.11	0.335	0.891	1.49	Z48	complex2.pdb.gz	13,14,15,17,19,32,34,36,81,82,83,84,85,132,134,144,145
3	0.66	3o0gB	0.702	1.61	0.373	0.735	1.22	3O0	complex3.pdb.gz	12,19,33,35,82,83,84,85,86,90,134,145
4	0.65	1j1cB	0.836	2.28	0.341	0.902	1.41	ADP	complex4.pdb.gz	12,15,18,32,34,65,82,83,84,87,131,132,134,145
5	0.64	1q41A	0.821	2.21	0.339	0.883	1.01	IXM	complex5.pdb.gz	12,18,33,81,82,83,84,85,87,134,144
6	0.64	3zrkB	0.829	2.45	0.331	0.902	1.06	ZRK	complex6.pdb.gz	16,19,32,34,82,83,84,134,145
7	0.61	3f88A	0.828	2.22	0.334	0.894	1.39	2HT	complex7.pdb.gz	12,19,131,132,145
8	0.54	1pmqA	0.724	2.66	0.245	0.799	1.13	880	complex8.pdb.gz	11,14,19,32,33,34,65,67,79,81,83,84,86,87,131,132,144
9	0.36	2p33A	0.708	2.26	0.259	0.765	0.93	J07	complex9.pdb.gz	11,12,13,19,32,65,81,82,84,85
10	0.35	3oxiA	0.705	2.26	0.266	0.768	0.80	SYY	complex10.pdb.gz	13,18,32,81,82,83,84,144

	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.