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I-TASSER results for job id S802038

(Click on S802038_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
MAAEIQPKPLTRKPILLQRMEGSQEVVNMAVIVPKEEGVISVSEDRSNGKHCKHTPVASI
LQ

  Predicted Secondary Structure

Sequence                  20                  40                  60
                   |                   |                   |  
MAAEIQPKPLTRKPILLQRMEGSQEVVNMAVIVPKEEGVISVSEDRSNGKHCKHTPVASILQ
PredictionCCCCCCCCCCCCCCSSSSSSCCCCCCSSSSSSSCCCCCSSSSSCCCCCCCCCCCCCHHHHCC
Conf.Score97523378888897877751377652446898438874599641567884245572355409
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60
                   |                   |                   |  
MAAEIQPKPLTRKPILLQRMEGSQEVVNMAVIVPKEEGVISVSEDRSNGKHCKHTPVASILQ
Prediction73443454644633310430543644131010025452103024444636414433234338
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		CCCCCCCCCCCCCCSSSSSSCCCCCCSSSSSSSCCCCCSSSSSCCCCCCCCCCCCCHHHHCC
MAAEIQPKPLTRKPILLQRMEGSQEVVNMAVIVPKEEGVISVSEDRSNGKHCKHTPVASILQ
13acpA 0.14 0.23 0.90 1.18Download VDTAKLQMRDSNFNLQREIDQAHVSEITKLKFFPSGEALISSSQDMQDGS-NPRTLI-----
21trjA 0.16 0.16 0.79 1.50Download ----------LNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGENLAAKKAMYTLS---
36pbgA 0.20 0.29 0.97 1.07Download ISGLRKKNLSPTDAVVKHVLEGHDRGVNWAAFHP--TMIVSGADDRQNESKAWHYNVSCAQE
45mqfF 0.22 0.13 0.66 1.12Download --------------------KGHTSFVNSCYPARRGPQVCTGSDDGTRKKAAIQT-FQNTYQ
54yvdA 0.11 0.11 0.73 1.44Download ----------LEYNKVIRHYHGHLSAVYGLDLHPTIDVLVTCSRDSTTKASVHTL-------
65mqfF 0.24 0.11 0.60 1.01Download ---------------------GHEGEVYCCKFHPNGSTLASAGFDRLYGD-CDNY---ATLK
71u2vC 0.19 0.18 0.76 1.44Download ----------GNKWVQVHELKEHNGQVTGVDWAPDSNRIVTCGTDRNKGRTWKPTLV-----
84g56B 0.14 0.21 0.90 1.01Download KTLSVFSDGTLSQKAVLKSYNAHSSEVNCVAACPGKDTFLSCGEDGRKPK-PATR-----ID
93acpA 0.15 0.23 0.77 1.42Download ---------DSNFNLQREIDQAHVSEITKLKFFPSGEALISSSQDMQKDGSNPRTLI-----
104j87A 0.25 0.23 0.84 1.01Download ILTRIQ----YRMGTLLDRFDGHDGPVRGIAFHPTQPIFVSGGDDYKSRK-LLFS-----LC
(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: MUSTER   2: Neff-PPAS   3: SP3   4: MUSTER   5: Neff-PPAS   6: MUSTER   7: Neff-PPAS   8: MUSTER   9: Neff-PPAS   10: MUSTER   

   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=-2.26 (Read more about C-score)
  • Estimated TM-score = 0.45±0.14
  • Estimated RMSD = 7.7±4.3Å

  • Download Model 2
  • C-score = -2.74

  • Download Model 3
  • C-score = -4.24

  • Download Model 4
  • C-score = -3.41

  • Download Model 5
  • C-score = -3.50


  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
13jcrL0.587 2.710.1020.871Download
21a0rB0.585 2.770.1380.855Download
37ruoA0.584 3.310.1860.935Download
46f3tA20.584 2.750.1720.855Download
54ozuA0.582 3.440.1150.919Download
62pbiD0.580 2.860.1550.855Download
76mzcG0.578 2.860.1690.871Download
82xzmR10.576 2.930.1690.887Download
92xznR0.575 2.950.1690.887Download
102zkqa20.575 2.810.1030.855Download

