I-TASSER results

Input Sequence in FASTA format

>protein (69 residues)
MVPVETLHSGDPITDVNGGGQRYIVLESKTVGDSCVVLELESRVNHQLQVIEKSFPAGYH
VGRAHHRIL

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MVPVETLHSGDPITDVNGGGQRYIVLESKTVGDSCVVLELESRVNHQLQVIEKSFPAGYHVGRAHHRIL
Prediction	CCCCCCCCCCCCCCCCCCCCEEEEEEEEEHCCCCEEEEEEHCHCHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	986443567998754689976899998655689679999744445578988876788755677777779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MVPVETLHSGDPITDVNGGGQRYIVLESKTVGDSCVVLELESRVNHQLQVIEKSFPAGYHVGRAHHRIL
Prediction	744254246443144144444311103454344201113045415431431455243424244454436
	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

CCCCCCCCCCCCCCCCCCCCEEEEEEEEEHCCCCEEEEEEHCHCHHHHHHHHHHCCCCCCCCCCCCCCC
MVPVETLHSGDPITDVNGGGQRYIVLESKTVGDSCVVLELESRVNHQLQVIEKSFPAGYHVGRAHHRIL

2eyqA

0.21

0.20

0.97

0.83

MUSTER

IRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGIYLMLTYDAKLVSSLHLISR-YAGGAEENAPLHK-L

2lxwA

0.18

0.14

0.80

0.75

dPPAS

----GSEFTSSPRGDKAA----YDIL--RRCSQCGILLPLPILNQHQEKCRWLASSKGKQVRNFS----

3treA1

0.18

0.14

0.83

0.88

wdPPAS

THSTNEFRGGLKVVD----GDPCSIIDNEFVGQAFNRVKFRNLKT---RVLERTFKSGETLPAA-----

2eyqA

0.22

0.20

0.93

wMUSTER

IRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGIYLMLTYDAKLVSSLHLISR-----YAGGAEENAPL

3treA1

0.21

0.16

0.77

0.65

wPPAS

THSTNEFRGG--VVD----GDPCSIIDNEFVGQAFNRVKFRN-----LRVLERTFKSGETLPAA-----

5j3bA1

0.19

0.16

0.86

dPPAS2

NYSTNDFKPGLKVM-LDS--NPCSIMENEYVGQAFNRVKLRNLKTG--KVLEKTFKSGDTLEAA-----

3treA1

0.18

0.14

0.83

0.77

PPAS

THSTNEFRGGLKVVD----GDPCSIIDNEFVGQAFNRVKFRNLKT---RVLERTFKSGETLPAA-----

5j3bA1

0.19

0.16

0.86

1.04

Env-PPAS

NYSTNDFKPGLKV-MLD--SNPCSIMENEYVGQAFNRVKLRNLKTG--KVLEKTFKSGDTLEAA-----

3dmqA

0.21

0.20

0.96

0.76

MUSTER

DSPVTVFNPGDTITS-HDGWQ--QVEEVKEENGLLTYIGTRLDTEESGVALREVFLDSKLVFSKPQRLF

2lwjA1

0.18

0.16

0.90

0.75

dPPAS

SHMQTSFKTGDKAVYPGQGVGEVMGIEHTEVAGQFYVLRILE-NGMRIMI-----PIN-KVGSVGLREI

(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=-1.59

Estimated TM-score = 0.52±0.15

Estimated RMSD = 6.4±3.9Å

Download Model 2

C-score=-2.09

Download Model 3

C-score=-3.89

Download Model 4

C-score=-2.43

Download Model 5

C-score=-4.55

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	1uebA1	0.621	2.04	0.211	0.826
2	3a5zB1	0.596	2.35	0.193	0.826
3	3oyyA1	0.593	2.15	0.143	0.812
4	5j3bA	0.592	2.45	0.097	0.855
5	1iz6A	0.587	2.42	0.133	0.841
6	3treA	0.585	2.29	0.140	0.812
7	1xtdA	0.583	2.52	0.148	0.841
8	1bkbA	0.582	2.45	0.148	0.841
9	3cpfA	0.578	2.51	0.098	0.841
10	3er0A1	0.576	2.32	0.105	0.826

(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	7	3a0gB	OXY	Rep, Mult	46,50
2	0.07	4	2vytA	MLZ	Rep, Mult	15,18,21,40,48,51
3	0.06	3	1oczB	HEA	Rep, Mult	24,51
4	0.06	3	4zj0A	RET	Rep, Mult	2,54,56
5	0.04	2	2as8A	MG	Rep, Mult	24,25,27,39
6	0.04	2	1zivA	CA	Rep, Mult	6,7,11
7	0.02	1	2e26A	ZN	Rep, Mult	39,41
8	0.02	1	2nqaA	CA	Rep, Mult	15,16,18,20
9	0.02	1	1hm9A	CA	Rep, Mult	11,33
10	0.02	1	1uwwA	CA	Rep, Mult	11,12
11	0.02	1	3q2qA	CA	Rep, Mult	52,54
12	0.02	1	3fqiA	MG	Rep, Mult	33,39,40

