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I-TASSER results for job id S776808

(Click on S776808_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

>seq
HTTPSQHANGLANCCMNMEDMICHEDITASSER

  Predicted Secondary Structure

Sequence                  20
                   |             
HTTPSQHANGLANCCMNMEDMICHEDITASSER
PredictionCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCC
Conf.Score967544431499886158988764012322469
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20
                   |             
HTTPSQHANGLANCCMNMEDMICHEDITASSER
Prediction854456424311411342643123642446688
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		CCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCC
HTTPSQHANGLANCCMNMEDMICHEDITASSER
16tdwN 0.16 0.18 0.94 1.20Download LSPIPEHLRLVKNVAQVQIDMLKLLNAQAAK--
23zeyA 0.26 0.24 0.94 1.20Download RANPSQEEESVARVLFELEGS--HKTLRAQLPR
35kc1C 0.22 0.21 0.97 1.12Download QDTLSPINDPLLMSILNRLQFNLNNDIQLKTE-
45b5iA 0.15 0.15 1.00 1.03Download FREPNVATECRSNCYNNPVFRQCMAYVVPAHLH
52gliA 0.24 0.24 0.88 1.04Download YMCEHE---GCSKAFSNASDRAKHQNRTHSNE-
62tmaA 0.16 0.15 0.97 1.03Download -ERAEERAELSEGKCAELEEEIKTVTNNLKSLE
75hyuA 0.06 0.06 1.00 1.01Download KLSEAELHDKIKNLEEEKAELFEKLDKVEEEHK
86m6xC 0.21 0.21 1.00 1.02Download KLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQK
91nvpB 0.09 0.09 0.97 1.00Download -TVPKLYRSVIEDVINDVRDIFLDDGVDEQVLM
106peqA 0.08 0.21 0.76 0.21Download FVHARERLRNIERICFLLRKLVLPE--------
(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: SP3   2: Neff-PPAS   3: SP3   4: Neff-PPAS   5: SP3   6: Neff-PPAS   7: SP3   8: Neff-PPAS   9: SP3   10: FFAS-3D   

   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=-1.05 (Read more about C-score)
  • Estimated TM-score = 0.58±0.14
  • Estimated RMSD = 3.8±2.6Å

  • Download Model 2
  • C-score = -3.32

  • Download Model 3
  • C-score = -2.93

  • Download Model 4
  • C-score = -5

  • Download Model 5
  • C-score = -5


  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
16ehqL20.614 2.020.0000.939Download
27ayxA0.589 2.090.0000.970Download
31jzsA20.588 1.860.0320.879Download
46vp9B20.585 2.500.0911.000Download
51zo4B0.578 2.150.0000.970Download
65nwsA0.578 2.180.0310.970Download
76w7tI0.575 1.960.1290.939Download
82j41D20.575 2.190.0330.909Download
96g5oA20.574 1.970.0940.970Download
108avvA0.574 2.100.0320.939Download

(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
10.20 33 3j5gV Nuc.Acid Rep, Mult 7,8,9,11
20.12 19 2zc5D ZN Rep, Mult 24,27
30.09 16 3ffuA MG Rep, Mult 25,28,29
40.08 12 5iqyA IOD Rep, Mult 20,21,24
50.06 10 3vk5A MG Rep, Mult 11,12,14


