D-I-TASSER Q7RTR0-D3

D-I-TASSER results for Q7RTR0-D3

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

Input Sequence in FASTA format

>Q7RTR0 (253 residues)
DLEINSQNTTYLYASFLTTVFKAGSQSFPPKVNRARLKSLCALAAEGIWTYTFVFSHGDL
RRNGLSESEGVMWVGMRLLQRRGDCFAFMHLCIQEFCAAMFYLLKRPKDDPNPAIGSITQ
LVRASVVQPQTLLTQVGIFMFGISTEEIVSMLETSFGFPLSKDLKQEITQCLESLSQCEA
DREAIAFQELFIGLFETQEKEFVTKVMNFFEEVFIYIGNIEHLVIASFCLKHCQHLTTLR
MCVENIFPDDSGC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| DLEINSQNTTYLYASFLTTVFKAGSQSFPPKVNRARLKSLCALAAEGIWTYTFVFSHGDLRRNGLSESEGVMWVGMRLLQRRGDCFAFMHLCIQEFCAAMFYLLKRPKDDPNPAIGSITQLVRASVVQPQTLLTQVGIFMFGISTEEIVSMLETSFGFPLSKDLKQEITQCLESLSQCEADREAIAFQELFIGLFETQEKEFVTKVMNFFEEVFIYIGNIEHLVIASFCLKHCQHLTTLRMCVENIFPDDSGC
Prediction	CCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHCHHHHHHHHHHHHHHHHHHCCSSSCHHHHHHHCCCHHHHHHHHHHHHHSCCCCSSSSSSHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCSSSSSCCCHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCC
Confidence	9765887579999999999738776678861019999999999999998697676299999969987773587500221058973898646899999999999962566764036799999999971568648999999997537378999998728977889999999999996214787664017999982504054999999997397699974987899999999995589708998624677645589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| DLEINSQNTTYLYASFLTTVFKAGSQSFPPKVNRARLKSLCALAAEGIWTYTFVFSHGDLRRNGLSESEGVMWVGMRLLQRRGDCFAFMHLCIQEFCAAMFYLLKRPKDDPNPAIGSITQLVRASVVQPQTLLTQVGIFMFGISTEEIVSMLETSFGFPLSKDLKQEITQCLESLSQCEADREAIAFQELFIGLFETQEKEFVTKVMNFFEEVFIYIGNIEHLVIASFCLKHCQHLTTLRMCVENIFPDDSGC
Prediction	8455324100100020011003455562567523510320030004003643120236104616053630211022300475651010012000000000000012456344421530450045126464210210010000002461153047205161266125201500551573764452430020010020142450043016205402031444300000000032044043030215401566758
	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                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHCHHHHHHHHHHHHHHHHHHCCSSSCHHHHHHHCCCHHHHHHHHHHHHHSCCCCSSSSSSHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCSSSSSCCCHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCC
DLEINSQNTTYLYASFLTTVFKAGSQSFPPKVNRARLKSLCALAAEGIWTYTFVFSHGDLRRNGLSESEGVMWVGMRLLQRRGDCFAFMHLCIQEFCAAMFYLLKRPKDDPNPAIGSITQLVRASVVQPQTLLTQVGIFMFGISTEEIVSMLETSFGFPLSKDLKQEITQCLESLSQCEADREAIAFQELFIGLFETQEKEFVTKVMNFFEEVFIYIGNIEHLVIASFCLKHCQHLTTLRMCVENIFPDDSGC

5irlA

0.18

0.17

5.42

1.33

DEthreader

QDGGSPKTTTDMYLLILQHFLRHASL--QG--RLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVD-PDDISLG---FLVQ--APLEFLHITFQCFLAAFYLVLSTD-----VPTASLRYLFNALQKTEPHNLQITAAFLAGLLSREHRDLLAACQASESLLRRRACARWCLARSLKHRSIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVHLKLTGVGPECAALAFVLRHL-R-RPVALQLDHNSDNNISG

