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I-TASSER results for job id S775506

(Click on S775506_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
LDCKPEGPNDRVGPLGAEGGPDYSHEMKLEDTMGPKDGKGPHSRALPTSVVFEKLFEGQK
QGPVEMDDNFEFGPCDAKPIVRGKFNTTLLNGGPANRDGPGNWTGPDQSRYTGGFIEGPY
KFQKGPCRLNNETGPDDTSCNREGGPQVIAMDTKLGPEGPIEKTACTFNYGPYFEPRDSY
FGPRHRDYASEAAAKEAAAKEAAAKSDTKEEGAVKKKQQKPDRLEKGRMKIVPKESEKDS
KTKPPDATIVVDGVKYQVKKKGKVKSKNTQDGLYHNKNKPPESRKKLEK

  Predicted Secondary Structure

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |         
LDCKPEGPNDRVGPLGAEGGPDYSHEMKLEDTMGPKDGKGPHSRALPTSVVFEKLFEGQKQGPVEMDDNFEFGPCDAKPIVRGKFNTTLLNGGPANRDGPGNWTGPDQSRYTGGFIEGPYKFQKGPCRLNNETGPDDTSCNREGGPQVIAMDTKLGPEGPIEKTACTFNYGPYFEPRDSYFGPRHRDYASEAAAKEAAAKEAAAKSDTKEEGAVKKKQQKPDRLEKGRMKIVPKESEKDSKTKPPDATIVVDGVKYQVKKKGKVKSKNTQDGLYHNKNKPPESRKKLEK
PredictionCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCSSSCCHHHHHCCCCCCCSSSSSCCCCCCCCSSSCCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSSSCCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCSSCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCHHHHHHHCC
Conf.Score9876756777422677764102458878510056501424302248872799983689988527777875447687824040113201038962532068884112003775875214788899761773111555775448987699967775378986203466304433358215777776578898888988643321111356666774446799527642860306654445456799996188723488887445235655655322468898667665229
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |         
LDCKPEGPNDRVGPLGAEGGPDYSHEMKLEDTMGPKDGKGPHSRALPTSVVFEKLFEGQKQGPVEMDDNFEFGPCDAKPIVRGKFNTTLLNGGPANRDGPGNWTGPDQSRYTGGFIEGPYKFQKGPCRLNNETGPDDTSCNREGGPQVIAMDTKLGPEGPIEKTACTFNYGPYFEPRDSYFGPRHRDYASEAAAKEAAAKEAAAKSDTKEEGAVKKKQQKPDRLEKGRMKIVPKESEKDSKTKPPDATIVVDGVKYQVKKKGKVKSKNTQDGLYHNKNKPPESRKKLEK
Prediction8714552456610102042043234614041100232033016321213020320363663433406441320114333213231334226341130001210000230414313064146243140314434434324053611020222355324724033101013034214233420453144200200000000330231115666544657553242154341423045446546442350310042131303441514456343021336632663354368
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                 240                 260                 280
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |         
Sec.Str
Seq		CCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCSSSCCHHHHHCCCCCCCSSSSSCCCCCCCCSSSCCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSSSCCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCSSCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCHHHHHHHCC
LDCKPEGPNDRVGPLGAEGGPDYSHEMKLEDTMGPKDGKGPHSRALPTSVVFEKLFEGQKQGPVEMDDNFEFGPCDAKPIVRGKFNTTLLNGGPANRDGPGNWTGPDQSRYTGGFIEGPYKFQKGPCRLNNETGPDDTSCNREGGPQVIAMDTKLGPEGPIEKTACTFNYGPYFEPRDSYFGPRHRDYASEAAAKEAAAKEAAAKSDTKEEGAVKKKQQKPDRLEKGRMKIVPKESEKDSKTKPPDATIVVDGVKYQVKKKGKVKSKNTQDGLYHNKNKPPESRKKLEK
12yq2A 0.41 0.49 0.87 1.60Download TGCKPEAKNDRIGPLGAEGWKDYSPEMTLEDTMVIRYLAILHSRALPTSVVFKKLFEGQKGDTVEMDDDFEFGPCDAKPIVRGKYNTTLLNGPAFQMVCPIGWTGTNRDTLDTAVVRTYRRSRPFPCITQKVLGEDLYDCILGGNWTCVTGDQLQYSGGSIESCWCGFKFQRS-EGLPHY--------------------PIGKCRLKNETGYRLVDNTSCNRVPQGTVKLGPKPYEIISSEGPVEKTACT----FNYTKTLKNKYFEPRDSYFQQ-------------
