D-I-TASSER C9JUS6-D1

D-I-TASSER results for C9JUS6-D1

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

Input Sequence in FASTA format

>C9JUS6 (153 residues)
MTIHILILLLLLAFSAQGDLDTAARRGQHQVPQHRGHVCYLGVCRTHRLAEIIYWIRCLH
QGALGEGQPRAPGPLQLWAPPVARGGSPARFPGFRPAARGLAQCPARWVTSGTARPLLGF
SLPICMLELLLHISSPLTPAPETVFPSPSPGCD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTIHILILLLLLAFSAQGDLDTAARRGQHQVPQHRGHVCYLGVCRTHRLAEIIYWIRCLHQGALGEGQPRAPGPLQLWAPPVARGGSPARFPGFRPAARGLAQCPARWVTSGTARPLLGFSLPICMLELLLHISSPLTPAPETVFPSPSPGCD
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCSSSSSSSCCCCCHHHHHHHHHHCHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHSCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	945899999999987427976312367652112137325554312342179999999722100037899999993345897335899877899997767756699234203777743356424799999997158899998765789999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTIHILILLLLLAFSAQGDLDTAARRGQHQVPQHRGHVCYLGVCRTHRLAEIIYWIRCLHQGALGEGQPRAPGPLQLWAPPVARGGSPARFPGFRPAARGLAQCPARWVTSGTARPLLGFSLPICMLELLLHISSPLTPAPETVFPSPSPGCD
Prediction	733200101311133234445444545455145444320100204344124002003123454147635665342413333344464435144343334333513330133334322222312302020123034323433543144455638
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCSSSSSSSCCCCCHHHHHHHHHHCHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHSCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
MTIHILILLLLLAFSAQGDLDTAARRGQHQVPQHRGHVCYLGVCRTHRLAEIIYWIRCLHQGALGEGQPRAPGPLQLWAPPVARGGSPARFPGFRPAARGLAQCPARWVTSGTARPLLGFSLPICMLELLLHISSPLTPAPETVFPSPSPGCD

3n8uA

0.12

0.11

3.95

0.46

CEthreader

IVDKCAEIANEVGTAKIGDPYNLYKAGNTEEALYAVESWYSWH-SRDDYTNNIYSIRNAYYGSLDGNINANS------LSTVIAGANSSLDTKIKNAIQKAAKAIQDIPQPFRNHIPSNETAADACAELESILKNDLKSYIANNSNNINTDAV

5ic0A

0.07

2.76

0.55

EigenThreader

SYFGCLDSVMENSKVLGEAMTGISQNAKNGNLPEFGDAIATASKALCGFTEAAAQAAYLVGVSDPNSQAGQQGLVEPTQFARANQAIQMACQSLGTIVAKHTSALCNSCRLASARTANPTAKRQFVQSAKEVANSTANLVKTIKALDGDFTEE

6traA5

0.24

0.20

6.12

0.45

FFAS-3D

IISHLNWVCIFLGFHSFGHNDTMRAFGRPQDMFSDTGIQLQPV--------FAQWVQNLHTLAPGGTAPNAAATASVAFGGVAVGGKVAMMP----IVLGTADFMVHHIHA--------FTIHVTVLILLKGV---LFARSSRLIPDKAN---

6ahfC1

0.09

0.08

3.22

0.88

SPARKS-K

RALTILTLAQKLAQHPQLQPIAFIETPEDGSVPYLQNLIEKGRYDYDLF-------KKVVNRNLVRIPQQQPAPAEITPSYAL--GKVLQDAAKIQKQQKDSFIAQDHILFALFNDSSIQQIIEAIKQQALERGNTRIDSRGADTNTPLE---

4kf7A

0.12

0.07

2.31

0.54

CNFpred

--STLALFGKRLEVNLM-----------------GAYDTALGYLSADELIEGISLLATVLRAETLRSSK-------------------------------DPDRGLRILTEASRLLSRGRDIMNVVCDTLDSLV-------------------

7knsA3

0.08

0.07

2.59

0.83

DEthreader

AAIGITTL--VGGGTCTPGKG-SS-SKPDLHEIIKAGAMGADIQINIIHTY--HS--------------EGAGGGAPDII--K--VCGIVLPSSTTLRKKTAAEDVLNGAIS-IIAKYTINPAINGFSIAFVSAVNLYGLNKRVEAV-SNVRK

6nxiA

0.08

3.29

0.89

MapAlign

LQTEIDRLLEEVNDQMVTVGPLVNLWGFGAITGIEHLTIEGNTLSKDIAKGWGVDVVADYLQSQGIENYMVEIGGEIRLKGLNRDGVPWRIAIEKPSVDQRSVPGDYAIATSTVLDKSCMTADGLATGLMVMGEERGMAVAEANQIPVLMIVK