5irlA

0.17

0.16

5.33

2.09

SPARKS-K

QDGGSPKTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDIS----LGFLVQAP--LEFLHITFQCFLAAFYLVLS--TDVPTASLRYLFTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASESLLRRRACARWCLARSLHKRSIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVEHLKGVGPAECAALAFVLRHLRRPVALQLDHNSVGDIGVEQ

5irlA

0.19

0.17

5.61

1.68

MapAlign

-----PKTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDI----SLGFLV--QAPLEFLHITFQCFLAAFYLVLSTD-----VPTASLRYLFCLLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASEL-LRRRACARWCLARSLHHRSIPAMPGFLWLIRSLYEMQEERLAQEAVLNVEHLKLTVG-PAECAALAFVLRHLRRPVALQLDHNSVGDIGVEQ

5irlA

0.16

0.15

5.13

1.54

CEthreader

QDGGSPKTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLGFLVQA------PLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLRRRACARWCLARSLHKRSIPAMPGFLWLIRSLYEMQEERLAQEAVVEHLKLTFCGVGPAECAALAFVLRHLRRPVALQLDHNSVGDIGVEQ

5irlA

0.16

5.23

1.60

MUSTER

QDGGSPKTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISL----GFLV--QAPLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLRRRACARWCLARSLHKRSIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVEHLKLVGPAECAALAFVLRHLRRPVALQLDHNSVGDIGVEQ

5irlA

0.16

5.23

4.44

HHsearch

QDGGSPKTTTDMYLLILQHF---LRHASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDIS----LGFLVQA--PLEFLHITFQCFLAAFYLVLSTDVPTASLLFN-CSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLLRRRCARWCLARSLHKHSIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVEHLTGVGPAECAALAFVLRHLRRPVALQLDHNSVGDIGVEC

5irlA4

0.17

0.13

4.29

2.20

FFAS-3D

------KTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLGFLV------QAPLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFNCTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLLRRRACARWCLAHKHFRSIPAMPGFLWLIRSLYEMQEERLAQEAVRGL-------------------------------------------

5irlA

0.16

0.15

4.86

1.20

EigenThreader

GSP---KTTTDMYLLILQHFLRHASL---LQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDIS----------LGFLVQEFLHITFQCFLAAFYLVLSTD----VPTASLRYLFNLLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERRACARWCLARSLHKHFRSIP--AMPGFLWLIRSLYEMQEERLAQEAVRNVEHLKLTFCGVGPAECAALAFVLRHLRRPVALQLDHNSVGDIGV

5irlA

0.16

0.15

5.00

1.50

CNFpred

QDGGSPKTTTDMYLLILQHFLRHA---SLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDIS----LGFLVQ--APLEFLHITFQCFLAAFYLVLSTDVPTASLRYL--STVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERLLRRRACARWCLARSLHKHFR-AMPGFLWLIRSLYEMQEERLAQEAVRGLNVEHLKL-GPAECAALAFVLRHLRRPVALQLDHNSVGDIGVEQ

6npyA

0.23

0.20

6.31

1.17

DEthreader

SLAQTSKTTTAVYVFFLSSLLQPRG-----G-LCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKCEKFYSFIHMTFQEFFAAMYYLLE----------N-VPGSRLKL--PSR---ENYGKFEKGYLIVRFLFGLVNQERT-AK-AKKLQIQPSQLELFYCMQEEFVQRAM--DYFPKIEIGFHNMPKEEEEEEKEGRHLDMVQ-CVLPSSSHAACSHGLVNSHLTS----S-G--

