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I-TASSER results for job id Rv1917c

[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
10.04 2 4ndhA NUC Rep, Mult 1324,1325,1326
20.04 2 2wscH CLA Rep, Mult 1449,1450,1454
30.02 1 2cixA MAN Rep, Mult 195,197
40.02 1 1pumB GOL Rep, Mult 263,376,377,380
50.02 1 1m34A SF4 Rep, Mult 14,15
60.02 1 2gx2B MG Rep, Mult 442,444
70.02 1 2v8eA SCR Rep, Mult 545,546,547,548,557
80.02 1 1z44A NPO Rep, Mult 65,66,69
90.02 1 1jv2A CA Rep, Mult 1020,1022,1028,1030
100.02 1 3wmm7 BCL Rep, Mult 10,14
110.02 1 3huzP MG Rep, Mult 230,232
120.02 1 3bbxL MG Rep, Mult 1388,1389
130.02 1 1vq9B MG Rep, Mult 297,299
140.02 1 1mtbB NTB Rep, Mult 447,448
150.02 1 4u0pB SAH Rep, Mult 1353,1354
160.02 1 3f1f1 MG Rep, Mult 1194,1195
170.02 1 2j6e4 III Rep, Mult 394,396,397,399,417
180.02 1 2i36C UUU Rep, Mult 1444,1451
190.02 1 3pyrG MG Rep, Mult 542,543
200.02 1 1zyrN STD Rep, Mult 494,495,499

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
10.0603eqlD0.18410.620.0330.2962.7.7.6NA
20.0602vkzG0.1849.970.0400.2802.3.1.38,3.1.2.14NA
30.0602vz9B0.17710.270.0290.2762.3.1.85NA
40.0602jfdA0.0737.390.0320.0952.3.1.85642
50.0602vz8B0.16810.460.0320.2652.3.1.85NA
60.0602hpiA0.1179.960.0220.1802.7.7.7236
70.0603ecqB0.1528.670.0330.2133.2.1.97NA
80.0601w36B0.1399.640.0220.2103.1.11.5NA
90.0602pdaA0.1459.830.0320.2191.2.7.1339,850
100.0602qf7A0.1439.400.0200.2106.4.1.1NA
110.0602vz8A0.18810.230.0230.2922.3.1.85NA
120.0601qssA0.0898.010.0330.1212.7.7.7NA
130.0601ej6A0.1549.920.0440.2352.7.7.50NA
140.0603c46B0.1499.470.0300.2212.7.7.6259,283,287
150.0602pffD0.13010.800.0090.2092.3.1.86229,291,345
160.0601ynnD0.1679.710.0370.2522.7.7.6744
170.0602pmzQ0.1509.590.0220.2282.7.7.6821,824
180.0601etuA0.0505.420.0150.0593.6.5.3NA
190.0602pffA0.14810.280.0510.2322.3.1.41,2.3.1.86767

