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I-TASSER results for job id Rv1190

[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
10.15 40 1a8uA BEZ Rep, Mult 49,50,114,115,116,141,213,270
20.13 38 1k63A BRP Rep, Mult 115,146,154,180,213
30.12 29 1k6eA 1BP Rep, Mult 115,146,154,172,176,180,270,271
40.07 19 4lyeA HPK Rep, Mult 49,50,51,52,56,114,115,116,151,180,194,270,271
50.02 7 2dhcA DCE Rep, Mult 115,116,119,158,161,210,211,214,246
60.01 2 1b6gA GOL Rep, Mult 5,7,31,82
70.01 2 1b6gA GOL Rep, Mult 59,276,277,278,279
80.01 3 1iupA ALQ Rep, Mult 55,56,194,271
90.01 2 1b6gA GOL Rep, Mult 179,180,184,245
100.01 2 3stvA 3HO Rep, Mult 50,156,157,160,270
110.01 4 2wj4A HQD Rep, Mult 52,114,115,116,156,176,198,206,209,213,270
120.01 3 2o2hA DCE Rep, Mult 146,147,244,245,270
130.01 3 2psjB CEI Rep, Mult 147,153,156,165,171,172,180,245,246,270
140.01 2 1ukbA BEZ Rep, Mult 58,176,179,190,271
150.01 4 1y37A MG Rep, Mult 88,89,90,93,209,212,217
160.01 3 1q0rA AKT Rep, Mult 115,116,119,139,140,141,151,212,213,218,220,246
170.01 2 3b12B FAH Rep, Mult 122,221,225,256
180.01 3 1xqyA III Rep, Mult 169,172,173,176,186,194,203
190.01 2 3hssB MLA Rep, Mult 175,197,201,271,274
200.01 2 1cijA BR Rep, Mult 116,158,161,210,211,214

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
10.3841b6gA0.8182.940.1610.9453.8.1.5115,270
20.3501mj5A0.8372.420.2550.9353.8.1.5115,270
30.3431a8qA0.7662.620.1930.8701.11.1.10245,270
40.3392qvbB0.8382.370.2470.9353.8.1.5115,270
50.3001iunB0.7822.760.1860.9013.7.1.9270
60.2912r11D0.7493.190.1590.8843.1.1.157,116,277
70.2861j1iA0.7642.360.1810.8533.7.1.851
80.2803e3aB0.7542.830.1450.8731.11.1.-35,51,74
90.2792ocgA0.7252.710.1650.8293.1.-.-111,117,237,270
100.2751a88B0.7662.800.1960.8731.11.1.10NA
110.2632vf2A0.7803.000.1810.9073.7.1.877,79,116
120.2362pu5A0.7872.990.1430.9073.7.1.8NA
130.1901c4xA0.7802.740.1600.9013.7.1.8NA
140.1621ehyA0.8012.790.1600.9183.3.2.10115,270
150.1591u2eA0.7793.110.1580.9073.7.1.-245,270
160.1233bf7A0.6793.600.1650.8293.1.-.-NA
170.0671i6wB0.4762.800.1520.5413.1.1.3NA
180.0601y37A0.8062.800.2060.9313.8.1.3205,207
190.0602psfA0.8123.020.1990.9451.13.12.5115,270
200.0601k8qA0.7913.310.1240.9423.1.1.3NA
210.0602v9zA0.8222.670.2140.9383.8.1.5NA
220.0603a2lA0.8212.460.1930.9253.8.1.558
230.0601vj5A0.7982.900.1440.9283.3.2.10,3.3.2.3110
240.0601va4A0.7712.750.1960.8733.1.1.2NA
250.0601zoiA0.7652.810.1800.8733.1.1.-245,270
260.0601mt3A0.7523.450.1120.9043.4.11.5270
270.0601ivyA0.7583.840.1130.9383.4.16.5NA
280.0602e3jA0.7842.750.1690.9043.3.2.3NA
290.0601hlgB0.7943.120.1330.9383.1.1.3NA
300.0603g0iA0.7983.190.1190.9523.3.2.3240
310.0602vavB0.7563.330.1190.9182.3.1.175174
