D-I-TASSER P10266-D1

D-I-TASSER results for P10266-D1

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

Input Sequence in FASTA format

>P10266 (197 residues)
NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKG
HIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGPLAEQDCEKFAFTIP
AINNKEPATRFQWKVLPSALIKAQELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQV
LHLPTQEAGVNPRGLCP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPSALIKAQELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCP
Prediction	CCCCCHHHHHHHHCSSSCCCCCCCCCCCSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSCCCCSSSSCCHHHHHHCCCCCCCCCCCCCCHHHHHHSSSSCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHCCCSSSSSSSCCSSCCCHHHHHHHHHHHHCCCCCCCCC
Confidence	95422023344426043279987654333137862204789799999999999999980882567898888448998348950011128887221467511125888855544123312566889996356751267655688678877545467886299779997402111111389999999981899777799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPSALIKAQELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCP
Prediction	86656433101302023413143163132414332165141466304103400541376351463542341100102446641330131440254246225132131366136210020213447421232314112421542320141241142046432301001113202124405303420362405364348
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHCSSSCCCCCCCCCCCSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSCCCCSSSSCCHHHHHHCCCCCCCCCCCCCCHHHHHHSSSSCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHCCCSSSSSSSCCSSCCCHHHHHHHHHHHHCCCCCCCCC
NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPSALIKAQELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCP

1rw3A1

0.18

0.17

5.60

1.17

DEthreader

--------AWAEGGMGLAVRQAPLIIPLKTSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKGTNDYRPVQDLREVNKRVEDIHPTFCLRLHPTSQPLFAFEW-RD--MGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIPILLQYVDDLLL-AATSELDCQQGTRALTLGNLGYRA

3drrA1

0.30

0.27

8.32

2.86

SPARKS-K

---------------SPISPIETVPVKLKPMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIENPYNTPVFAIKKKSTKWRKLVDFRELNKRTQDFWEVQLGPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFNPDIVICQYMDDLYVGSDLQHRTKIEELRQHLLRWGLTT

1rw3A

0.18

0.17

5.61

1.76

MapAlign

---------AETGGMGLAVRQAPLIIPLKTSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNYRPVQDLREVNKRVEDIDAFFCLRLHPTSQPLFAFEWRDPE-MGISGQLTWTRLPQGFKNSPTLFDEALHRDLRIQHPDLILLQYVDDLLLAATSELDCQQGTLLQTLGNLGYRA

1rw3A1

0.18

5.79

1.51

CEthreader

WLSDFPQAWAETGGMGLAVRQAPLIIPLKASTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGNDYRPVQDLREVNKRVEDIHPTVPLRLHPTSQPLFAFEWRDPEMGISG-QLTWTRLPQGFKNSPTLFDEALHRDLADFRIQLILLQYVDDLLLAATSDCQQGTRALLQTLGNLGYRA

3drrA1

0.31

0.28

8.45

2.14

MUSTER

---------------SPISPIETVPVKLKPMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGNPYNTPVFAIKKKSTKWRKLVDFRELNKRTQDFWEVQLGPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPKQNPDIVICQYMDDLYVGSDIEELRQHLLRWGLT---TPD

3drrA

0.27

0.25

7.63

3.94

HHsearch

---------------SPISPIETVPVKLKPMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKPENPYNTPVFAIKKKDSTWRKLVDFRELNKRT-QDFWEVQLPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKDIVICQYMDDLYVGSDLEGQHRTKILRQHLLRWGLTT

1rw3A1

0.21

0.19

6.14

1.69

FFAS-3D

-------TWLSDFGLAVRQAPLIIPLKA-TSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTDYRPVQDLREVNKRVEDIHPTVPNPYNLLSLKDAFFCLRLDPEMGISGQLTWTRLPQGFKNSPTFDEALHRDLADFRQYVDDLLLAATSELDCQQGTRALLQTLGNLGYR------

3drrA1

0.19

0.18

5.72

1.67

EigenThreader

--------------SPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKPENPYNTPVFAIKKKDSTKRKLVDFRELNKRTQDFWEVQLGVPLDERKYTAFTIPSINNETPGIR-YQYNVLPQGWKGSPAIFQSSMTKPFRKQNPDIVICQYMLYVGSDLEIGQHRTKIEELRQHLLRWGLT

1ikvB

0.29

0.25

7.73

2.55

CNFpred

-----------------------VPVKLKPMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGNPYNTPVFAIKKKDTKWRKLVDFRELNKRTQEVQLGIP-PLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKPDIVIYQYMDDLYVGSDEIGQHRTKIERQHLLRWGLTT

