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I-TASSER results for job id S802021

(Click on S802021_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
LPSLVNKPLTKVPLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
LLLLLL

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| LPSLVNKPLTKVPLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
Prediction	CHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	912315853441499999999999999999999999999999999999999999999999999879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| LPSLVNKPLTKVPLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
Prediction	644336431341312323333333333333333333333333333333333333333333333334
	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
                   |                   |                   |      

Sec.Str
Seq

CHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
LPSLVNKPLTKVPLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL

1p49A

0.34

0.30

0.88

1.35

Download

--------FTTGFKRLVFLPLQIVGVTLLTLAALNCLGLLHVPLGVFFSLLFLAALILTLFLGFLH

6b85J

0.23

0.26

0.98

1.06

Download

-DTEDSRKIWRTIMLLLVFAILLSAIIWYQITTNPDTSQIATLLSMQLLLIALMLVVIALLLSRQT

5lnkM

0.36

0.33

1.00

1.21

Download

IPTMMLMPLTWLSIWINTTLHSLLISLTSLLLTPLLILTMWLLPLMLMASQLFISMLILLQLFLIM

2mxbA

0.32

0.24

0.71

1.67

Download

EPASLLTASDLDPLILTLSLILVLISLLLTVLALLSHRRTLQQKIWP-------------------

6b85J

0.27

0.26

0.97

1.32

Download

--SKDTEDSRKIWRTIMLLLVFAILLSAIIWYQITTTSQIATLLSMQLLLIALMLVVIALLLSRQT

5lnkM

0.36

0.33

1.00

1.21

Download

IPTMMLMPLTWLSIWINTTLHSLLISLTSLLLTPLLILTMWLLPLMLMASQLFISMLILLQLFLIM

2yevC

0.33

0.27

0.79

1.55

Download

--------------VYIALFALGAALVTLFFYLILNPRVLFDLRFVLFMLLLILLAAGTVALMLLI

5t4oK

0.23

0.21

1.00

1.23

Download

LISLLSKPVSGLRLFGNMYAGELIFILIAGLLWWSQWILNVPWAIFHILIITLQAFIFMVLTIVYL

3rkoG

0.28

0.29

0.92

1.18

Download

-----MIPLQHGLILAAILFVLGLTGLVIRLLFMLIGLEIMINASALAFVVAGSYWSIGLALLLQL

6zkaK

0.27

0.26

0.89

1.33

Download

-------SLVYMNIMMAFTVSLTGLLMLMSSLLCLEGMMLSLFILATLMILNSHFTLASMMPIILL

(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: pGenTHREADER 4: SP3 5: MUSTER 6: pGenTHREADER 7: SP3 8: MUSTER 9: pGenTHREADER 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=-1.69 (Read more about C-score) Estimated TM-score = 0.51±0.15 Estimated RMSD = 6.6±4.0Å	Download Model 2 C-score = -1.89	Download Model 3 C-score = -3.77	Download Model 4 C-score = -4.14	Download Model 5 C-score = -3.62

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	3k66A	0.815	1.46	0.092	0.985	Download
2	3capB	0.809	1.59	0.091	1.000	Download
3	6b85J	0.807	1.39	0.266	0.970	Download
4	4dvyP4	0.792	1.47	0.127	0.955	Download
5	7vugR	0.790	1.83	0.092	0.985	Download
6	1wdzB	0.789	1.89	0.121	1.000	Download
7	6u7hA	0.787	1.98	0.106	0.985	Download
8	6kobC	0.787	2.08	0.092	0.985	Download
9	1i49B	0.787	1.70	0.106	1.000	Download
10	6fpdA	0.786	1.40	0.079	0.955	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	0.10	9	2eimC	CDL	Rep, Mult	20,24,27,28,47,50,51
2	0.07	6	3ny9A	CLR	Rep, Mult	27,44,48,52,55
3	0.04	3	3rrpA	LMR	Rep, Mult	30,31,40,41,46
4	0.04	4	3r9vA	DXC	Rep, Mult	26,47
5	0.04	4	3b71C	PEPTIDE	Rep, Mult	17,20,21,24,51,54,58,62

