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I-TASSER results for job id Rv2507

[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 3 3etdA B1T Rep, Mult 223,224
20.06 3 2a07F MG Rep, Mult 232,233,234
30.06 3 3w68B PBU Rep, Mult 227,228,230
40.06 3 2cizA MAN Rep, Mult 165,167,168,171
50.04 2 1hn1B NA Rep, Mult 28,29,30,96,97,98
60.02 1 5tglA HEE Rep, Mult 73,135
70.02 1 2ahiC NUC Rep, Mult 171,175
80.02 1 3iylA MYR Rep, Mult 196,212
90.02 1 2pflB NA Rep, Mult 109,143,144,145
100.02 1 2v5pA UUU Rep, Mult 133,135
110.02 1 3begB ALA Rep, Mult 41,45
120.02 1 2pyhB CA Rep, Mult 155,158
130.02 1 1yf8B UUU Rep, Mult 157,242
140.02 1 1h18B DTL Rep, Mult 189,190,192,195
150.02 1 3pe7A CA Rep, Mult 1,37

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
10.0601h16A0.4206.180.0350.7032.3.1.54NA
20.0603eifA0.3915.750.0430.6373.4.21.110NA
30.0601t3qB0.3906.650.0680.7141.3.99.17NA
40.0601jroB0.3856.590.0420.6891.1.1.204NA
50.0601mx9D0.3876.230.0270.6593.1.1.1NA
60.0602pflA0.4206.190.0350.7032.3.1.54NA
70.0601llwA0.3986.530.0450.7001.4.7.1NA
80.0602pm8A0.3876.270.0470.6673.1.1.8NA
90.0601yq2A0.4255.960.0720.7073.2.1.23NA
100.0602r7oA0.4186.950.0490.7842.7.7.48155
110.0601n1hA0.3366.960.0410.6342.7.7.4827
120.0601maaD0.3886.010.0640.6483.1.1.7NA
130.0603c46B0.3146.840.0330.5682.7.7.6NA
140.0603czkA0.3865.860.0480.6343.2.1.48NA
150.0601mpyA0.3985.620.0310.6371.13.11.2NA
160.0601ti2A0.3806.880.0280.7181.97.1.248
170.0603ecjA0.3995.640.0300.6411.13.11.15NA
180.0601jrpB0.3856.680.0450.7031.17.1.4220
190.0601ofdA0.3256.430.0260.5861.4.7.1NA

(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
00.180.8262.180.090.904nl6A GO:0000245 GO:0000387 GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006353 GO:0006397 GO:0007399 GO:0008380 GO:0015030 GO:0030018 GO:0032797 GO:0034719 GO:0036464 GO:0042802 GO:0043005 GO:0043204 GO:0051170 GO:0097504
10.060.4255.960.070.711yq2A GO:0003824 GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0030246 GO:0046872
20.060.3216.230.040.542okxA GO:0003824
30.060.4285.860.090.705a1aA GO:0000287 GO:0003824 GO:0004553 GO:0004565 GO:0005975 GO:0005990 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0030246 GO:0031420 GO:0043231 GO:0046872
40.060.3496.210.040.592je8B GO:0004553 GO:0004567 GO:0005975 GO:0043231
50.060.4056.040.060.673decA GO:0003824 GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0030246 GO:0043231
60.060.4055.990.060.673bgaA GO:0003824 GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0030246 GO:0043231 GO:0046872
70.060.2776.100.030.454jkkA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
80.060.3306.610.040.591bhgA GO:0004553 GO:0004566 GO:0005102 GO:0005615 GO:0005764 GO:0005975 GO:0006027 GO:0008152 GO:0016020 GO:0016787 GO:0016798 GO:0019904 GO:0030214 GO:0043202 GO:0043231 GO:0070062
90.060.3196.160.040.535c70A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
100.060.2946.420.060.524ew6A GO:0016491 GO:0019151 GO:0055114
110.060.3285.960.040.544jkmA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
120.060.3276.150.050.553lpfA GO:0004553 GO:0004566 GO:0005829 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0019391 GO:0043231
130.060.3536.080.040.603gm8A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
140.060.3246.050.060.544e6pA GO:0003939 GO:0016491 GO:0055114
150.060.3276.720.040.614cu7A GO:0004553 GO:0004565 GO:0005576 GO:0005618 GO:0005975 GO:0008152 GO:0016020 GO:0016787 GO:0016798
160.060.3025.950.050.504dnsA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
170.060.3056.300.040.523up8A GO:0016491 GO:0050580 GO:0055114
180.060.3636.330.040.613fn9C GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0016787 GO:0016798


Consensus prediction of GO terms
 
Molecular Function GO:0016798 GO:0003676 GO:0005515
GO-Score 0.36 0.35 0.35
Biological Processes GO:0006351 GO:0006913 GO:0048731 GO:0022618 GO:0000398
GO-Score 0.35 0.35 0.35 0.35 0.35
Cellular Component GO:0043234 GO:0042995 GO:0035770 GO:0043025 GO:0016604 GO:0031674
GO-Score 0.35 0.35 0.35 0.35 0.35 0.35

(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.