320.0601a7uA0.7712.490.1780.8631.11.1.10245,270
330.0601a8sA0.7652.810.1690.8731.11.1.10270
340.0601a88A0.7662.800.1960.8731.11.1.10245,270
350.0602og1A0.7872.990.1430.9073.7.1.8NA
360.0602pl5A0.7543.270.0910.9012.3.1.31270

(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
00.470.8332.780.200.964nvrA GO:0016740 GO:0016746 GO:0016787 GO:0046872
10.440.8232.800.190.955esrA GO:0003824 GO:0016787 GO:0018786
20.420.8352.580.230.953u1tB GO:0003824
30.410.7752.390.150.873fobA GO:0003824 GO:0004601 GO:0009636 GO:0016491 GO:0016691 GO:0016787 GO:0019806 GO:0055114 GO:0098869
40.410.8242.440.210.934k2aC GO:0003824 GO:0016787 GO:0018786
50.400.8232.700.220.943sk0A GO:0003824 GO:0009636 GO:0016787 GO:0018786
60.370.8332.560.200.944kajA GO:0003824 GO:0009636 GO:0016787 GO:0018786
70.350.8002.960.170.924ccyB GO:0005737 GO:0016787 GO:0052689
80.330.7792.420.200.884x00A GO:0016787
90.330.7972.950.190.925bovB GO:0003824 GO:0016787
100.330.7592.540.170.863wzlA GO:0016787
110.330.8322.730.220.954mj3B GO:0003824 GO:0016787 GO:0018786
120.330.8162.830.200.944b9aA GO:0003824 GO:0009062 GO:0016298 GO:0016787
130.320.8771.960.210.953wi7A GO:0016787 GO:0018786
140.320.7833.180.160.924psuA GO:0016787
150.310.8012.790.160.921ehyA GO:0003824 GO:0016787
160.300.7472.940.180.861womA GO:0016787
170.300.7562.900.200.884rncA GO:0016787 GO:0052689
180.300.8102.660.190.933qyjA GO:0003824
190.300.7853.070.200.924io0A GO:0003824 GO:0008152 GO:0016787 GO:0016798 GO:0047405
200.300.7662.800.200.871a88A GO:0003824 GO:0004601 GO:0016491 GO:0016691 GO:0055114 GO:0098869
210.300.7443.300.220.893kxpA GO:0016787 GO:0042803 GO:0042820 GO:0047411
220.290.7383.410.170.893p2mA GO:0052689
230.290.8242.690.160.954dlnB GO:0016787
240.290.7702.780.150.894ns4A GO:0016787 GO:0016788
250.280.7992.890.140.934haiA GO:0000287 GO:0003824 GO:0004301 GO:0005102 GO:0005737 GO:0005777 GO:0005829 GO:0006629 GO:0006805 GO:0006874 GO:0006954 GO:0008152 GO:0008217 GO:0009636 GO:0010628 GO:0015643 GO:0016311 GO:0016787 GO:0016791 GO:0017144 GO:0019373 GO:0019439 GO:0033885 GO:0042577 GO:0042632 GO:0042803 GO:0045909 GO:0046272 GO:0046839 GO:0046872 GO:0070062 GO:0072593 GO:0090181
260.280.7803.000.180.912vf2A GO:0005618 GO:0005886 GO:0006629 GO:0006694 GO:0016042 GO:0016787 GO:0018774 GO:0019439 GO:0034820 GO:0044117 GO:0102296
270.280.7272.630.170.834nmwA GO:0005737 GO:0009102 GO:0016787 GO:0052689
280.280.7822.760.190.901iunB GO:0003824 GO:0016787
290.280.8102.700.200.933b12A GO:0003824 GO:0016787 GO:0018785
300.280.7662.620.190.871a8qA GO:0003824 GO:0004601 GO:0016491 GO:0017000 GO:0055114 GO:0098869
310.280.7782.800.170.894lxhA GO:0016787
320.270.8162.580.190.933afiB GO:0003824 GO:0016787 GO:0018786 GO:0042206 GO:0042802
