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I-TASSER results for job id S778844

(Click on S778844_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
YDFMGSCVYQLAGVCSKNPALTPFLVTVENIIRGNKAVSFTKAVTLEVYNMTISLSKSAP
RRIEVNGVLVYLPFS

  Predicted Secondary Structure

Sequence                  20                  40                  60
                   |                   |                   |               
YDFMGSCVYQLAGVCSKNPALTPFLVTVENIIRGNKAVSFTKAVTLEVYNMTISLSKSAPRRIEVNGVLVYLPFS
PredictionCCCCCSSSSSSSSSCCCCCCCCCSSSSSSSCCCCCCCCSSSSSSSSSSCCSSSSSSCCCCCSSSSCCSSSSCCCC
Conf.Score975737469996730899988788999997579999617999999999999999951998989999999728979
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60
                   |                   |                   |               
YDFMGSCVYQLAGVCSKNPALTPFLVTVENIIRGNKAVSFTKAVTLEVYNMTISLSKSAPRRIEVNGVLVYLPFS
Prediction873724141301331377653430303041373644412122303030462303034646330303445343448
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                  40                  60
                   |                   |                   |               
Sec.Str
Seq		CCCCCSSSSSSSSSCCCCCCCCCSSSSSSSCCCCCCCCSSSSSSSSSSCCSSSSSSCCCCCSSSSCCSSSSCCCC
YDFMGSCVYQLAGVCSKNPALTPFLVTVENIIRGNKAVSFTKAVTLEVYNMTISLSKSAPRRIEVNGVLVYLPFS
18qciA 0.43 0.47 1.00 1.25Download FDFQGTCNYVLATTGCPGVSTTPFTVTTKNQNRGNPAVSYVRVVTVAALGTNISIHKDEIGKVRVNGVLTALPVS
28qciB 0.43 0.47 1.00 1.57Download FDFQGTCNYVLATTGCPGVSTTPFTVTTKNQNRGNPAVSYVRVVTVAALGTNISIHKDEIGKVRVNGVLTALPVS
37pmv 0.25 0.45 0.92 2.20Download FTFSGICQYLLARDCQD----HSFSIVIETVQCADRDAVCTRSVTVRLPGSLVKLKHG--AGVAMDGQDVQLPLL
48qci 0.44 0.47 1.00 1.52Download FDFQGTCNYVLATTGCPTQGLTPFTVTTKNQNRGNPAVSYVRVVTVAALGTNISIHKDEIGKVRVNGVLTALPVS
56rbfA 0.24 0.33 1.00 1.28Download YDFDGHCSYVAVQDYGQNSSLGSFSIITENVPCGTTGVTCSKAIKIFMGRTELKLEDKHRVVIQRDHVAYTTREV
68qci 0.43 0.47 0.99 2.39Download FDFQGTCNYVLATTGCPTQGLTPFTVTTKNQNRGNPAVSYVRVVTVAALGTNISIHKDEIGKVRVNGVLTALPV-
76rbfA 0.27 0.31 1.00 0.69Download YDFDGHCSYVAVQDCGQNSSLGSFSIITENVPCGTTGVTCSKAIKIFMGRTELKLEDKSTGIVIWDKVFIKLAPS
86rbfA 0.25 0.33 0.97 0.95Download YDFDGHCSYVAVQDYGQNSSLGSFSIITENVPCGTTGVTCSKAIKIFMGRTELKLEDK--HRVVIQRDHVAYTTR
98qciB 0.43 0.47 1.00 0.98Download FDFQGTCNYVLATTGCPGQGLTPFTVTTKNQNRGNPAVSYVRVVTVAALGTNISIHKDEIGKVRVNGVLTALPVT
106rbfA 0.25 0.40 1.00 2.35Download YDFDGHCSYVAVQDCGQNSSLGSFSIITENVPCGTTGVTCSKAIKIFMGRTELKLEDKHRVVIQRDHVAYTTREV
(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: FFAS-3D   2: SPARKS-X   3: HHSEARCH2   4: HHSEARCH I   5: Neff-PPAS   6: HHSEARCH   7: pGenTHREADER   8: wdPPAS   9: PROSPECT2   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=-0.22 (Read more about C-score)
  • Estimated TM-score = 0.68±0.12
  • Estimated RMSD = 3.8±2.6Å

