I-TASSER results

Input Sequence in FASTA format

>protein (74 residues)
MNPGFDAVDQETAAAQAVADAHGVPFLGIRGMSDGPGDPLHLPGFPVQFFVYKQIAANNA
ARVTEAFLQNWAGV

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MNPGFDAVDQETAAAQAVADAHGVPFLGIRGMSDGPGDPLHLPGFPVQFFVYKQIAANNAARVTEAFLQNWAGV
Prediction	CCCCCCEEHHHHHHHHHHHHHHCCCEEEEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	99887544356899999999989988999997557998777776646788899999999999999999986689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MNPGFDAVDQETAAAQAVADAHGVPFLGIRGMSDGPGDPLHLPGFPVQFFVYKQIAANNAARVTEAFLQNWAGV
Prediction	86473423424321122114446121100121233444646357343333214421563224003301551577
	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

CCCCCCEEHHHHHHHHHHHHHHCCCEEEEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
MNPGFDAVDQETAAAQAVADAHGVPFLGIRGMSDGPGDPLHLPGFPVQFFVYKQIAANNAARVTEAFLQNWAGV

4g41A

0.29

0.27

0.92

1.86

MUSTER

AFSNVLAVEMEGAAIAQAAHTAGKPFIVVRAMSDTAAHDANIT-----FDQFIIEAGKRSAQILMTFLENLP-V

3dp9C2

0.21

0.19

0.89

1.01

dPPAS

HFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

3dp9C2

0.21

0.19

0.89

1.60

wdPPAS

HFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

4g41A

0.29

0.27

0.92

2.27

wMUSTER

AFSNVLAVEMEGAAIAQAAHTAGKPFIVVRAMSDTAAHDANIT-----FDQFIIEAGKRSAQILMTFLENLP-V

3dp9C2

0.21

0.19

0.89

1.95

wPPAS

IFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

3dp9C2

0.21

0.19

0.89

1.86

dPPAS2

HFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

3dp9C2

0.21

0.19

0.89

1.67

PPAS

HFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

3dp9C2

0.21

0.19

0.89

1.61

Env-PPAS

HFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESP-----LSFEEFLPLAAKSSSAMVLKMVELL---

3nm4A

0.21

0.19

0.89

1.84

MUSTER

SEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAG-----MSFDEFLEKSAHTSAKFLKSMVDEL---

4pr3A

0.27

0.24

0.91

0.76

dPPAS

AYERIEADVDETYACLRACQAVGVPLLGLRGISDGASTQH-----LHVIDEKLAGAVARVERAVADGLLSPS--

(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=-0.46

Estimated TM-score = 0.65±0.13

Estimated RMSD = 4.3±2.8Å

Download Model 2

C-score=-0.98

Download Model 3

C-score=-1.65

Download Model 4

C-score=-3.26

Download Model 5

C-score=-1.31

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	1nc3A	0.795	1.43	0.265	0.919
2	3eeiA	0.787	1.29	0.258	0.892
3	1zosA	0.777	1.42	0.313	0.905
4	4qezB	0.771	1.80	0.275	0.932
5	3dp9C	0.771	1.32	0.200	0.878
6	5dk6A	0.770	1.54	0.303	0.892
7	3nm4A	0.762	1.23	0.219	0.865
8	3bl6A	0.757	1.43	0.231	0.878
9	4l0mA	0.752	1.35	0.302	0.851
10	4jwtA	0.752	1.21	0.206	0.851

(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	0.48	23	3dp9A	BIG	Rep, Mult	8,9,10,11,33,34,49
2	0.04	2	3u40A	ADN	Rep, Mult	8,9,10,11
3	0.03	2	2xquB	CVM	Rep, Mult	57,61
4	0.02	1	3nm6B	TRS	Rep, Mult	9,10,11,30,49
5	0.02	1	3mnnG	PTW	Rep, Mult	61,62,65
6	0.02	1	1vf5S	III	Rep, Mult	67,68