5x6oG

0.12

4.17

0.58

MUSTER

IISYSFDLLEGILRVLQSHPKQTYMEFFDENLKSFEFVYKLALTISFSAVEVVNIITSIILNMDNSSDLKSLISGSWWRDCITRLYALLEKEIKSGDVYNENVDTTTLHMS-KYHDFFGLIRNIGDNELGGLISKLIYTDRLQSVPRVISKED

2l7sA

0.25

0.08

2.63

1.36

HHsearch

-----------------------YRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTD-K---DKDN--VAPR--SKISP---QGY-------------------------------------------------------------------

3d41A

0.09

3.45

0.43

CEthreader

DDDAVTRFARNFARLAETYRGRMVSGGGAFGHGAIRDHDSTHAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLAAMCTLRNGIPQLRSEVLRDVLDHGALP---VLAGDALFDEHGKLWAFSSDRVPEVLLPMVEGRLRVVTLTDVDGIV

(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	0.5025

(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	3cf4A	0.49	4.72	0.061	0.824	model1_3cf4A.pdb.gz
2	1ru3A1	0.48	4.67	0.062	0.824	model1_1ru3A1.pdb.gz
3	1uwyA1	0.48	4.97	0.076	0.817	model1_1uwyA1.pdb.gz
4	3mn8A1	0.48	4.90	0.099	0.817	model1_3mn8A1.pdb.gz
5	3v4cA	0.48	4.21	0.054	0.686	model1_3v4cA.pdb.gz
6	1eb6A	0.48	4.15	0.043	0.712	model1_1eb6A.pdb.gz
7	2nsmA1	0.47	4.98	0.077	0.804	model1_2nsmA1.pdb.gz
8	1ez0A1	0.47	4.29	0.076	0.693	model1_1ez0A1.pdb.gz
9	1ayeA2	0.47	4.73	0.054	0.771	model1_1ayeA2.pdb.gz
10	1ad3A1	0.47	4.16	0.102	0.673	model1_1ad3A1.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:0051540	0.47	metal cluster binding
GO:0043167	0.44	ion binding
GO:0043169	0.42	cation binding
GO:0003824	0.40	catalytic 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:0008152	0.94	metabolic process
GO:0009987	0.91	cellular process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.90	primary metabolic process
GO:0044237	0.90	cellular metabolic process
GO:0043170	0.89	macromolecule metabolic process
GO:0006139	0.89	nucleobase-containing compound metabolic process
GO:0006396	0.88	RNA processing
GO:0008380	0.87	RNA splicing
GO:0044699	0.58	single-organism process
GO:0044710	0.50	single-organism metabolic 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	0.97	cell part
GO:0044424	0.90	intracellular part
GO:0005737	0.58	cytoplasm
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.52	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	2j6lB	0.467	4.39	0.057	0.686	1.2.1.31 1.2.1.3	NA
2	0.060	2o2pA	0.453	4.28	0.071	0.673	1.5.1.6	NA
3	0.060	1cpbA	0.211	4.34	0.076	0.333	3.4.17.2	94
4	0.060	1obrA	0.452	4.84	0.062	0.745	3.4.17.18	NA
5	0.060	1uwyA	0.479	5.02	0.068	0.824	3.4.17.12	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	1ez0B	0.473	4.29	0.076	0.693	0.11	NAP	complex1.pdb.gz	3,55,56
2	0.01	1ru3A	0.483	4.78	0.061	0.830	0.14	SF4	complex2.pdb.gz	5,63,65
3	0.01	1ez0D	0.473	4.29	0.076	0.693	0.13	NAP	complex3.pdb.gz	54,57,58
4	0.01	1zlh0	0.462	4.69	0.054	0.752	0.16	III	complex4.pdb.gz	5,6,86,87
5	0.01	1bavC	0.460	4.90	0.053	0.771	0.15	BIP	complex5.pdb.gz	4,61,65,66
6	0.01	3fx6A	0.464	4.81	0.061	0.765	0.15	BPX	complex6.pdb.gz	1,2,128
7	0.01	3rhhC	0.458	4.27	0.039	0.667	0.24	NAP	complex7.pdb.gz	1,2,5,6,57,61,62,65
8	0.01	2jg7A	0.466	4.24	0.049	0.680	0.14	NAD	complex8.pdb.gz	74,113,128
9	0.01	3rhhA	0.460	4.09	0.039	0.660	0.29	NAP	complex9.pdb.gz	1,2,58,62,63,66
10	0.01	3fvlC	0.464	4.77	0.061	0.765	0.15	BHK	complex10.pdb.gz	5,128,135

	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.