D-I-TASSER Q17RQ9

D-I-TASSER results for Q17RQ9

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

Summary of the Protein

Uniprot ID: Q17RQ9
Protein Name: NTPase KAP family P-loop domain-containing protein 1
Gene Name: NKPD1

Input Sequence in FASTA format

>Q17RQ9 (610 residues)
MQQEAAQRESEELQHVQWRPRAVSGWGVPQLLWYLVFLQPIITEVHLRRRNVQFLFIRFS
AWQYAGTDKLWAGLVTTLCEGIRRHYGALPFSVYSVLGNKPATRQDCCQSEWHCRRRVCL
GLLALLAALGLGVGLLYLSLGGHALGHGSPSGSLLKVFGGAATTLSGSGLLMAVYSVGKH
LFVSQRKKIERLVSREKFGSQLGFMCEVKKEVELLTDFLCFLEIYQRRRLRVVLEVTGLD
TCYPERVVGVLNAINTLLSDSHAPFIFILVVDPSILAACLESAGNMKGTADNGYLFLNRT
VTLPFSVPIMGRRTKLQFLHDAVQSRDDLLYREMTRKPWLPGDAGGESAQLLAVQAQAGT
ERGQGRIDDEAARRIQEALFCLHDERDCLYEYVPDNVVSMRRIVNTVPITVRLLQQQQQQ
GDFGGPTPRQAVAWVVLANQWPCRLSWALQCLEDRQQTGGAPEGRARLWDVFRDNSRELH
TMTKALQNVLDLDGDPELFERFLGADFPFTVAEAQSLLRCTVNLDHSIRRRMGLIRAVSA
LKPPSPPKSPTRDTPHAAHRANSASRAPPSGRASGQAGEGHHTGDLAHRGKLWPVACALF
RPGQSSPGGP

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	Q17RQ9-D1	1-302	302		MQQEAAQRESEELQHVQWRPRAVSGWGVPQLLWYLVFLQPIITEVHLRRRNVQFLFIRFSAWQYAGTDKLWAGLVTTLCEGIRRHYGALPFSVYSVLGNKPATRQDCCQSEWHCRRRVCLGLLALLAALGLGVGLLYLSLGGHALGHGSPSGSLLKVFGGAATTLSGSGLLMAVYSVGKHLFVSQRKKIERLVSREKFGSQLGFMCEVKKEVELLTDFLCFLEIYQRRRLRVVLEVTGLDTCYPERVVGVLNAINTLLSDSHAPFIFILVVDPSILAACLESAGNMKGTADNGYLFLNRTVT
2	Q17RQ9-D2	303-610	308		LPFSVPIMGRRTKLQFLHDAVQSRDDLLYREMTRKPWLPGDAGGESAQLLAVQAQAGTERGQGRIDDEAARRIQEALFCLHDERDCLYEYVPDNVVSMRRIVNTVPITVRLLQQQQQQGDFGGPTPRQAVAWVVLANQWPCRLSWALQCLEDRQQTGGAPEGRARLWDVFRDNSRELHTMTKALQNVLDLDGDPELFERFLGADFPFTVAEAQSLLRCTVNLDHSIRRRMGLIRAVSALKPPSPPKSPTRDTPHAAHRANSASRAPPSGRASGQAGEGHHTGDLAHRGKLWPVACALFRPGQSSPGGP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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	5gm6B	0.39	7.62	0.052	0.613	model1_5gm6B.pdb.gz
2	6wjvA	0.37	7.69	0.050	0.600	model1_6wjvA.pdb.gz
3	6bq1A	0.37	7.80	0.049	0.587	model1_6bq1A.pdb.gz
4	6z2wE	0.36	7.46	0.052	0.556	model1_6z2wE.pdb.gz
5	5m59A	0.35	8.37	0.024	0.592	model1_5m59A.pdb.gz
6	4kf7A	0.35	7.79	0.037	0.562	model1_4kf7A.pdb.gz
7	7lheA	0.35	7.53	0.049	0.554	model1_7lheA.pdb.gz
8	5yz0A	0.35	8.05	0.066	0.574	model1_5yz0A.pdb.gz
9	2uvcG	0.34	8.37	0.029	0.592	model1_2uvcG.pdb.gz
10	4f91B	0.34	8.23	0.039	0.577	model1_4f91B.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:0030165	0.98	PDZ domain binding
GO:0019887	0.98	protein kinase regulator 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:0065007	0.89	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0031323	0.84	regulation of cellular metabolic process
GO:0032268	0.83	regulation of cellular protein metabolic process
GO:0045859	0.82	regulation of protein kinase activity
GO:0007165	0.78	signal transduction
GO:0038180	0.75	nerve growth factor signaling pathway
GO:0009987	0.60	cellular process
GO:0044699	0.50	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	0.95	intracellular part
GO:0016020	0.79	membrane
GO:0044444	0.72	cytoplasmic part
GO:0043226	0.66	organelle
GO:0043229	0.64	intracellular organelle
GO:0032991	0.61	macromolecular complex
GO:0043234	0.60	protein complex
GO:0043227	0.59	membrane-bounded organelle
GO:0043231	0.57	intracellular membrane-bounded organelle

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	1l1lA	0.294	8.32	0.035	0.497	1.17.4.2	NA
2	0.060	2vuaA	0.224	7.31	0.071	0.346	3.4.24.69	NA
3	0.060	3ecqB	0.300	8.12	0.030	0.498	3.2.1.97	NA
4	0.060	2vkzG	0.339	8.40	0.038	0.582	2.3.1.38 3.1.2.14	NA
5	0.060	1fohC	0.293	7.70	0.039	0.470	1.14.13.7	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	1ydiA	0.177	6.09	0.081	0.241	0.24	III	complex1.pdb.gz	118,121,124,125,128,132,163
2	0.01	3tj5A	0.170	5.89	0.058	0.233	0.11	III	complex2.pdb.gz	26,29,30,32
3	0.01	1rke0	0.182	5.75	0.061	0.243	0.21	III	complex3.pdb.gz	26,29,30,33,34,37
4	0.01	2ibfA	0.170	6.01	0.068	0.233	0.18	III	complex4.pdb.gz	28,191,194,195
5	0.01	1syqA	0.174	5.89	0.047	0.234	0.24	III	complex5.pdb.gz	125,132,136,140,143
6	0.01	3rf3A	0.165	6.24	0.069	0.228	0.24	III	complex6.pdb.gz	34,35,119,122,123,126,129,130,133
7	0.01	1rkcA	0.167	5.84	0.057	0.223	0.12	III	complex7.pdb.gz	24,27,28,31,34,38
8	0.01	1zvzA	0.177	5.73	0.058	0.238	0.11	III	complex8.pdb.gz	27,28,93,117

	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.