I-TASSER results

Input Sequence in FASTA format

>protein (68 residues)
MAVSVAAQKLRLALDMYEVGEQMQRMRLGRERPNADVVEIEAAIDAWRMTRPGAEEGDSA
GPTSTRFT

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MAVSVAAQKLRLALDMYEVGEQMQRMRLGRERPNADVVEIEAAIDAWRMTRPGAEEGDSAGPTSTRFT
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Conf.Score	94448999999999999999999999875668999744578889999867888666788888766679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MAVSVAAQKLRLALDMYEVGEQMQRMRLGRERPNADVVEIEAAIDAWRMTRPGAEEGDSAGPTSTRFT
Prediction	64343335414111412523641543434474463423404321431434444375467444564538
	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

                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
MAVSVAAQKLRLALDMYEVGEQMQRMRLGRERPNADVVEIEAAIDAWRMTRPGAEEGDSAGPTSTRFT

1qmiA1

0.29

0.28

0.97

0.88

MUSTER

IALAQGGQILRSALSLSITGQTITSIRAGRAKPGLLRQHLTAVKAATEIC--GATEGAELGSQRLLFR

2oblA2

0.17

0.16

0.96

0.69

dPPAS

SEHLRAAAECKKLIATYK--NPELLIRIGEYTMGQD-PEADKAIKNRKLIQQSTKDISSYEKTIESLF

2avuE1

0.21

0.16

0.78

0.76

wdPPAS

-SIVQEARDIQLAMELITLG----RLQM---------LESETQLSRGRLIKLYKERGSPPPKGMLPF-

1qmiA1

0.28

0.26

0.96

0.87

wMUSTER

LDGAQ-GQILRSALSLSITGQTITSIRAGRAKPGLLRQHLTAVKAATEIC--GATEGAELGSQRLLFR

2avuE1

0.28

0.19

0.68

0.65

wPPAS

-SIVQEARDIQLAMELITLG----RLQM---------LESETQLSRGRLIK---ERGSPPGP----F-

2oblA2

0.17

0.16

0.96

0.77

dPPAS2

SEHLRAAAECKKLIATYK--NPELLIRIGEYTMGQD-PEADKAIKNRKLIQQSTKDISSYEKTIESLF

2oblA2

0.17

0.16

0.93

0.80

PPAS

SEHLRAAAECKKLIATYK--NPELLIRIGEYTMGQD--EADKAIKNRKL-QQSTKDISSYEKTIESLF

3g36A

0.25

0.19

0.75

0.93

Env-PPAS

--VDLQSLPTRAYLDQTVVPILLQGAVLAKERPP-NPIEFLASYLLKNK--AQFED------------

4o89A1

0.21

0.97

0.78

MUSTER

MITSYGGQILRTSVALSTITGEIVNIRANRPNPGLRPQHLHAILALKHLA--NAEKGAHVGSRELVFI

2avuE1

0.16

0.13

0.81

0.69

dPPAS

-SIVQEARDIQLAMELITLGARLQMLESETQLS------RGRLIKLYKELR-----GSPPPKGMLPF-

(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=-2.06

Estimated TM-score = 0.47±0.15

Estimated RMSD = 7.5±4.3Å

Download Model 2

C-score=-3.20

Download Model 3

C-score=-4.62

Download Model 4

C-score=-3.81

Download Model 5

C-score=-2.01

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	2uy1A2	0.615	2.31	0.030	0.897
2	4yodA	0.596	2.62	0.061	0.897
3	4e6hA	0.594	2.50	0.015	0.897
4	2wpvC	0.592	2.95	0.092	0.897
5	3lpzA	0.591	3.20	0.090	0.941
6	2a2fX2	0.590	2.89	0.090	0.926
7	2ooeA	0.589	2.75	0.076	0.897
8	5l4kP	0.588	2.86	0.078	0.882
9	4rfsS	0.587	3.37	0.044	0.971
10	3urzA	0.584	2.65	0.063	0.882

