D-I-TASSER Q8TDR2-D3

D-I-TASSER results for Q8TDR2-D3

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

Input Sequence in FASTA format

>Q8TDR2 (217 residues)
CEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRDLKPDNILITERSGTPIL
KVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDFYMAPEVWEGHYTAKADI
FALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEALLENPKMELHIPQKRRTS
MSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| CEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRDLKPDNILITERSGTPILKVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDFYMAPEVWEGHYTAKADIFALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEALLENPKMELHIPQKRRTSMSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA
Prediction	CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCSCCCCCHHHHSSCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCHCHCCHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHCCCC
Confidence	9961569999982999999999999999999999981873578994561107899998668860574222133444433233334456788751521789910146578728999455467788999999819999899988999999997177778742010124553032488766769999999999966799323999999999899833489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| CEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRDLKPDNILITERSGTPILKVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDFYMAPEVWEGHYTAKADIFALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEALLENPKMELHIPQKRRTSMSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA
Prediction	6743400330275514173024002100300410374400000020100001367851401000000022044344444433443444445442041202232300000044525450201003001000000200232733440043014334433444444453452505045640550164024004400443174123063015105525268
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCSCCCCCHHHHSSCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCHCHCCHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHCCCC
CEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRDLKPDNILITERSGTPILKVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDFYMAPEVWEGHYTAKADIFALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEALLENPKMELHIPQKRRTSMSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA

6z3uB

0.26

0.23

6.96

1.33

DEthreader

LPLGDLEMLIRDVRYGAADIKAWMGMLTRAVWWCHENFILHRDIKPNNLLIAAD---GEVKLADFGLARSFADP---------------GR--RMTANVITRWYRPPELLGAHYGGAVDIWSVGMVFAELIIRSPFLPG--NT--EMEQITL--ICKHIGTPTNIPVWGKDAYMA-RFGAVGSEGVDLLWRTLQLDPKKRITAREMLEH--RWWRTD

6x8fA2

0.22

0.20

6.24

1.72

SPARKS-K

VPLGSLRDYLPRHSIGLAQLLLFAQQICEGMAYLHSQHYIHRDLAARNVLLDNDR---LVKIGDFGLAKAV----PEGHEYRVREDGD-----------SPVFWYAPECLKEYFYYASDVWSFGVTLYELLTHCD--SSQSPPTKFLELIGIAQGQ-MTVLRLTELLERGERLP--RPDKCPAEVYHLMKNCWETEASFRPTFENLIPILKTVHEKY

3a7hB2

0.24

0.19

6.03

0.34

MapAlign

LGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSE---HGEVKLADFGVAGQLT-----------------DTQIKRN-FVGTPFWMAPEVIKQAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIP----------------KNNPPTL----EGNYSKPLKEFVEACLNKEPSFRPTAKELLKHILRNAK--

3hx4A

0.28

0.24

7.18

0.23

CEthreader

YTGGELFDEIISKRFSEVDAARIIRQVLSGITYMHKNKIVHRDLKPENLLLESKSKDANIRIIDFGLSTHFEASK------------------KMKDKIGTAYYIAPEVLHGTYDEKCDVWSTGVILYILLSGCPPFNGANEYDILKKVEKGKYT-----------------FELPQWKKVSESAKDLIRKMLTYVPSMRISARDALEWIQTYTKEQ

3hx4A

0.28

0.24

7.18

1.31

MUSTER

YTGGELFDEIISRKFSEVDAARIIRQVLSGITYMHKNKIVHRDLKPENLLLESKSKDANIRIIDFGLSTHFE------------------ASKKMKDKIGTAYYIAPEVLHGTYDEKCDVWSTGVILYILLSGCPPFNGANEYDILKKVEKG-----------------KYTFELPQWKKVSESAKDLIRKMLTYVPSMRISARDALDHEWIQTYTK

6ygnA

0.19

0.16

5.19

0.66

HHsearch

ISGLDIFERINTSELNEREIVSYVHQVCEALQFLHSHNIGHFDIRPENIIYQTRR-SSTIKIIEFGQARQLKPGD------------------NFRLLFTAPEYYAPEVHQHVVSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAE-----------------YTFDEEAFKEISIEAMDFVDRLLVKERKSRMTASEALQHLKQKIERV

7akgA2

0.24

0.19

6.02

2.59

FFAS-3D

AAGGEIFSLCLPEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKIGHACEL------------------REIMGTPEYLAPEILNYDITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQV-----------------NVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLS---------

5z33A

0.20

0.19

6.03

0.57

EigenThreader

MECDLAAIIRSGQPLTDAHFQSFIYQILCGLKYIHSANVLHRDLKPGNLLVN---ADCELKICDFGLARGFSVDP-------------EENAGYMTEYVATRWYRAPEIMLQSYTKAIDVWSVGCILAELLGGRPFFKGRDYVDQLNQILHILGTPNEETLSRRNLPFMAKKPFPTLFPNANPDALDLLDRMLAFDPSSRISVEQALEHPYLHIWHD

3i79A

0.28

0.24

7.18

1.99

CNFpred

YTGGELFDEIISRRFSEVDAARIIRQVLSGITYMHKNKIVHRDLKPENLLLESKSKDANIRIIDFGLSTHFEASK------------------KMKDKIGTAYYIAPEVLHGTYDEKCDVWSTGVILYILLSGCPPFNGANEYDILKKVEKG-----------------KYTFELPQWKKVSESAKDLIRKMLTYVPSMRISARDALD-HEWIQTYT