(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
10.14 5 3sfzA GBL Rep, Mult 27,28,41
20.07 3 1a0rB FAR Rep, Mult 21,23,25,41,43,45,47,49
30.05 2 1icrA NIO N/A 21,22
40.05 2 3mksD C1C Rep, Mult 18,19,21,28,29,30,40,42,43
50.05 2 2x9xA IMD N/A 7,9


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
10.1471g72A0.529 3.280.0500.887 1.1.99.8  NA
20.1421lrwC0.510 2.840.0330.839 1.1.99.8  NA
30.1421lrwA0.514 3.270.0340.871 1.1.99.8  NA
40.1363kf5A0.525 3.600.0170.952 3.2.1.26  NA
50.1352fpcA0.435 3.300.1060.694 4.3.3.2  33,56

 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 0.150.5798 2.86 0.15 0.852pbiD GO:0005515
2 0.150.5803 2.78 0.14 0.851b9xA GO:0050909 GO:0006184 GO:0007200 GO:0007186 GO:0007165 GO:0005834 GO:0003924 GO:0005515 GO:0004871 GO:0008283 GO:0001750 GO:0007596 GO:0007213 GO:0006112 GO:0031702 GO:0001664 GO:0005886 GO:0007265 GO:0030168 GO:0007204 GO:0007268 GO:0071377 GO:0051020
3 0.140.5613 2.97 0.19 0.871vyhC GO:0021540 GO:0043005 GO:0071445 GO:0030154 GO:0000226 GO:0042598 GO:0048471 GO:0006810 GO:0030036 GO:0021819 GO:0019226 GO:0007017 GO:0033267 GO:0045505 GO:0005829 GO:0030426 GO:0007049 GO:0005737 GO:0016042 GO:0005625 GO:0005815 GO:0016020 GO:0008090 GO:0005813 GO:0042803 GO:0031513 GO:0007405 GO:0031512 GO:0015630 GO:0031252 GO:0007611 GO:0005938 GO:0032403 GO:0051660 GO:0051081 GO:0051219 GO:0045773 GO:0045931 GO:0007420 GO:0017145 GO:0007399 GO:0007067 GO:0007275 GO:0001675 GO:0005634 GO:0051301 GO:0050885 GO:0000132 GO:0031023 GO:0001764 GO:0007097 GO:0005875 GO:0007268 GO:0008017 GO:0005626 GO:0005635 GO:0045502 GO:0010977 GO:0043025 GO:0005874 GO:0048854 GO:0005819 GO:0021895 GO:0005871 GO:0005856 GO:0031965 GO:0032319 GO:0021766 GO:0005515 GO:0000235 GO:0000776 GO:0021987 GO:0008344 GO:0016477
4 0.140.5722 3.13 0.14 0.891u2vC GO:0005856 GO:0003779 GO:0005737 GO:0005515 GO:0030833
5 0.140.5757 2.95 0.17 0.892xzmR GO:0005840 GO:0005515
6 0.140.5686 3.32 0.03 0.902aq5A GO:0005515
7 0.140.5684 3.13 0.12 0.893acpA GO:0003674 GO:0006511 GO:0005829 GO:0070682 GO:0005634 GO:0005515 GO:0000502 GO:0005737
8 0.130.5561 2.90 0.15 0.851erjC GO:0005515
9 0.130.5598 2.93 0.21 0.873dm0A GO:0009845 GO:0005829 GO:0006417 GO:0022626 GO:0004871 GO:0015423 GO:0043190 GO:0006810 GO:0042597 GO:0008643 GO:0042956 GO:0015609 GO:0015768 GO:0007165 GO:0005634 GO:0042254 GO:0009507 GO:0046686 GO:0071215 GO:0005515 GO:0005215 GO:0005363
10 0.130.5543 3.01 0.08 0.873izbA GO:0001965 GO:0005737 GO:0005515 GO:0010255 GO:0005092 GO:0017148 GO:0007186 GO:0001403 GO:0022627 GO:0004871


Consensus prediction of GO terms		 
Molecular Function GO:0005515
GO-Score 0.54
Biological Process GO:0019226 GO:0007267
GO-Score 0.54 0.54
Cellular Component GO:0043232
GO-Score 0.53

(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 S802038_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.