I-TASSER results

I-TASSER results for job id Rv3861

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (108 residues)
MTWLADPVGNSRIARAQACKTSISAPIVESWRAQRGAQCGQREKSCRCSRAVHIQGISPP
LFRRPLEPAVQAAVASCRLGRHPVVAHRVTVALGQGSQLAQRECPRPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MTWLADPVGNSRIARAQACKTSISAPIVESWRAQRGAQCGQREKSCRCSRAVHIQGISPPLFRRPLEPAVQAAVASCRLGRHPVVAHRVTVALGQGSQLAQRECPRPA
Prediction	CCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCCHHHHHHCCCCCC
Conf.Score	986567888656666665455556645678899886677555544444655776679976567886489999988766578864456676643556566775589999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MTWLADPVGNSRIARAQACKTSISAPIVESWRAQRGAQCGQREKSCRCSRAVHIQGISPPLFRRPLEPAVQAAVASCRLGRHPVVAHRVTVALGQGSQLAQRECPRPA
Prediction	742234434554134143144414242254144644451465555141432141442434214431432153113414344332223302222344451355616668
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(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

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCCHHHHHHCCCCCC
MTWLADPVGNSRIARAQACKTSISAPIVESWRAQRGAQCGQREKSCRCSRAVHIQGISPPLFRRPLEPAVQAAVASCRLGRHPVVAHRVTVALGQGSQLAQRECPRPA

3bkxA

0.31

0.28

0.91

0.72

MUSTER

ITDLAGPANARTIQRRQTAHR---LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNTN--LSDDLGPIAD

1f0xA1

0.09

0.07

0.79

0.58

dPPAS

-----------------------NKAFLNELARLVGSSHDPAKTARYRKGFRSGQGDALAVVFPGSLLELWRVLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDV

3bkxA1

0.27

0.24

0.91

0.62

wdPPAS

IT-ALGPANARTIQRRQTAH----LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNTNLSDDLGPIADQH

3a5cA

0.37

0.29

0.78

0.75

wMUSTER

QGFMADST--SRWAEALR---EISSPAEEGYLAARLAAFYERAGKVITGEAVTIVGVSPP-MS---EPVTQSTLRIVG----------AFWRLD--ASLAFR---RPA

3bkxA1

0.29

0.25

0.86

0.60

wPPAS

IT-ALGPANARTIQRRQTAH----LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNT----NLSD-PIAD

3bkxA1

0.29

0.26

0.89

0.73

dPPAS2

ITDLLGPANARTIQRRQTAHR---LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNT----NLSDDLGPI

3bkxA1

0.29

0.26

0.88

0.76

PPAS

ITDLLGPANARTIQRRQTAH----LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNT----NLSDDLGPI

3bkxA1

0.29

0.26

0.89

0.84

Env-PPAS

ITDLLGPANARTIQRRQTAHR---LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNT----NLSDDLGPI

3bkxA1

0.29

0.26

0.89

0.72

MUSTER

ITDLLGPANARTIQRRQTAHR---LAIAEAWQVKPGEKCGQGDLSAVLADQVHVTGIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNT----NLSDDLGPI

3bkxA1

0.21

0.19

0.93

0.58

dPPAS

ITALGPTANARTIQRRQTAHR---LAIAEAWQVKPGDLSAVLADQVGSSGHVTGIDIASPDYGAPLT----LGQAWNHLLAGPL-GDRLTVHFNTNLSDDLGPIADQH

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

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 higher value signifies a model with a high 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.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-2.48

Estimated TM-score = 0.43±0.14

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-3.60

Download Model 3

C-score=-3.72

Download Model 4

C-score=-3.30

Download Model 5

C-score=-4.91

Proteins structureally close to the target in 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
1	1ccwB1	0.501	4.37	0.069	0.898
2	4ityA	0.500	4.26	0.139	0.852
3	4nl4H	0.495	3.84	0.054	0.824
4	1cevA	0.495	4.40	0.070	0.852
5	4bloA	0.493	4.29	0.071	0.870
6	4k92A	0.490	4.28	0.105	0.852
7	1g5aA	0.490	4.37	0.029	0.889
8	3gmzA	0.490	4.50	0.069	0.861
9	5dkxA	0.490	4.03	0.034	0.787
10	5aedA	0.489	4.31	0.078	0.870