(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
00.060.1619.630.040.243gauA GO:0002376 GO:0005576 GO:0005615 GO:0006956 GO:0006957 GO:0008201 GO:0030449 GO:0043395 GO:0045087 GO:0070062 GO:0072562
10.060.1099.270.030.164a5wB GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
20.060.1229.190.030.184e0sB GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
30.060.1268.020.030.173t5oA GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
40.060.1196.180.050.151ntjA GO:0002376 GO:0006958 GO:0007275 GO:0007565 GO:0016020 GO:0016021 GO:0045087 GO:0045916
50.060.1025.600.040.121c1zA GO:0001937 GO:0001948 GO:0002576 GO:0005543 GO:0005576 GO:0005615 GO:0005737 GO:0005886 GO:0006641 GO:0007568 GO:0007596 GO:0007597 GO:0008201 GO:0008289 GO:0009986 GO:0010596 GO:0010898 GO:0016525 GO:0030193 GO:0030194 GO:0030195 GO:0031012 GO:0031089 GO:0031100 GO:0031639 GO:0033033 GO:0034014 GO:0034197 GO:0034361 GO:0034364 GO:0034392 GO:0042627 GO:0042802 GO:0051006 GO:0051917 GO:0051918 GO:0060230 GO:0060268 GO:0070062
60.060.1086.880.040.144aqbA GO:0001867 GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006956 GO:0008233 GO:0008236 GO:0016787 GO:0042803 GO:0045087 GO:0045916 GO:0046872 GO:0048306
70.060.1115.570.080.133o8eB GO:0001618 GO:0001669 GO:0001848 GO:0002079 GO:0002250 GO:0002376 GO:0002456 GO:0004175 GO:0004857 GO:0004872 GO:0005737 GO:0005794 GO:0005886 GO:0005887 GO:0005925 GO:0006508 GO:0006958 GO:0007338 GO:0008593 GO:0009986 GO:0010628 GO:0010629 GO:0016020 GO:0016021 GO:0016032 GO:0016323 GO:0030449 GO:0031410 GO:0032613 GO:0032733 GO:0035581 GO:0042102 GO:0043086 GO:0043382 GO:0045087 GO:0045296 GO:0045591 GO:0045916 GO:0046718 GO:0070062 GO:0071636
80.060.1064.980.040.121ojvA GO:0000139 GO:0001618 GO:0002376 GO:0005576 GO:0005886 GO:0005887 GO:0006888 GO:0006958 GO:0007204 GO:0008289 GO:0009986 GO:0016020 GO:0016032 GO:0030133 GO:0030449 GO:0031225 GO:0031664 GO:0033116 GO:0035743 GO:0045087 GO:0045121 GO:0045730 GO:0045916 GO:0046718 GO:0070062 GO:2000516 GO:2000563
90.060.1217.580.040.161ntlA GO:0001701 GO:0002376 GO:0006958 GO:0007275 GO:0007565 GO:0009897 GO:0016020 GO:0016021 GO:0030449 GO:0043235 GO:0045087 GO:0045916
100.060.1568.260.030.222gsxA GO:0001618 GO:0001848 GO:0002376 GO:0002430 GO:0003677 GO:0004875 GO:0004888 GO:0005886 GO:0006955 GO:0006958 GO:0007165 GO:0016020 GO:0016021 GO:0016032 GO:0030183 GO:0042100 GO:0042803 GO:0043235 GO:0045087 GO:0046718 GO:0070062
110.060.1017.900.030.142xwbF GO:0001848 GO:0002376 GO:0004252 GO:0005576 GO:0005615 GO:0005886 GO:0006508 GO:0006956 GO:0006957 GO:0008233 GO:0008236 GO:0016787 GO:0030449 GO:0045087 GO:0070062 GO:0072562
120.060.0866.720.020.114j1yA GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0042802 GO:0045087 GO:0046872 GO:0070062 GO:0072562
130.060.0874.590.070.105fo9C GO:0001618 GO:0001851 GO:0001855 GO:0001861 GO:0002376 GO:0002430 GO:0004877 GO:0005886 GO:0005887 GO:0006958 GO:0009986 GO:0016020 GO:0016021 GO:0016032 GO:0030449 GO:0045087 GO:0045957 GO:0045959 GO:0046718 GO:0070062 GO:1900004 GO:1900005
140.060.0877.100.040.111gpzA GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006955 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0070062 GO:0072562
150.060.0917.450.030.122atyA
160.060.0855.420.070.101ridA GO:0001848 GO:0005576 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0020002 GO:0030683 GO:0033644 GO:0039573 GO:0045916 GO:0055036
170.060.0938.110.050.133vm5A GO:0003824 GO:0004556 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
180.060.0936.520.060.124igdA GO:0001867 GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006956 GO:0008233 GO:0008236 GO:0016787 GO:0042803 GO:0045087 GO:0045916 GO:0046872 GO:0048306


Consensus prediction of GO terms		 
Molecular Function GO:0043395 GO:0008201
GO-Score 0.06 0.06
Biological Processes GO:0002455 GO:0045765 GO:0043009 GO:0002699 GO:2000259 GO:0001969 GO:0010954 GO:1904018 GO:0002922
GO-Score 0.45 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35
Cellular Component GO:1903561 GO:0031988 GO:0046930 GO:0098797 GO:0005887
GO-Score 0.45 0.45 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.