I-TASSER results

Input Sequence in FASTA format

>protein (72 residues)
MPKAAMAKPAAAEQATGYVVGGISPFGQRKRLRTVVDVSALSWDRVLRCRQTALGRHGGP
AGPDHLDQRDHR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MPKAAMAKPAAAEQATGYVVGGISPFGQRKRLRTVVDVSALSWDRVLRCRQTALGRHGGPAGPDHLDQRDHR
Prediction	CCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCEEHHHHHHHCCEEEHCCEHCCCCCCEEEHCCHHHHHHCC
Conf.Score	985544998999876698789989765557897444577887874444444456766677667988876579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MPKAAMAKPAAAEQATGYVVGGISPFGQRKRLRTVVDVSALSWDRVLRCRQTALGRHGGPAGPDHLDQRDHR
Prediction	754354254750473242331121133344523020141046244124332121232235042556356648
	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

CCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCEEHHHHHHHCCEEEHCCEHCCCCCCEEEHCCHHHHHHCC
MPKAAMAKPAAAEQATGYVVGGISPFGQRKRLRTVVDVSALSWDRVLRCRQTALGRHGGPAGPDHLDQRDHR

1wdvA

0.22

0.21

0.94

1.72

MUSTER

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

4.70

dPPAS

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRK----KVYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

3.21

wdPPAS

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

1.77

wMUSTER

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

1.85

wPPAS

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

6.34

dPPAS2

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

2.11

PPAS

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

1wdvA

0.22

0.21

0.94

2.26

Env-PPAS

GKPVRLARANEVVELTGYPVGGVPPVALPPNIVLVVDRILLSRKK----VYGGGGRENALLEFSPRELVEAT

3op6A

0.20

0.18

0.92

1.59

MUSTER

TSDLELATESEFEGKFAECDVGAPPFGNLYGLPVLVSTKLSAQDNIL----FNAGSHS-ELQLSFGDFEK-K

1dbxA

0.35

0.33

0.94

4.45

dPPAS

GVKKVEADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFE----TIYVSGGKRGLSVEIAPQDLAKVL

(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 3 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=0.62

Estimated TM-score = 0.80±0.09

Estimated RMSD = 2.2±1.7Å

Download Model 2

C-score=-2.25

Download Model 3

C-score=0.28

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	1wdvA	0.896	0.74	0.221	0.944
2	1dbxA	0.797	1.36	0.358	0.931
3	2dxaA	0.796	1.28	0.364	0.917
4	2cx5A	0.766	1.54	0.191	0.944
5	1vkiB	0.680	2.00	0.147	0.944
6	2j3lB1	0.672	2.17	0.103	0.917
7	3op6A	0.657	2.36	0.200	0.903
8	1vjfA	0.650	2.16	0.134	0.931
9	3memA1	0.567	2.42	0.131	0.847
10	5im3A3	0.523	3.29	0.015	0.861

(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	0.10	5	4i18H	CA	Rep, Mult	37,39
2	0.08	4	1xjfA	DTP	Rep, Mult	36,51,52,53,54,62,63,64
3	0.08	4	2z0xA	5CA	Rep, Mult	6,7,9,20,21,53,60
4	0.08	4	1shkA	MG	Rep, Mult	14,15,17
5	0.06	3	3i8gP	MG	Rep, Mult	16,17,23,42
6	0.04	2	5l43A	MG	Rep, Mult	64,67
7	0.02	1	2v0nA	GAV	Rep, Mult	21,22
8	0.02	1	2a19C	MG	Rep, Mult	44,64
9	0.02	1	2iyxA	MG	Rep, Mult	13,19,20
10	0.02	1	1mbxA	YBT	Rep, Mult	6,12

