I-TASSER results

Input Sequence in FASTA format

>protein (63 residues)
MAFVDLRYPWCRGDGWISPPVVAVALGWAMRRKPFSRFNEYVGSASNTCWFARALELRTL
LIR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MAFVDLRYPWCRGDGWISPPVVAVALGWAMRRKPFSRFNEYVGSASNTCWFARALELRTLLIR
Prediction	CCEEHCCCCEHCCCCCCCCCEEEEEHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHC
Conf.Score	975555675555788788855566545677648747888765667663688899999999878
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MAFVDLRYPWCRGDGWISPPVVAVALGWAMRRKPFSRFNEYVGSASNTCWFARALELRTLLIR
Prediction	633342423214463214232201122312445325414522343543121242352442348
	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

CCEEHCCCCEHCCCCCCCCCEEEEEHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHC
MAFVDLRYPWCRGDGWISPPVVAVALGWAMRRKPFSRFNEYVGSASNTCWFARALELRTLLIR

2x27X

0.18

0.17

0.95

0.88

MUSTER

QVDVKGLLDGKLADIKQLPPTLLLQ--YYPMGGTNSAFQPYGGLGVNYTTFFDE-DLASNRKA

3j27B

0.20

0.19

0.97

0.94

dPPAS

MGLETATETWMSSEGAWKH--AQRIETWILRHPGFTIMAAILAYTIGTTHFQRALIFILLTAV

2m5zA

0.24

0.14

0.60

0.89

wdPPAS

--------------GAIA---LVAKFGWPIVKKYYKQIMQFIGEAINIDWIKKHI--------

4btgA

0.20

0.19

0.94

0.85

wMUSTER

SASMTSELLWEVGKGNIDPVMYALFFQYAQAGGALS-VDELV---NQFTEYHQSTACNPEIWR

2m5zA

0.24

0.14

0.60

0.67

wPPAS

--------------GAIA---LVAKFGWPIVKKYYKQIMQFIGEAINIDWIKKHI--------

2m5zA

0.18

0.11

0.62

1.02

dPPAS2

--------------GAIAK--LVAKFGWPIVKKYYKQIMQFIGEGWAIDWIKKHI--------

3j27B

0.22

0.21

0.94

0.80

PPAS

MG-LETATTWMSSEGWKHAQRI---ETWILRHPGFTIMAAILAYTIGTTHFQRALIFILLTAV

1qd7D2

0.25

0.22

0.90

0.85

Env-PPAS

AGEIILK-PASEGTGVIAGGPAAV-LELAGISDILSK---SIGS-NTPINMVRATFDGLKQLK

4btgA

0.20

0.19

0.94

0.74

MUSTER

SASMTSELLWEVGKGNIDPVMYALFFQYAQAGGALS-VDELV---NQFTEYHQSTACNPEIWR

2m5zA

0.09

0.06

0.68

0.94

dPPAS

----------------GAIAKLVAKFGWPIVKKYYKQIMQFIGEGWAINKIIDWIKKHI----

(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=-2.40

Estimated TM-score = 0.43±0.14

Estimated RMSD = 8.0±4.4Å

Download Model 2

C-score=-3.31

Download Model 3

C-score=-4.26

Download Model 4

C-score=-3.98

Download Model 5

C-score=-3.75

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	3vvnA	0.589	2.93	0.081	0.905
2	4lz6A	0.558	3.12	0.049	0.873
3	3mktA2	0.543	2.95	0.098	0.873
4	3k7dA3	0.540	3.18	0.032	0.889
5	4hukA	0.539	2.88	0.048	0.889
6	3e9lA	0.537	2.98	0.069	0.809
7	2pgsA	0.536	3.15	0.033	0.841
8	4z3nA	0.535	3.12	0.081	0.873
9	1l8wD	0.533	3.72	0.050	0.905
10	5klpA	0.533	3.20	0.133	0.873

(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	0.24	7	1iw7F	MG	Rep, Mult	57,58,61
2	0.10	3	5da5A	CA	Rep, Mult	53,56
3	0.06	2	4xk8K	CLA	Rep, Mult	55,62
4	0.06	2	2zo5A	HEC	Rep, Mult	17,20,22,26,34,38,39,42,43
5	0.03	1	3lg1A	NA	Rep, Mult	40,43,49
6	0.03	1	2jfsA	CAC	Rep, Mult	5,6,8,25

