D-I-TASSER Q5T9C9

D-I-TASSER results for Q5T9C9

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

Summary of the Protein

Uniprot ID: Q5T9C9
Protein Name: Phosphatidylinositol 4-phosphate 5-kinase-like protein 1
Gene Name: PIP5KL1

Input Sequence in FASTA format

>Q5T9C9 (394 residues)
MAAPSPGPREVLAPSPEAGCRAVTSSRRGLLWRLRDKQSRLGLFEISPGHELHGMTCMMQ
AGLWAATQVSMDHPPTGPPSRDDFSEVLTQVHEGFELGTLAGPAFAWLRRSLGLAEEDYQ
AALGPGGPYLQFLSTSKSKASFFLSHDQRFFLKTQGRREVQALLAHLPRYVQHLQRHPHS
LLARLLGVHSLRVDRGKKTYFIVMQSVFYPAGRISERYDIKGCEVSRWVDPAPEGSPLVL
VLKDLNFQGKTINLGPQRSWFLRQMELDTTFLRELNVLDYSLLIAFQRLHEDERGPGSSL
IFRTARSVQGAQSPEESRAQNRRLLPDAPNALHILDGPEQRYFLGVVDLATVYGLRKRLE
HLWKTLRYPGRTFSTVSPARYARRLCQWVEAHTE

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	Q5T9C9-D1	1-205	205		MAAPSPGPREVLAPSPEAGCRAVTSSRRGLLWRLRDKQSRLGLFEISPGHELHGMTCMMQAGLWAATQVSMDHPPTGPPSRDDFSEVLTQVHEGFELGTLAGPAFAWLRRSLGLAEEDYQAALGPGGPYLQFLSTSKSKASFFLSHDQRFFLKTQGRREVQALLAHLPRYVQHLQRHPHSLLARLLGVHSLRVDRGKKTYFIVMQ
2	Q5T9C9-D2	206-394	189		SVFYPAGRISERYDIKGCEVSRWVDPAPEGSPLVLVLKDLNFQGKTINLGPQRSWFLRQMELDTTFLRELNVLDYSLLIAFQRLHEDERGPGSSLIFRTARSVQGAQSPEESRAQNRRLLPDAPNALHILDGPEQRYFLGVVDLATVYGLRKRLEHLWKTLRYPGRTFSTVSPARYARRLCQWVEAHTE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	1bo1A	0.72	2.16	0.227	0.759	model1_1bo1A.pdb.gz
2	4tz7A	0.68	2.04	0.247	0.718	model1_4tz7A.pdb.gz
3	7k2vP	0.58	2.39	0.257	0.619	model1_7k2vP.pdb.gz
4	6z2wE	0.42	4.93	0.055	0.548	model1_6z2wE.pdb.gz
5	4u94A	0.41	5.50	0.094	0.584	model1_4u94A.pdb.gz
6	5jy7I	0.41	5.19	0.075	0.564	model1_5jy7I.pdb.gz
7	5yz0A	0.40	5.20	0.045	0.548	model1_5yz0A.pdb.gz
8	2y3aA	0.40	5.75	0.057	0.576	model1_2y3aA.pdb.gz
9	5fvmA	0.40	5.22	0.060	0.546	model1_5fvmA.pdb.gz
10	6nctA	0.40	5.47	0.051	0.553	model1_6nctA.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:0016307	0.96	phosphatidylinositol phosphate kinase activity
GO:0016308	0.79	1-phosphatidylinositol-4-phosphate 5-kinase activity
GO:1901363	0.50	heterocyclic compound binding
GO:0097159	0.50	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:0044699	0.88	single-organism process
GO:0008152	0.85	metabolic process
GO:0065007	0.84	biological regulation
GO:0044237	0.84	cellular metabolic process
GO:0044763	0.83	single-organism cellular process
GO:0006796	0.82	phosphate-containing compound metabolic process
GO:0050794	0.80	regulation of cellular process
GO:0071704	0.74	organic substance metabolic process
GO:0044710	0.74	single-organism metabolic process
GO:0044238	0.74	primary metabolic process
GO:0019637	0.71	organophosphate metabolic process
GO:0006644	0.70	phospholipid metabolic process
GO:0046488	0.69	phosphatidylinositol metabolic process
GO:0016310	0.57	phosphorylation
GO:0051128	0.56	regulation of cellular component organization
GO:0048518	0.54	positive regulation of biological process
GO:0048522	0.53	positive regulation of cellular 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	0.90	intracellular part
GO:0044444	0.69	cytoplasmic part
GO:0016020	0.69	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	0.495	2gk9B	0.573	1.48	0.247	0.596	2.7.1.149 2.7.1.68	153,279
2	0.136	1bo1A	0.716	2.16	0.227	0.759	2.7.1.149	153,279
3	0.060	3epsA	0.370	5.78	0.040	0.533	2.7.11.5	NA
4	0.060	2xalA	0.385	5.69	0.081	0.551	2.7.1.158	229
5	0.060	2zvaA	0.320	5.29	0.119	0.449	2.7.10.2	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	0.01	3ibeA	0.389	4.63	0.059	0.508	0.17	L64	complex1.pdb.gz	115,116,118,119,204
2	0.01	3apcA	0.396	5.13	0.049	0.528	0.16	MMD	complex2.pdb.gz	113,115,201,203
3	0.01	3qjzA	0.390	4.49	0.059	0.505	0.19	QJZ	complex3.pdb.gz	62,98,99,101,104,202
4	0.01	3csfA	0.393	5.01	0.039	0.520	0.21	DW2	complex4.pdb.gz	103,104,105,204
5	0.01	1e8zA	0.387	4.91	0.047	0.510	0.17	STU	complex5.pdb.gz	66,102,103,104,111,186
6	0.01	1e8xA	0.384	5.07	0.057	0.515	0.13	ATP	complex6.pdb.gz	117,123,184
7	0.01	2wxoA	0.391	5.15	0.056	0.528	0.18	ZZP	complex7.pdb.gz	115,183,203
8	0.01	3t8mA	0.386	4.94	0.036	0.510	0.18	3T8	complex8.pdb.gz	143,202,204,205
9	0.01	2wxkA	0.397	5.06	0.072	0.538	0.13	RW4	complex9.pdb.gz	186,187,188
10	0.01	2chzA	0.387	5.11	0.050	0.520	0.15	093	complex10.pdb.gz	104,201,203

	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.