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I-TASSER results for job id S802915

(Click on S802915_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

  Submitted Sequence in FASTA format

>protein
GFPRAGSNPADY

  Predicted Secondary Structure

Sequence
            
GFPRAGSNPADY
PredictionCCCCCCCCCCCC
Conf.Score977666786769
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence
            
GFPRAGSNPADY
Prediction744646644577
Values range from 0 (buried residue) to 9 (highly exposed residue)

   Predicted normalized B-factor

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. Click here to read more about predicted normalized B-factor)


  Top 10 threading templates used by I-TASSER

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank PDB
Hit		Iden1Iden2CovNorm.
Z-score		Download
Align.		 
            
Sec.Str
Seq		CCCCCCCCCCCC
GFPRAGSNPADY
17ml0A 0.08 0.17 1.00 1.30Download TIDDFNGDLVEY
25w4kA 0.33 0.42 1.00 1.98Download SPGNASSNSASA
36z7nA 0.45 0.42 0.92 3.02Download LAPRHGSRPFM-
43vqjA 0.27 0.25 0.92 1.49Download -AGKASASPAAF
54ld3B 0.33 0.17 1.00 2.41Download LSPRPSPNPHPV
66fkrA 0.36 0.33 0.92 1.39Download -LPRPGRRPRFP
75hkpC 0.27 0.42 0.92 2.38Download -SPRGCADGRDA
81ho9A 0.11 0.17 0.75 1.35Download ---WSITQAIEY
95itzD 0.25 0.25 1.00 2.25Download PFLKRGEGLARF
101byvA 0.17 0.17 1.00 1.26Download TYPRTDVGAGTP
(a)All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)Rank of templates represents the top ten threading templates used by I-TASSER.
(c)Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
       1: SPARKS-X   2: Neff-PPAS   3: SP3   4: Neff-PPAS   5: SP3   6: Neff-PPAS   7: SP3   8: Neff-PPAS   9: SP3   10: Neff-PPAS   

   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 a higher value signifies a model with a higher 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.)
    (By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)
  • Download Model 1
  • C-score=-0.83 (Read more about C-score)
  • Estimated TM-score = 0.61±0.14
  • Estimated RMSD = 1.6±1.4Å

  • Download Model 2
  • C-score = -2.76

  • Download Model 3
  • C-score = -2.72

  • Download Model 4
  • C-score = -0.99

  • Download Model 5
  • C-score = -3.86


  Proteins structurally close to the target in the 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.)


Top 10 Identified stuctural analogs in PDB

Click
to view		RankPDB HitTM-scoreRMSDaIDENaCovAlignment
12nlyA0.459 2.190.0000.917Download
22q7bA0.454 1.140.0000.917Download
33sli_0.451 2.210.1671.000Download
41k66A0.449 0.730.0000.917Download
54hppA20.447 2.150.0000.833Download
62ew2B10.446 1.960.0000.833Download
72a87B20.444 1.960.0000.833Download
83d8xA20.442 1.920.0000.833Download
95xj1A0.438 2.710.0830.917Download
104jnqA20.437 1.920.0000.833Download

(a)Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(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 the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.


  Predicted function using COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs.)

  Ligand binding sites


Click
to view		RankC-scoreCluster
size		 PDB
Hit		 Lig
Name		 Download
Complex		 Ligand Binding Site Residues
10.29 467 1jxpA PEPTIDE N/A 3,4,5,6,7,8,9,10,11
20.12 192 1pirA CA N/A 2,3,4,5,6,7
30.09 136 3ihkB TPP N/A 7,8,9,10,11
40.05 86 1i95G WO2 N/A 8,9,10,11,12
50.03 41 2y8nA SF4 Rep, Mult 3,4


Download the residue-specific ligand binding probability, which is estimated by SVM.
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


Click
to view		RankCscoreECPDB
Hit		TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.2162e5vA0.411 0.720.0000.667 1.4.3.16  NA
20.2082e5vB0.256 3.060.0001.000 1.4.3.16  NA
30.1993lk5A0.429 2.800.0831.000 2.5.1.1  NA
40.1681dihA0.411 2.740.0830.917 1.3.1.26  NA
50.1681didA0.419 2.010.0000.833 5.3.1.5  NA

 Click on the radio buttons to visualize predicted active site residues.
(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
Top 10 homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
1 0.200.4295 2.80 0.08 1.003lk5A GO:0016740 GO:0004161 GO:0008299
2 0.180.4594 2.19 0.00 0.922nlyA GO:0046872 GO:0003824 GO:0005975 GO:0016810
3 0.170.4236 2.65 0.00 0.832jscB GO:0003700 GO:0003677 GO:0046870 GO:0010288 GO:0006355 GO:0016564 GO:0005622 GO:0032791 GO:0006351 GO:0042803 GO:0046872 GO:0046686 GO:0010468 GO:0051260 GO:0097063
4 0.170.4186 2.01 0.00 0.831didA GO:0042732 GO:0009045 GO:0016853 GO:0005737 GO:0046872 GO:0005975 GO:0006098
5 0.150.4252 2.81 0.00 0.832rd5B GO:0003991 GO:0004349 GO:0005737 GO:0006526 GO:0006561 GO:0008652
6 0.140.4233 1.69 0.00 0.671fqjC GO:0047555 GO:0045745 GO:0016787 GO:0007601 GO:0050896 GO:0000187 GO:0045742 GO:0004114 GO:0030553
7 0.130.2093 2.95 0.00 0.673qqvA GO:0008299 GO:0004161 GO:0016740
8 0.120.4187 2.38 0.08 0.923eqnA GO:0004338 GO:0016787 GO:0016798 GO:0008152
9 0.120.4192 1.95 0.08 0.922r48A GO:0005351 GO:0008982 GO:0009401 GO:0016020
10 0.120.3869 1.72 0.17 0.921sliA GO:0008152 GO:0016787 GO:0033995 GO:0005615 GO:0016798 GO:0016829 GO:0005576 GO:0004308 GO:0005975


Consensus prediction of GO terms		 
Molecular Function GO:0004659 GO:0042802 GO:0046870 GO:0001071 GO:0016861
GO-Score 0.40 0.35 0.35 0.35 0.33
Biological Process GO:0006720 GO:0010038 GO:0051259 GO:0010468 GO:0051252 GO:2000112 GO:0019321 GO:0006740 GO:0006007
GO-Score 0.40 0.35 0.35 0.35 0.35 0.35 0.33 0.33 0.33
Cellular Component GO:0044424
GO-Score 0.58

(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 S802915_results.tar.bz2 to download the tarball file including all modeling results listed on this page]


Please cite the following articles when you use the I-TASSER server:
  • Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1: 100014 (2021).
  • Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
  • Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.