(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	0.13	5	1g0iA	MN	Rep, Mult	36,55
2	0.07	3	5c2xB	CO3	Rep, Mult	11,46
3	0.07	3	4dmzA	MG	Rep, Mult	8,11
4	0.04	2	3mpjD	FAD	Rep, Mult	29,36,39
5	0.04	2	5komA	DMU	Rep, Mult	13,17
6	0.02	1	1imcB	MN	Rep, Mult	55,68
7	0.02	1	2r9eB	SDX	Rep, Mult	48,51
8	0.02	1	4nhvB	2O6	Rep, Mult	4,42
9	0.02	1	3aqtA	RCO	Rep, Mult	10,23,26,43,44,47
10	0.02	1	1egcC	FAD	Rep, Mult	16,18,23,25,26
11	0.02	1	3rf4A	ZN	Rep, Mult	41,45
12	0.02	1	4d2eC	78M	Rep, Mult	10,14
13	0.02	1	4ryoA	MPG	Rep, Mult	1,5

	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	2okcB	0.530	3.27	0.045	0.926	2.1.1.72	NA
2	0.060	2ix6E	0.552	3.37	0.065	0.853	1.3.3.6	NA
3	0.060	2il3A	0.528	3.64	0.119	0.897	2.5.1.18	NA
4	0.060	3f6fA	0.532	3.14	0.076	0.868	2.5.1.18	NA
5	0.060	1ivhA	0.530	3.55	0.062	0.897	1.3.99.10	43
6	0.060	1gq2A	0.532	3.13	0.082	0.838	1.1.1.40	NA
7	0.060	1wz2A	0.557	3.32	0.060	0.868	6.1.1.4	NA
8	0.060	2c3tC	0.528	3.20	0.118	0.897	2.5.1.18	5,10
9	0.060	2owmA	0.542	3.38	0.078	0.912	3.6.4.4	NA
10	0.060	1e6zB	0.542	3.50	0.048	0.882	3.2.1.14	NA
11	0.060	2c4mC	0.557	2.75	0.049	0.838	2.4.1.1	NA
12	0.060	3etdA	0.543	3.17	0.047	0.882	1.4.1.3	11
13	0.060	2c3nA	0.528	3.19	0.118	0.897	2.5.1.18	NA
14	0.060	1ljrA	0.551	3.04	0.044	0.897	2.5.1.18	NA
15	0.060	2gtqA	0.552	3.28	0.077	0.912	3.4.11.2	NA
16	0.060	3einA	0.533	3.03	0.091	0.868	2.5.1.18	NA
17	0.060	2jifA	0.537	3.38	0.075	0.926	1.3.99.-	NA
18	0.060	1lw1A	0.533	3.22	0.048	0.868	1.11.1.15	NA
19	0.060	2ix6A	0.552	3.37	0.065	0.853	1.3.3.6	NA

