[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv0779c

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

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 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.)


 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
10.08 4 4ujmE MG Rep, Mult 135,139
20.04 2 1o6pA III Rep, Mult 140,143,144,188,191,194,195
30.04 2 1jm0A DMS Rep, Mult 158,159,162,184
40.04 2 1o6pA III Rep, Mult 104,156,160
50.02 1 4llhA CM5 Rep, Mult 129,133
60.02 1 2hcvA ZN Rep, Mult 40,79
70.02 1 4jxtA III Rep, Mult 54,57,58,61,111,114,115,118,161,165,171
80.02 1 1jb0M CLA Rep, Mult 110,114
90.02 1 1f59A III Rep, Mult 40,43,44,47,48,91,95
100.02 1 3gwzD CA Rep, Mult 18,22
110.02 1 1fx4A MG Rep, Mult 22,79
120.02 1 1h2u0 III Rep, Mult 71,75,76,120,121,128
130.02 1 4ryoA MPG Rep, Mult 112,127,134
140.02 1 1g5bA MN Rep, Mult 22,40,79
150.02 1 5jvgN MG Rep, Mult 180,184
160.02 1 4e5uB CA Rep, Mult 192,197
170.02 1 2bptA III Rep, Mult 90,93,94,97,98,137,140
180.02 1 2id3B CA Rep, Mult 48,52
190.02 1 4tt0A IOD Rep, Mult 138,139,142
200.02 1 3k7tA GP7 Rep, Mult 12,13

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

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0661ujkB0.4803.490.0440.6503.4.23.46NA
20.0603c5wA0.5863.790.0470.7963.1.3.16NA
30.0603dsxA0.5294.070.0520.7282.5.1.60NA
40.0602ejaA0.5194.280.0410.7384.1.1.37NA
50.0603draA0.5574.170.0420.7822.5.1.58,2.5.1.59NA
60.0602hsaA0.5064.430.0680.7381.3.1.42NA
70.0602oykB0.4984.680.1190.7433.2.1.123NA
80.0602infC0.5144.300.0640.7434.1.1.37NA
90.0601uroA0.5394.600.0660.7914.1.1.37NA
100.0601e1eB0.5055.170.0650.8013.2.1.2183
110.0602x6fA0.5174.650.0360.8012.7.1.137,2.7.1.153,2.7.1.154176
120.0602v1yA0.1904.790.0120.2912.7.1.153135
130.0601jphA0.5005.050.0870.7914.1.1.37NA
140.0602infA0.5044.640.0800.7484.1.1.37NA
150.0601ayxA0.5065.390.0780.8543.2.1.3NA
160.0601q45B0.5094.600.0630.7521.3.1.42NA
170.0601b1yA0.5055.030.0900.7673.2.1.2NA
180.0602o1dA0.5065.270.0500.8454.2.2.2NA
190.0602gtqA0.5084.140.0850.7433.4.11.2NA
200.0601h7aA0.5034.970.0810.8061.17.4.2NA

(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.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.120.5464.850.110.844uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
10.090.6394.200.080.924by6A GO:0046872
20.070.6314.090.060.885fu7A GO:0000122 GO:0000289 GO:0000932 GO:0004535 GO:0005615 GO:0005634 GO:0005737 GO:0005778 GO:0005829 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007275 GO:0010606 GO:0016020 GO:0017148 GO:0019904 GO:0030014 GO:0030015 GO:0030331 GO:0031047 GO:0032947 GO:0033147 GO:0035195 GO:0042974 GO:0043231 GO:0044822 GO:0048387 GO:0060213 GO:0061014 GO:0070016 GO:0090503 GO:1900153 GO:2000036
30.060.4485.480.040.753renA GO:0003824 GO:0004553 GO:0005975 GO:0016020 GO:0016021 GO:0016787
40.060.3854.430.180.581n0rA
50.060.4065.180.050.653l0oA GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0006351 GO:0006353 GO:0006355 GO:0008186 GO:0016787
60.060.3985.050.080.632y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
70.060.3605.040.050.553wwpA GO:0016829 GO:0046872
80.060.4035.400.060.672bklB GO:0004252 GO:0006508 GO:0008236 GO:0070008
90.060.3105.470.040.514p3lA GO:0006810 GO:0008643 GO:0030288 GO:0042597
100.060.3655.170.080.594wjiA GO:0000166 GO:0004665 GO:0006571 GO:0008977 GO:0055114
110.060.3195.800.060.554p7kA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
120.060.3265.140.030.522f6uA GO:0000287 GO:0002094 GO:0005737 GO:0006629 GO:0006650 GO:0008654 GO:0016740 GO:0016765 GO:0046474 GO:0046872 GO:0047294
130.060.2834.650.030.414k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
140.060.2294.760.030.343idoA GO:0004725 GO:0006470 GO:0035335
150.060.3266.280.070.622cuzA GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039
160.060.2412.750.040.291qsdA GO:0005737 GO:0005856 GO:0005874 GO:0007021 GO:0007023 GO:0015631 GO:0048487
170.060.2244.620.040.344ccvA GO:0002839 GO:0004869 GO:0005102 GO:0005576 GO:0007162 GO:0007596 GO:0007599 GO:0008201 GO:0008270 GO:0008285 GO:0010468 GO:0010543 GO:0010593 GO:0010755 GO:0010951 GO:0016525 GO:0019865 GO:0020037 GO:0030168 GO:0030193 GO:0030308 GO:0032956 GO:0033629 GO:0042730 GO:0043065 GO:0043254 GO:0043395 GO:0043537 GO:0046872 GO:0050730 GO:0050832 GO:0051894 GO:1900747 GO:2000504 GO:2001027
180.060.2244.500.030.342fc3A GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502


Consensus prediction of GO terms
 
Molecular Function GO:0003682 GO:0046872 GO:0004535 GO:0032947 GO:0070016 GO:0044822 GO:0030331 GO:0042974 GO:0004553
GO-Score 0.12 0.09 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Biological Processes GO:0000755 GO:0031505 GO:0006473 GO:0007064 GO:0009847 GO:0035195 GO:0033147 GO:0007275 GO:2000036 GO:0000122 GO:0060213 GO:0010606 GO:0090503 GO:0006977 GO:0048387 GO:0005975
GO-Score 0.12 0.12 0.12 0.12 0.12 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0044444 GO:0043231
GO-Score 0.36 0.36

(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.