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I-TASSER results for job id Rv1028A

[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 3 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
10.17 774 1l6lQ BOG Rep, Mult 8,9,11,12,13
20.14 665 1gtwB NUC Rep, Mult 10,13,14,16,17,18,20
30.13 632 1jb0B CLA Rep, Mult 6,9,10,12,13,15,16
40.10 460 5t6jA III Rep, Mult 1,4,5,7,8,11
50.09 433 3d5d2 MG Rep, Mult 17,18,19,20,21,22
60.07 310 4eoyA CA Rep, Mult 1,2,3,4,5,6
70.06 278 5e7cZ CLA Rep, Mult 22,23,26,27
80.05 243 5d56C 78M Rep, Mult 20,21,24,25
90.00 5 1ne7A GLC Rep, Mult 19,30
100.00 4 4gx1D GLC Rep, Mult 27,29

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
10.3173brtA0.7631.470.0670.9332.7.11.106,10
20.2911r7cA0.5131.640.0670.9003.6.1.1512,16,19
30.2852k1lA0.5321.920.0690.9332.7.10.17,16,20
40.2663brvC0.8120.470.0330.9002.7.11.1023
50.2612jwaA0.7871.540.1331.0002.7.10.111,16
60.2341z8yN0.5551.710.1000.9333.4.21.9020,22
70.1971xtcC0.7201.130.0670.9332.4.2.3614,19
80.1792o98P0.7190.970.0690.9673.6.3.625
90.1771qleD0.7930.480.1000.9001.9.3.1NA
100.1743e7kH0.7880.630.1000.9002.7.11.120
110.1472fyuK0.6581.940.0670.9331.10.2.2NA
120.1312k9yA0.6062.020.1000.9672.7.10.1NA
130.0811vzjF0.5201.330.0340.8673.1.1.7NA
140.0601mhlC0.8590.990.1331.0001.11.1.7NA
150.0603k92A0.8310.860.0340.9671.4.1.2NA
160.0601e1yA0.8541.620.1001.0002.4.1.1NA
170.0603ilwA0.8391.430.0330.9675.99.1.3NA
180.0601xppA0.8300.380.0330.9002.7.7.6NA
190.0601ay4A0.8551.480.0331.0002.6.1.57NA
200.0602zaeD0.7500.770.0380.8673.1.26.58,12
210.0603bllA0.8371.140.0001.0002.4.2.29NA
220.0601cfrA0.8460.830.0000.9673.1.21.4NA
230.0601t8rA0.8410.650.1001.0003.2.2.4NA
240.0602qllA0.7291.170.0330.9332.4.1.1NA
250.0602wl2B0.8311.280.1001.0005.99.1.3NA
260.0602o6yA0.8310.780.1330.9674.3.1.-NA
270.0602rgrA0.8351.810.0331.0005.99.1.3NA
280.0603k9fA0.8291.090.0330.9335.99.1.-NA
290.0603fofA0.7771.270.0330.9335.99.1.-NA
300.0601is2A0.8300.910.0671.0001.3.3.6NA
310.0601h12A0.8321.070.1001.0003.2.1.8NA
320.0602w90B0.8471.490.1001.0001.1.1.44NA

