I-TASSER results

Input Sequence in FASTA format

>protein (99 residues)
MAPGMKWAAKTDHLAIVLLPRHHRRHSRRGRALPARSRSALGWIIERYRVTTDKASGIVN
DPNDWCDEHDDPTYIVDLIKKVTTVSVETMKIVDGLAGG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAPGMKWAAKTDHLAIVLLPRHHRRHSRRGRALPARSRSALGWIIERYRVTTDKASGIVNDPNDWCDEHDDPTYIVDLIKKVTTVSVETMKIVDGLAGG
Prediction	CCCCCCCCCCCCCEEEEHCCCEEHCCCHHHHEEEHCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
Conf.Score	998777777788679997796786587666455437877799999986435787778777856788875997357899999999999999999976589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAPGMKWAAKTDHLAIVLLPRHHRRHSRRGRALPARSRSALGWIIERYRVTTDKASGIVNDPNDWCDEHDDPTYIVDLIKKVTTVSVETMKIVDGLAGG
Prediction	745514255674312022146212522460351425642103000432435466644146314401573744400040033003011402511562588
	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                  80

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCEEEEHCCCEEHCCCHHHHEEEHCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
MAPGMKWAAKTDHLAIVLLPRHHRRHSRRGRALPARSRSALGWIIERYRVTTDKASGIVNDPNDWCDEHDDPTYIVDLIKKVTTVSVETMKIVDGLAGG

4xqkA

0.34

0.33

0.97

3.03

MUSTER

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEF---SDDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

1.46

dPPAS

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEF---SDDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

1.48

wdPPAS

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEFS---DDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA

0.34

0.33

0.97

3.67

wMUSTER

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEF---SDDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

0.92

wPPAS

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEFS---DDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

4.34

dPPAS2

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEFS---DDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

0.96

PPAS

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEFS---DDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

1.06

Env-PPAS

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEFS---DDPKYILNLLLSVITVSMRTLELIDELPEF

4xqkA2

0.34

0.33

0.97

2.93

MUSTER

RVKKMKHPKKGVLDTIIYNESITIKIPEKAYEYVVNGRPAIEWIINQYQVKTDKKSGITDDPNEF---SDDPKYILNLLLSVITVSMRTLELIDELPEF

5dooA3

0.15

0.14

0.92

0.87

dPPAS

QAKHAHFNNVTNMFSITNRLNDMIGIPEKYILEMLDGTHNIDDIKKSIIEKINSKLLTACD-------VTDPKLLKEFVDYVVAVSLEKFRINYLLVG-

(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 5 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=0.65

Estimated TM-score = 0.80±0.09

Estimated RMSD = 2.7±2.0Å

Download Model 2

C-score=-3.67

Download Model 3

C-score=-4.28

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	4xqkA2	0.920	0.89	0.344	0.970
2	1iduA	0.532	3.75	0.079	0.838
3	2ddzE	0.527	4.45	0.116	0.919
4	4twaA	0.525	3.49	0.010	0.768
5	2c2nA	0.523	3.96	0.025	0.768
6	3vvnA	0.522	3.92	0.057	0.838
7	4citA	0.521	3.77	0.023	0.828
8	1nj1A	0.520	3.68	0.063	0.788
9	3mk7A	0.520	3.87	0.140	0.798
10	3rkoL	0.519	4.20	0.053	0.859

(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	0.08	3	3keuB	MPD	Rep, Mult	50,51,52,59
2	0.08	3	1q90M	BCR	Rep, Mult	83,87
3	0.08	3	1fbmD	RTL	Rep, Mult	78,85
4	0.05	2	1rwkB	158	Rep, Mult	39,43,47
5	0.05	2	2yxtA	MPD	Rep, Mult	41,42,45,78
6	0.03	1	3nteA	FE	Rep, Mult	63,67
7	0.03	1	2w9nA	ZN	Rep, Mult	71,81
8	0.03	1	2e2hA	NUC	Rep, Mult	10,43
9	0.03	1	2zfeA	XE	Rep, Mult	44,45,48,75,78,79
10	0.03	1	3h87B	IMD	Rep, Mult	46,47
11	0.03	1	4brbB	78N	Rep, Mult	92,96

	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	1nj6A	0.521	3.67	0.063	0.788	6.1.1.15	NA
2	0.060	2ewnA	0.487	4.53	0.054	0.818	6.3.4.15	NA
3	0.060	2hvgA	0.482	3.77	0.093	0.758	4.3.2.2	46
4	0.060	3kb9A	0.509	3.50	0.076	0.768	4.2.3.37	NA
5	0.060	3ckeD	0.374	4.78	0.023	0.697	4.2.3.9	NA
6	0.060	3eenA	0.490	4.12	0.026	0.737	2.3.1.39	NA
7	0.060	1v8aA	0.500	3.72	0.050	0.768	2.7.1.50	30,42
8	0.060	1yisA	0.490	3.39	0.053	0.717	4.3.2.2	NA
9	0.060	1esjA	0.513	3.67	0.123	0.788	2.7.1.50	42,79
10	0.060	1nj1A	0.520	3.68	0.063	0.788	6.1.1.15	NA
11	0.060	3h0pB	0.486	4.05	0.051	0.727	2.3.1.39	NA
12	0.060	1nj8D	0.518	3.80	0.062	0.798	6.1.1.15	NA
13	0.060	3f2bA	0.499	4.57	0.062	0.899	2.7.7.7	NA
14	0.060	2c2nA	0.523	3.96	0.025	0.768	2.3.1.39	NA
15	0.060	3im9A	0.491	3.94	0.040	0.727	2.3.1.39	37
16	0.060	1b0aA	0.484	4.09	0.041	0.808	1.5.1.5,3.5.4.9	NA
17	0.060	1nm2A	0.488	3.89	0.026	0.717	2.3.1.39	NA
18	0.060	2oa6D	0.509	3.16	0.050	0.758	4.2.3.9	NA
19	0.060	1rfuA	0.516	3.80	0.087	0.778	2.7.1.35	NA

