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I-TASSER results for job id Rv2049c

[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
10.16 65 3bknC HEM Rep, Mult 30,33,34,37,56,60,63,64,66,67
20.10 41 4garY NUC Rep, Mult 12,13,16,49,51,53,54,56,57,60,61,64,65,67,68,71,72
30.06 22 2p06A MG Rep, Mult 32,35,59,62
40.06 25 1tkoA FE Rep, Mult 37,38,41
50.05 23 5etzB 22B Rep, Mult 33,36,40,43,53,56,60,63
60.05 19 4s1xE III Rep, Mult 29,32,33,36,39,40
70.03 13 1brrC ARC Rep, Mult 40,43,52,53,56,57
80.03 12 1nf4G FEC Rep, Mult 22,29,30,33,37,60,67,71
90.02 9 4or2A CLR Rep, Mult 31,35,39,42,51,55
100.02 8 1vf5S III Rep, Mult 39,40
110.01 6 2e50A TRE Rep, Mult 32,35,39
120.00 1 2hn2A CA Rep, Mult 23,27
130.00 2 2eulA ZN Rep, Mult 67,70
140.00 1 3fofB QNA Rep, Mult 16,62,69,72

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
10.1841cxzB0.6722.140.0820.8242.7.11.1337
20.1701urfA0.5681.970.1230.7702.7.11.1332,67
30.0671wcrA0.6332.840.0560.9732.7.1.69NA
40.0603eabA0.6672.240.0480.8513.6.4.3NA
50.0602zr3B0.6681.750.0540.7846.1.1.1114,31
60.0602ckpB0.3972.620.1210.5812.7.1.32NA
70.0601sssB0.6332.030.0680.7841.15.1.1NA
80.0602ckpA0.6203.060.0290.9192.7.1.32NA
90.0601hzfA0.6662.250.0630.8383.4.21.43NA
100.0603hf1B0.6283.030.0540.9321.17.4.1NA
110.0601sk6C0.5152.950.0550.8244.6.1.15,64
120.0601zvuA0.6592.150.1080.7845.99.1.-NA
130.0602vuxB0.6072.820.0410.8921.17.4.1NA
140.0602dq3A0.7041.520.0950.7846.1.1.11NA
150.0603fofA0.6702.100.0680.7845.99.1.-NA
160.0601gaxA0.7362.650.1110.9196.1.1.9NA
170.0603k9fA0.6881.900.0680.7845.99.1.-NA
180.0601chuA0.6612.670.0900.9051.4.3.168
190.0601jkuA0.6962.510.0950.8781.11.1.6NA
200.0602vn7A0.6472.900.0690.9193.2.1.342
210.0603ee4A0.6523.110.0680.9461.17.4.1NA
220.0601y5nC0.6652.920.0590.8921.7.99.471