28pagA 0.16 0.26 0.66 1.39Download KVDRPDQKDLKGVLSGKKVWTGGSVIITDEFVMTTPIEMDYCIKVIDTAKFFCVMVGTPQRDLVKPPEM--LCGCGALEVQDNNSTGLISPGNVLPSKCINGWTGVEPTKLPYEDIQECPHKPLGWCRVGENEPTNRKSCVQGGVIKVGNFNETASFRGPTT---CTYKYNKIYDEKDRYWGQYMVKGEYQYWFD----------------------------------------------------------------------------------------------
37w7iA 0.07 0.21 0.88 1.15Download NDVATAKATGETSAKVSINKVLNIAEG---------------ITTPEATFTFTFTPKTGTS-----SNGAPYETIDSSNGQITDKNVSYSGTD------VLATGQTNIKKDTGDIFREVNYTHAGEYVYTKQNVGWKVIQKNGSPIDFMTYDNRNKTTGGTYISSVYFKQVSPSVNGKVKPSESGTTYKYDLFTNIYRKNAGKITDPNEPNPNKPSKVTKASTETSQSITGKIGETSKTFVYGQETTAYKENGASKNQAGTVSTNFTQDSILIGEKPDVTP--------
42yq2 0.70 0.49 0.68 7.94Download TGCKPEAKNDRIGPLGAEGLKDYSPEMTLEDTMVIASGAILHSRALPTSVVFKKLFEGQKQGDVEMDDDFEFGPCDAKPIVRGKYNTTLLNGPAANRDLGGNWTCGDQLQYSGGSIESGFKFQRGKCRLKNETGVDNTSCNREGVVQVIALDTKLGPEGPVEKTACTFNYTKYFEPRDSYFQQLKGEY----------QYWFDLEVT----------------------------------------------------------------------------------
57egyA 0.22 0.23 0.70 1.30Download ----------------------------------------------------------TNPSTEEMGDDFGFGPFDTSPVVKGKYNTTLLNGSAFYLVCPIGWTGVSPTTLRTEVVKTFRREKPFPCVTTTVENEDLFYCKLGGNWTCVKGEPVVYTGGQVKQCWCGFDFNEP-DGLPHY--------------------PIGKCILANETGYRIVDSTDCNRSAKGSHECLIGNTTSDERLGPPKEIVSSTSCTFNYAKTLKNKYYEPRDSYFQQYMLKGE-------
62yq2 0.65 0.49 0.68 5.23Download TGCKPEAKNDRIGPLGAEGWKDYSPEMTLEDTMSCRYLAILHSRALPTSVVFKKLFEGQKGDTVEMDDDFEFGPCDAKPIVRGKYNTTLLNGPAFQMVCPINWTCVDQLQYSGGSIESCPHYPIGKCRLKNETGVDNTSCNREGVVQVIALDTKLGPEGPVEKTACTFNYNKYFEPRDSYFQQYMGEYQYWFD------LEVT--------------------------------------------------------------------------------------
78deoA 0.10 0.27 1.00 1.08Download IDIPPESNPTDLNATNNNRQSNTTGADGWGFMFSKKDGDDFREKGTPSAAGFRIDTGYYNNDFVKNDSQGNTSKVGSGTPSTDFLNYADNTTNDLDGKFHGQKLNNVNLKYNASNQTGLSPTDSYNFLVTSSQYSGVMRADLDGATLTYTPKAVDGDSTKEIPFNKKREFDPNLAPGTEKVVQKGEPGIETTTTPTYVNPNTGEKVGEGEPTEKITKQPVDEIVHYGGEEIKPGHKDEFDPNAPKGSQTTQPGKPGVKNPDTGEVVTPPVDDVKNPLTGEKVGEGEPTE
82yq2A 0.65 0.49 0.68 2.20Download -GCKPEAKNDRIGPLGAEGWKDYSPEMTLEDIASCRYLAILHSRALPTSVVFKKLFEGQKQDTVEMDDDFEFGPCDAKPIVRGKYNTTLLNGPAFQMVCPGNWTCVDQLQYSGGSIESCPHYPIGKCRLKNETGVDNTSCNREGTVQVIALDTKLGPEGPVEKTACTFNYNKYFEPRDSYFQQYMGEYQYWFDLEVT--------------------------------------------------------------------------------------------
98pagA 0.15 0.26 0.90 1.23Download KVDRPDQKDLKGVLSGKDGWTGGSVIITDEFAVTTPIEMDYCIKVIDTAKFFCVMVGTPTRDLVKPPEML--CGCGALEVQDNNSTGLISPGNVLPSKCINGWTGVVTCHCTDIKMKFLENTTPQKCPGTYLSDQNFHDCKYGSQESCIDPEPTKLPYEDIQECWCSYYIKDHKGPLGWCRVGENEPY---------YLTNRKSCVQGGVQGTTKIKVGNFNETAISFMPCNPIKEASRG---PTTCTY-----KYAKTLKNKIDEKDRYWGQYMVKGE----------
102yq2 0.70 0.49 0.63 8.67Download TGCKPEAKNDRIGPLGAEGWKDYSPEMTLEDTMSCRYLAILHSRALPTSVVFKKLFEGQKQDTVEMDDDFEFGPCDAKPIVRGKYNTTLLNGPAFQMVCPIGWTGGDQLQYSGGSIEGLPHYPIGKCRLKNETGVDNTSCNREGVVQVIALDTKLGPEGPVEKTACTFNYNKYFEPRDSYFQQ----------------------------------------------------------------------------------------------------------
(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: PROSPECT2   4: HHSEARCH2   5: FFAS-3D   6: HHSEARCH I   7: PROSPECT2   8: Neff-PPAS   9: FFAS-3D   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=-2.29 (Read more about C-score)
  • Estimated TM-score = 0.45±0.14
  • Estimated RMSD = 11.5±4.5Å

