I-TASSER results

Input Sequence in FASTA format

>protein (73 residues)
MSGRWEAGNADGNGGSAGLIGSGGAGGDGGSGGATGAGGEGGDAGASGSINGNAGDPGNS
GERGAVGKPGAPG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSGRWEAGNADGNGGSAGLIGSGGAGGDGGSGGATGAGGEGGDAGASGSINGNAGDPGNSGERGAVGKPGAPG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9988888999999999999999999999999999999999999998899999999999999999999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSGRWEAGNADGNGGSAGLIGSGGAGGDGGSGGATGAGGEGGDAGASGSINGNAGDPGNSGERGAVGKPGAPG
Prediction	7644564664736616536435736636625744635737515544725471663643772664643654688
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60

                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSGRWEAGNADGNGGSAGLIGSGGAGGDGGSGGATGAGGEGGDAGASGSINGNAGDPGNSGERGAVGKPGAPG

3boiA

0.32

1.00

4.14

MUSTER

ADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3boiA

0.32

1.00

5.14

dPPAS

ADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3boiA

0.34

1.00

5.43

wdPPAS

CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKG

3boiA

0.32

1.00

7.82

wMUSTER

ADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3boiA

0.34

1.00

4.64

wPPAS

CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKG

3boiA

0.32

1.00

8.70

dPPAS2

ADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3boiA

0.32

1.00

5.31

PPAS

ADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3bogA

0.32

0.99

2.11

Env-PPAS

ADGAHG-VGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3bogA

0.32

0.99

3.81

MUSTER

ADGAHG-VGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

3bogA

0.32

0.99

4.67

dPPAS

ADGAHG-VGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADG

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 2 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=1.80

Estimated TM-score = 0.97±0.05

Estimated RMSD = 0.5±0.5Å

Download Model 2

C-score=-4.38

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	3boiA	0.889	1.11	0.315	1.000
2	5awfA	0.613	2.70	0.155	0.973
3	2zu0A	0.595	2.87	0.099	0.973
4	4dn7A2	0.579	2.98	0.153	0.986
5	2odlA1	0.548	3.00	0.081	0.836
6	3pk0A	0.532	3.68	0.123	0.973
7	4rm6A1	0.528	3.21	0.066	0.836
8	3orfA	0.522	3.82	0.083	0.945
9	4lvuA	0.514	3.87	0.070	0.959
10	3wxbA	0.513	3.84	0.110	0.973

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.11	5	2ml3A	CA	Rep, Mult	16,30,32,45,47,62
2	0.11	5	1c9uA	CA	Rep, Mult	2,3,4,6,40
3	0.07	3	2ml1A	CA	Rep, Mult	34,35,36,43,63,64,65,70
4	0.04	2	2ztiA	MN	Rep, Mult	6,64
5	0.04	2	3eqnA	ZN	Rep, Mult	9,67
6	0.02	1	3nmvB	MG	Rep, Mult	24,52
7	0.02	1	1izlB	CLA	Rep, Mult	41
8	0.02	1	3svtA	NA	Rep, Mult	18,27,58
9	0.02	1	3bbxL	MG	Rep, Mult	38,39
10	0.02	1	2vn4A	MAN	Rep, Mult	60,61
11	0.02	1	3pk0A	CA	Rep, Mult	52,54,55

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1rkxC	0.381	3.91	0.029	0.740	4.2.1.45	NA
2	0.060	2bfpD	0.464	3.84	0.060	0.877	1.5.1.33	28
3	0.060	1kcdA	0.496	3.25	0.048	0.836	3.2.1.15	8,68
4	0.060	1hxhD	0.468	3.63	0.046	0.822	1.1.1.51	NA
5	0.060	2zeaD	0.488	3.58	0.055	0.890	1.1.1.30	NA
6	0.060	2p68A	0.487	4.18	0.083	0.918	1.1.1.100	NA
7	0.060	1iy8A	0.485	3.72	0.100	0.877	1.1.1.-	47
8	0.060	2yz7A	0.465	3.70	0.123	0.863	1.1.1.30	68
9	0.060	2ze4A	0.477	3.80	0.045	0.904	3.1.4.4	NA
10	0.060	1ae1B	0.490	3.65	0.069	0.877	1.1.1.206	68
11	0.060	3ftpA	0.487	3.46	0.068	0.863	1.1.1.100	NA
12	0.060	2ztlA	0.489	3.72	0.028	0.890	1.1.1.30	NA
13	0.060	1vdzA	0.489	3.48	0.075	0.890	3.6.3.14	NA
14	0.060	1w0cA	0.509	3.90	0.055	0.986	1.5.1.33	NA
15	0.060	3f9iB	0.489	3.80	0.111	0.904	1.1.1.100	NA
16	0.060	1wvgA	0.489	3.64	0.070	0.904	4.2.1.45	NA
17	0.060	1p33B	0.513	4.01	0.055	1.000	1.5.1.33,1.1.1.253	NA
18	0.060	2fwmX	0.487	3.64	0.082	0.877	1.3.1.28	NA
19	0.060	3gvcB	0.505	3.51	0.096	0.890	1.-.-.-	68