	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	2qttA	0.676	2.33	0.188	0.932	3.2.2.16	NA
2	0.060	2dwoA	0.569	2.96	0.069	0.838	2.7.1.105,3.1.3.46	11,53
3	0.060	3dpsF	0.560	2.42	0.103	0.757	2.4.2.3	NA
4	0.060	3b8eA	0.611	2.79	0.014	0.932	3.6.3.9	NA
5	0.060	3ixzA	0.604	2.73	0.027	0.919	3.6.3.10	NA
6	0.060	1u1dA	0.663	2.22	0.091	0.892	2.4.2.3	NA
7	0.060	1yqqA	0.640	2.32	0.118	0.919	2.4.2.1	NA
8	0.060	1bifA	0.550	3.14	0.069	0.851	3.1.3.46,2.7.1.105	15,31,63
9	0.060	3bjeA	0.592	2.38	0.109	0.865	2.4.2.-	NA
10	0.060	1v4nB	0.635	2.38	0.058	0.919	2.4.2.28	NA
11	0.060	3ipiA	0.588	3.27	0.044	0.905	2.5.1.-	NA
12	0.060	1wtaA	0.610	2.91	0.113	0.960	2.4.2.28	NA
13	0.060	1k3fA	0.498	3.15	0.113	0.838	2.4.2.3	NA
14	0.060	1t8rA	0.688	2.32	0.203	0.932	3.2.2.4	11
15	0.060	2guwB	0.694	2.32	0.200	0.946	3.2.2.4	NA
16	0.060	1tcuC	0.624	2.59	0.087	0.932	2.4.2.1	NA
17	0.060	1k6mA	0.571	3.20	0.056	0.851	2.7.1.105,3.1.3.46	31,63
18	0.060	2p8uA	0.564	3.11	0.113	0.865	2.3.3.10	9
19	0.060	1fpsA	0.590	3.32	0.058	0.919	2.5.1.1,2.5.1.10	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	0.19	0.800	1.54	0.29	0.93	5dk6A	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
1	0.19	0.792	1.44	0.28	0.92	4g89A	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
2	0.18	0.787	1.29	0.26	0.89	3eeiA	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019284 GO:0019509
3	0.18	0.800	1.39	0.27	0.92	4f2pB	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
4	0.17	0.777	1.42	0.31	0.91	1zosA	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
5	0.17	0.796	1.39	0.19	0.92	4wkbA	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
6	0.16	0.763	1.21	0.22	0.86	4yo8B	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0009234 GO:0016787 GO:0019509 GO:0102246
7	0.16	0.774	1.36	0.29	0.88	4l0mA	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
8	0.16	0.794	1.25	0.19	0.91	4jwtA	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
9	0.15	0.757	1.43	0.23	0.88	3bl6A	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
10	0.14	0.771	1.80	0.28	0.93	4qezB	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
11	0.14	0.698	2.34	0.20	0.95	1t8rA	GO:0003824 GO:0005829 GO:0008152 GO:0008714 GO:0009116 GO:0016787 GO:0044209 GO:0046033
12	0.13	0.759	1.25	0.19	0.86	4josB	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
13	0.12	0.694	2.32	0.20	0.95	2guwB	GO:0003824 GO:0008152 GO:0008714 GO:0009116 GO:0016787 GO:0016798 GO:0044209 GO:0046033
14	0.12	0.689	2.01	0.20	0.89	3of3A	GO:0003824 GO:0004731 GO:0006139 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0042278
15	0.12	0.676	2.33	0.19	0.93	2qttA	GO:0000003 GO:0001944 GO:0003824 GO:0005829 GO:0005886 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0016787 GO:0019509
16	0.12	0.686	1.99	0.20	0.89	3occD	GO:0003824 GO:0004731 GO:0006139 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0042278
17	0.10	0.678	2.31	0.20	0.93	3bsfA	GO:0000003 GO:0001944 GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0016787 GO:0019509
18	0.10	0.619	2.68	0.19	0.92	2iscD	GO:0003824 GO:0004731 GO:0006139 GO:0009116

Consensus prediction of GO terms

Molecular Function	GO:0008782	GO:0008930
GO-Score	0.63	0.63
Biological Processes	GO:0009164	GO:0019509	GO:0019284
GO-Score	0.63	0.63	0.56
Cellular Component
GO-Score

(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 Rv2292c

[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]