(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 COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results 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	0.09	3	5egoA	NUC	Rep, Mult	9,70,71,74,75,78,81,82
2	0.06	2	4y49A	G4P	Rep, Mult	47,72
3	0.06	2	1hqgA	ORN	Rep, Mult	30,32,42,46
4	0.06	2	2b5zA	BGS	Rep, Mult	81,82
5	0.06	2	1zs2A	GLC	Rep, Mult	3,4,6,23,74,75
6	0.03	1	3olxA	BEF	Rep, Mult	17,18
7	0.03	1	4kt0M	CLA	Rep, Mult	69,70,73
8	0.03	1	3bz1Z	CLA	Rep, Mult	79,83
9	0.03	1	1pprM	PID	Rep, Mult	61,69
10	0.03	1	4f8hA	LMD	Rep, Mult	73,76
11	0.03	1	2icsA	ZN	Rep, Mult	20,53,87

	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	0.060	2eabA	0.468	4.49	0.031	0.852	3.2.1.63	NA
2	0.060	1eh9A	0.469	4.76	0.040	0.907	3.2.1.141	29
3	0.060	3ebgA	0.458	4.17	0.052	0.787	3.4.11.-	NA
4	0.060	1vlqA	0.456	4.27	0.062	0.806	3.1.1.41	87
5	0.060	1cb7B	0.493	4.22	0.058	0.861	5.4.99.1	NA
6	0.060	2jlcB	0.444	4.61	0.082	0.843	2.2.1.9	24,27
7	0.060	1on3E	0.482	4.51	0.050	0.870	2.1.3.1	NA
8	0.060	3gmzA	0.490	4.50	0.069	0.861	3.5.3.1	68
9	0.060	2jlaA	0.466	4.33	0.089	0.824	2.2.1.9	NA
10	0.060	1cevA	0.495	4.40	0.070	0.852	3.5.3.1	6
11	0.060	3flmA	0.449	4.42	0.043	0.824	2.2.1.9	36
12	0.060	3i39X	0.463	4.64	0.030	0.843	1.2.99.2	74
13	0.060	1s5jA	0.461	4.33	0.058	0.824	2.7.7.7	NA
14	0.060	1dioA	0.462	4.63	0.070	0.861	4.2.1.28	NA
15	0.060	1n0hA	0.457	4.96	0.056	0.898	2.2.1.6	NA
16	0.060	1g5aA	0.490	4.37	0.029	0.889	2.4.1.4	16
17	0.060	1iwpA	0.443	4.42	0.010	0.806	4.2.1.30	NA
18	0.060	3ifh6	0.459	4.22	0.071	0.768	1.2.1.16	NA
19	0.060	1ayxA	0.449	4.41	0.061	0.778	3.2.1.3	103

