D-I-TASSER Q8N4T4-D2

D-I-TASSER results for Q8N4T4-D2

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

Input Sequence in FASTA format

>Q8N4T4 (162 residues)
SPDHQQLTRAARLISETAQRVHTIGQKQKNDQHLRRVQALLSGRQAKGLTSGRWFLRQGW
LLVVPPHGEPRPRMFFLFTDVLLMAKPRPPLHLLRSGTFACKALYPMAQCHLSRVFGHSG
GPCGGLLSLSFPHEKLLLMSTDQEELSRWYHSLTWAISSQKN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| SPDHQQLTRAARLISETAQRVHTIGQKQKNDQHLRRVQALLSGRQAKGLTSGRWFLRQGWLLVVPPHGEPRPRMFFLFTDVLLMAKPRPPLHLLRSGTFACKALYPMAQCHLSRVFGHSGGPCGGLLSLSFPHEKLLLMSTDQEELSRWYHSLTWAISSQKN
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSSSSSSCCCCCCCSSSSSSSCCSSSSSSSCCCCCCCCCCSSSSSSSSSCCCCSSSSCCCCCCCCCCCSSSSSSCCSSSSSSCCCHHHHHHHHHHHHHHHHHHHC
Confidence	952899999999999999999999999999999999999737999874557733688634999869998414899996989999997477664444317887788647839998068998877857999939959999929999999999999999998549
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| SPDHQQLTRAARLISETAQRVHTIGQKQKNDQHLRRVQALLSGRQAKGLTSGRWFLRQGWLLVVPPHGEPRPRMFFLFTDVLLMAKPRPPLHLLRSGTFACKALYPMAQCHLSRVFGHSGGPCGGLLSLSFPHEKLLLMSTDQEELSRWYHSLTWAISSQKN
Prediction	865274045015203500530354156453352035015305646361043224113413023336655534100000110000013456444253430313120406604045134676552420020314742010105357114642523451056358
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSSSSSSCCCCCCCSSSSSSSCCSSSSSSSCCCCCCCCCCSSSSSSSSSCCCCSSSSCCCCCCCCCCCSSSSSSCCSSSSSSCCCHHHHHHHHHHHHHHHHHHHC
SPDHQQLTRAARLISETAQRVHTIGQKQKNDQHLRRVQALLSGRQAKGLTSGRWFLRQGWLLVVPPHGEPRPRMFFLFTDVLLMAKPRPPLHLLRSGTFACKALYPMAQCHLSRVFGHSGGPCGGLLSLSFPHEKLLLMSTDQEELSRWYHSLTWAISSQKN

4xh9A

0.15

0.14

4.79

1.33

DEthreader

TPKEHPDVQLLEDAILIIQGVLSDINLKKGESECQYYIDKLEYQRDPRIEASKVLLCHGELRSK----SGHKLYIFLFQDILVLTRPVTRNE--R-HSYQVYRPIPVQELVLEDLQDGDVRMAKNIFRIRFDAQSHTLQANDVFHKQQWFNCIRAAIAHHHH

4gzuA

0.22

0.21

6.61

1.92

SPARKS-K

HRDYADCHEALKAITEVTTELQQSLTRLENLQKLTELQRDLVGVEN-LIAPGREFIREGCLHKLTKK-GLQQRMFFLFSDMLLYTSKS----VTGASHFRIRGFLPLRGMLVEESNEWSVL---HCFTIYAAQKTIVVAASTRLEKEKWMQDLNAAIQAAKP

4c0aA

0.13

0.12

4.29

0.76

MapAlign

-AQKVERLIEAFSQRYCICIFILAFAIILHVSQVQKVEKLIVGLGCVLSLPHRRLVCYCRLFEVPQKLGLHQREIFLFNDLLVVTKIFQK--KKNSVTYSFRQSFSLYGMQVLLF---ENQYYPNGIRLTSSKVLINFNAPNPQDRKKFTDDLRESIAEVQ-

4c0aA

0.14

4.64

0.57

CEthreader

VDDGEDIPREMLMGIYERIRKRELKTNEDHVSQVQKVEKLIVGLGCVLSLPHRRLVCYCRLFEVPDPNKLHQREIFLFNDLLVVTKIFQKKK--NSVTYSFRQSFSLYGMQVLLFENQY---YPNGIRLTSSVVLINFNAPNPQDRKKFTDDLRESIAEVQE

4gzuA

0.23

0.22

6.78

1.54

MUSTER

HRDYADCHEALKAITEVTTELQQSLTRLENLQKLTELQRDLVGVE-NLIAPGREFIREGCLHKLTKKG-LQQRMFFLFSDMLLYTSKSVT----GASHFRIRGFLPLRGMLVEESNEWS---VLHCFTIYAAQKTIVVAASTRLEKEKWMQDLNAAIQAAKP

4gzuA

0.22

0.21

6.61

1.56

HHsearch

HRDYADCHEALKAITEVTTELQQSLTRLENLQKLTELQRDLVGVE-NLIAPGREFIREGCLHKLTKKG-LQQRMFFLFSDMLLYTSKSV----TGASHFRIRGFLPLRGMLVEESNE---WSVLHCFTIYAAQKTIVVAASTRLEKEKWMQDLNAAIQAAKP