  • Download Model 2
  • C-score = -4.48

  • Download Model 3
  • C-score = -2.19

  • Download Model 4
  • C-score = -5

  • Download Model 5
  • C-score = -2.49


  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
18qciB0.873 1.440.4401.000Download
27zwhD0.804 1.340.2610.920Download
37wn4E20.802 1.350.2610.920Download
47wn3A20.794 1.380.2460.920Download
58oesA30.767 1.660.2900.920Download
67pp6B30.756 1.790.2320.920Download
77a5oA0.755 1.860.2170.920Download
86rbfA0.701 2.570.2220.920Download
97qclA0.692 2.300.1740.880Download
106n29A0.652 2.690.2460.880Download

(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
10.19 10 3b2jA IOD Rep, Mult 27,43,44,45,54
20.09 5 2x56A C8E Rep, Mult 25,26,27,45,46,52,53,66
30.09 5 4p99A CA Rep, Mult 47,52
40.05 3 2qtkB C8E Rep, Mult 26,53,54
50.03 2 2x55A C8E Rep, Mult 48,53,55,63


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
10.2502bjiA0.565 3.110.0300.880 3.1.3.25  NA
20.2471ftaA0.588 3.030.1290.893 3.1.3.11  NA
30.2341awbA0.556 2.910.0450.880 3.1.3.25  NA
40.2331j2gC0.577 3.140.0430.907 1.7.3.3  NA
50.2292cziA0.579 2.850.0460.867 3.1.3.25  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 0.250.5652 3.11 0.03 0.882bjiA GO:0005737 GO:0046872 GO:0006661 GO:0042802 GO:0042803 GO:0004437 GO:0007165 GO:0008934 GO:0046855 GO:0006796 GO:0016787
2 0.250.5876 3.03 0.13 0.891ftaA GO:0004331 GO:0042132 GO:0003824 GO:0005515 GO:0046872 GO:0005975 GO:0032869 GO:0005625 GO:0005829 GO:0006094 GO:0042802 GO:0006002 GO:0016787 GO:0008152 GO:0006006 GO:0048029 GO:0006000 GO:0042578
3 0.240.5783 3.69 0.04 0.932qzuA GO:0003824 GO:0008152 GO:0008484
4 0.240.5794 3.06 0.07 0.881r56C GO:0005777 GO:0006144 GO:0004846 GO:0055114 GO:0016491
5 0.240.5809 3.22 0.06 0.923ifaA GO:0008152 GO:0006094 GO:0004331 GO:0005975 GO:0016787 GO:0042132 GO:0046872 GO:0003824 GO:0005829 GO:0006006 GO:0006000 GO:0042578
6 0.230.5561 2.91 0.04 0.881awbA GO:0005737 GO:0004437 GO:0016787 GO:0006796 GO:0042802 GO:0043025 GO:0046855 GO:0046872 GO:0008934 GO:0030424 GO:0042803 GO:0007165 GO:0010226 GO:0006661
7 0.230.5759 3.14 0.04 0.911j2gA GO:0004846 GO:0006144 GO:0016491 GO:0055114
8 0.230.5790 2.85 0.05 0.872cziA GO:0008934 GO:0006796 GO:0005737 GO:0007165 GO:0016787 GO:0046855 GO:0042803 GO:0046872 GO:0004437
9 0.220.4685 2.96 0.02 0.761fj1E GO:0005886 GO:0009279 GO:0016020
10 0.220.5488 2.56 0.05 0.733ckgA GO:0009279


Consensus prediction of GO terms		 
Molecular Function GO:0046872 GO:0052745 GO:0016663 GO:0042802 GO:0004331 GO:0042132
GO-Score 0.57 0.50 0.48 0.43 0.42 0.42
Biological Process GO:0050794 GO:0071545 GO:0046474 GO:0007154 GO:0046838 GO:0023052 GO:0046488 GO:0032868 GO:0071375 GO:0072521
GO-Score 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.49 0.49 0.48
Cellular Component GO:0000267 GO:0042579 GO:0005829
GO-Score 0.49 0.48 0.42

(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 S778844_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.