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I-TASSER results for job id S693414

[Click on S693414_results.tar.bz2 to download the tarball file including all modeling results listed on this page]

  Submitted Sequence in FASTA format


  Predicted Secondary Structure

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                 
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                 
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
                   20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360
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(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=1.13 (Read more about C-score)
  • Estimated TM-score = 0.87±0.07
  • Estimated RMSD = 4.3±2.9Å

  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

to view
RankPDB HitTM-scoreRMSDaIDENaCovAlignment
13eksA0.984 0.640.9300.992Download
21yagA0.960 1.310.8600.981Download
34eahD0.908 1.470.9940.944Download
45aftA0.902 2.250.5280.971Download
53qb0A0.900 2.220.3150.968Download
64fo0A0.900 2.230.2070.966Download
74am6A0.884 2.390.2100.952Download
86w17B0.879 1.870.4720.934Download
96kw5f0.879 2.220.2160.944Download
106gejR0.874 2.320.2510.950Download

(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

to view
Ligand Binding Site Residues
10.87 328 4pl7A ATP Rep, Mult 15,16,17,18,20,158,159,160,161,184,212,215,216,303,304,305,307,308,338
20.24 61 1qz6A JAS Rep, Mult 25,26,27,141,145,146,147,148,149,170,171,336,343,346,347,348,350,357
30.13 38 4h03B LAR Rep, Mult 17,18,34,36,58,61,69,71,159,185,188,208,209,212
40.08 21 1wuaA AP8 Rep, Mult 135,145,146,147,148,149,150,170,171,336,347,351,353,354,357
50.08 39 1qhaA G6P Rep, Mult 13,17,139,158,159,302,303,304,340,341

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

to view
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.7603cjcA0.945 1.670.9950.981  12,16,20,31,34,36,56,71,78,80,82,86,90,92,94,96,124
20.3503f9mA0.617 4.110.0920.769  NA
30.3402e2oA0.550 3.650.1200.666  NA
40.3062nztA0.612 4.220.0980.769  NA
50.3051bdgA0.604 3.930.0990.745  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 0.780.9515 1.22 0.90 0.971c0fA GO:0001891 GO:0016192 GO:0032010 GO:0000902 GO:0000910 GO:0006897 GO:0031143 GO:0005524 GO:0005737 GO:0017022 GO:0006935 GO:0042331 GO:0015629 GO:0005856 GO:0005200 GO:0032009 GO:0005515 GO:0006928 GO:0000166 GO:0005884 GO:0006972 GO:0031252
2 0.770.9063 2.42 0.97 0.982y83O GO:0005884 GO:0006915 GO:0001725 GO:0030240 GO:0005856 GO:0055003 GO:0030048 GO:0031032 GO:0031674 GO:0060047 GO:0005524 GO:0006200 GO:0005515 GO:0005737 GO:0000166 GO:0055008 GO:0017022 GO:0016887 GO:0005865 GO:0042643 GO:0030017 GO:0048741 GO:0007517 GO:0006898 GO:0009792 GO:0040007 GO:0000910 GO:0040035 GO:0000003 GO:0030036 GO:0071688 GO:0002119 GO:0009790 GO:0040039 GO:0048545 GO:0006936 GO:0005200 GO:0030049 GO:0009991 GO:0005829 GO:0016049 GO:0010226 GO:0009612 GO:0015629 GO:0043531 GO:0043503 GO:0042802 GO:0035267 GO:0006457 GO:0051086 GO:0016319 GO:0006911 GO:0005875 GO:0032507 GO:0031011 GO:0002121 GO:0007291 GO:0005623 GO:0005811 GO:0044267 GO:0034329 GO:0045216 GO:0034332 GO:0019901 GO:0050998 GO:0030529 GO:0007596 GO:0043234 GO:0006928 GO:0007409 GO:0070688 GO:0019894 GO:0051084 GO:0030424 GO:0007411
3 0.760.9596 1.31 0.86 0.981yagA GO:0031011 GO:0031505 GO:0000123 GO:0006357 GO:0034599 GO:0007119 GO:0000916 GO:0030050 GO:0005515 GO:0000142 GO:0005856 GO:0005524 GO:0032432 GO:0006897 GO:0000132 GO:0005737 GO:0030479 GO:0035267 GO:0006887 GO:0000011 GO:0016573 GO:0001300 GO:0000910 GO:0000001 GO:0000166 GO:0006281 GO:0030476 GO:0000812
4 0.690.6802 1.25 0.54 0.702p9kB GO:0005856 GO:0005737 GO:0003779 GO:0005524 GO:0042995 GO:0000166
5 0.650.8556 3.03 0.38 0.981u2vA GO:0003779 GO:0005515 GO:0005524 GO:0030030 GO:0030833 GO:0005737 GO:0005856 GO:0060271 GO:0000166 GO:0042995 GO:0030027
6 0.580.7742 3.30 0.40 0.913dwlA GO:0030479 GO:0000147 GO:0005737 GO:0051666 GO:0005856 GO:0000915 GO:0005515 GO:0030833 GO:0003779 GO:0007163 GO:0000166 GO:0005829 GO:0005524 GO:0006897 GO:0034314
7 0.560.8991 2.31 0.31 0.973qb0B GO:0006357 GO:0005634 GO:0051382 GO:0006351 GO:0000790 GO:0035267 GO:0003682 GO:0031011 GO:0016573 GO:0004402 GO:0006355 GO:0006338 GO:0006325 GO:0006281 GO:0016568 GO:0043140 GO:0006974 GO:0000812 GO:0005515
8 0.520.7364 3.23 0.14 0.841jcfA GO:0000902 GO:0005524
9 0.500.6589 3.02 0.13 0.752fsjA GO:0000166 GO:0016787 GO:0005524
10 0.440.6977 3.22 0.14 0.803kvgB GO:0005524

Consensus prediction of GO terms
Molecular Function GO:0005524 GO:0017022 GO:0005200 GO:0003779 GO:0050998 GO:0019894 GO:0016887 GO:0019901 GO:0042802 GO:0043531
GO-Score 1.00 0.95 0.95 0.89 0.77 0.77 0.77 0.77 0.77 0.77
Biological Process GO:0042331 GO:0006972 GO:0071688 GO:0009792 GO:0034329 GO:0032507 GO:0006200 GO:0010226 GO:0002121 GO:0016319
GO-Score 0.78 0.78 0.77 0.77 0.77 0.77 0.77 0.77 0.77 0.77
Cellular Component GO:0035267 GO:0031011 GO:0031143 GO:0032010 GO:0001891 GO:0032009 GO:0042643 GO:0001725 GO:0031674 GO:0005829
GO-Score 0.94 0.94 0.78 0.78 0.78 0.78 0.77 0.77 0.77 0.77

(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 S693414_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.