  • Download Model 2
  • C-score = -3.35

  • Download Model 3
  • C-score = -3.55

  • Download Model 4
  • C-score = -3.13

  • Download Model 5
  • C-score = -3.78


  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
12yq2A0.753 3.350.3120.889Download
27egyA0.490 3.610.1640.595Download
38pagA0.444 5.420.0670.675Download
48rc4a0.422 6.040.0330.706Download
55f0oA0.418 6.410.0460.716Download
66um1A0.413 6.830.0800.741Download
77t7rA0.410 6.780.0470.723Download
86bcuW0.403 6.790.0400.727Download
98a19A0.403 6.410.0470.696Download
102zxqA0.403 6.420.0420.696Download

(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
10.06 2 3q2wA MAN Rep, Mult 138,153
20.06 2 2dexX CA Rep, Mult 87,98,99,100,102
30.06 2 2z7cA ARG Rep, Mult 130,137,138,139
40.04 1 4ildA CA Rep, Mult 67,69
50.03 1 3vggA GLC Rep, Mult 14,16


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
10.0932np0A0.378 6.410.0320.644 3.4.24.69  NA
20.0901wd8A0.352 6.620.0700.633 3.5.3.15  NA
30.0892vkzG0.363 6.860.0410.668 2.3.1.38 3.1.2.14  NA
40.0892zxqA0.403 6.420.0420.696 3.2.1.97  68
50.0871w27A0.341 6.720.0480.606 4.3.1.24  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 0.200.3720 6.12 0.05 0.622q7nA GO:0005515
2 0.100.4009 6.00 0.05 0.651cwvA GO:0005488 GO:0009405 GO:0009986
3 0.100.3661 6.52 0.05 0.642ww8A GO:0046872 GO:0005488 GO:0005515
4 0.100.3760 6.37 0.05 0.641fnfA GO:0005515
5 0.090.3685 6.23 0.04 0.623apnA GO:0006355 GO:0016787 GO:0006464 GO:0006351 GO:0046872 GO:0004668 GO:0005737 GO:0016568 GO:0005634 GO:0005509 GO:0018101
6 0.090.4027 6.42 0.04 0.702zxqA GO:0007155
7 0.090.3821 6.23 0.05 0.653q2wA GO:0005509 GO:0005886 GO:0007155 GO:0007156 GO:0016020
8 0.080.3794 6.60 0.05 0.672uv8G GO:0016829 GO:0004318 GO:0016409 GO:0008152 GO:0016491 GO:0004317 GO:0005737 GO:0004314 GO:0005811 GO:0004313 GO:0004320 GO:0003824 GO:0008610 GO:0004312 GO:0016296 GO:0055114 GO:0005739 GO:0005829 GO:0004319 GO:0004321 GO:0016297 GO:0019171 GO:0006633 GO:0005835 GO:0005515 GO:0016295 GO:0016740 GO:0016787
9 0.080.3761 6.84 0.03 0.693p8cA GO:0051015 GO:0030032 GO:0003779 GO:0048675 GO:0045202 GO:0031529 GO:0030027 GO:0005515 GO:0042995 GO:0005845 GO:0001726 GO:0005737 GO:0019717 GO:0048471 GO:0048365 GO:0030154 GO:0008360 GO:0007275 GO:0030054 GO:0007399
10 0.080.3741 6.31 0.05 0.632dewX GO:0004668 GO:0005737 GO:0016568 GO:0046872 GO:0005634 GO:0016787 GO:0006464 GO:0006351 GO:0006355 GO:0005509 GO:0018101


Consensus prediction of GO terms		 
Molecular Function GO:0043167 GO:0005515
GO-Score 0.36 0.34
Biological Process GO:0009405 GO:0006355 GO:0018101 GO:0016568
GO-Score 0.10 0.09 0.09 0.09
Cellular Component GO:0009986 GO:0005737 GO:0005634
GO-Score 0.10 0.09 0.09

(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 S775506_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.