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I-TASSER results for job id S693396

(Click on S693396_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
HHHHHHDPDKDGTIDLKE

  Predicted Secondary Structure

Sequence
                  
HHHHHHDPDKDGTIDLKE
PredictionCCCCCCCCCCCCCSSCCC
Conf.Score965557878687410369
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence
                  
HHHHHHDPDKDGTIDLKE
Prediction854444546572436368
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
CCCCCCCCCCCCCSSCCC
HHHHHHDPDKDGTIDLKE
17msjA 0.06 0.33 1.00 1.04Download PGYFCENQDGSHCSTCLQ
21uzjA 0.18 0.17 0.94 1.32Download -PDFELNPTRVGCVDTRS
35lztA 0.27 0.22 0.83 1.20Download GMWRFYTEDSPG---LKV
45hu3B 0.27 0.22 0.83 1.88Download ATLARQDIDEGGEVD---
57opcY 0.17 0.28 1.00 1.00Download DSQLLVTASDDGYIKIYD
63u1iA 0.33 0.33 1.00 1.23Download SHNLMITVDDDGTMRIKD
73kv6D 0.39 0.44 1.00 1.14Download HRHDYTEIDDGGTTFIKE
86ae8C 0.33 0.22 0.67 1.81Download ------DDEDEEDDDFKE
91ctdA 0.46 0.33 0.72 1.12Download -----FDKNADGYIDIEE
104xzrA 0.40 0.17 0.83 1.68Download TRKKRKDPDKENKID---
(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: wdPPAS   4: SP3   5: SPARKS-X   6: Neff-PPAS   7: wdPPAS   8: SP3   9: Neff-PPAS   10: SP3   

   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=-1.04 (Read more about C-score)
  • Estimated TM-score = 0.58±0.14
  • Estimated RMSD = 2.7±2.0Å

  • Download Model 2
  • C-score = -3.61

  • Download Model 3
  • C-score = -2.25

  • Download Model 4
  • C-score = -3.26

  • Download Model 5
  • C-score = -1.63


  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
11nyaA10.361 2.170.1670.944Download
21y1xA0.355 1.870.1111.000Download
37pqcO0.339 0.480.0630.556Download
43cs1A0.335 1.780.1180.944Download
52aaoA0.333 1.760.3530.944Download
63if8A0.330 2.140.0590.667Download
73f73A0.326 2.800.0000.944Download
85e37A30.325 2.340.2220.944Download
94tncA10.325 1.800.3331.000Download
103dtpC0.323 2.430.1880.889Download

(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
10.51 13 3akaA CA Rep, Mult 7,9,11,13


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
10.1213im9A0.296 1.770.1000.556 2.3.1.39  NA
20.1031rv8B0.136 2.630.0560.611 4.1.2.13  NA
30.0922qezF0.280 2.390.1180.944 4.3.1.7  NA
40.0902nqaB0.158 1.730.0000.667 3.4.22.53 3.4.22.52  NA
50.0863iydD0.301 1.250.0000.667 2.7.7.6  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 0.110.3258 2.80 0.00 0.943f73A GO:0003676 GO:0005515 GO:0046872
2 0.110.2646 3.09 0.00 0.943hm9A GO:0005515 GO:0003676 GO:0046872
3 0.110.2983 1.73 0.23 0.941bmoA GO:0005509 GO:0005515 GO:0005578 GO:0005615 GO:0007165
4 0.100.2638 2.22 0.28 0.943fbyA GO:0005509 GO:0005515 GO:0005576 GO:0007155
5 0.100.2492 2.25 0.18 0.941m8qC GO:0005509 GO:0016459
6 0.090.2986 2.88 0.00 0.943hxmA GO:0005515 GO:0003676 GO:0046872
7 0.090.1892 2.09 0.33 0.722l5yA GO:0005515
8 0.090.3008 1.25 0.00 0.673iydD GO:0016740 GO:0005515 GO:0006351 GO:0016779 GO:0016020 GO:0003899 GO:0005737 GO:0003677
9 0.080.1513 1.70 0.00 0.672g8eA GO:0004198 GO:0005622 GO:0006508 GO:0004197
10 0.080.2469 1.86 0.23 0.941sraA GO:0005509 GO:0005578 GO:0005615 GO:0007165


Consensus prediction of GO terms
 
Molecular Function GO:0043167 GO:0005515
GO-Score 0.56 0.37
Biological Process GO:0007165 GO:0007155
GO-Score 0.11 0.10
Cellular Component GO:0005615 GO:0005578 GO:0016459
GO-Score 0.11 0.11 0.10

(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 S693396_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.