330.270.7572.590.160.864g8bA GO:0003824 GO:0016787 GO:0016788
340.270.7772.480.180.874qesA GO:0003723 GO:0003824 GO:0004601 GO:0005198 GO:0005576 GO:0005654 GO:0005829 GO:0005886 GO:0016020 GO:0016032 GO:0016491 GO:0017000 GO:0019012 GO:0019061 GO:0019062 GO:0019064 GO:0019065 GO:0019068 GO:0019070 GO:0019072 GO:0019076 GO:0019083 GO:0030666 GO:0030683 GO:0031904 GO:0039573 GO:0039660 GO:0042025 GO:0046761 GO:0055036 GO:0055114 GO:0075733 GO:0098869
350.270.7073.220.140.844gdmC GO:0005829 GO:0009234 GO:0016787 GO:0016829 GO:0070205
360.250.7572.600.170.862xuaH GO:0016787 GO:0042952 GO:0047570
370.240.7642.360.180.851j1iA GO:0016787
380.240.7732.740.200.881hkhA GO:0003824 GO:0004601 GO:0098869
390.240.7702.770.200.873heaA GO:0003824 GO:0004064 GO:0004601 GO:0016491 GO:0016787 GO:0055114 GO:0098869
400.200.6852.990.150.801r3dA GO:0005829 GO:0009234 GO:0016787 GO:0016829 GO:0070205
410.190.7763.210.150.912r11D GO:0016787 GO:0052689
420.180.8372.420.260.931mj5A GO:0003824 GO:0009636 GO:0016787 GO:0018786 GO:0042597
430.180.8172.950.160.951be0A GO:0003824 GO:0009636 GO:0016787 GO:0018786 GO:0019260
440.180.8382.370.250.932qvbB GO:0003824 GO:0005618 GO:0005886 GO:0016787 GO:0018786 GO:0042206
450.180.7932.950.140.925aljA GO:0000287 GO:0003824 GO:0004301 GO:0005102 GO:0005737 GO:0005777 GO:0005829 GO:0006629 GO:0006805 GO:0006874 GO:0006954 GO:0008152 GO:0008217 GO:0009636 GO:0010628 GO:0015643 GO:0016311 GO:0016787 GO:0016791 GO:0017144 GO:0019373 GO:0019439 GO:0033885 GO:0042577 GO:0042632 GO:0042803 GO:0045909 GO:0046272 GO:0046839 GO:0046872 GO:0070062 GO:0072593 GO:0090181
460.170.7992.820.190.932xt0A GO:0003824
470.170.8123.020.200.952psfA GO:0003824 GO:0004497 GO:0008218 GO:0016491 GO:0016829 GO:0016831 GO:0050248 GO:0055114
480.160.7652.810.170.871a8sA GO:0003824 GO:0004601 GO:0016491 GO:0016691 GO:0055114 GO:0098869
490.160.7872.990.140.912og1A GO:0003824 GO:0016787 GO:0016823 GO:0018771 GO:0018774 GO:0019439
500.150.7442.880.140.864htaA GO:0005634 GO:0005737 GO:0005829 GO:0009640 GO:0009704 GO:0016787 GO:0080167
510.140.7242.590.200.831m33A GO:0005737 GO:0009102 GO:0016787 GO:0052689 GO:0090499
520.140.7893.120.170.924ufoA GO:0003824 GO:0016787
530.130.7723.100.150.914f0jA GO:0003824 GO:0016787
540.130.7232.970.130.842xmzA GO:0009234 GO:0016787 GO:0016829 GO:0070205
550.130.7842.750.170.902e3jA GO:0003824 GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0018786 GO:0046872 GO:0016746 GO:0016691 GO:0019806
GO-Score 0.67 0.47 0.47 0.41 0.41
Biological Processes GO:0055114 GO:0098869
GO-Score 0.41 0.41
Cellular Component
GO-Score

(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.