6z3uB2

0.26

0.23

6.96

1.33

DEthreader

LPLGDLEMLIRDVRYGAADIKAWMGMLTRAVWWCHENFILHRDIKPNNLLIAAD---GEVKLADFGLARSFADP---------------GR--RMTANVITRWYRPPELLGAHYGGAVDIWSVGMVFAELIIRSPFLPG--NT--EMEQITL--ICKHIGTPTNIPVWGKDAYMA-RFGAVGSEGVDLLWRTLQLDPKKRITAREMLEH--RWWRTD

(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	0.917

(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	4iw0A	0.75	2.41	0.162	0.853	model1_4iw0A.pdb.gz
2	6xdbA	0.74	2.51	0.258	0.834	model1_6xdbA.pdb.gz
3	5l2qC	0.74	2.18	0.230	0.820	model1_5l2qC.pdb.gz
4	3c0gB	0.73	2.58	0.220	0.839	model1_3c0gB.pdb.gz
5	2qkwB	0.73	2.64	0.194	0.830	model1_2qkwB.pdb.gz
6	3e62A	0.73	2.78	0.215	0.853	model1_3e62A.pdb.gz
7	5ig1A2	0.73	2.59	0.258	0.839	model1_5ig1A2.pdb.gz
8	3lijA	0.73	2.54	0.276	0.834	model1_3lijA.pdb.gz
9	3soaA	0.73	2.60	0.235	0.843	model1_3soaA.pdb.gz
10	3lxnA2	0.73	2.89	0.199	0.853	model1_3lxnA2.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	0.99	catalytic activity
GO:0004672	0.98	protein kinase activity
GO:0004674	0.91	protein serine/threonine kinase activity
GO:1901363	0.79	heterocyclic compound binding
GO:0097159	0.79	organic cyclic compound binding
GO:0035639	0.77	purine ribonucleoside triphosphate binding
GO:0032555	0.77	purine ribonucleotide binding
GO:0032550	0.77	purine ribonucleoside binding
GO:0005524	0.76	ATP binding
GO:0003676	0.51	nucleic acid binding
GO:0043167	0.50	ion 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	0.96	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0008152	0.90	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0050794	0.88	regulation of cellular process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0006796	0.87	phosphate-containing compound metabolic process
GO:0019538	0.85	protein metabolic process
GO:0006468	0.84	protein phosphorylation
GO:0007165	0.78	signal transduction
GO:0044699	0.73	single-organism process
GO:0044763	0.68	single-organism cellular process
GO:0035556	0.67	intracellular signal transduction
GO:0050896	0.62	response to stimulus
GO:0051179	0.58	localization
GO:0006950	0.58	response to stress
GO:0048519	0.57	negative regulation of biological process
GO:0018193	0.57	peptidyl-amino acid modification
GO:0048523	0.56	negative regulation of cellular process
GO:0048518	0.56	positive regulation of biological process
GO:0031323	0.56	regulation of cellular metabolic process
GO:0048522	0.53	positive regulation of cellular process
GO:0044710	0.53	single-organism metabolic process
GO:0033036	0.53	macromolecule localization
GO:0032502	0.53	developmental process
GO:0006807	0.53	nitrogen compound metabolic process
GO:0051716	0.52	cellular response to stimulus
GO:0044767	0.52	single-organism developmental process
GO:0042325	0.52	regulation of phosphorylation
GO:0034641	0.52	cellular nitrogen compound metabolic process
GO:0009058	0.52	biosynthetic process
GO:1901576	0.51	organic substance biosynthetic process
GO:0044281	0.51	small molecule metabolic process
GO:0044249	0.51	cellular biosynthetic process
GO:0006139	0.51	nucleobase-containing compound metabolic process
GO:1901362	0.50	organic cyclic compound biosynthetic process
GO:0090304	0.50	nucleic acid metabolic process
GO:0048856	0.50	anatomical structure development
GO:0044271	0.50	cellular nitrogen compound biosynthetic process
GO:0034645	0.50	cellular macromolecule biosynthetic process
GO:0033554	0.50	cellular response to stress
GO:0022402	0.50	cell cycle process
GO:0019438	0.50	aromatic compound biosynthetic process
GO:0018130	0.50	heterocycle biosynthetic 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	0.96	intracellular part
GO:0043226	0.73	organelle
GO:0005737	0.71	cytoplasm
GO:0043229	0.70	intracellular organelle
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044444	0.62	cytoplasmic part
GO:0016020	0.57	membrane
GO:0005634	0.55	nucleus

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	0.438	1ia8A	0.695	3.19	0.251	0.820	2.7.11.1	43,45,48
2	0.437	2zv2A	0.704	2.54	0.241	0.802	2.7.11.17	43,45,48
3	0.393	2iwiB	0.676	2.09	0.255	0.760	2.7.11.1	43,45,48
4	0.377	1uwhA	0.671	2.89	0.233	0.779	2.7.11.1	43,45,48,101
5	0.361	3is5F	0.673	2.91	0.304	0.779	2.7.11.17	43,45,48

	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	0.27	2v7aB	0.722	2.22	0.239	0.811	0.71	627	complex1.pdb.gz	1,2,4,5,46,48,50,63,64
2	0.25	3dk6B	0.718	2.26	0.227	0.811	0.69	SX7	complex2.pdb.gz	1,4,50,65
3	0.05	3hx4A	0.728	2.55	0.276	0.830	0.60	CA	complex3.pdb.gz	43,45,104

	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.