	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	3e47U	0.491	3.18	0.054	0.809	3.4.25.1	NA
2	0.060	1br2A	0.490	3.32	0.054	0.825	3.6.1.32	NA
3	0.060	2dknB	0.379	3.76	0.075	0.714	1.1.1.50	NA
4	0.060	1uliC	0.491	3.54	0.019	0.794	1.14.12.18	NA
5	0.060	2h7fX	0.509	3.05	0.051	0.841	5.99.1.2	NA
6	0.060	2dknA	0.501	3.60	0.155	0.857	1.1.1.50	NA
7	0.060	2c82B	0.468	3.47	0.050	0.841	1.1.1.267	18
8	0.060	1dofA	0.504	3.96	0.119	0.889	4.3.2.2	NA
9	0.060	1ezfB	0.495	2.42	0.065	0.682	2.5.1.21	54
10	0.060	3focA	0.505	3.24	0.066	0.857	6.1.1.2	NA
11	0.060	3bp1D	0.503	3.43	0.130	0.841	1.7.1.13	16,18,31
12	0.060	1txoB	0.521	3.28	0.103	0.857	3.1.3.16	21
13	0.060	1hqdA	0.419	3.43	0.035	0.714	3.1.1.3	NA
14	0.060	3bjxA	0.502	3.58	0.082	0.968	3.8.1.10	23
15	0.060	3bvlF	0.506	2.88	0.032	0.794	1.16.3.1	NA
16	0.060	2ts1A	0.493	3.56	0.051	0.794	6.1.1.1	44
17	0.060	3d6nB	0.513	3.62	0.033	0.905	2.1.3.2	NA
18	0.060	2lipA	0.415	3.83	0.034	0.746	3.1.1.3	3,5
19	0.060	1jilA	0.491	3.40	0.085	0.794	6.1.1.1	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	0.07	0.543	2.95	0.10	0.87	3mktA
1	0.07	0.535	3.12	0.08	0.87	4z3nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
2	0.07	0.569	3.00	0.08	0.90	3vvpA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
3	0.07	0.440	3.88	0.05	0.86	5c6nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
4	0.07	0.429	2.96	0.02	0.75	1v4aA	GO:0000166 GO:0000287 GO:0000820 GO:0005524 GO:0005829 GO:0008882 GO:0016740 GO:0016779
5	0.06	0.540	3.18	0.03	0.89	3k7dA	GO:0000166 GO:0000287 GO:0000820 GO:0005524 GO:0005829 GO:0008882 GO:0016740 GO:0016779
6	0.06	0.396	2.67	0.04	0.62	2ejeA	GO:0000981 GO:0003677 GO:0003700 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0007165 GO:0014886 GO:0016020 GO:0016525 GO:0042995 GO:0043025 GO:0051019 GO:0051481
7	0.06	0.352	4.36	0.07	0.83	1u3iA	GO:0004364 GO:0016740
8	0.06	0.454	3.58	0.02	0.73	4ffcA	GO:0003824 GO:0003867 GO:0008483 GO:0009448 GO:0016740 GO:0030170
9	0.06	0.434	2.50	0.04	0.59	2i9eB	GO:0003824 GO:0004807 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
10	0.06	0.491	3.16	0.08	0.86	5c6pA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
11	0.06	0.337	3.64	0.04	0.63	4wlpB	GO:0002020 GO:0003677 GO:0005634 GO:0005654 GO:0006281 GO:0006310 GO:0006351 GO:0006355 GO:0006366 GO:0006954 GO:0006974 GO:0031011
12	0.06	0.310	4.17	0.04	0.71	2kq2A	GO:0003676 GO:0004523 GO:0090502
13	0.06	0.586	3.03	0.08	0.92	4mlbB	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
14	0.06	0.339	3.31	0.04	0.59	3a0bE	GO:0005506 GO:0009055 GO:0009523 GO:0009539 GO:0009579 GO:0009767 GO:0015979 GO:0016020 GO:0016021 GO:0019684 GO:0020037 GO:0042651 GO:0046872 GO:0055114
15	0.06	0.331	2.98	0.02	0.54	4x5mB	GO:0005886 GO:0006810 GO:0008643 GO:0016020 GO:0016021
16	0.06	0.259	4.22	0.10	0.60	5a9zAS	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
17	0.06	0.277	1.05	0.03	0.30	1h88B	GO:0000779 GO:0000790 GO:0000977 GO:0000978 GO:0001077 GO:0001541 GO:0001889 GO:0001892 GO:0002432 GO:0003677 GO:0003682 GO:0003700 GO:0003705 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006366 GO:0006953 GO:0006954 GO:0006955 GO:0007613 GO:0008134 GO:0016363 GO:0019900 GO:0030154 GO:0030182 GO:0032496 GO:0032753 GO:0033598 GO:0034976 GO:0035035 GO:0035259 GO:0035711 GO:0036488 GO:0042130 GO:0042742 GO:0042803 GO:0042826 GO:0043524 GO:0043565 GO:0044212 GO:0044389 GO:0045408 GO:0045444 GO:0045600 GO:0045669 GO:0045670 GO:0045892 GO:0045893 GO:0045944 GO:0046982 GO:0050873 GO:0060644 GO:0060850 GO:0070059 GO:0071222 GO:0071230 GO:0071347 GO:0071407 GO:0072574 GO:0097421 GO:1990440
18	0.06	0.270	3.68	0.00	0.51	4yuuE2	GO:0005506 GO:0009055 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009539 GO:0009579 GO:0009767 GO:0015979 GO:0016020 GO:0016021 GO:0019684 GO:0020037 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0090484	GO:0015291
GO-Score	0.37	0.37
Biological Processes	GO:0044763	GO:0015893
GO-Score	0.37	0.37
Cellular Component	GO:0016021	GO:0005829
GO-Score	0.18	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.

I-TASSER results for job id Rv2307A

[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]