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I-TASSER results for job id S776316

(Click on S776316_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
VRVRRVRRRRVRVRRVRRRRVVRRRRRRRRVRVVRR

  Predicted Secondary Structure

Sequence                  20
                   |                
VRVRRVRRRRVRVRRVRRRRVVRRRRRRRRVRVVRR
PredictionCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCC
Conf.Score930378777789999999999999875341122229
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20
                   |                
VRVRRVRRRRVRVRRVRRRRVVRRRRRRRRVRVVRR
Prediction743442454434344244443344444444343358
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.		                   20
                   |                
Sec.Str
Seq		CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCC
VRVRRVRRRRVRVRRVRRRRVVRRRRRRRRVRVVRR
18p0vK 0.17 0.19 1.00 1.35Download DLDRRYNMEKEKLYKIRLLQARRNREIAILHRKIDE
21ohf 0.50 0.39 0.50 1.22Download KIAARVR-----ARRDRRR--------AARM-----
35o5jB 0.30 0.25 0.83 1.36Download ----VIKKRRKRMSKKKHRKLLRRTRVQRRKLGK--
45o5jB 0.28 0.25 0.89 1.21Download --GSVIKKRRKRMSKKKHRKLLRRTRVQRR-KLGK-
54ce4A 0.20 0.25 0.97 1.44Download SNIKRKHKWVRRLRTPTGVQVILRRMHKGRKSLSH-
67znkG 0.08 0.08 1.00 1.18Download KELEALGKELEHLSHIKESVEDKLELRRKQFHVLLS
71ohfA 0.43 0.39 0.58 1.17Download IPGKIA--ARVRARRDRRR--------AARM-----
85mmmA 0.22 0.22 1.00 1.23Download KLEQKMKMKMAKKIRLRRNRLMRKRKLRKRGAWPPS
95mmiA 0.22 0.22 1.00 1.40Download KLEQKMKMKMAKKIRLRRNRLMRKRKLRKRGAKMKK
107tryU 0.15 0.11 0.92 1.16Download DLTFHLLRTLLELARTQSQRERAEQNRIIFDSV---
(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: HHSEARCH2   3: Neff-PPAS   4: wdPPAS   5: SP3   6: SPARKS-X   7: HHSEARCH2   8: Neff-PPAS   9: SP3   10: SPARKS-X   

   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=-0.88 (Read more about C-score)
  • Estimated TM-score = 0.60±0.14
  • Estimated RMSD = 3.7±2.5Å

  • Download Model 2
  • C-score = -3.21

  • Download Model 3
  • C-score = -2.24

  • Download Model 4
  • C-score = -2.03

  • Download Model 5
  • C-score = -2.50


  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
14mt4A0.855 0.950.0570.972Download
28tqmA0.843 1.050.0001.000Download
38c0eA0.841 1.070.1710.972Download
47khbD20.839 1.190.0561.000Download
53htkC0.838 1.190.0000.972Download
67qkrA30.838 1.020.0000.972Download
77aalA20.837 1.040.1140.972Download
87mknD0.836 1.240.0561.000Download
97r91D0.835 0.850.0860.972Download
106thkA0.835 0.770.1140.972Download

(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
10.28 425 4fe1B CLA Rep, Mult 17,21,23,24,26,27
20.22 327 4y281 CLA Rep, Mult 16,19,20,23,24
30.21 363 4eoyA CA Rep, Mult 16,17,18,19,20,21
40.11 236 2zp9H PEPTIDE Rep, Mult 21,24,25,27,28,29
50.02 36 1ud5A RB Rep, Mult 27,28,31


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
10.3053ilwA0.816 1.190.1430.972 5.99.1.3  NA
20.2842wl2B0.796 1.290.2000.972 5.99.1.3  NA
30.2832x6fA0.814 0.910.1140.972 2.7.1.137 2.7.1.153 2.7.1.154  NA
40.2811gpjA0.810 1.500.0860.972 1.2.1.70  NA
50.2742c5uB0.801 1.140.0831.000 6.5.1.3  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 0.330.8228 1.45 0.06 0.971f5nA GO:0060333 GO:0006184 GO:0016020 GO:0005886 GO:0005525 GO:0019221 GO:0000166 GO:0003924
2 0.280.8341 1.25 0.06 0.972q13A GO:0005515
3 0.280.8378 1.19 0.00 0.973htkC GO:0006974 GO:0016874 GO:0046872 GO:0005635 GO:0005634 GO:0006281 GO:0005737 GO:0008270 GO:0019789 GO:0006310
4 0.280.8069 1.15 0.11 0.972xcrD GO:0003677 GO:0003700 GO:0003918 GO:0005524 GO:0005694 GO:0006259 GO:0006265 GO:0006355
5 0.270.8335 0.96 0.06 0.973c98B GO:0030141 GO:0043234 GO:0030672 GO:0070032 GO:0043008 GO:0043005 GO:0006836 GO:0005886 GO:0016081 GO:0043229 GO:0017156 GO:0006887 GO:0042641 GO:0005515 GO:0009629 GO:0001956 GO:0001948 GO:0030054 GO:0000149 GO:0006810 GO:0045202 GO:0005624 GO:0032028 GO:0019904 GO:0046982 GO:0017157 GO:0045921 GO:0070044 GO:0048306 GO:0017022 GO:0016021 GO:0030674 GO:0016020 GO:0019717 GO:0019855 GO:0031410 GO:0047485 GO:0005484 GO:0006886 GO:0007268 GO:0016192
6 0.270.7911 1.32 0.14 1.003kz1A GO:0005089 GO:0005515 GO:0005622 GO:0035023
7 0.270.8156 1.34 0.11 0.972xcqA GO:0003677 GO:0003700 GO:0003918 GO:0005524 GO:0005694 GO:0006259 GO:0006265 GO:0006355
8 0.270.7740 1.51 0.03 0.941gk7A GO:0005198
9 0.270.8181 1.26 0.08 1.001yvlB GO:0014070 GO:0006917 GO:0042493 GO:0005515 GO:0000983 GO:0007584 GO:0034097 GO:0043330 GO:0060334 GO:0009615 GO:0051591 GO:0003677 GO:0008284 GO:0009612 GO:0006355 GO:0005730 GO:0006366 GO:0043565 GO:0000979 GO:0007165 GO:0048661 GO:0005829 GO:0030425 GO:0006351 GO:0043434 GO:0006919 GO:0005737 GO:0003700 GO:0060338 GO:0030424 GO:0060337 GO:0008015 GO:0060333 GO:0032869 GO:0044419 GO:0042542 GO:0007259 GO:0032496 GO:0005654 GO:0005634 GO:0009617 GO:0004871 GO:0007260 GO:0031663 GO:0007249 GO:0019221 GO:0005509
10 0.270.8170 0.63 0.09 0.923iedA GO:0005524 GO:0006457 GO:0006950 GO:0051082


Consensus prediction of GO terms		 
Molecular Function GO:0019787 GO:0032559 GO:0001071 GO:0005246 GO:0008200 GO:0032036 GO:0060090 GO:0046914 GO:0008094 GO:0003924
GO-Score 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.42 0.37 0.33
Biological Process GO:0033554 GO:0071103 GO:0010468 GO:2000112 GO:0051252 GO:0016079 GO:0046928 GO:0009628 GO:0051047 GO:0006904
GO-Score 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55
Cellular Component GO:0044428 GO:0031967 GO:0005626 GO:0008021 GO:0031224 GO:0042995 GO:0044430 GO:0015629 GO:0030665 GO:0031201
GO-Score 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55

(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 S776316_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.