(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
00.190.6942.080.110.863cc2V GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
10.140.7522.380.100.912mbgA GO:0005096 GO:0005829 GO:0006810 GO:0006897 GO:0006935 GO:0007165 GO:0007264 GO:0016020 GO:0016887 GO:0017160 GO:0022857 GO:0043087 GO:0043492 GO:0043547 GO:0048365 GO:0051056 GO:0055085
20.110.6422.270.100.813j9wB1 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625 GO:0030529
30.100.7542.190.110.973nvoA GO:0005385 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006829 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085 GO:0071577 GO:0098655
40.070.6532.450.080.884v63B2 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0030529
50.070.7412.480.081.004cy4E GO:0005886 GO:0006810 GO:0006811 GO:0006824 GO:0015087 GO:0015095 GO:0015693 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085 GO:0098655 GO:1903830
60.070.6132.730.070.962ct8A GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
70.070.6062.990.080.973jcfA GO:0000287 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006824 GO:0015087 GO:0015095 GO:0015693 GO:0016020 GO:0016021 GO:0030001 GO:0046872 GO:0046873 GO:0050897 GO:0051260 GO:0055085 GO:1903830
80.070.6481.860.050.783k9aA
90.070.7091.680.080.843j793 GO:0000463 GO:0003729 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015934 GO:0022625
100.070.6062.920.110.883ck6E GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
110.070.4934.140.050.854b2tg GO:0000166 GO:0002199 GO:0005524 GO:0005737 GO:0005832 GO:0005874 GO:0005886 GO:0006457 GO:0007339 GO:0043209 GO:0044297 GO:0044822 GO:0046931 GO:0051082 GO:0070062 GO:1901998
120.070.5353.670.060.864u3kA GO:0005096 GO:0005546 GO:0005737 GO:0005933 GO:0007165 GO:0007231 GO:0010314 GO:0010447 GO:0030479 GO:0032266 GO:0043547 GO:0070273 GO:0080025
130.070.6651.960.070.804wceV GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625 GO:0030529
140.070.7171.930.050.884v8pBU GO:0000463 GO:0003729 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625 GO:0030529
150.070.7162.000.080.894v3pLc GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0030529
160.070.7111.950.080.884v6xCh GO:0000184 GO:0000463 GO:0003729 GO:0003735 GO:0005622 GO:0005730 GO:0005737 GO:0005829 GO:0005840 GO:0006364 GO:0006412 GO:0006413 GO:0006614 GO:0016020 GO:0019083 GO:0022625 GO:0030529 GO:0044822
170.070.5223.290.040.811pbwB GO:0001678 GO:0001953 GO:0005068 GO:0005158 GO:0005159 GO:0005168 GO:0005634 GO:0005737 GO:0005801 GO:0005829 GO:0005886 GO:0005911 GO:0005942 GO:0005943 GO:0006468 GO:0006661 GO:0006810 GO:0007162 GO:0007165 GO:0007173 GO:0008134 GO:0008286 GO:0008625 GO:0008630 GO:0014065 GO:0014066 GO:0015031 GO:0016020 GO:0016032 GO:0016303 GO:0019903 GO:0030168 GO:0030183 GO:0030335 GO:0031295 GO:0032760 GO:0032869 GO:0033120 GO:0034644 GO:0034976 GO:0035014 GO:0036092 GO:0036312 GO:0038095 GO:0038096 GO:0038128 GO:0042993 GO:0043066 GO:0043125 GO:0043548 GO:0043551 GO:0043559 GO:0043560 GO:0045671 GO:0045944 GO:0046326 GO:0046854 GO:0046934 GO:0046935 GO:0046982 GO:0048009 GO:0048010 GO:0048015 GO:0050821 GO:0050852 GO:0050900 GO:0051492 GO:0051531 GO:0060396 GO:0090003 GO:0090004 GO:1900103 GO:1990578 GO:2001275
180.070.4283.960.050.785jcpA GO:0000166 GO:0001726 GO:0003924 GO:0005096 GO:0005525 GO:0005547 GO:0005737 GO:0005768 GO:0005789 GO:0005829 GO:0005856 GO:0005886 GO:0005925 GO:0005938 GO:0007010 GO:0007049 GO:0007165 GO:0007179 GO:0007264 GO:0007266 GO:0008360 GO:0016020 GO:0016032 GO:0016192 GO:0016477 GO:0017022 GO:0021762 GO:0030027 GO:0030036 GO:0030054 GO:0030168 GO:0030334 GO:0030336 GO:0030496 GO:0031234 GO:0031532 GO:0031982 GO:0032154 GO:0032467 GO:0032956 GO:0033688 GO:0035021 GO:0035024 GO:0035385 GO:0036089 GO:0038027 GO:0042346 GO:0042995 GO:0043123 GO:0043149 GO:0043296 GO:0043297 GO:0043325 GO:0043542 GO:0043547 GO:0043931 GO:0044319 GO:0045666 GO:0046872 GO:0048010 GO:0048013 GO:0048015 GO:0050771 GO:0050772 GO:0050919 GO:0051056 GO:0051301 GO:0051496 GO:0060071 GO:0060193 GO:0061383 GO:0070062 GO:0071902 GO:0071944 GO:0090051 GO:0090307 GO:0097498 GO:1902766 GO:1903673 GO:2000145
190.070.4233.970.060.723kuqA GO:0001843 GO:0003007 GO:0005096 GO:0005634 GO:0005737 GO:0005829 GO:0005901 GO:0005925 GO:0006915 GO:0006919 GO:0007165 GO:0008285 GO:0008289 GO:0008360 GO:0016020 GO:0021575 GO:0030036 GO:0030054 GO:0030336 GO:0030864 GO:0030900 GO:0032587 GO:0032956 GO:0035023 GO:0035024 GO:0035307 GO:0042169 GO:0043547 GO:0048041 GO:0051056 GO:0051497 GO:0051895 GO:1900119
200.070.6741.770.030.815it7hh GO:0003735 GO:0005622 GO:0005730 GO:0005829 GO:0005840 GO:0006412
210.070.6312.020.010.773p30A
220.070.6802.290.080.884v6wCh GO:0000022 GO:0000463 GO:0003729 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0007052 GO:0022625 GO:0051298
230.070.5303.710.080.863qisA GO:0001701 GO:0001750 GO:0004439 GO:0005096 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005795 GO:0005798 GO:0005802 GO:0005829 GO:0005886 GO:0005905 GO:0005929 GO:0006629 GO:0006661 GO:0007165 GO:0016020 GO:0016023 GO:0016787 GO:0030030 GO:0030136 GO:0030670 GO:0031410 GO:0031901 GO:0042384 GO:0042995 GO:0043087 GO:0043547 GO:0043647 GO:0046856 GO:0048365 GO:0051056 GO:0052658 GO:0052659 GO:0052745 GO:0070062
240.070.4313.970.060.813msxB GO:0005096 GO:0005829 GO:0007165 GO:0043547 GO:0051056
250.070.5133.950.090.891am4A GO:0005070 GO:0005096 GO:0005737 GO:0005829 GO:0005913 GO:0007165 GO:0007264 GO:0007266 GO:0009967 GO:0017124 GO:0043547 GO:0048471 GO:0051056 GO:0070062 GO:0098609 GO:0098641
260.070.4543.780.040.811f7cA GO:0005096 GO:0005543 GO:0005737 GO:0005856 GO:0005925 GO:0007165 GO:0030036 GO:0030054 GO:0043547 GO:0051056
270.070.5053.640.040.853cxlA GO:0005070 GO:0005096 GO:0005737 GO:0005829 GO:0007165 GO:0007399 GO:0008045 GO:0009967 GO:0035556 GO:0043087 GO:0043547 GO:0046872 GO:0046875 GO:0048013 GO:0050770 GO:0051056
280.070.5212.420.050.661lshA GO:0005319 GO:0006869 GO:0045735
290.070.5283.620.010.843eapA GO:0005096 GO:0005829 GO:0007165 GO:0043547 GO:0051056
300.070.4553.690.070.703byiA GO:0005096 GO:0005737 GO:0005829 GO:0007165 GO:0008360 GO:0016020 GO:0043547 GO:0051056


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0003735
GO-Score 0.38 0.33
Biological Processes GO:0044763 GO:0044765 GO:0006412
GO-Score 0.45 0.45 0.33
Cellular Component GO:0005840
GO-Score 0.33

(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.