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
10.2083hf2A0.574 2.240.0000.970 1.14.14.1 1.6.2.4  NA
20.1982j41D0.575 2.190.0330.909 2.7.4.8  NA
30.1871tqnA0.560 2.060.0000.970 1.14.13.67 1.14.13.32 1.14.13.97  NA
40.1871w0eA0.519 2.480.0310.970 1.14.13.67 1.14.14.1  NA
50.1831eemA0.545 2.350.0650.909 2.5.1.18  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 0.210.5743 2.24 0.00 0.973hf2A GO:0005506 GO:0009055 GO:0016705 GO:0020037 GO:0055114
2 0.200.5468 1.89 0.03 0.851tt9A GO:0007010 GO:0019215 GO:0005737 GO:0005542 GO:0005814 GO:0005794 GO:0003824 GO:0044237 GO:0016740 GO:0030412 GO:0016829 GO:0005856 GO:0030409 GO:0006547 GO:0008152
3 0.200.5746 2.19 0.03 0.912j41D GO:0004385 GO:0016740 GO:0000166 GO:0016301 GO:0005524 GO:0006163 GO:0005737 GO:0005515 GO:0016310
4 0.200.5436 2.20 0.03 0.853dwcB GO:0004180 GO:0016787 GO:0004181 GO:0006508 GO:0046872
5 0.190.5599 2.06 0.00 0.971tqnA GO:0047638 GO:0009822 GO:0005737 GO:0008395 GO:0070576 GO:0006629 GO:0050649 GO:0042359 GO:0042737 GO:0070989 GO:0008202 GO:0033780 GO:0005783 GO:0055114 GO:0017144 GO:0019899 GO:0050591 GO:0016491 GO:0046483 GO:0016021 GO:0042738 GO:0016098 GO:0005496 GO:0005792 GO:0009986 GO:0046872 GO:0006805 GO:0034875 GO:0005506 GO:0006706 GO:0005789 GO:0004497 GO:0016020 GO:0030343 GO:0008209 GO:0019825 GO:0009055 GO:0016705 GO:0016712 GO:0020037
6 0.190.5194 2.48 0.03 0.971w0eA GO:0042738 GO:0016021 GO:0005496 GO:0005792 GO:0009986 GO:0046872 GO:0006805 GO:0034875 GO:0005506 GO:0006706 GO:0005789 GO:0004497 GO:0016020 GO:0030343 GO:0008209 GO:0009822 GO:0047638 GO:0019825 GO:0005737 GO:0008395 GO:0070576 GO:0006629 GO:0050649 GO:0042359 GO:0042737 GO:0070989 GO:0008202 GO:0033780 GO:0005783 GO:0055114 GO:0017144 GO:0019899 GO:0050591 GO:0016491 GO:0046483 GO:0016098 GO:0009055 GO:0016705 GO:0016712 GO:0020037
7 0.190.5476 2.94 0.09 0.972a11A GO:0004518 GO:0003723 GO:0040007 GO:0004525 GO:0005737 GO:0004519 GO:0016787 GO:0003725 GO:0005622 GO:0006396 GO:0016075
8 0.180.4622 2.34 0.03 0.911c1gA GO:0031941 GO:0005856 GO:0060048 GO:0030016 GO:0003779 GO:0009790 GO:0005737 GO:0003065 GO:0001701 GO:0055010
9 0.180.5447 2.35 0.07 0.911eemA GO:0016740 GO:0019853 GO:0005515 GO:0005829 GO:0008152 GO:0016656 GO:0005737 GO:0006805 GO:0008150 GO:0004364
10 0.170.5606 2.07 0.03 0.973k9vA GO:0033280 GO:0070561 GO:0030342 GO:0008403 GO:0042369 GO:0016709 GO:0016491 GO:0001649 GO:0046872 GO:0005739 GO:0055114 GO:0004497 GO:0042359 GO:0005506 GO:0009055 GO:0016705 GO:0020037


Consensus prediction of GO terms		 
Molecular Function GO:0019842 GO:0032559 GO:0016776 GO:0019239 GO:0031406 GO:0035639 GO:0019201 GO:0032403 GO:0043176 GO:0016841
GO-Score 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40
Biological Process GO:0006796 GO:0072521 GO:0006996 GO:0009075 GO:0009117 GO:0044270 GO:0034754 GO:0017144 GO:0006775 GO:0016042
GO-Score 0.40 0.40 0.40 0.40 0.40 0.38 0.38 0.38 0.38 0.38
Cellular Component GO:0044450 GO:0005813 GO:0042598 GO:0031090 GO:0031224 GO:0044432 GO:0042175
GO-Score 0.40 0.40 0.38 0.38 0.38 0.38 0.38

(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 S776808_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.