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I-TASSER results for job id S776332

(Click on S776332_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
MAKSSFKISNPLEARMSESSRIREKYPDRIPVIVEKAGQSDVPDIDKKKYLVPADLTVGQ
FVYVVRKRIKLGAEKAIFVFVKNTLPPTAALMSAIYEEHKDEDGFLYMTYSGENTFGSLT
VA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAKSSFKISNPLEARMSESSRIREKYPDRIPVIVEKAGQSDVPDIDKKKYLVPADLTVGQFVYVVRKRIKLGAEKAIFVFVKNTLPPTAALMSAIYEEHKDEDGFLYMTYSGENTFGSLTVA
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCSSSCCCCCCHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCCHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCC
Conf.Score	98653233189999999999999878765157887636257852245237606997088999997643256988619999898516654759999998348778779996178656885659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAKSSFKISNPLEARMSESSRIREKYPDRIPVIVEKAGQSDVPDIDKKKYLVPADLTVGQFVYVVRKRIKLGAEKAIFVFVKNTLPPTAALMSAIYEEHKDEDGFLYMTYSGENTFGSLTVA
Prediction	87645147633155036405412741473030103326756145153432113472323302310443171466310101024322464330340156344421000000132412233648
	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

Iden1

Iden2

Cov

Norm.
Z-score

Download
Align.

                  20                  40                  60                  80                 100                 120
                   |                   |                   |                   |                   |                   |  

Sec.Str
Seq

CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCSSSCCCCCCHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCCHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCC
MAKSSFKISNPLEARMSESSRIREKYPDRIPVIVEKAGQSDVPDIDKKKYLVPADLTVGQFVYVVRKRIKLGAEKAIFVFVKNTLPPTAALMSAIYEEHKDEDGFLYMTYSGENTFGSLTVA

7dhtA

0.77

0.75

0.98

2.85

Download

MAKSSFKQEHDLEKRRAEAARIREKYPDRIPVIVEKAEKSDIPTIDKKKYLVPADLTVGQFVYVIRKRIKLSAEKAIFIFVDNVLPPAGALMSSVYEEKKDDDGFLYVTYSGENTFGFGS--

7elgA

0.36

0.35

0.95

2.96

Download

FSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVVSTPISEVYESEKDEDGFLYMVYASQETF------

7dht

0.76

0.75

0.99

3.54

Download

MAKSSFKQEHDLEKRRAEAARIREKYPDRIPVIVEKAEKSDIPTIDKKKYLVPADLTVGQFVYVIRKRIKLSAEKAIFIFVDNVLPPAGALMSSVYEEKKDDDGFLYVTYSGENTFGFGSP-

7dht

0.76

0.75

0.99

2.70

Download

MAKSSFKQEHDLEKRRAEAARIREKYPDRIPVIVEKAEKSDIPTIDKKKYLVPADLTVGQFVYVIRKRIKLSAEKAIFIFVDNVLPPAGALMSSVYEEKKDDDGFLYVTYSGENTFGFGSP-

3h9dA

0.53

0.51

0.95

3.78

Download

-KDSKYKMSHTFESRQSDAAKVRERHPDRLPIICEKVYNSDIGELDRCKFLVPSDLTVGQFVSVLRKRVQLEAESALFVYTNDTVLPSSAQMADIYSKYKDEDGFLYMKYSGEATFG-----

7dht

0.77

0.75

0.98

4.15

Download

MAKSSFKQEHDLEKRRAEAARIREKYPDRIPVIVEKAEKSDIPTIDKKKYLVPADLTVGQFVYVIRKRIKLSAEKAIFIFVDNVLPPAGALMSSVYEEKKDDDGFLYVTYSGENTFGFGS--

1eo6A

0.60

0.57

0.95

2.98

Download

M-KWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFG-----

3h9dA

0.53

0.51

0.95

3.20

Download

-KDSKYKMSHTFESRQSDAAKVRERHPDRLPIICEKVYNSDIGELDRCKFLVPSDLTVGQFVSVLRKRVQLEAESALFVYTNDTVLPSSAQMADIYSKYKDEDGFLYMKYSGEATFG-----

7dhtA

0.76

0.75

0.99

1.56

Download

MAKSSFKQEHDLEKRRAEAARIREKYPDRIPVIVEKAEKSDIPTIDKKKYLVPADLTVGQFVYVIRKRIKLSAEKAIFIFVDNVLPPAGALMSSVYEEKKDDDGFLYVTYSGENTFGF-GSP

1gnuA

0.56

0.54

0.96

5.17

Download

-MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL----

(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=0.67 (Read more about C-score) Estimated TM-score = 0.80±0.09 Estimated RMSD = 3.0±2.2Å	Download Model 2 C-score = -2.20	Download Model 3 C-score = -2.78	Download Model 4 C-score = -1.60

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	Alignment
1	1eo6B	0.879	1.24	0.564	0.926	Download
2	3h9dA	0.876	1.44	0.517	0.943	Download
3	1kotA	0.867	1.49	0.551	0.934	Download
4	2zjdC	0.860	1.79	0.345	0.926	Download
5	2zpnA	0.856	1.29	0.712	0.902	Download
6	3eciA	0.849	1.24	0.355	0.902	Download
7	5azhA	0.837	1.56	0.316	0.910	Download
8	7dhtA	0.825	1.99	0.742	0.984	Download
9	4eoyA	0.805	1.92	0.442	0.910	Download
10	3vvwB	0.799	1.31	0.400	0.869	Download