	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	3hm7B	0.469	3.61	0.063	0.792	3.5.2.5	NA
2	0.060	2ftwA	0.455	3.46	0.065	0.792	3.5.2.2	NA
3	0.060	1a5kC	0.467	3.81	0.069	0.847	3.5.1.5	NA
4	0.060	1mo7A	0.341	4.55	0.061	0.750	3.6.3.9	22,54
5	0.060	1jq5A	0.456	4.09	0.114	0.958	1.1.1.6	NA
6	0.060	2a1aB	0.463	3.84	0.000	0.847	2.7.11.1	8
7	0.060	3m6yA	0.471	3.78	0.088	0.847	4.1.3.16	25
8	0.060	3b8eA	0.347	4.29	0.071	0.694	3.6.3.9	NA
9	0.060	3d6nA	0.483	3.18	0.081	0.764	3.5.2.3	64
10	0.060	2v40A	0.398	4.25	0.106	0.833	6.3.4.4	12
11	0.060	2j3lB	0.672	2.17	0.103	0.917	6.1.1.15	NA
12	0.060	1ql6A	0.457	3.78	0.049	0.833	2.7.11.19,2.7.1.38	NA
13	0.060	3la4A	0.489	3.52	0.095	0.833	3.5.1.5	NA
14	0.060	2z00A	0.455	3.69	0.081	0.778	3.5.2.3	NA
15	0.060	2c30A	0.321	4.57	0.063	0.750	2.7.11.1	NA
16	0.060	1xrtA	0.361	4.25	0.071	0.750	3.5.2.3	NA
17	0.060	3ihnA	0.449	3.38	0.081	0.750	3.5.2.3	NA
18	0.060	1pumA	0.446	3.84	0.050	0.819	3.2.2.22	13
19	0.060	3e74B	0.458	3.69	0.031	0.792	3.5.2.5	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	0.22	0.896	0.74	0.22	0.94	1wdvA	GO:0002161 GO:0006450 GO:0016787
1	0.17	0.802	1.37	0.37	0.94	1dbuA	GO:0002161 GO:0005737 GO:0006412 GO:0006450 GO:0016829 GO:0043906
2	0.16	0.819	1.28	0.37	0.94	2dxaA	GO:0002161 GO:0005737 GO:0005829 GO:0006412 GO:0006450 GO:0016829 GO:0043906 GO:0043907
3	0.15	0.766	1.54	0.19	0.94	2cx5A	GO:0002161 GO:0006450
4	0.12	0.672	2.17	0.10	0.92	2j3lB	GO:0000166 GO:0002161 GO:0004812 GO:0004827 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006433 GO:0006450 GO:0016874
5	0.10	0.665	2.07	0.12	0.94	1vjfA	GO:0002161 GO:0003677 GO:0006450
6	0.10	0.683	2.33	0.19	0.93	3op6A	GO:0002161 GO:0006450
7	0.08	0.680	2.00	0.15	0.94	1vkiB	GO:0002161 GO:0006450
8	0.06	0.414	3.97	0.03	0.76	1vpbA	GO:0006508 GO:0008237
9	0.06	0.383	3.69	0.06	0.71	2ychA	GO:0000166 GO:0005524
10	0.06	0.356	4.80	0.04	0.82	3i5aA	GO:0000160 GO:0000166 GO:0005622
11	0.06	0.332	4.41	0.12	0.75	1y11A	GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0008289 GO:0009190 GO:0009268 GO:0009405 GO:0016829 GO:0016849 GO:0030145 GO:0035556 GO:0046872
12	0.06	0.334	4.61	0.09	0.75	2yjtD	GO:0000027 GO:0000166 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0008143 GO:0008186 GO:0010501 GO:0016787 GO:0033592 GO:0042254
13	0.06	0.325	3.90	0.15	0.56	2mswA	GO:0000160 GO:0005622 GO:0016301 GO:0016310
14	0.06	0.317	4.28	0.06	0.67	4cagA	GO:0016829 GO:0046872
15	0.06	0.318	4.95	0.01	0.76	1zc1A	GO:0000837 GO:0000839 GO:0005634 GO:0006511 GO:0030433 GO:0030970 GO:0031593 GO:0034098 GO:0043130 GO:0043161 GO:0051974 GO:0070651 GO:0071629 GO:0071712 GO:1900182 GO:1990112 GO:1990116
16	0.06	0.223	4.15	0.08	0.47	1n7eA	GO:0005102 GO:0005737 GO:0005783 GO:0005789 GO:0005886 GO:0007399 GO:0012505 GO:0014069 GO:0015031 GO:0016020 GO:0016358 GO:0030054 GO:0030159 GO:0043025 GO:0045202 GO:0045211
17	0.06	0.274	4.86	0.09	0.69	5dmzA	GO:0000166 GO:0000775 GO:0000776 GO:0000777 GO:0000942 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0007049 GO:0007059 GO:0007062 GO:0007063 GO:0007067 GO:0007093 GO:0007094 GO:0008283 GO:0016020 GO:0016032 GO:0016301 GO:0016310 GO:0016740 GO:0051301 GO:0051983 GO:0071173
18	0.06	0.356	3.58	0.14	0.62	1c0wB	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0046914 GO:0046983

Consensus prediction of GO terms

Molecular Function	GO:0043906	GO:0016829
GO-Score	0.30	0.30
Biological Processes	GO:0006450
GO-Score	0.59
Cellular Component	GO:0044444
GO-Score	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 Rv3224B

[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]