1ki1D2

0.18

0.17

5.62

1.66

FFAS-3D

HPDHSHLKHALEKAEELCSQVNEGVREKENSDRLEWIQAHVQCEGLSNCLGPRKFLHSG---KLYKAKNNKELYGFLFNDFLLLTQITKPKVFSPKSNLQYMYPIFLNEVLVK-----LPTDPSGDFHISHIDRVYTLRAESINERTAWVQKIKAASELYIE

4gzuA

0.18

0.17

5.44

0.93

EigenThreader

HRDYADCHEALKAITEVTTELQQSLTRLENLQKLTELQRDLVGVENLIAPGREFIREGCLHKLT--KKGLQQRMFFLFSDMLLYTSKSVTGASH----FRIRGFLPLRGMLVEES----NEWSVLHCFTIYAQKTIVVAASTRLEKEKWMQDLNAAIQAAKP

4mt7A

0.16

0.15

5.14

1.68

CNFpred

HSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGDILDRSSELIYTGEMAWIYQYGRNQQRVFFLFDHQMVLCKKDL----IRRDILYYKGRIDMDKYEVIDIEDGRDVSMKNAFKLHNKEEVHLFFAKKLEEKIRWLRAFREERKMVQE

3odoA

0.15

0.14

4.57

1.33

DEthreader

PTEREKVELAAECCREILHHVNQAVRDMEDLLRLKDYQRRLDLLKNLDITK-KKLVHEGPLTWRVTKDKAVEVHVLLLDDLLLLLQRQD-------ERLLLKPVLRLTSAMTREV-AT----DHKAFYVLFTAQIYELVAQTVSERKNWCALITETAGS---

(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	0.8123

(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	1ki1D2	0.85	2.31	0.201	0.951	model1_1ki1D2.pdb.gz
2	4xh9A	0.85	2.00	0.144	0.944	model1_4xh9A.pdb.gz
3	7csoA	0.82	2.20	0.161	0.932	model1_7csoA.pdb.gz
4	3ky9B	0.81	2.24	0.158	0.932	model1_3ky9B.pdb.gz
5	4d0nB	0.79	2.05	0.129	0.907	model1_4d0nB.pdb.gz
6	2pz1A	0.78	2.72	0.158	0.957	model1_2pz1A.pdb.gz
7	3odoA	0.78	2.03	0.144	0.901	model1_3odoA.pdb.gz
8	2dfkA	0.76	3.08	0.135	0.963	model1_2dfkA.pdb.gz
9	1xcgE	0.75	2.54	0.143	0.889	model1_1xcgE.pdb.gz
10	4c0aA	0.75	2.71	0.121	0.876	model1_4c0aA.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:0098772	0.78	molecular function regulator
GO:0005085	0.77	guanyl-nucleotide exchange factor activity
GO:0005089	0.73	Rho guanyl-nucleotide exchange factor activity
GO:0019899	0.60	enzyme binding
GO:0031267	0.57	small GTPase binding
GO:0003824	0.57	catalytic activity
GO:0016301	0.53	kinase activity
GO:0005198	0.53	structural molecule activity
GO:0043169	0.52	cation binding
GO:0019900	0.52	kinase binding
GO:0004672	0.52	protein kinase activity
GO:0035591	0.51	signaling adaptor activity
GO:0017048	0.51	Rho GTPase binding
GO:0004674	0.51	protein serine/threonine kinase activity
GO:0032947	0.50	protein complex scaffold
GO:0004690	0.50	cyclic nucleotide-dependent protein 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:0050794	1.00	regulation of cellular process
GO:0030335	0.90	positive regulation of cell migration
GO:0009987	0.65	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:0005886	0.91	plasma membrane
GO:0044424	0.83	intracellular part

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	0.170	1bakA	0.495	3.19	0.165	0.624	2.7.11.15	59,78,82,104,127,146
2	0.163	1p6sA	0.508	3.03	0.183	0.636	2.7.11.1	60,72,144
3	0.159	2ys1A	0.510	3.02	0.176	0.624	3.6.5.5	60,102,149
4	0.150	2dynA	0.532	2.16	0.200	0.605	3.6.5.5	60,102
5	0.066	1bwnA	0.575	2.00	0.151	0.648	2.7.10.2	146

	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	0.09	2uvmA	0.568	2.38	0.200	0.648	0.42	GVF	complex1.pdb.gz	51,53,80,82
2	0.08	1h10A	0.567	2.17	0.181	0.642	0.43	4IP	complex2.pdb.gz	48,53,55,82,83
3	0.07	2z0pC	0.580	2.03	0.143	0.648	0.49	4PT	complex3.pdb.gz	45,53,78,81
4	0.03	2uzsA	0.565	2.31	0.181	0.648	0.43	4IP	complex4.pdb.gz	62,64,65,69,73,75
5	0.02	2bcj2	0.542	2.55	0.124	0.636	0.46	III	complex5.pdb.gz	27,30,31,34,35,36,37,38,39,40,41,53
6	0.01	2jkqA	0.310	5.75	0.047	0.605	0.43	VG8	complex6.pdb.gz	113,114,125,127,140

	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.