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I-TASSER results for job id S693184

(Click on S693184_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
MARGKIQIKMIENATNRQVTYSKRRHGLFKKAHELSVLCDAKVSIIMVSSTKKLHEFITP
NLSQKQFYDQYQKAKPCDLWSNHYQAMQEQLRKLREVNRNLRNEISHRKGESLNGLSHEE
LYILEQKMQEAVDITRAQKMKTITNQIEKSKKKVRNGEQVQRTLLQDLELFKEEDPHYGL
VDNGGDYETVFGCSNAYPGLLALRLQSNHYNFHGGAGSDLTFA

  Predicted Secondary Structure

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |   
MARGKIQIKMIENATNRQVTYSKRRHGLFKKAHELSVLCDAKVSIIMVSSTKKLHEFITPNLSQKQFYDQYQKAKPCDLWSNHYQAMQEQLRKLREVNRNLRNEISHRKGESLNGLSHEELYILEQKMQEAVDITRAQKMKTITNQIEKSKKKVRNGEQVQRTLLQDLELFKEEDPHYGLVDNGGDYETVFGCSNAYPGLLALRLQSNHYNFHGGAGSDLTFA
PredictionCCCCCCSSSSSCCCCCCCCHHHHHHCCHHHHHHHHHHHHCCSSSSSSSCCCCCSSCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score9976415676147654545014755025676777753306558899971898711035860567899999987116773045679999999999999999999986235788654999999999999999998699999999999999999999999999999999999987456553444378875433567889998702367999986789998767379
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |   
MARGKIQIKMIENATNRQVTYSKRRHGLFKKAHELSVLCDAKVSIIMVSSTKKLHEFITPNLSQKQFYDQYQKAKPCDLWSNHYQAMQEQLRKLREVNRNLRNEISHRKGESLNGLSHEELYILEQKMQEAVDITRAQKMKTITNQIEKSKKKVRNGEQVQRTLLQDLELFKEEDPHYGLVDNGGDYETVFGCSNAYPGLLALRLQSNHYNFHGGAGSDLTFA
Prediction7733321023261633210000123320122031000002230000000342201001134432341131034247551445424403410430364144014422423032157043720340053025114402432342044205413532441363044034414434543442323444432433343434332321030003021113323310337
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                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |   
Sec.Str
Seq
CCCCCCSSSSSCCCCCCCCHHHHHHCCHHHHHHHHHHHHCCSSSSSSSCCCCCSSCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MARGKIQIKMIENATNRQVTYSKRRHGLFKKAHELSVLCDAKVSIIMVSSTKKLHEFITPNLSQKQFYDQYQKAKPCDLWSNHYQAMQEQLRKLREVNRNLRNEISHRKGESLNGLSHEELYILEQKMQEAVDITRAQKMKTITNQIEKSKKKVRNGEQVQRTLLQDLELFKEEDPHYGLVDNGGDYETVFGCSNAYPGLLALRLQSNHYNFHGGAGSDLTFA
11n6jA 0.33 0.17 0.40 1.96Download -GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD--MDRVLLKYTEYSEPHESRTNTDILETLKRR----------------------------------------------------------------------------------------------------------------------------------
27tz7B 0.08 0.15 0.65 1.01Download KEDNIEAVGK---------KLHEYNTQFQEKSREYDRL----------------------YEEYTRTSQEIQMK------RTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQ-----------------------------------------
37x1nB 0.33 0.17 0.39 1.00Download ----KIQIQRITDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNHSNKLFQYASTD--MDKVLLKYTEYNEPHESRTNADIIETLRKKG---------------------------------------------------------------------------------------------------------------------------------
44ox0A 0.24 0.14 0.40 1.79Download --------------------------------------------------------------------------------LAVELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRLAD-----------------------------------------------------
51n6j 0.34 0.17 0.42 4.96Download -GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD--MDRVLLKYTEYSEPHESRTNT-DI---LETLKRR------GIG---------------------------------------------------------------------------------------------------------------------
64ox0A 0.24 0.14 0.41 1.01Download ----------------------------------------------------------------------------SREALAVELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRL-------------------------------------------------------
71n6j 0.33 0.17 0.42 3.48Download -GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD--MDRVLLKYTEYSEPHESRTNTDI--LETLKRRGIG-----------------------------------------------------------------------------------------------------------------------------
84ox0A 0.25 0.14 0.42 1.18Download ---------------------------------------------------------------------------PSREALAVELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRL-------------------------------------------------------
91n6jA 0.33 0.17 0.42 1.05Download -GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAS--TDMDRVLLKYTEYSEPH--ESRTNTDILETLKRRGIG-----------------------------------------------------------------------------------------------------------------------------
101mnm 0.49 0.19 0.29 5.73Download KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPI--------------------------------------------------------------------------------------------------------------------------------------------------------------
(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: PROSPECT2   3: SPARKS-X   4: FFAS-3D   5: HHSEARCH2   6: Neff-PPAS   7: HHSEARCH I   8: wdPPAS   9: Neff-PPAS   10: HHSEARCH   

