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I-TASSER results for job id Rv1374c

[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
10.06 2 4q54z CLA Rep, Mult 98,106
20.06 2 3wmnQ BCL Rep, Mult 87,98,102
30.06 2 3a0bX CLA Rep, Mult 89,92,93,96
40.06 2 4pj0X CLA Rep, Mult 88,89,93
50.06 2 3wmoS BCL Rep, Mult 87,98
60.06 2 1kfvA QNA Rep, Mult 14,57,58,59,60
70.03 1 1rpsA NO Rep, Mult 34,86,90
80.03 1 3tmdA FE Rep, Mult 28,31,83
90.03 1 4pdiA 2ON Rep, Mult 66,67,69,128,151
100.03 1 1q39A CA Rep, Mult 76,150

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
10.0601iduA0.4615.170.0870.7631.11.1.10NA
20.0601xrtA0.4214.200.0270.6513.5.2.3NA
30.0601ygeA0.3695.940.0720.7301.13.11.12NA
40.0601mx9D0.4535.460.0670.8093.1.1.1NA
50.0602iukB0.3815.120.0340.6911.13.11.1287
60.0601pm5A0.6004.030.1100.8623.2.2.23NA
70.0601qo9A0.4575.270.0670.8093.1.1.7NA
80.0601aqfE0.4534.650.1140.7502.7.1.40NA
90.0601ee8A0.6054.200.1160.8953.2.2.23NA
100.0603gpyA0.6144.050.1540.8823.2.2.2352
110.0603a45A0.5644.560.0810.8753.2.2.23NA
120.0603juvA0.4624.380.0650.6781.14.13.706,34,64
130.0602ve3A0.4634.090.0400.6581.14.-.-64
140.0601k4yA0.3515.340.0220.6383.1.1.1NA
150.0602zf5Y0.4725.080.0480.8362.7.1.3010
160.0602vr2A0.4604.530.0230.7303.5.2.2NA
170.0601pjjA0.6024.150.1040.8683.2.2.2362,64
180.0601ak0A0.4605.190.0530.8163.1.30.138
190.0603i3kA0.3954.820.0730.6711.14.13.7016

(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
00.160.6054.200.120.891ee8A GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
10.140.5844.120.100.861k82A GO:0000703 GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0004519 GO:0006281 GO:0006284 GO:0006285 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0046872 GO:0090305
20.130.5763.740.120.821q3bA GO:0000703 GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0004519 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872 GO:0090305
30.090.5644.560.080.883a45A GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829
40.080.6133.660.110.863w0fA GO:0000405 GO:0003676 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0003824 GO:0003906 GO:0005634 GO:0005654 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0046872
50.080.6174.010.150.882f5qA GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
60.070.6014.070.100.874pd2A GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
70.070.6024.100.110.914mb7A GO:0003676 GO:0003684 GO:0003906 GO:0006284 GO:0006289 GO:0008270 GO:0016799 GO:0046872
80.070.5593.970.150.794g4nA GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
90.070.5644.000.090.823twkA GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0005634 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0006979 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104
100.060.4284.770.040.701ffyA GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
110.060.3265.290.030.613a3tA GO:0005623 GO:0045454
120.060.3645.610.020.693cogD GO:0000098 GO:0003824 GO:0003962 GO:0004123 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0006534 GO:0008652 GO:0016829 GO:0016846 GO:0018272 GO:0019343 GO:0019344 GO:0019346 GO:0030170 GO:0030968 GO:0043066 GO:0043123 GO:0044524 GO:0044540 GO:0047982 GO:0051092 GO:0051289 GO:0070062 GO:0070814 GO:0071266 GO:0080146 GO:1904831 GO:2001234
130.060.3825.040.040.663p09A GO:0008800 GO:0016787 GO:0030655 GO:0046677
140.060.5554.490.110.891tdhA GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005815 GO:0005856 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0006979 GO:0008022 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0032074 GO:0045008
150.060.2944.340.060.454aqyM GO:0000049 GO:0003676 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
160.060.3044.320.060.454g7nA GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0005814 GO:0005856 GO:0006468 GO:0007052 GO:0007099 GO:0007140 GO:0007288 GO:0016301 GO:0016310 GO:0016740 GO:0031647 GO:0035186 GO:0045732 GO:0046599 GO:0046777 GO:0051297 GO:0051298
170.060.1901.910.070.204dhxA GO:0000166 GO:0002376 GO:0003677 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006260 GO:0006606 GO:0006810 GO:0015031 GO:0016740 GO:0016746 GO:0031965 GO:0051028
180.060.2084.700.040.362l7yA GO:0005576 GO:0005618 GO:0005737 GO:0016020 GO:0033925


Consensus prediction of GO terms
 
Molecular Function GO:0003684 GO:0008270 GO:0008534
GO-Score 0.48 0.48 0.35
Biological Processes GO:0006284 GO:0006289
GO-Score 0.48 0.48
Cellular Component GO:0005654
GO-Score 0.08

(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.