I-TASSER results

Input Sequence in FASTA format

>protein (50 residues)
MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ

Predicted Secondary Structure

Sequence	20 40 \| \| MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ
Prediction	CCHHHHHHHHHHHHHHHHHHHHEEEEEEEEHCCHHHHHHHCCCCHHHCCC
Conf.Score	95788999999999987776456688888645778999986565677689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ
Prediction	65232323233213333333131112020343556532462455464568
	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

                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHEEEEEEEEHCCHHHHHHHCCCCHHHCCC
MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ

3d1bA1

0.26

0.24

0.92

1.00

wMUSTER

NDLYINWLKSLSFFQTNSSCAEALVKVI-KLIDFSQVLQLVFSASEK---

2l6wA

0.14

0.10

0.72

1.00

PPAS

LPFKVVVISAILALVVLTIISLIILIMLWQKKPRYE--------------

5aonE

0.20

0.18

0.90

1.01

Env-PPAS

EKRVSNAVEFLLSRVRRTPTSSKVHFLKSKGLSAEEICEAF---TKVG--

2hpvA

0.24

1.00

0.71

MUSTER

KDFASQYIKAILNFIGVDQVDGLFIEIDHFPDRAEELLNTATKATEYGKT

2n7qA

0.09

0.08

0.92

0.85

dPPAS

----ASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY

2l6wA

0.14

0.10

0.72

0.87

wdPPAS

LPFKVVVISAILALVVLTIISLIILIMLWQKKPRYE--------------

5eduB4

0.20

0.14

0.70

0.97

wMUSTER

---QMSAFWYAVRTAVINAAS---------RQTVDAALAAA--QTNAAA-

3g9rA

0.23

0.14

0.60

0.87

wPPAS

LDNITNWLWYIKIEELKSKIKRI----EIKRIKK----------------

5eduB4

0.23

0.16

0.70

0.90

dPPAS2

---QMSAFWYAVRTAVINAAS--------GRQTVDAALAA----AQTNAA

5eduB4

0.24

0.16

0.68

0.97

PPAS

---QMSAFWYAVRTAVINAAS---------RQTVDAALAA----AQTNAA

(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=-1.94

Estimated TM-score = 0.48±0.15

Estimated RMSD = 6.5±3.9Å

Download Model 2

C-score=-2.83

Download Model 3

C-score=-4.27

Download Model 4

C-score=-1.97

Download Model 5

C-score=-2.66

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	3c6gB	0.657	1.62	0.041	0.860
2	2j7oA2	0.634	2.36	0.120	0.980
3	1q57A	0.621	2.75	0.085	0.920
4	2qagC	0.609	2.51	0.042	0.920
5	1xr2B1	0.599	2.86	0.061	0.980
6	3h6fR	0.591	2.10	0.133	0.900
7	1e0kA	0.589	2.52	0.087	0.880
8	2id3A	0.589	2.85	0.082	0.980
9	2zy4F3	0.588	2.92	0.083	0.960
10	2k0dX	0.586	2.54	0.128	0.880

(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	0.17	49	5e7cH	CLA	Rep, Mult	7,10,11,14
2	0.13	37	4xk8g	CLA	Rep, Mult	4,8
3	0.08	22	4l6vK	CLA	Rep, Mult	10,13,14,17,18,20
4	0.08	23	5sy7A	NUC	Rep, Mult	2,5,6,9
5	0.02	5	3v2d2	MG	Rep, Mult	15,19
6	0.01	4	2dr3A	ADP	Rep, Mult	28,29,30,32,33,37
7	0.01	3	4il6H	CLA	Rep, Mult	11,15,18
8	0.01	4	1jhgA	TRP	Rep, Mult	8,11,12,40,43,44,47
9	0.01	2	3rszB	GLC	Rep, Mult	16,17
10	0.01	2	3wmoP	BCL	Rep, Mult	20,21
11	0.01	4	5hhjB	GLY	Rep, Mult	38,41
12	0.01	2	1nm0A	SO4	Rep, Mult	33,35,39
13	0.00	1	2nr9A	PA6	Rep, Mult	23,27
14	0.00	1	1cgpA	NUC	Rep, Mult	2,4,47