(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	0.21	0.903	1.05	0.33	0.97	5ffjB	GO:0000166 GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0006306 GO:0008168 GO:0008170 GO:0016787 GO:0032259 GO:0090305
1	0.20	0.899	1.08	0.33	0.97	5ffjA	GO:0000166 GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0006306 GO:0008168 GO:0008170 GO:0016787 GO:0032259 GO:0090305
2	0.07	0.454	3.83	0.06	0.76	4rxoD	GO:0002376 GO:0003676 GO:0003723 GO:0003824 GO:0005622 GO:0005634 GO:0005654 GO:0005886 GO:0006203 GO:0006955 GO:0008152 GO:0008270 GO:0008832 GO:0016787 GO:0032567 GO:0045087 GO:0045088 GO:0046061 GO:0046872 GO:0051289 GO:0051607 GO:0060337
3	0.06	0.397	4.19	0.05	0.65	3crvA	GO:0000166 GO:0003676 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0006139 GO:0006281 GO:0006351 GO:0006974 GO:0008026 GO:0016787 GO:0016818 GO:0032508 GO:0043139 GO:0046872 GO:0051536 GO:0051539
4	0.06	0.432	4.42	0.03	0.73	2c4wA	GO:0003855 GO:0008652 GO:0009073 GO:0009423 GO:0016829
5	0.06	0.418	4.31	0.10	0.71	4nmnA	GO:0000166 GO:0003677 GO:0003678 GO:0004386 GO:0005524 GO:0005829 GO:0006260 GO:0006268 GO:0006269 GO:0016787 GO:0046872 GO:1990077
6	0.06	0.360	5.06	0.03	0.75	5adzA	GO:0003824 GO:0005730 GO:0005739 GO:0005777 GO:0005778 GO:0006629 GO:0008609 GO:0008610 GO:0008611 GO:0016020 GO:0016491 GO:0016614 GO:0016740 GO:0043231 GO:0050660 GO:0055114 GO:0071949
7	0.06	0.428	4.33	0.08	0.82	3abzA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
8	0.06	0.355	4.68	0.07	0.65	4a2wA	GO:0000166 GO:0003677 GO:0005524 GO:0005737 GO:0016787 GO:0016817 GO:0046872
9	0.06	0.360	4.91	0.05	0.72	3i32A	GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
10	0.06	0.328	4.77	0.07	0.66	2b5xA	GO:0000103 GO:0005737 GO:0006457 GO:0015035 GO:0016209 GO:0016491 GO:0016671 GO:0034599 GO:0045454 GO:0055114 GO:0098869
11	0.06	0.394	4.05	0.07	0.66	1o81A
12	0.06	0.375	3.97	0.03	0.57	1t5lA	GO:0000166 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009381 GO:0009432 GO:0016787 GO:0090305
13	0.06	0.373	3.91	0.03	0.56	2fdcA	GO:0000166 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009381 GO:0009432 GO:0016787 GO:0090305
14	0.06	0.365	4.84	0.06	0.71	3mwyW	GO:0000124 GO:0000166 GO:0000182 GO:0000790 GO:0001178 GO:0003677 GO:0004386 GO:0005524 GO:0005634 GO:0006351 GO:0006355 GO:0006363 GO:0006368 GO:0006369 GO:0008094 GO:0016568 GO:0016584 GO:0016787 GO:0030874 GO:0031490 GO:0034728 GO:0035064 GO:0042766 GO:0043044 GO:0044212 GO:0046695 GO:0060303 GO:0070615 GO:0071441 GO:0071894 GO:1900050 GO:1902275 GO:2000104 GO:2000616
15	0.06	0.396	4.49	0.01	0.71	2fh7A	GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0006470 GO:0007155 GO:0007268 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0021510 GO:0021549 GO:0021766 GO:0021987 GO:0022038 GO:0035335 GO:0070062 GO:0090557
16	0.06	0.366	3.77	0.02	0.56	1d2mA	GO:0000166 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009381 GO:0009432 GO:0016787 GO:0090305
17	0.06	0.360	4.30	0.05	0.66	1vj7A	GO:0000166 GO:0005524 GO:0005525 GO:0008152 GO:0008728 GO:0008893 GO:0015969 GO:0015970 GO:0016301 GO:0016310 GO:0016597 GO:0016740 GO:0016787 GO:0046872
18	0.06	0.336	5.05	0.03	0.68	3h1tA	GO:0000166 GO:0003677 GO:0003824 GO:0005524 GO:0006304 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0003677	GO:0008170	GO:0004519
GO-Score	0.41	0.41	0.37	0.37
Biological Processes	GO:0090305	GO:0006306
GO-Score	0.37	0.37
Cellular Component	GO:0005886	GO:0005654
GO-Score	0.07	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 Rv2020c

[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]