(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	0.10	0.598	2.58	0.01	0.90	4ebaA	GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005849 GO:0006378 GO:0006379 GO:0006396 GO:0006397 GO:0046982 GO:0072423
1	0.07	0.589	2.75	0.08	0.90	2ooeA	GO:0003729 GO:0005634 GO:0005654 GO:0006379 GO:0006396 GO:0006397 GO:0031123 GO:0044822
2	0.07	0.449	3.60	0.07	0.76	4lliA	GO:0000146 GO:0000166 GO:0001726 GO:0001750 GO:0003774 GO:0003779 GO:0005509 GO:0005516 GO:0005524 GO:0005737 GO:0005764 GO:0005769 GO:0005770 GO:0005777 GO:0005783 GO:0005794 GO:0005829 GO:0005882 GO:0005884 GO:0006582 GO:0006810 GO:0006887 GO:0006892 GO:0007268 GO:0007601 GO:0015031 GO:0016020 GO:0016192 GO:0016459 GO:0017137 GO:0030048 GO:0030050 GO:0030073 GO:0030141 GO:0030318 GO:0030426 GO:0031585 GO:0031982 GO:0031987 GO:0032252 GO:0032400 GO:0032402 GO:0032433 GO:0032593 GO:0032869 GO:0035371 GO:0042438 GO:0042470 GO:0042476 GO:0042552 GO:0042641 GO:0042759 GO:0043005 GO:0043025 GO:0043473 GO:0044822 GO:0048066 GO:0050808 GO:0051643 GO:0055037 GO:0070062 GO:0072659 GO:1903358
3	0.07	0.521	3.37	0.06	0.91	3jb9R	GO:0000245 GO:0000974 GO:0005634 GO:0005681 GO:0006396 GO:0006397 GO:0008380 GO:0045292 GO:0071004 GO:0071010 GO:0071011 GO:0071012 GO:0071013 GO:0071014
4	0.07	0.465	2.97	0.09	0.74	3dnmA	GO:0008152 GO:0016787
5	0.07	0.614	2.28	0.03	0.90	2uy1B	GO:0005634 GO:0005739 GO:0005829 GO:0005849 GO:0006378 GO:0006379 GO:0006396 GO:0006397 GO:0046982 GO:0072423
6	0.07	0.472	3.87	0.01	0.87	3cu7B	GO:0000187 GO:0001701 GO:0002376 GO:0004866 GO:0005102 GO:0005576 GO:0005579 GO:0005615 GO:0006935 GO:0006950 GO:0006954 GO:0006956 GO:0006957 GO:0006958 GO:0007166 GO:0007186 GO:0008009 GO:0010575 GO:0010760 GO:0010951 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0060326 GO:0070062 GO:0090197 GO:0098779
7	0.07	0.615	2.31	0.03	0.90	2uy1A	GO:0005634 GO:0005739 GO:0005829 GO:0005849 GO:0006378 GO:0006379 GO:0006396 GO:0006397 GO:0046982 GO:0072423
8	0.07	0.456	3.64	0.03	0.76	5hccA	GO:0000187 GO:0001701 GO:0002376 GO:0004866 GO:0005102 GO:0005576 GO:0005579 GO:0005615 GO:0006935 GO:0006950 GO:0006954 GO:0006956 GO:0006957 GO:0006958 GO:0007166 GO:0007186 GO:0008009 GO:0010575 GO:0010760 GO:0010951 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0060326 GO:0070062 GO:0090197 GO:0098779
9	0.07	0.437	3.86	0.07	0.74	2g50D	GO:0000166 GO:0000287 GO:0003824 GO:0004743 GO:0005524 GO:0005634 GO:0005737 GO:0006096 GO:0008152 GO:0016301 GO:0016310 GO:0016740 GO:0030955 GO:0046872
10	0.07	0.437	3.81	0.07	0.74	3me3B	GO:0000166 GO:0000287 GO:0001666 GO:0001889 GO:0003824 GO:0004743 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0005913 GO:0005929 GO:0006006 GO:0006096 GO:0006754 GO:0007584 GO:0008152 GO:0009629 GO:0010033 GO:0012501 GO:0014870 GO:0016301 GO:0016310 GO:0016740 GO:0023026 GO:0030955 GO:0031012 GO:0031100 GO:0031982 GO:0032868 GO:0042866 GO:0043209 GO:0043403 GO:0043531 GO:0044822 GO:0046872 GO:0061621 GO:0070062 GO:0098609 GO:0098641 GO:1903561
11	0.07	0.399	3.73	0.09	0.81	3wn6A	GO:0003824 GO:0004556 GO:0005509 GO:0005975 GO:0005983 GO:0005987 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
12	0.06	0.408	3.83	0.04	0.75	2ljaA	GO:0016491 GO:0055114
13	0.06	0.431	3.90	0.03	0.82	1h4pA	GO:0004338 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0006073 GO:0008152 GO:0009251 GO:0009277 GO:0009986 GO:0016787 GO:0016798 GO:0031505 GO:0071555
14	0.06	0.437	3.57	0.05	0.76	2ls5A	GO:0016491 GO:0055114
15	0.06	0.385	3.32	0.08	0.68	1vzyA	GO:0005737 GO:0006457 GO:0051082
16	0.06	0.436	3.39	0.06	0.75	2cfaA	GO:0006231 GO:0008168 GO:0009165 GO:0016740 GO:0032259 GO:0050660 GO:0050797
17	0.06	0.427	3.85	0.09	0.78	4nmuA	GO:0005886 GO:0015036 GO:0016020 GO:0016021 GO:0016209 GO:0016491 GO:0017004 GO:0045454 GO:0055114 GO:0098869
18	0.06	0.410	3.88	0.07	0.75	3hczA	GO:0016209 GO:0016491 GO:0016853 GO:0055114 GO:0098869

Consensus prediction of GO terms

Molecular Function	GO:0046982	GO:0003729	GO:0017137	GO:0005524	GO:0000146	GO:0005509	GO:0005516	GO:0003779
GO-Score	0.10	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0016071	GO:0010467	GO:0090501
GO-Score	0.43	0.43	0.32
Cellular Component	GO:0043231	GO:0044444
GO-Score	0.43	0.32

(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.

I-TASSER results for job id Rv0078B

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

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