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I-TASSER results for job id Rv2149c

[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 1 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
10.20 2 1u05A ZN Rep, Mult 77,114,131
20.17 3 1wb4A SXX Rep, Mult 77,78,79,135,136,140
30.17 2 1t8hA ZN Rep, Mult 170,171,224,227
40.06 1 1gklA FER Rep, Mult 135,137,138,139,182
50.06 1 1oi8A CO3 Rep, Mult 166,225,226

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
10.0603b9eA0.4435.780.0430.7403.2.1.14NA
20.0602hs4A0.4495.060.0530.6686.3.5.3164
30.0602ddtA0.4126.080.0810.7203.1.4.12NA
40.0601t3tA0.4965.030.0850.7366.3.5.3133
50.0601w0iA0.4305.460.0750.6802.3.1.41NA
60.0601tz7A0.4495.490.0310.7122.4.1.25NA
70.0601e5tA0.4575.390.0580.7203.4.21.26234
80.0601ho5A0.4395.390.0530.6763.1.3.5,3.6.1.45NA
90.0601c7jA0.3106.560.0390.5963.1.1.-NA
100.0601thgA0.4455.820.0510.7643.1.1.3112
110.0601maaD0.4326.040.0710.7323.1.1.7NA
120.0601w9pA0.4325.850.0730.7203.2.1.14NA
130.0602a3eA0.4315.860.0780.7203.2.1.1474,226
140.0602w22A0.4565.900.0600.7763.1.1.3206
150.0601eveA0.4325.940.0340.7403.1.1.7NA
160.0601qo9A0.4326.010.0630.7523.1.1.7NA
170.0602pffD0.4525.580.0600.7082.3.1.86NA
180.0601edqA0.4395.670.0820.7203.2.1.14NA
190.0601mx9D0.4356.040.0540.7523.1.1.1NA

(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
00.660.9281.240.360.961u05A GO:0046872
10.330.9132.190.321.001t8hA GO:0046872
20.070.4475.240.080.683viuA GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874 GO:0046872
30.070.4265.220.070.632hruA GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
40.060.4282.870.180.502f9zC GO:0006935 GO:0008984 GO:0016787 GO:0050568
50.060.4095.640.070.651r9jB GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
60.060.3754.780.080.564q1tD GO:0000166 GO:0003723 GO:0004349 GO:0005524 GO:0005737 GO:0006561 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0055129
70.060.4014.970.060.601e3wD GO:0001540 GO:0003857 GO:0004303 GO:0005496 GO:0005739 GO:0007569 GO:0008033 GO:0016491 GO:0018454 GO:0030283 GO:0030331 GO:0033327 GO:0042802 GO:0047015 GO:0051287 GO:0051289 GO:0055114
80.060.4745.190.070.712hs3A GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
90.060.3786.300.040.671jy1A GO:0000012 GO:0003690 GO:0003697 GO:0004518 GO:0004527 GO:0005634 GO:0005737 GO:0005886 GO:0006281 GO:0006302 GO:0006974 GO:0008081 GO:0016787 GO:0017005 GO:0043231 GO:0090305
100.060.3506.330.030.631a12A GO:0000082 GO:0000790 GO:0000794 GO:0003677 GO:0003682 GO:0005085 GO:0005087 GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0007052 GO:0007059 GO:0007067 GO:0007088 GO:0016032 GO:0031492 GO:0031965 GO:0042393 GO:0043547 GO:0051225 GO:0051301
110.060.3556.250.050.624ufoA GO:0003824 GO:0016787
120.060.4175.260.080.643vdqA GO:0000166 GO:0003858 GO:0016491 GO:0055114
130.060.3215.760.060.541pmiA GO:0004476 GO:0005737 GO:0005975 GO:0008270 GO:0009298 GO:0016853 GO:0031505 GO:0046872
140.060.3455.950.050.584zhtA GO:0000166 GO:0003824 GO:0004553 GO:0005524 GO:0005737 GO:0005829 GO:0006045 GO:0006047 GO:0006054 GO:0007155 GO:0008152 GO:0008761 GO:0009384 GO:0016301 GO:0016310 GO:0016740 GO:0016787 GO:0046835 GO:0046872
150.060.3586.090.040.643ikmD GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
160.060.3325.940.060.561a5zA GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
170.060.3306.290.040.601vr0C GO:0000287 GO:0016311 GO:0016787 GO:0019295 GO:0050532
180.060.2955.060.090.451ztcA


Consensus prediction of GO terms
 
Molecular Function GO:0046872
GO-Score 0.80
Biological Processes GO:0006189 GO:0006935 GO:0006541
GO-Score 0.13 0.07 0.07
Cellular Component GO:0005737
GO-Score 0.13

(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.