(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
Homologous GO templates in PDB
0	0.11	0.450	4.42	0.05	0.81	1wogA	GO:0016787 GO:0016813 GO:0046872
1	0.07	0.492	3.86	0.04	0.82	4nl8E	GO:0000166 GO:0003676 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0006260 GO:0006268 GO:0006269 GO:0008270 GO:0016787 GO:0032508 GO:0046872 GO:1990077
2	0.07	0.490	4.50	0.07	0.86	3gmzA	GO:0000050 GO:0001889 GO:0001938 GO:0004053 GO:0005615 GO:0005634 GO:0005737 GO:0005741 GO:0005829 GO:0006525 GO:0006527 GO:0007565 GO:0007568 GO:0009611 GO:0009635 GO:0010042 GO:0010043 GO:0010269 GO:0010963 GO:0014075 GO:0016787 GO:0016813 GO:0019547 GO:0030145 GO:0030324 GO:0032496 GO:0032964 GO:0033189 GO:0033197 GO:0042493 GO:0043005 GO:0043025 GO:0043200 GO:0043434 GO:0046686 GO:0046872 GO:0048545 GO:0048678 GO:0051597 GO:0060056 GO:0060135 GO:0070062 GO:0070207 GO:0070301 GO:0071222 GO:0071353 GO:0071377 GO:0071549 GO:0071560
3	0.07	0.490	4.36	0.08	0.85	5hj9A	GO:0004053 GO:0006525 GO:0016787 GO:0016813 GO:0046872
4	0.07	0.407	4.66	0.06	0.75	1hqfA	GO:0000050 GO:0001889 GO:0001938 GO:0004053 GO:0005615 GO:0005634 GO:0005737 GO:0005741 GO:0006525 GO:0007565 GO:0007568 GO:0009611 GO:0009635 GO:0010042 GO:0010043 GO:0010269 GO:0010963 GO:0014075 GO:0016787 GO:0016813 GO:0019547 GO:0030145 GO:0030324 GO:0032496 GO:0032964 GO:0033189 GO:0033197 GO:0042493 GO:0043005 GO:0043025 GO:0043200 GO:0043434 GO:0046686 GO:0046872 GO:0048545 GO:0048678 GO:0051597 GO:0060056 GO:0060135 GO:0070062 GO:0070207 GO:0070301 GO:0071222 GO:0071353 GO:0071377 GO:0071549 GO:0071560
5	0.07	0.493	4.22	0.06	0.86	1cb7B	GO:0003824 GO:0008152 GO:0016853 GO:0016866 GO:0019553 GO:0019670 GO:0031419 GO:0050097
6	0.07	0.446	4.67	0.04	0.82	4nasB	GO:0000287 GO:0015977 GO:0016829 GO:0016984 GO:0046872
7	0.07	0.492	3.91	0.04	0.82	4nl8A	GO:0000166 GO:0003676 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0006260 GO:0006268 GO:0006269 GO:0008270 GO:0016787 GO:0032508 GO:0046872 GO:1990077
8	0.07	0.435	4.81	0.04	0.81	3pzlB	GO:0016787 GO:0016813 GO:0046872
9	0.07	0.439	4.51	0.03	0.80	1gq6B	GO:0016787 GO:0016813 GO:0033050 GO:0033972 GO:0046872
10	0.07	0.388	4.66	0.03	0.73	4q3vC	GO:0000050 GO:0004053 GO:0006525 GO:0016787 GO:0016813 GO:0046872
11	0.07	0.437	4.23	0.07	0.77	2a0mA	GO:0046872
12	0.07	0.449	4.32	0.05	0.78	3lhlA	GO:0008783 GO:0016787 GO:0016813 GO:0046872
13	0.07	0.444	4.40	0.03	0.79	3m1rD	GO:0006547 GO:0006548 GO:0016787 GO:0016813 GO:0019556 GO:0019557 GO:0030145 GO:0046872 GO:0050415
14	0.07	0.414	4.54	0.13	0.77	2z0mA	GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
15	0.06	0.458	4.26	0.07	0.77	4v6h1	GO:0008152 GO:0009013 GO:0009450 GO:0016491 GO:0016620 GO:0055114
16	0.06	0.420	4.83	0.05	0.81	5elxA	GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0005634 GO:0005643 GO:0005737 GO:0006810 GO:0015031 GO:0016020 GO:0016787 GO:0031965 GO:0051028
17	0.06	0.367	4.21	0.06	0.63	1eyxA	GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015979 GO:0016020 GO:0018298 GO:0030089 GO:0055114
18	0.06	0.364	4.98	0.06	0.73	2p6rA

Consensus prediction of GO terms

Molecular Function	GO:0016810	GO:0046872
GO-Score	0.55	0.32
Biological Processes	GO:0009064	GO:0006520
GO-Score	0.37	0.37
Cellular Component	GO:0043005	GO:0005634	GO:0070062	GO:0005741	GO:0005615	GO:0043025	GO:1990077	GO:0005829
GO-Score	0.13	0.13	0.13	0.13	0.13	0.13	0.07	0.07

(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 result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.