(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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.90	45	5azfA	PEPTIDE	Rep, Mult	18,22,29,31,47,49,50,51,52,53,61,64,65,68,105
2	0.28	10	3d32A	PEPTIDE	Rep, Mult	18,22,26,31,45,49,50,51,52,53,55,56,57,60,61,64,65,68,105
3	0.03	2	2l8jA	PEPTIDE	Rep, Mult	13,17,18,22,26,29,49,50,51,52,53,105
4	0.01	1	4eoyC	MG	Rep, Mult	36,42,43,44,110
5	0.01	1	2ZPNC	2ZPNC00	Rep, Mult	78,85,113

	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

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.276	2j0mA	0.557	3.41	0.065	0.754	2.7.10.2	NA
2	0.270	2j0kB	0.561	3.05	0.068	0.721	2.7.10.2	NA
3	0.257	3i9vA	0.544	4.10	0.074	0.877	1.6.99.5	NA
4	0.249	3it6B	0.510	3.72	0.095	0.787	2.3.1.1 2.3.1.35	NA
5	0.244	2jrhA	0.488	3.33	0.059	0.664	2.7.11.25	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC 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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Top 10 homologous GO templates in PDB
1	0.66	0.6481	1.91	0.59	0.73	2kq7A	GO:0019898 GO:0005515 GO:0005829 GO:0000407 GO:0031410 GO:0006914 GO:0000329 GO:0033110 GO:0015031 GO:0006944 GO:0005773 GO:0006810 GO:0005774 GO:0032258 GO:0000421 GO:0003674 GO:0006888 GO:0034727 GO:0000045 GO:0005776 GO:0005737 GO:0016020 GO:0000422
2	0.59	0.8493	1.24	0.35	0.90	3eciA	GO:0000045 GO:0005543 GO:0031410 GO:0000421 GO:0006914 GO:0005776 GO:0005737 GO:0005874 GO:0008429 GO:0005856 GO:0005515 GO:0012505 GO:0005829 GO:0031090 GO:0016020
3	0.40	0.8792	1.24	0.56	0.93	1eo6B	GO:0000421 GO:0005829 GO:0006810 GO:0000139 GO:0005794 GO:0032781 GO:0005622 GO:0051117 GO:0006891 GO:0000149 GO:0015031 GO:0005624
4	0.40	0.8668	1.49	0.55	0.93	1kotA	GO:0008017 GO:0006810 GO:0005515 GO:0005886 GO:0016020 GO:0005790 GO:0005764 GO:0005875 GO:0050811 GO:0007268 GO:0005737 GO:0015629 GO:0005874 GO:0048487 GO:0005856 GO:0005794 GO:0015031 GO:0000421 GO:0000226 GO:0000139 GO:0006605 GO:0012505 GO:0048471 GO:0044297 GO:0004872
5	0.40	0.8595	1.79	0.34	0.93	2zjdC	GO:0005776 GO:0005622 GO:0012505 GO:0000421 GO:0005737 GO:0006914 GO:0016020 GO:0031090 GO:0005515 GO:0005856 GO:0031410 GO:0005874
6	0.35	0.7710	1.98	0.54	0.90	2l8jA	GO:0048487 GO:0005622 GO:0016020 GO:0005783 GO:0005856 GO:0005776 GO:0005794 GO:0050811 GO:0005515 GO:0005874 GO:0005737
7	0.33	0.6920	2.69	0.18	0.86	2dyoA	GO:0000407 GO:0006914 GO:0034045 GO:0016787 GO:0005776 GO:0016236 GO:0006501 GO:0006810 GO:0005829 GO:0015031 GO:0019776 GO:0016020 GO:0000422 GO:0032258 GO:0034727 GO:0034274 GO:0005737 GO:0005515
8	0.28	0.5615	2.80	0.18	0.71	1e5wA	GO:0005488 GO:0005515 GO:0005737 GO:0005856 GO:0008092 GO:0019898
9	0.28	0.5874	2.97	0.08	0.76	3ddcB	GO:0007165
10	0.27	0.5607	2.91	0.08	0.71	1isnA	GO:0005488 GO:0005515 GO:0005737 GO:0005856 GO:0008092 GO:0019898

Consensus prediction of GO terms

Molecular Function GO:0008429 GO:0051117 GO:0000149 GO:0048487 GO:0050811 GO:0004872 GO:0008017

GO-Score 0.59 0.40 0.40 0.40 0.40 0.40 0.40

Biological Process GO:0000045 GO:0000422 GO:0034727 GO:0006888 GO:0006944 GO:0032258 GO:0006891 GO:0032781 GO:0000226 GO:0007268

GO-Score 0.86 0.66 0.66 0.66 0.66 0.66 0.40 0.40 0.40 0.40

Cellular Component GO:0000421 GO:0005829 GO:0005874 GO:0033110 GO:0000329 GO:0000407 GO:0019898 GO:0000139 GO:0005624 GO:0005886

GO-Score 0.97 0.92 0.85 0.66 0.66 0.66 0.66 0.64 0.40 0.40

(a) Cscore^GO 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) RMSD^a is the RMSD between residues that are structurally aligned by TM-align.

(d) IDEN^a 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 Cscore^GO of the template.

[Click on S776332_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.