I-TASSER results

Input Sequence in FASTA format

>protein (114 residues)
MAVILLPQVERWFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNDSTFHNMKELRPA
GTSIRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQRSENWLASEHGGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAVILLPQVERWFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNDSTFHNMKELRPAGTSIRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQRSENWLASEHGGG
Prediction	CEEEHCHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCEEEEEEEHCCEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	989985568999998999999999999999999899899986545688767775567768986999999959968999986557888875799999999999999999998769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAVILLPQVERWFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNDSTFHNMKELRPAGTSIRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQRSENWLASEHGGG
Prediction	630431640350166046721540240042037423724312143054352560450347454110001124433000000233546654215510540362155105636888
	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                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEHCHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCEEEEEEEHCCEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
MAVILLPQVERWFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNDSTFHNMKELRPAGTSIRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQRSENWLASEHGGG

2kheA

0.14

0.11

0.76

1.34

MUSTER

MRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARDVYR------------------------

2kheA

0.13

0.10

0.76

1.83

dPPAS

YRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARDVYR------------------------

2kheA

0.13

0.10

0.76

2.02

wdPPAS

YRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARDVYR------------------------

2kheA

0.13

0.10

0.75

1.65

wMUSTER

YRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARD----YR---------------------

2kheA

0.14

0.11

0.75

1.85

wPPAS

MRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARD----YR---------------------

2kheA

0.13

0.10

0.76

3.82

dPPAS2

YRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARDVYR------------------------

2kheA

0.14

0.11

0.75

1.67

PPAS

MRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARD----YR---------------------

2kheA

0.13

0.10

0.76

1.73

Env-PPAS

YRIEFDPRAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRVGD--YRLICHIQDREATVLVLRVGHARDV---YR---------------------

1wmiA

0.19

0.14

0.75

1.29

MUSTER

MRVKIHKQVVKALQSLPKAHYRRFLEFRDILEYEPVPREKFDVIKLEGTGDLDLYRARL--GDYRVIYSVNWKDKVIKILKLKPRGRA--------------------------

1wmiA

0.17

0.13

0.75

1.76

dPPAS

YRVKIHKQVVKALQSLPKAHYRRFLEFRDILEYEPVPREKFDVIKLEGTGDLDLYRARLG--DYRVIYSVNWKDKVIKILKLKPRGRA--------------------------

(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=-0.27

Estimated TM-score = 0.68±0.12

Estimated RMSD = 4.7±3.1Å

Download Model 2

C-score=-1.70

Download Model 3

C-score=-4.31

Download Model 4

C-score=-2.05

Download Model 5

C-score=-1.22

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	2kc9A	0.671	2.08	0.086	0.816
2	2kheA	0.661	1.85	0.116	0.754
3	3a3jA	0.611	3.62	0.072	0.956
4	3itbD	0.607	3.60	0.082	0.947
5	1tvfA	0.607	3.69	0.046	0.947
6	5fsrA	0.606	3.61	0.110	0.939
7	1nrjA	0.606	3.46	0.089	0.868
8	3bebA	0.605	3.63	0.073	0.947
9	3g5oC	0.605	1.97	0.162	0.702
10	2o9aA	0.605	3.45	0.098	0.895

(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	0.10	4	3kiuy	RQA	Rep, Mult	46,47,56,58,65,92
2	0.08	3	3kisy	UUU	Rep, Mult	58,85,86,88,92
3	0.06	2	2a6sB	IPA	Rep, Mult	4,5,6,78,79,80
4	0.05	2	1wmi0	III	Rep, Mult	23,56,58,85
5	0.05	2	1wmi4	III	Rep, Mult	1,3,4,5,6,7,18,21,22,25,28,33,34,36,44,45,46,47,48,54,55,56,65,67,69,72,75,78,80,81,83,86
6	0.03	1	3g5oB	IMD	Rep, Mult	69,71,78
7	0.03	1	2v9jE	MG	Rep, Mult	6,65
8	0.03	1	1usyB	HIS	Rep, Mult	53,56
9	0.03	1	1lv8A	CA	Rep, Mult	49,56
10	0.03	1	3it9A	SUC	Rep, Mult	47,49,51
11	0.03	1	3c25B	CA	Rep, Mult	56,71