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.07	0.595	2.87	0.10	0.97	2zu0A	GO:0006979 GO:0016226
1	0.07	0.613	2.70	0.15	0.97	5awfA	GO:0016226 GO:0051539
2	0.07	0.579	2.86	0.14	0.97	4dn7A	GO:0005524 GO:0016226
3	0.07	0.533	3.12	0.10	0.86	2odlA
4	0.07	0.494	3.38	0.08	0.85	4rt6A	GO:0005576 GO:0006810
5	0.06	0.433	4.01	0.15	0.81	4i84B	GO:0005576 GO:0006810
6	0.06	0.351	4.15	0.00	0.74	4e5xG	GO:0005537 GO:0016020 GO:0016021 GO:0016032 GO:0030246 GO:0030683 GO:0033644 GO:0039504 GO:0039591 GO:0044165 GO:0044167 GO:0050690
7	0.06	0.304	4.55	0.05	0.67	2l0dA	GO:0004181 GO:0004185 GO:0005509 GO:0005615 GO:0006518 GO:0016485
8	0.06	0.335	4.31	0.06	0.68	4icqA	GO:0004177 GO:0006508 GO:0016787
9	0.06	0.343	4.92	0.00	0.74	3hjpA	GO:0016209 GO:0016491 GO:0055114 GO:0098869
10	0.06	0.371	4.39	0.13	0.81	3icuA	GO:0005737 GO:0005770 GO:0005783 GO:0005794 GO:0005856 GO:0008270 GO:0012505 GO:0016020 GO:0016021 GO:0016567 GO:0016874 GO:0031647 GO:0042036 GO:0042787 GO:0046872 GO:0048471 GO:0061462 GO:0061630 GO:1904352
11	0.06	0.330	4.72	0.07	0.71	1fr1A	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
12	0.06	0.296	4.40	0.09	0.60	2fxhA	GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
13	0.06	0.307	5.20	0.03	0.84	2x6kA	GO:0000166 GO:0000421 GO:0005524 GO:0005769 GO:0006897 GO:0006914 GO:0009267 GO:0010506 GO:0016301 GO:0016303 GO:0016310 GO:0016322 GO:0016740 GO:0033227 GO:0034271 GO:0035004 GO:0035005 GO:0035032 GO:0035096 GO:0036092 GO:0045850 GO:0046854 GO:0046934 GO:0048015
14	0.06	0.300	4.64	0.03	0.68	4tkkA	GO:0000287 GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0006281 GO:0006310 GO:0006974 GO:0008821 GO:0016787 GO:0046872 GO:0090305
15	0.06	0.286	4.78	0.03	0.70	2dwrA	GO:0016032 GO:0019012 GO:0019028 GO:0019058 GO:0019062 GO:0039624 GO:0039665 GO:0044165 GO:0044168 GO:0046718
16	0.06	0.385	3.82	0.05	0.75	1fo1A	GO:0000166 GO:0000346 GO:0003723 GO:0003727 GO:0003729 GO:0005487 GO:0005622 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006405 GO:0006406 GO:0006810 GO:0016032 GO:0016607 GO:0016973 GO:0042405 GO:0044822 GO:0051028
17	0.06	0.308	4.00	0.02	0.60	1s9hC	GO:0000166 GO:0005524 GO:0006260 GO:0016032 GO:0016787 GO:0019079 GO:0039592 GO:0039645 GO:0039665 GO:0039693 GO:0046718 GO:0060153
18	0.06	0.253	4.38	0.04	0.52	1wg1A	GO:0000166 GO:0000398 GO:0003676 GO:0003723 GO:0005634 GO:0005737 GO:0044822

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0051539
GO-Score	0.07	0.07
Biological Processes	GO:0006790	GO:0051188	GO:0031163
GO-Score	0.37	0.37	0.37
Cellular Component	GO:0005576
GO-Score	0.07

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.

I-TASSER results for job id Rv0378

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]