1rw3A

0.18

0.17

5.60

1.17

DEthreader

--------AWAEGGMGLAVRQAPLIIPLKTSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKGTNDYRPVQDLREVNKRVEDIHPTFCLRLHPTSQPLFAFEW-RD--MGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIPILLQYVDDLLL-AATSELDCQQGTRALTLGNLGYRA

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.773

(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	1rw3A	0.93	1.81	0.179	0.995	model1_1rw3A.pdb.gz
2	3drrA1	0.86	1.65	0.275	0.919	model1_3drrA1.pdb.gz
3	1mu2A1	0.79	1.60	0.263	0.843	model1_1mu2A1.pdb.gz
4	4ol8A	0.74	2.79	0.188	0.883	model1_4ol8A.pdb.gz
5	3ig1B	0.64	3.24	0.274	0.772	model1_3ig1B.pdb.gz
6	2fm1D	0.29	6.15	0.044	0.564	model1_2fm1D.pdb.gz
7	1st0A	0.28	5.38	0.057	0.482	model1_1st0A.pdb.gz
8	3uxuA	0.26	5.16	0.042	0.421	model1_3uxuA.pdb.gz
9	3gfrD	0.26	5.25	0.044	0.436	model1_3gfrD.pdb.gz
10	1l5gA6	0.26	5.30	0.068	0.431	model1_1l5gA6.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	0.75	catalytic activity
GO:0004518	0.61	nuclease activity
GO:0003964	0.60	RNA-directed DNA polymerase activity
GO:0004523	0.59	RNA-DNA hybrid ribonuclease activity
GO:0008233	0.57	peptidase activity
GO:0008270	0.50	zinc ion binding
GO:0004190	0.50	aspartic-type endopeptidase activity
GO:0003887	0.50	DNA-directed DNA polymerase activity
GO:0003723	0.50	RNA binding
GO:0003677	0.50	DNA 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:0006259	1.00	DNA metabolic process
GO:0006278	0.69	RNA-dependent DNA biosynthetic process
GO:0051701	0.66	interaction with host
GO:0016032	0.66	viral process
GO:0075713	0.65	establishment of integrated proviral latency
GO:0006310	0.60	DNA recombination
GO:0051169	0.56	nuclear transport
GO:0019068	0.54	virion assembly
GO:0039663	0.52	membrane fusion involved in viral entry into host cell
GO:0090502	0.50	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0015074	0.50	DNA integration

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	0.91	intracellular part
GO:0016020	0.73	membrane
GO:0044428	0.67	nuclear part
GO:0005829	0.67	cytosol
GO:0005654	0.61	nucleoplasm
GO:0005886	0.59	plasma membrane
GO:0005576	0.59	extracellular region

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	0.139	1qajA	0.906	2.07	0.179	0.980	3.1.26.4	146,170
2	0.060	1mu2A	0.794	1.60	0.263	0.843	3.4.23.47	NA
3	0.060	1tp7A	0.505	4.10	0.074	0.726	3.4.22.28	105,114
4	0.060	3ikmD	0.404	5.11	0.049	0.650	2.7.7.7	NA
5	0.060	1xr5A	0.508	4.18	0.091	0.746	3.4.22.28	138

	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	0.36	3qo9A	0.842	2.01	0.275	0.914	0.20	QO9	complex1.pdb.gz	96,99,101,102,105,115
2	0.35	3tamA	0.837	1.68	0.264	0.898	0.30	M06	complex2.pdb.gz	96,97,98,99,102,140,141
3	0.35	1tl1A	0.815	1.65	0.277	0.873	0.18	H18	complex3.pdb.gz	105,107,111,136,137
4	0.34	1fkoA	0.849	1.69	0.282	0.914	0.23	EFZ	complex4.pdb.gz	100,108,136,137
5	0.32	3is9A	0.848	1.74	0.282	0.909	0.20	AC7	complex5.pdb.gz	99,100,105,139
6	0.32	3c6tA	0.860	1.68	0.273	0.924	0.21	M14	complex6.pdb.gz	99,105,106,111
7	0.23	3irxA	0.850	1.91	0.280	0.914	0.21	UDR	complex7.pdb.gz	99,106,107,108,135,136
8	0.21	3lalA	0.853	1.63	0.276	0.914	0.25	KRV	complex8.pdb.gz	100,106,108,136
9	0.21	3dmjA	0.828	1.62	0.263	0.883	0.25	GWE	complex9.pdb.gz	93,102,103,104,105,106,112
10	0.21	1s9gA	0.844	1.77	0.276	0.914	0.28	ABZ	complex10.pdb.gz	96,99,100,105,111

	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.