(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	0.8152

(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	5irlA	0.87	2.08	0.168	0.941	model1_5irlA.pdb.gz
2	6npyA	0.74	3.19	0.231	0.889	model1_6npyA.pdb.gz
3	4kxfK	0.67	4.34	0.123	0.877	model1_4kxfK.pdb.gz
4	6b5bA	0.62	4.38	0.123	0.866	model1_6b5bA.pdb.gz
5	6tc0C2	0.55	4.77	0.074	0.775	model1_6tc0C2.pdb.gz
6	6m6xC	0.55	4.52	0.055	0.767	model1_6m6xC.pdb.gz
7	6sytA	0.54	5.23	0.096	0.850	model1_6sytA.pdb.gz
8	4kf7A	0.53	5.01	0.069	0.790	model1_4kf7A.pdb.gz
9	5dlqB	0.53	5.06	0.080	0.798	model1_5dlqB.pdb.gz
10	4knhA	0.53	4.70	0.084	0.771	model1_4knhA.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:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0019899	0.59	enzyme binding
GO:0097367	0.57	carbohydrate derivative binding
GO:0003676	0.57	nucleic acid binding
GO:0000166	0.53	nucleotide binding
GO:0035639	0.52	purine ribonucleoside triphosphate binding
GO:0032559	0.52	adenyl ribonucleotide binding
GO:0032550	0.52	purine ribonucleoside 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:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0009987	0.81	cellular process
GO:0019222	0.78	regulation of metabolic process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0080090	0.74	regulation of primary metabolic process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0050896	0.69	response to stimulus
GO:0048518	0.69	positive regulation of biological process
GO:0044699	0.69	single-organism process
GO:0048522	0.68	positive regulation of cellular process
GO:0009893	0.65	positive regulation of metabolic process
GO:0008152	0.64	metabolic process
GO:0071704	0.63	organic substance metabolic process
GO:0044238	0.63	primary metabolic process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0048583	0.61	regulation of response to stimulus
GO:0044763	0.61	single-organism cellular process
GO:0031325	0.61	positive regulation of cellular metabolic process
GO:0043170	0.60	macromolecule metabolic process
GO:0065009	0.59	regulation of molecular function
GO:0010468	0.58	regulation of gene expression
GO:0032268	0.57	regulation of cellular protein metabolic process
GO:0006950	0.56	response to stress
GO:2000112	0.55	regulation of cellular macromolecule biosynthetic process
GO:0050790	0.55	regulation of catalytic activity
GO:0048519	0.55	negative regulation of biological process
GO:0019219	0.55	regulation of nucleobase-containing compound metabolic process
GO:0051049	0.54	regulation of transport
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0051223	0.53	regulation of protein transport
GO:0048523	0.53	negative regulation of cellular process
GO:0042221	0.53	response to chemical
GO:0010941	0.53	regulation of cell death
GO:0042981	0.52	regulation of apoptotic process
GO:0006952	0.52	defense response
GO:0019538	0.51	protein metabolic process
GO:0044093	0.50	positive regulation of molecular function
GO:0043281	0.50	regulation of cysteine-type endopeptidase activity involved in apoptotic 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:0044446	1.00	intracellular organelle part
GO:0043226	0.97	organelle
GO:0043227	0.96	membrane-bounded organelle
GO:0005737	0.92	cytoplasm
GO:0043229	0.91	intracellular organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus
GO:0044444	0.83	cytoplasmic part
GO:0032991	0.74	macromolecular complex
GO:0043234	0.72	protein complex
GO:0044428	0.66	nuclear part
GO:0005829	0.55	cytosol
GO:0016020	0.51	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	0.060	1h54B	0.455	6.04	0.033	0.787	2.4.1.8	NA
2	0.060	1f1sA	0.489	5.21	0.048	0.731	4.2.2.1	NA
3	0.060	2oykB	0.442	5.55	0.040	0.723	3.2.1.123	46,90
4	0.060	1ojnA	0.481	5.17	0.068	0.727	4.2.2.1	191
5	0.060	2jg0A	0.466	5.56	0.077	0.747	3.2.1.28	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	0.02	3ebbC	0.511	4.86	0.082	0.751	0.67	III	complex1.pdb.gz	96,138,142,189,193
2	0.01	1w9c0	0.432	4.99	0.048	0.644	0.40	III	complex2.pdb.gz	143,144,166,168,171,174,175,178,183,185,186,189,193
3	0.01	1iq1C	0.463	5.30	0.042	0.700	0.44	III	complex3.pdb.gz	95,135,139,141,142,143,144,194,198,224,228
4	0.01	1q1tC	0.451	4.99	0.065	0.672	0.44	III	complex4.pdb.gz	100,135,139,141,142,144,195,221
5	0.01	2ot8A	0.485	5.19	0.051	0.739	0.42	III	complex5.pdb.gz	143,186,188,189,192,222

	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.