D-I-TASSER Q9BYH1-D4

D-I-TASSER results for Q9BYH1-D4

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

Input Sequence in FASTA format

>Q9BYH1 (92 residues)
NQDSFEHALEVAEAAAETSLEGGNMALAIFIPVLIISLLLGGAYIYITRCRYYSNLRLPL
MYSHPYSQITVETEFDNPIYETGETREYEVSI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| NQDSFEHALEVAEAAAETSLEGGNMALAIFIPVLIISLLLGGAYIYITRCRYYSNLRLPLMYSHPYSQITVETEFDNPIYETGETREYEVSI
Prediction	CCCCCCCSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHSSSSSSSSCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCSSSSSCC
Confidence	98655541354316897765443224679999999999971105788862477653455567999886302114688642378741577529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| NQDSFEHALEVAEAAAETSLEGGNMALAIFIPVLIISLLLGGAYIYITRCRYYSNLRLPLMYSHPYSQITVETEFDNPIYETGETREYEVSI
Prediction	86445744141463456352444422101323333333233323111131444431413344344344143434254332544644626357
	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 AttentionPotential. 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

                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHSSSSSSSSCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCSSSSSCC
NQDSFEHALEVAEAAAETSLEGGNMALAIFIPVLIISLLLGGAYIYITRCRYYSNLRLPLMYSHPYSQITVETEFDNPIYETGETREYEVSI

6yvuA

0.07

0.05

2.29

1.00

DEthreader

-----E--KESIASLIKKYANTEKDYKMVQEQLSKQRDLYKRKEELVS-TLADGGYNQLAKAKLEVSLAKKSSMKMELKKELLT--------

1w5cJ1

0.08

3.05

0.49

CEthreader

AERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDF

3hd7B

0.04

2.15

0.58

EigenThreader

ETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVE--RAVSDTKKAVKYQSKARRKKIMIIICCVILGIIIASTIGG

6t15k

0.15

0.14

4.76

0.35

FFAS-3D

DKVAAQKFKESLMATEKHAKDTSNMWVKISVWVALPAIALTAVNTYFVEKELKHVPDSEWPRDYEFMNIRSKTLFWNPVVNRHIEHD-----

4yhcA1

0.13

0.11

3.76

0.72

SPARKS-K

NSKLNVFWMPGTHKD----DEWKNFELVVVES---------SGEIQVFSLTIEEKFQL---SSPIIKSISIVSTANRIASLTESGEVTVYSK

3rkoD

0.10

0.03

1.22

0.60

CNFpred

--------------------QGAPAPVSTFLATASKIAIFGVVMRLFLYAP-----------------------------------------

3ffzA

0.02

1.49

1.00

DEthreader

---YTLEEKNELNKYQNNQKVSIAMNNIDRFLTESSISYLMKIINEVKINKREYDELNSIPFFKSVLN-MRYYNKNQ-FGG-EHGWQEK---

3e6uA

0.08

3.02

0.84

MapAlign

ITRLIHLNKIDPHAPNEMLYGRIGYIYALLFVIQQICETILTSGENLARKRNFTAKSPLMYEWYQEYYVGAAHGLAGIYYYLMQPSLQV---

3ixzA4

0.10

3.64

0.64

MUSTER

EKAESDIMHLRPRNPKRDRLVNEPLAAYSYFIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYT

6jxrf

0.14

0.08

2.61

0.58

HHsearch

GSKDANFYLYLRARVCENEMDVMSVATIVIVDICITGGLLLLVY--YWSKNRK---------------------------------------

(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	0.487

(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 AttentionPotential, 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	6wxrA3	0.55	3.44	0.058	0.837	model1_6wxrA3.pdb.gz
2	4gbyA1	0.55	3.51	0.100	0.848	model1_4gbyA1.pdb.gz
3	6bd4A	0.55	3.96	0.048	0.859	model1_6bd4A.pdb.gz
4	5yepB	0.55	3.80	0.044	0.826	model1_5yepB.pdb.gz
5	4ut1A	0.54	3.88	0.111	0.848	model1_4ut1A.pdb.gz
6	6kkiA	0.54	3.53	0.075	0.837	model1_6kkiA.pdb.gz
7	4nleA	0.54	3.47	0.033	0.815	model1_4nleA.pdb.gz
8	6vbu93	0.54	4.14	0.056	0.902	model1_6vbu93.pdb.gz
9	5l7dA3	0.54	3.90	0.023	0.837	model1_5l7dA3.pdb.gz
10	2yyjA	0.54	3.21	0.069	0.826	model1_2yyjA.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	0.46	heterocyclic compound binding
GO:0097159	0.46	organic cyclic compound binding
GO:0003824	0.42	catalytic activity
GO:0016872	0.37	intramolecular lyase activity
GO:0000166	0.37	nucleotide binding
GO:0097367	0.34	carbohydrate derivative binding
GO:0005524	0.33	ATP 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:0048856	1.00	anatomical structure development
GO:0044767	1.00	single-organism developmental process
GO:0009987	0.86	cellular process
GO:0065007	0.83	biological regulation
GO:0044763	0.82	single-organism cellular process
GO:0050794	0.81	regulation of cellular process
GO:0044708	0.76	single-organism behavior
GO:0044707	0.76	single-multicellular organism process
GO:0023051	0.76	regulation of signaling
GO:0010646	0.76	regulation of cell communication
GO:0090036	0.75	regulation of protein kinase C signaling
GO:0060074	0.75	synapse maturation
GO:0021680	0.75	cerebellar Purkinje cell layer development
GO:0008344	0.75	adult locomotory behavior

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:0043025	1.00	neuronal cell body
GO:0005783	1.00	endoplasmic reticulum

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	3mddA	0.513	3.73	0.036	0.826	1.3.99.3	69
2	0.060	1fa9A	0.455	4.24	0.046	0.793	2.4.1.1	NA
3	0.060	1t9gC	0.412	3.80	0.067	0.630	1.3.99.3	NA
4	0.060	2fenD	0.540	3.76	0.011	0.826	5.5.1.2	NA
5	0.060	1ig8A	0.489	3.43	0.081	0.772	2.7.1.1	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	1mskA	0.544	3.91	0.058	0.880	0.16	SAM	complex1.pdb.gz	41,75,76,77,80
2	0.01	2hpyA	0.501	4.18	0.044	0.859	0.11	RET	complex2.pdb.gz	74,81,82
3	0.01	1m56A	0.526	4.28	0.043	0.935	0.15	HEA	complex3.pdb.gz	24,30,31,34,35,38,41,45
4	0.01	3omaA	0.459	4.04	0.044	0.772	0.21	HEA	complex4.pdb.gz	14,33,36,37,40,41
5	0.01	1m57A	0.526	4.25	0.043	0.935	0.10	HEA	complex5.pdb.gz	8,24,25,28,33,36,40
6	0.01	1ln6A	0.400	4.90	0.080	0.870	0.13	RET	complex6.pdb.gz	38,42,43,59
7	0.01	1m56G	0.526	4.26	0.043	0.935	0.17	HEA	complex7.pdb.gz	43,47,48,74,75
8	0.01	3dtuA	0.463	3.85	0.045	0.750	0.13	HEA	complex8.pdb.gz	22,26,29,30,33,34,36,37,69,85

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.