	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	0.219	3kkbB	0.724	1.75	0.133	0.909	2.7.13.3	NA
2	0.215	1jqiA	0.708	2.34	0.092	0.970	1.3.99.2	NA
3	0.213	3gm1B	0.712	1.75	0.138	0.924	2.7.10.2	NA
4	0.212	1wcrA	0.717	1.57	0.133	0.909	2.7.1.69	NA
5	0.209	1c3cA	0.721	2.45	0.076	0.985	4.3.2.2	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	0.22	0.7702	2.05	0.09	0.98	1m56C	GO:0016021 GO:0055114 GO:0016020 GO:0006123 GO:0004129 GO:0022904 GO:0016491
2	0.22	0.7440	1.87	0.08	1.00	2o98B	GO:0019904
3	0.22	0.7681	1.79	0.12	1.00	1y2oA	GO:0007165 GO:0008093 GO:0017124 GO:0046847
4	0.22	0.7659	2.22	0.11	1.00	1occC	GO:0016020 GO:0022904 GO:0005743 GO:0006123 GO:0004129 GO:0005739 GO:0016021
5	0.21	0.7372	1.95	0.09	1.00	2br9A	GO:0005737 GO:0006605 GO:0005622 GO:0005739 GO:0000278 GO:0048011 GO:0032403 GO:0019904 GO:0001764 GO:0021987 GO:0033267 GO:0035308 GO:0050815 GO:0006915 GO:0008624 GO:0042470 GO:0051219 GO:0044419 GO:0000086 GO:0042826 GO:0005871 GO:0005515 GO:0035556 GO:0019899 GO:0005829 GO:0021766
6	0.20	0.7595	2.03	0.08	0.98	1qleC	GO:0055114 GO:0016021 GO:0005886 GO:0016491 GO:0004129 GO:0016020 GO:0006123 GO:0022904
7	0.20	0.7474	1.95	0.12	1.00	1orqC	GO:0005249 GO:0006813 GO:0008076
8	0.19	0.6146	2.77	0.25	0.95	1p49A	GO:0007565 GO:0043588 GO:0008284 GO:0005635 GO:0008544 GO:0043434 GO:0005764 GO:0005792 GO:0005789 GO:0005783 GO:0008484 GO:0008202 GO:0007611 GO:0004773 GO:0014070 GO:0046872 GO:0009268 GO:0016021 GO:0043627 GO:0005886 GO:0006706 GO:0006629 GO:0016020 GO:0016787 GO:0005624 GO:0005768 GO:0000299 GO:0005794 GO:0003824 GO:0008152
9	0.19	0.7394	2.24	0.06	0.97	1cunA	GO:0005515
10	0.19	0.6366	2.78	0.08	0.91	2x2vA	GO:0015078 GO:0016020 GO:0015992 GO:0033177 GO:0006810 GO:0015986 GO:0016021 GO:0008289 GO:0006754 GO:0006811 GO:0045263 GO:0005886 GO:0015991

Consensus prediction of GO terms

Molecular Function GO:0008092 GO:0030674 GO:0031406 GO:0045309 GO:0019899 GO:0043176 GO:0004129 GO:0019904

GO-Score 0.43 0.43 0.42 0.42 0.42 0.42 0.39 0.38

Biological Process GO:0030035 GO:0031400 GO:0035305 GO:0046907 GO:0021761 GO:0048699 GO:0016477 GO:0045184 GO:0006917 GO:0021543

GO-Score 0.43 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42

Cellular Component GO:0019866 GO:0030424 GO:0005875 GO:0044463 GO:0031966 GO:0048770 GO:0016021

GO-Score 0.43 0.42 0.42 0.42 0.42 0.42 0.39

(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 S802021_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.