   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=-4.10 (Read more about C-score)
  • Estimated TM-score = 0.28±0.09
  • Estimated RMSD = 15.6±3.3Å

  • Download Model 2
  • C-score = -4.17

  • Download Model 3
  • C-score = -4.45

  • Download Model 4
  • C-score = -4.79

  • Download Model 5
  • C-score = -4.76


  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
16rz6A0.473 5.280.0530.753Download
24phuA0.471 5.200.0360.731Download
34mt0A0.470 4.950.0810.727Download
44ntjA0.465 5.050.0630.709Download
52rakA0.465 4.940.0560.709Download
66w1sR0.464 5.160.0650.735Download
71nktA0.462 5.370.0320.735Download
86e59A0.461 5.160.0440.727Download
97s9yA30.460 4.860.0870.700Download
101wp1A0.460 5.020.0690.727Download

(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 8 1nwqC Nuc.Acid Rep, Mult 127,128,131,132,134,135,136
20.05 2 4ntjA CLR Rep, Mult 23,26,27,30
30.02 1 3pp5A CA Rep, Mult 126,129
40.02 1 4l3yA NO2 Rep, Mult 117,121
50.02 1 N/A N/A N/A 10,17,21,48,50,52,53,55,139


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
10.0651pixA0.455 5.730.0950.789 4.1.1.70  NA
20.0653gmaB0.450 5.570.0700.762 4.1.1.70  NA
30.0653gf7A0.449 5.560.0610.762 4.1.1.70  NA
40.0653bnjA0.420 5.160.0440.641 1.7.2.2  NA
50.0653e04D0.417 5.590.0200.682 4.2.1.2  130

 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 0.070.4599 5.02 0.07 0.731wp1A GO:0009279 GO:0016020 GO:0046677 GO:0005886 GO:0016021 GO:0006810 GO:0005215 GO:0008289
2 0.070.4594 4.99 0.06 0.712rajA GO:0005515 GO:0007154 GO:0035091
3 0.070.4397 5.58 0.05 0.723dinA GO:0005524 GO:0017038 GO:0006605 GO:0005886 GO:0006810 GO:0006886 GO:0003676 GO:0000166 GO:0016020 GO:0005737 GO:0055085 GO:0015031 GO:0004386
4 0.070.4341 5.50 0.05 0.693pikA GO:0005886 GO:0016021 GO:0046688 GO:0016020 GO:0010272 GO:0009279 GO:0060003 GO:0005215 GO:0006810 GO:0008289
5 0.070.4503 5.57 0.07 0.763gmaB GO:0016874
6 0.070.4493 5.56 0.06 0.763gf7A GO:0016874
7 0.070.3553 5.46 0.07 0.561nl3A GO:0040007 GO:0006810 GO:0005886 GO:0016887 GO:0005576 GO:0005737 GO:0043952 GO:0016020 GO:0000166 GO:0042803 GO:0015031 GO:0005829 GO:0005524 GO:0031522 GO:0006200 GO:0055085 GO:0006605 GO:0006886 GO:0017038
8 0.070.4498 5.67 0.05 0.763rzeA GO:0005737 GO:0004872 GO:0007186 GO:0016021 GO:0010894 GO:0042742 GO:0008152 GO:0016798 GO:0003796 GO:0019835 GO:0003824 GO:0009253 GO:0016787 GO:0016998 GO:0004930 GO:0009629 GO:0045907 GO:0005887 GO:0045429 GO:0006954 GO:0005730 GO:0004969 GO:0051381 GO:0007165 GO:0007200 GO:0004871 GO:0005634 GO:0016020 GO:0005624 GO:0007268 GO:0005886
9 0.070.4309 5.80 0.05 0.712xubA GO:0003899 GO:0003677 GO:0009615 GO:0006351 GO:0005666 GO:0045089 GO:0006359 GO:0045087 GO:0005634 GO:0032728
10 0.060.4434 5.63 0.08 0.743qnqD GO:0005886 GO:0016740 GO:0008643 GO:0016020 GO:0006810 GO:0008982 GO:0016021 GO:0005351 GO:0009401


Consensus prediction of GO terms
 
Molecular Function GO:0005215 GO:0016874 GO:0005524 GO:0003676 GO:0005515 GO:0004386 GO:0035091
GO-Score 0.13 0.07 0.07 0.07 0.07 0.07 0.07
Biological Process GO:0051234
GO-Score 0.38
Cellular Component GO:0071944
GO-Score 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 S693184_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.