	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	1iyqA	0.523	4.02	0.077	0.842	3.5.2.6	99
2	0.060	2blmA	0.528	4.35	0.064	0.886	3.5.2.6	23
3	0.060	3fwmA	0.391	4.49	0.076	0.667	2.4.1.129,	NA
4	0.060	3bydA	0.523	4.08	0.077	0.851	3.5.2.6	NA
5	0.060	2j9oD	0.566	4.14	0.056	0.930	3.4.16.4	NA
6	0.060	3fwlA	0.518	4.05	0.028	0.842	2.4.1.129	NA
7	0.060	2wafA	0.538	4.23	0.045	0.930	3.4.-.-	NA
8	0.060	1skfA	0.529	3.81	0.060	0.833	3.4.16.4	NA
9	0.060	1d9qB	0.520	3.83	0.045	0.816	3.1.3.11	NA
10	0.060	1spiA	0.466	4.68	0.064	0.798	3.1.3.11	NA
11	0.060	3cg5A	0.526	3.85	0.049	0.860	3.5.2.6	NA
12	0.060	2ex2A	0.518	4.35	0.029	0.895	3.4.16.4	NA
13	0.060	2vgkD	0.548	3.73	0.084	0.860	3.4.16.4	NA
14	0.060	1dy6A	0.524	4.18	0.058	0.877	3.5.2.6	NA
15	0.060	2bcfA	0.533	4.03	0.067	0.886	3.4.16.4	28,31
16	0.060	1e25A	0.572	4.03	0.055	0.930	3.5.2.6	NA
17	0.060	1rqiA	0.531	4.01	0.110	0.860	2.5.1.10	NA
18	0.060	3c4pA	0.533	3.84	0.080	0.868	3.5.2.6	85
19	0.060	1z6fA	0.603	3.64	0.073	0.947	3.4.16.4	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	0.22	0.601	2.26	0.05	0.73	2kc8A	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006402 GO:0016787 GO:0017148 GO:0019843 GO:0034198 GO:0043022 GO:0046677 GO:0090305 GO:0090502
1	0.20	0.585	2.53	0.11	0.74	3bpqD	GO:0004518 GO:0016787 GO:0090305
2	0.18	0.572	2.24	0.13	0.69	3oeiC	GO:0003677 GO:0004518 GO:0004519 GO:0006351 GO:0006355 GO:0006401 GO:0016787 GO:0040008 GO:0045892 GO:0090305
3	0.18	0.560	2.28	0.11	0.69	2a6qE	GO:0003714 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006401 GO:0006402 GO:0016787 GO:0016892 GO:0043024 GO:0044010 GO:0045947 GO:0090502 GO:0098795 GO:1903507
4	0.15	0.607	3.60	0.08	0.95	3itbD	GO:0004175 GO:0004180 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0008658 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0042493 GO:0071555
5	0.13	0.605	1.97	0.16	0.70	3g5oC	GO:0003677 GO:0004518 GO:0004519 GO:0006351 GO:0006355 GO:0006401 GO:0016787 GO:0040008 GO:0045892 GO:0045926 GO:0090305
6	0.07	0.611	3.62	0.07	0.96	3a3jA	GO:0004175 GO:0004180 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0071555
7	0.07	0.601	3.66	0.07	0.95	3mzfA	GO:0000270 GO:0004175 GO:0004180 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0008658 GO:0008800 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0044036 GO:0071555
8	0.07	0.606	3.61	0.11	0.94	5fsrA	GO:0004175 GO:0004180 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0008658 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0071555
9	0.07	0.607	3.69	0.05	0.95	1tvfA	GO:0004180 GO:0006508 GO:0009002 GO:0016020 GO:0016021
10	0.07	0.566	4.14	0.06	0.93	2j9oD
11	0.07	0.573	3.82	0.06	0.89	3mfdA	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0030435 GO:0071555
12	0.07	0.589	3.78	0.08	0.93	1xp4A	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016787
13	0.07	0.539	3.95	0.05	0.90	4pprA	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016020 GO:0016021 GO:0016787
14	0.07	0.573	3.78	0.07	0.91	4k91A	GO:0004180 GO:0006508 GO:0009002
15	0.07	0.554	3.56	0.06	0.87	1xp4D	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016787
16	0.07	0.531	3.91	0.13	0.87	4id4A	GO:0008800 GO:0016787 GO:0030655 GO:0046677
17	0.07	0.544	3.89	0.08	0.89	4ryeA	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016787
18	0.07	0.539	4.13	0.09	0.89	2v1zA	GO:0008800 GO:0016787 GO:0030655 GO:0046677
19	0.07	0.386	4.78	0.06	0.72	3e7pA	GO:0046872 GO:0051536 GO:0051539
20	0.06	0.529	3.81	0.06	0.83	1skfA	GO:0004180 GO:0005576 GO:0006508 GO:0008233 GO:0008360 GO:0009002 GO:0009252 GO:0016787 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0043021	GO:0004521	GO:0003723	GO:0003712	GO:0016894	GO:0043177	GO:0008144	GO:0033218	GO:0004185	GO:1901681
GO-Score	0.45	0.36	0.36	0.36	0.36	0.31	0.31	0.31	0.31	0.31
Biological Processes	GO:0006355	GO:0034249	GO:2000113	GO:0042221	GO:0032269	GO:0009267	GO:0040007	GO:1903507	GO:0006402	GO:0090502	GO:0006446	GO:0042710	GO:0006379	GO:0016458	GO:0009273	GO:0022604	GO:0065008	GO:0045229	GO:0044038	GO:0000270	GO:0006024
GO-Score	0.48	0.45	0.45	0.45	0.45	0.45	0.37	0.37	0.36	0.36	0.36	0.36	0.36	0.36	0.31	0.31	0.31	0.31	0.31	0.31	0.31
Cellular Component	GO:0031226
GO-Score	0.31

(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 Rv3182

[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]