	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	2g8eA	0.571	3.07	0.079	0.913	3.4.22.52	NA
2	0.060	2o6xA	0.545	3.35	0.106	0.942	3.4.22.15	NA
3	0.060	1cb5A	0.544	3.31	0.031	0.927	3.4.22.40	NA
4	0.060	3d6sA	0.530	3.46	0.061	0.927	3.4.22.65	NA
5	0.060	1yt5A	0.525	3.33	0.077	0.913	2.7.1.23	NA
6	0.060	1gecE	0.528	3.44	0.106	0.942	3.4.22.25	NA
7	0.060	1cqdA	0.539	3.49	0.104	0.957	3.4.22.67	NA
8	0.060	1pciA	0.536	3.11	0.063	0.899	3.4.22.30	NA
9	0.060	1cv8A	0.529	3.07	0.129	0.884	3.4.22.48	NA
10	0.060	1icfA	0.305	3.23	0.022	0.536	3.4.22.15	NA
11	0.060	1qxpB	0.549	3.23	0.111	0.913	3.4.22.53,3.4.22.52	45
12	0.060	7pckA	0.534	3.35	0.061	0.927	3.4.22.38	NA
13	0.060	2efmA	0.539	3.28	0.046	0.927	3.4.22.51	NA
14	0.060	2fo5A	0.529	3.54	0.090	0.957	3.4.22.-	NA
15	0.060	1xkgA	0.539	3.16	0.046	0.899	3.4.22.65	NA
16	0.060	1aecA	0.535	3.49	0.075	0.957	3.4.22.14	NA
17	0.060	7pckD	0.534	3.35	0.061	0.927	3.4.22.38	NA
18	0.060	1by8A	0.524	3.40	0.061	0.927	3.4.22.38	NA
19	0.060	1cqdC	0.539	3.49	0.104	0.957	3.4.22.67	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	0.26	0.585	2.35	0.07	0.84	3a5zD	GO:0003746 GO:0005737 GO:0005829 GO:0006412 GO:0006414 GO:0043022 GO:0043043
1	0.24	0.587	2.34	0.17	0.86	1uebA	GO:0003746 GO:0005737 GO:0006412 GO:0006414 GO:0043043
2	0.16	0.587	2.41	0.14	0.84	3treA	GO:0003746 GO:0005737 GO:0006412 GO:0006414 GO:0043043
3	0.14	0.584	2.47	0.12	0.84	5gakq	GO:0003723 GO:0003743 GO:0003746 GO:0005737 GO:0006412 GO:0006413 GO:0006414 GO:0006452 GO:0022626 GO:0043022 GO:0045901 GO:0045905 GO:0045948 GO:1903272
4	0.10	0.587	2.42	0.13	0.84	1iz6A	GO:0003723 GO:0003743 GO:0003746 GO:0005737 GO:0006412 GO:0006413 GO:0006452 GO:0043022 GO:0045901 GO:0045905
5	0.08	0.505	3.10	0.11	0.88	2eifA	GO:0003723 GO:0003743 GO:0003746 GO:0005737 GO:0006412 GO:0006413 GO:0006452 GO:0043022 GO:0045901 GO:0045905
6	0.07	0.521	2.67	0.14	0.86	3oyyA	GO:0003746 GO:0005737 GO:0006412 GO:0006414 GO:0043043
7	0.07	0.575	2.57	0.11	0.86	1ybyB	GO:0003746 GO:0005737 GO:0006412 GO:0006414 GO:0043043
8	0.07	0.578	2.31	0.13	0.84	5j3bB	GO:0003746 GO:0005737 GO:0006412 GO:0006414 GO:0043043
9	0.07	0.565	2.60	0.12	0.84	5dlqF	GO:0003723 GO:0003746 GO:0005634 GO:0005642 GO:0005643 GO:0005737 GO:0005783 GO:0005789 GO:0005829 GO:0006406 GO:0006412 GO:0006414 GO:0006452 GO:0006611 GO:0006810 GO:0006913 GO:0006915 GO:0008284 GO:0008612 GO:0015031 GO:0016020 GO:0017070 GO:0043022 GO:0044822 GO:0045901 GO:0045905 GO:0047485 GO:0051028 GO:0070062
10	0.07	0.522	2.49	0.11	0.78	3j9zLN	GO:0002181 GO:0003723 GO:0003735 GO:0005622 GO:0005829 GO:0005840 GO:0006412 GO:0008270 GO:0015934 GO:0016740 GO:0019843 GO:0022625 GO:0030529
11	0.07	0.417	3.99	0.10	0.84	2f1mC	GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015721 GO:0016020 GO:0030288 GO:0031226 GO:0042802 GO:0046677 GO:0055085
12	0.07	0.470	3.59	0.05	0.81	4lk4A	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016787
13	0.06	0.537	2.42	0.13	0.78	4wfbA	GO:0002181 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015934 GO:0016740 GO:0019843 GO:0022625 GO:0030529
14	0.06	0.343	4.21	0.08	0.65	5ijaA	GO:0006508 GO:0008047 GO:0008233 GO:0043085
15	0.06	0.396	3.61	0.05	0.78	2f1mD	GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015721 GO:0016020 GO:0030288 GO:0031226 GO:0042802 GO:0046677 GO:0055085
16	0.06	0.398	2.96	0.02	0.65	5bweB	GO:0046872 GO:0051536 GO:0051539
17	0.06	0.339	4.25	0.09	0.65	1cx4A	GO:0000166 GO:0001932 GO:0004862 GO:0005737 GO:0005743 GO:0005813 GO:0005886 GO:0005952 GO:0006631 GO:0007612 GO:0008603 GO:0016020 GO:0019901 GO:0019904 GO:0030425 GO:0030552 GO:0031625 GO:0034236 GO:0043025 GO:0043197 GO:0043198 GO:0045121 GO:0045859 GO:0048471 GO:0070062 GO:0097332 GO:0097338 GO:0097546 GO:2000480

Consensus prediction of GO terms

Molecular Function	GO:0003746	GO:0043022
GO-Score	0.64	0.43
Biological Processes	GO:0006448	GO:0006449	GO:0045727	GO:0043243
GO-Score	0.46	0.46	0.46	0.46
Cellular Component	GO:0044444
GO-Score	0.51

(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 Rv0108c

[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]