Input Sequence in FASTA format
>protein (75 residues)
MVDRDPNTIKQEIDQTRDQLAATIDSLAERANPRRLADDAKTRVIAFLRKPIVTVSLVGI
GSVVVVVVIHKIRNR
|
Predicted Secondary Structure
| Sequence |
20 40 60
| | |
MVDRDPNTIKQEIDQTRDQLAATIDSLAERANPRRLADDAKTRVIAFLRKPIVTVSLVGIGSVVVVVVIHKIRNR |
|
Prediction | CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHHCC |
|
Conf.Score | 999999999999999999999999999985786789999999999999788755676557899999999998769 |
| H:Helix;
S:Strand; C:Coil |
Predicted Solvent Accessibility
| Sequence |
20 40 60
| | |
MVDRDPNTIKQEIDQTRDQLAATIDSLAERANPRRLADDAKTRVIAFLRKPIVTVSLVGIGSVVVVVVIHKIRNR |
|
Prediction | 746543741453156127511521441164352541265135403631664403210023333211100332478 |
| 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 | DownloadAlign. | | 20 40 60
| | | |
|---|
| Sec.Str
Seq | CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHHCC
MVDRDPNTIKQEIDQTRDQLAATIDSLAERANPRRLADDAKTRVIAFLRKPIVTVSLVGIGSVVVVVVIHKIRNR |
|---|
| 1 | 5j0iA | 0.15 | 0.15 | 0.96 | 0.90 | MUSTER | | MGTKELRRALEELEKALQELREMLRKLKES--LEELKKNPSEDALVRNNELIVEVLRVIVEVLSIIARVLEINA- |
| 2 | 4lhxC | 0.10 | 0.09 | 0.95 | 0.83 | dPPAS | | ----GYERLKEELAKAQRELKLKDEECERLSKVRDQLGQELEELTASLFEEAHKMVRANIKQATAEKQLKEAQGK |
| 3 | 4pu3D | 0.17 | 0.15 | 0.84 | 0.77 | wdPPAS | | IMASNQQSLGLLIKERRKSAALTQDVAAMLCG-------VTKKTLIRVEKGE-----VYISTVFKILDGLGIDIV |
| 4 | 5iy7M | 0.07 | 0.07 | 0.95 | 0.57 | wMUSTER | | QNRRTMSSSDRAMMNAFKEITTMADRIN----PRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGV |
| 5 | 4pu3D | 0.13 | 0.11 | 0.81 | 0.83 | wPPAS | | IMASNQQSLGLLIKERRKSAALTQDVAAMLCG--------TKKTLIRVEKGE------DVYISTVFKILDGLGID |
| 6 | 2yn7A3 | 0.19 | 0.13 | 0.71 | 1.01 | dPPAS2 | | ----------KEWSRQADGLIANASSNSSLSDSKSLAEYIKKRYLDNMQN-------ARQSVLEAYISIM----- |
| 7 | 4lhxC | 0.10 | 0.09 | 0.93 | 0.93 | PPAS | | ----GYERLKEELAKAQRELKLKDEECERLSKVRDQLGQELEELTASLFEEAHKMV-ANIKQATAEKQLKEAQGK |
| 8 | 3dnvB | 0.09 | 0.08 | 0.87 | 0.90 | Env-PPAS | | QKIYSPTQLANAMKLVRQQNGWTQSELAKKIG---IKQATISNFENNPDNTT-------LTTFFKILQSLTLCDA |
| 9 | 4tqlA2 | 0.12 | 0.12 | 0.97 | 0.90 | MUSTER | | -MKKLYDEAKKKIEQMIQQIKQGGDKQKME-ELLKRAKEEMKKVKDKMEKAKQVAEELIKKILQLIEKAKEIAEK |
| 10 | 5ajsA | 0.17 | 0.15 | 0.84 | 0.75 | dPPAS | | ---TTEEELLRKLNEQRDILALMEVKMKEMKGSIRHLRLTEAKLREELR---------EKDRLLAMAVIRKKHGM |
| (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.)
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 | RMSDa | IDENa | Cov |
|---|
1 | 5cwcA1 | 0.659 | 2.40 | 0.087 | 0.920 | |
2 | 3kbcA | 0.635 | 2.62 | 0.097 | 0.920 | |
3 | 1jswB | 0.632 | 3.05 | 0.125 | 0.933 | |
4 | 3saeA | 0.628 | 2.62 | 0.069 | 0.827 | |
5 | 1s8nA | 0.627 | 2.57 | 0.029 | 0.853 | |
6 | 3jd8A | 0.621 | 2.99 | 0.114 | 0.920 | |
7 | 3p5pA | 0.619 | 2.64 | 0.014 | 0.813 | |
8 | 4pgrA | 0.618 | 3.03 | 0.110 | 0.973 | |
9 | 4jkvA | 0.614 | 3.22 | 0.056 | 0.920 | |
10 | 3mktA1 | 0.613 | 3.14 | 0.055 | 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align. |
| (d) | IDENa 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.)
| Rank |
C-score |
Cluster
size |
PDB
Hit |
Lig
Name |
Download
Complex |
Ligand Binding Site Residues |
| 1 | 0.27 | 29 | 2akfB | ZN | Rep, Mult | 25,29 |
| 2 | 0.07 | 8 | 5bpsK | EFO | Rep, Mult | 13,17,20,21,23,24,27 |
| 3 | 0.06 | 7 | 4tt0A | IOD | Rep, Mult | 16,17,20 |
| 4 | 0.05 | 5 | 3qzcB | ZN | Rep, Mult | 21,25 |
| 5 | 0.05 | 6 | 4evdA | CD | Rep, Mult | 11,12,15 |
| 6 | 0.02 | 2 | 3ho8D | COA | Rep, Mult | 31,37,38,43 |
| 7 | 0.01 | 1 | 2zxeB | CLR | Rep, Mult | 9,13 |
| 8 | 0.01 | 1 | 2eulA | ZN | Rep, Mult | 15,19 |
| 9 | 0.01 | 1 | 3rrpA | LMR | Rep, Mult | 26,28,35,36,37 |
| 10 | 0.01 | 1 | 3zk1I | DMU | Rep, Mult | 5,8 |
| 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
|
| (a) | CscoreEC is the confidence score for the EC number prediction. CscoreEC 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align. |
| (d) | IDENa 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. |
Consensus prediction of GO terms | | |
|---|
|
|
| (a) | CscoreGO 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align. |
| (d) | IDENa 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 CscoreGO 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. |