	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	2veaA	0.550	2.72	0.163	0.840	2.7.13.3	NA
2	0.060	2acxA	0.550	3.78	0.042	0.940	2.7.11.16	30
3	0.060	1u22A	0.569	2.90	0.061	0.960	2.1.1.14	NA
4	0.060	1szqA	0.576	2.12	0.071	0.840	4.2.1.79	NA
5	0.060	1bqbA	0.560	2.14	0.047	0.780	3.4.21.19,3.4.24.29	NA
6	0.060	2nq5A	0.570	2.31	0.042	0.840	2.1.1.14	NA
7	0.060	2gq3A	0.552	2.53	0.065	0.920	2.3.3.9	NA
8	0.060	3hdlA	0.573	2.48	0.022	0.900	1.11.1.-	NA
9	0.060	1espA	0.490	3.62	0.085	0.900	3.4.24.28	8
10	0.060	2gblA	0.548	2.95	0.064	0.880	2.7.11.1	43
11	0.060	1eb6A	0.561	2.28	0.070	0.860	3.4.24.39	NA
12	0.060	3dojA	0.573	2.64	0.085	0.920	1.1.1.79	NA
13	0.060	1mj9A	0.549	2.34	0.095	0.840	2.3.1.48	6,35
14	0.060	1fj3A	0.412	3.75	0.102	0.800	3.4.24.27	NA
15	0.060	2gq1A	0.449	2.45	0.048	0.680	3.1.3.11	NA
16	0.060	1trlB	0.396	3.85	0.109	0.900	3.4.24.27	12,45
17	0.060	3c6gB	0.657	1.62	0.041	0.860	1.14.13.15	NA
18	0.060	3l24A	0.566	2.70	0.063	0.940	3.1.8.2,3.4.13.9,3.1.8.1	NA
19	0.060	1q57A	0.621	2.75	0.085	0.920	3.6.4.12	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	0.24	0.425	3.31	0.06	0.80	3kw4A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0031090 GO:0043231 GO:0046872 GO:0055114 GO:0070330
1	0.10	0.512	3.07	0.18	0.88	3v8dA	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006629 GO:0006699 GO:0006707 GO:0008123 GO:0008202 GO:0008203 GO:0016020 GO:0016125 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0042632 GO:0043231 GO:0046872 GO:0055114 GO:0070857 GO:0071333 GO:0071397
2	0.09	0.495	3.52	0.06	0.98	1z11A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005881 GO:0008202 GO:0008389 GO:0008392 GO:0008395 GO:0009804 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019373 GO:0019899 GO:0020037 GO:0031090 GO:0042738 GO:0043231 GO:0046226 GO:0046872 GO:0055114
3	0.08	0.657	1.62	0.04	0.86	3c6gB	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006766 GO:0008395 GO:0010038 GO:0010164 GO:0010212 GO:0016020 GO:0016491 GO:0016705 GO:0020037 GO:0030343 GO:0031090 GO:0036378 GO:0042359 GO:0043231 GO:0046872 GO:0055114
4	0.07	0.434	3.47	0.11	0.90	3awmA	GO:0005506 GO:0016705 GO:0020037 GO:0046872 GO:0055114
5	0.07	0.414	2.72	0.07	0.76	3juvA	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005886 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008398 GO:0016020 GO:0016021 GO:0016125 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033488 GO:0043231 GO:0046872 GO:0055114 GO:0070988
6	0.07	0.415	3.64	0.05	0.72	1izoA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
7	0.07	0.443	2.55	0.09	0.76	4uylA	GO:0004497 GO:0005506 GO:0008144 GO:0008168 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0020037 GO:0032259 GO:0035690 GO:0046872 GO:0055114
8	0.07	0.449	2.03	0.05	0.62	4ck8B	GO:0004497 GO:0005506 GO:0006629 GO:0006694 GO:0008202 GO:0008398 GO:0016020 GO:0016021 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0070988
9	0.07	0.558	2.58	0.02	0.96	5hdiA	GO:0004497 GO:0005506 GO:0005618 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
10	0.07	0.417	3.73	0.04	0.90	1uedA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0033072 GO:0046872 GO:0055114
11	0.07	0.517	2.85	0.09	0.94	5ikiB	GO:0004497 GO:0005506 GO:0005737 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
12	0.07	0.519	3.48	0.02	0.92	5d3uA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
13	0.07	0.453	3.63	0.09	0.86	3eqmA	GO:0002677 GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006694 GO:0006703 GO:0008209 GO:0008395 GO:0009055 GO:0010760 GO:0016020 GO:0016125 GO:0016491 GO:0016705 GO:0016712 GO:0019825 GO:0020037 GO:0046872 GO:0055114 GO:0060736 GO:0070330
14	0.07	0.446	3.14	0.07	0.66	3ejbH	GO:0004497 GO:0005506 GO:0009102 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
15	0.07	0.476	3.33	0.02	0.96	4tpnA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
16	0.07	0.433	3.58	0.10	0.82	2x5lA	GO:0004497 GO:0005506 GO:0005886 GO:0006707 GO:0008395 GO:0016491 GO:0016705 GO:0020037 GO:0036199 GO:0044117 GO:0046872 GO:0055114
17	0.07	0.461	2.18	0.05	0.62	3l4dB	GO:0004497 GO:0005506 GO:0008168 GO:0008398 GO:0016491 GO:0016705 GO:0020037 GO:0032259 GO:0046872 GO:0055114 GO:0070988
18	0.07	0.433	3.37	0.07	0.76	4j14A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006629 GO:0006699 GO:0006707 GO:0006805 GO:0007399 GO:0008202 GO:0008203 GO:0008395 GO:0016020 GO:0016021 GO:0016125 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033781 GO:0043231 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0005506	GO:0020037	GO:0016712
GO-Score	0.46	0.46	0.30
Biological Processes	GO:0055114	GO:0006629	GO:1901360
GO-Score	0.46	0.36	0.36
Cellular Component	GO:0031090	GO:0005789
GO-Score	0.42	0.42

(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 Rv0900

[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]