(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
00.310.8090.950.130.933ni0A GO:0002376 GO:0002737 GO:0004871 GO:0005737 GO:0005768 GO:0005770 GO:0005771 GO:0005794 GO:0005886 GO:0007165 GO:0008191 GO:0009615 GO:0009986 GO:0010951 GO:0016020 GO:0016021 GO:0016324 GO:0030308 GO:0030336 GO:0031225 GO:0032956 GO:0034341 GO:0035455 GO:0035456 GO:0042803 GO:0043123 GO:0044822 GO:0045071 GO:0045087 GO:0045121 GO:0051607 GO:0070062 GO:1901253
10.290.8420.360.030.904cpcG GO:0000775 GO:0000800 GO:0003677 GO:0005634 GO:0005694 GO:0007049 GO:0007141 GO:0035093 GO:0051301 GO:0051321
20.280.8170.990.030.934om3D GO:0000122 GO:0001106 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0007165 GO:0007275 GO:0008134 GO:0009887 GO:0010628 GO:0016055 GO:0030178 GO:0042802 GO:0043124 GO:0045892 GO:1904837 GO:2000811
30.280.8131.050.000.931debA GO:0000281 GO:0000776 GO:0001708 GO:0005634 GO:0005654 GO:0005737 GO:0005813 GO:0005829 GO:0005856 GO:0005874 GO:0005881 GO:0005886 GO:0005912 GO:0005913 GO:0005923 GO:0005938 GO:0006461 GO:0006921 GO:0006974 GO:0007026 GO:0007050 GO:0007094 GO:0007155 GO:0007163 GO:0007389 GO:0008013 GO:0008017 GO:0008285 GO:0016020 GO:0016055 GO:0016328 GO:0016342 GO:0016477 GO:0019887 GO:0019901 GO:0030027 GO:0030054 GO:0030178 GO:0030335 GO:0030425 GO:0030426 GO:0030877 GO:0031016 GO:0031175 GO:0031274 GO:0031965 GO:0032403 GO:0032587 GO:0032886 GO:0042493 GO:0042995 GO:0043005 GO:0043025 GO:0043065 GO:0043161 GO:0043234 GO:0044295 GO:0044306 GO:0045202 GO:0045295 GO:0045296 GO:0045595 GO:0045732 GO:0045736 GO:0051010 GO:0051988 GO:0060070 GO:0070830 GO:0070852 GO:0090090 GO:0097305 GO:1904885 GO:1904886 GO:1990090 GO:1990909 GO:2000211
40.260.8321.010.000.934ntjA GO:0001609 GO:0001621 GO:0001973 GO:0004871 GO:0004930 GO:0005085 GO:0005506 GO:0005622 GO:0005739 GO:0005886 GO:0005887 GO:0005901 GO:0006930 GO:0007165 GO:0007186 GO:0007188 GO:0007193 GO:0007596 GO:0007599 GO:0008347 GO:0009055 GO:0009897 GO:0009925 GO:0009986 GO:0010700 GO:0016020 GO:0016021 GO:0020037 GO:0022900 GO:0030030 GO:0030168 GO:0031224 GO:0035589 GO:0042597 GO:0043270 GO:0043491 GO:0043547 GO:0045028 GO:0045596 GO:0046872 GO:0051924 GO:0055114 GO:0070527 GO:0070588 GO:0071318 GO:0071407 GO:0071805 GO:1904139
50.230.7341.420.130.933miwC GO:0005576 GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0033644 GO:0044155 GO:0044165 GO:0044169 GO:0046872
60.230.7911.280.000.934i6mC GO:0000166 GO:0000182 GO:0001102 GO:0003677 GO:0004386 GO:0005524 GO:0005634 GO:0005987 GO:0006261 GO:0006302 GO:0006338 GO:0006351 GO:0006355 GO:0008094 GO:0015616 GO:0016514 GO:0016787 GO:0031492 GO:0031496 GO:0042148 GO:0042393 GO:0042766 GO:0043044 GO:0044109 GO:0045944 GO:0061412 GO:0070577 GO:1900189 GO:2000219
70.200.8410.870.071.005fu7A 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
80.160.7201.440.030.904by6A GO:0046872
90.150.8151.020.000.931qsdA GO:0005737 GO:0005856 GO:0005874 GO:0007021 GO:0007023 GO:0015631 GO:0048487
100.150.6930.810.130.905apxA GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
110.140.6211.160.030.803nufA GO:0006355
120.140.8121.150.030.932x7rC GO:0002223 GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512
130.140.7901.360.000.933lidA GO:0000155 GO:0000160 GO:0005622 GO:0023014
140.130.7670.920.000.931ykeB GO:0000122 GO:0001103 GO:0001105 GO:0001106 GO:0005634 GO:0006351 GO:0006355 GO:0016592 GO:0045944 GO:0070847
150.130.6531.900.000.904a79A GO:0005739 GO:0005740 GO:0005741 GO:0005743 GO:0008131 GO:0009055 GO:0009636 GO:0010044 GO:0010269 GO:0014063 GO:0016020 GO:0016021 GO:0016491 GO:0021762 GO:0032496 GO:0042420 GO:0042493 GO:0042803 GO:0045471 GO:0045964 GO:0048545 GO:0050660 GO:0050665 GO:0051412 GO:0055114 GO:0070062
160.130.7460.910.030.901b54A GO:0005622 GO:0030170
170.120.7561.570.070.972d8eA GO:0003824 GO:0009058 GO:0009073 GO:0016740 GO:0016832 GO:0046417
180.110.6931.430.070.773sy1A GO:0005829 GO:0030170
190.100.7331.190.100.903tmbB GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003714 GO:0001191 GO:0001104 GO:0019207 GO:0019900 GO:0050839 GO:0044877 GO:0008017 GO:0046914 GO:0001608 GO:0001614 GO:0046906 GO:0044822 GO:0042803 GO:0008191
GO-Score 0.57 0.57 0.57 0.55 0.55 0.55 0.55 0.55 0.52 0.52 0.52 0.52 0.31 0.31 0.31
Biological Processes GO:0035092 GO:0007127 GO:0043486 GO:0007140 GO:0010629 GO:0006461 GO:0043066 GO:2000113 GO:1902532 GO:1903507 GO:2000209 GO:0048513 GO:0006357 GO:0009653 GO:2000147 GO:0051247 GO:0010498 GO:0060828 GO:0042127 GO:0043068 GO:0000820 GO:0071174 GO:0006536 GO:0097194 GO:1901880 GO:0048666 GO:1990089 GO:0071173 GO:0031114 GO:0043297 GO:0071901 GO:1904030 GO:0031111 GO:0031346 GO:0071363 GO:0042176 GO:0008608 GO:0045165 GO:0006511 GO:0009896 GO:0031272 GO:0044089 GO:0000079 GO:0033554 GO:0061640 GO:0006929 GO:0014061 GO:0051345 GO:0002685 GO:0071804 GO:0007596 GO:0007187 GO:0006091 GO:0033198 GO:1901701 GO:1904124 GO:0033604 GO:0098662 GO:0010959 GO:0051050 GO:1903975 GO:0001775 GO:0043087 GO:0035588 GO:0006816 GO:0034109 GO:0035590 GO:0071417 GO:0030178 GO:0045071 GO:0030336 GO:1901253 GO:0002737 GO:0035456 GO:0010951 GO:0032956 GO:0030308 GO:0051607 GO:0043123 GO:0035455 GO:0034341
GO-Score 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.48 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31
Cellular Component GO:0098687 GO:0000795 GO:0031090 GO:0033267 GO:0031253 GO:0036477 GO:0005874 GO:0005815 GO:0099568 GO:0030427 GO:0070161 GO:0005635 GO:0098797 GO:0044297 GO:0070160 GO:0031256 GO:0043296 GO:0019897 GO:0001726 GO:0045178 GO:0031226 GO:0016323 GO:0098552 GO:0044853 GO:0009986 GO:0016021 GO:0005829 GO:0005654 GO:0031225 GO:0005771 GO:0005794 GO:0070062 GO:0016324
GO-Score 0.57 0.57 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.52 0.52 0.52 0.52 0.52 0.49 0.49 0.48 0.48 0.31 0.31 0.31 0.31 0.31

(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.