I-TASSER results

Input Sequence in FASTA format

>protein (71 residues)
MTMTASVAKVTAARPEPSAAWAEARRRVRQRREDMLRHPAFLSKQLPAEPADDDGVAAVY
DIAIARRRRPA

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MTMTASVAKVTAARPEPSAAWAEARRRVRQRREDMLRHPAFLSKQLPAEPADDDGVAAVYDIAIARRRRPA
Prediction	CCCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCCCCCCEEEEHHHHHHHHCCC
Conf.Score	98654455566568887589999999999999999868667665689888887774344456666654789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MTMTASVAKVTAARPEPSAAWAEARRRVRQRREDMLRHPAFLSKQLPAEPADDDGVAAVYDIAIARRRRPA
Prediction	75344423413444464533145145424644653263233135614463376631111231222455568
	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

CCCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCCCCCCEEEEHHHHHHHHCCC
MTMTASVAKVTAARPEPSAAWAEARRRVRQRREDMLRHPAFLSKQLPAEPADDDGVAAVYDIAIARRRRPA

2qioA1

0.18

1.00

1.07

Env-PPAS

MELQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQESNDEELTACFETIKQEVGTIH

3onrA

0.22

0.20

0.92

1.02

Env-PPAS

VSV-YKVIDIIGTSPT-S--WEQAAAEAVQRARDSVDDRVARVIEQDMA-VDSAGK-ITYRIKVSFKMRPS

4y0lA

0.25

0.23

0.89

0.78

MUSTER

------PVQVLVRFDAGGASAPEHSQTIAAIRHRIAQAPNVVS--APPRFADDNGLSAVLTITWMRTQLPR

2qioA1

0.17

1.00

0.83

dPPAS

ELLQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQESNDEELTACFETIKQEVGTIH

2qioA1

0.18

1.00

0.78

wdPPAS

MELQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQESNDEELTACFETIKQEVGTIH

4y0lA

0.25

0.23

0.89

0.82

wMUSTER

------PVQVLVRFDAGGASAPEHSQTIAAIRHRIAQAPNVVS--APPRFADDNGLSAVLTITWMRTQLPR

2qioA1

0.22

0.21

0.96

0.65

wPPAS

M-LQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQPCDNDELTACFETIKQEVGT--

2qioA1

0.18

1.00

0.89

dPPAS2

MELQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQESNDEELTACFETIKQEVGTIH

2qioA1

0.18

1.00

0.83

PPAS

MELQGKTFVVMGVANQRSIAWGIARSLHNAAGERLERNVRELADTLEGQESNDEELTACFETIKQEVGTIH

3gr6D1

0.15

1.00

0.94

Env-PPAS

LAAENKTYVIMGIANKRSIAFGVAKVLDQLRKERSRKELEKLLEQLNQPEASDEEVINGFEQIGKDVGNID

(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=-1.42

Estimated TM-score = 0.54±0.15

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-1.92

Download Model 3

C-score=-3.57

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	3hpdA	0.557	3.26	0.087	0.887
2	3t33A	0.557	3.13	0.050	0.831
3	4l7qC	0.555	3.21	0.086	0.944
4	3j9pD	0.553	3.38	0.045	0.930
5	2a5uA	0.551	3.43	0.101	0.887
6	4gdhA	0.551	3.12	0.029	0.915
7	3gvcB	0.545	3.49	0.119	0.915
8	1l9xB	0.545	3.60	0.058	0.958
9	2dplA1	0.543	3.56	0.074	0.915
10	2e18A	0.542	3.05	0.061	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	0.10	3	3luhB	5GP	Rep, Mult	25,29
2	0.10	3	5ezmA	MPG	Rep, Mult	19,22
3	0.07	2	2v5kB	MG	Rep, Mult	49,61
4	0.07	2	5l1gD	GYB	Rep, Mult	21,28
5	0.07	2	2np5C	NDS	Rep, Mult	50,51,53,57
6	0.03	1	1i503	III	Rep, Mult	7,9,10,12,26,29,30,57
7	0.03	1	1e1cB	DCA	Rep, Mult	28,31
8	0.03	1	4h10B	NUC	Rep, Mult	23,26

	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	3gafA	0.521	3.67	0.030	0.887	1.1.1.159	NA
2	0.060	3cq0A	0.524	3.70	0.101	0.972	2.2.1.2	NA
3	0.060	3i1jA	0.518	3.63	0.090	0.915	1.1.1.-	NA
4	0.060	3gr6D	0.526	3.55	0.108	0.873	1.3.1.9	NA
5	0.060	1y5mA	0.518	3.58	0.030	0.901	1.1.1.146	NA
6	0.060	2e1rA	0.523	3.47	0.090	0.915	3.6.5.3	NA
7	0.060	2eggA	0.522	3.12	0.131	0.859	1.1.1.25	NA
8	0.060	2v5hB	0.531	3.52	0.091	0.930	2.7.2.8	NA
9	0.060	1sy7A	0.517	3.39	0.075	0.901	1.11.1.6	NA
10	0.060	2e76A	0.521	3.35	0.029	0.887	1.10.99.1	66
11	0.060	2vz8A	0.523	3.05	0.079	0.873	2.3.1.85	9,41
12	0.060	2eggB	0.401	3.94	0.113	0.817	1.1.1.25	NA
13	0.060	1gpmA	0.537	3.41	0.045	0.915	6.3.5.2	NA
14	0.060	2jfdA	0.392	4.35	0.059	0.859	2.3.1.85	32
15	0.060	1v8aA	0.557	3.26	0.087	0.887	2.7.1.50	NA
16	0.060	2cdqA	0.521	2.89	0.121	0.831	2.7.2.4	NA
17	0.060	2dplA	0.543	3.56	0.074	0.915	6.3.5.2	NA
18	0.060	2et6A	0.527	3.73	0.076	0.901	1.1.1.-	NA
19	0.060	3gvcB	0.545	3.49	0.119	0.915	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	0.511	3.37	0.04	0.92	2lxnA	GO:0000166 GO:0003921 GO:0003922 GO:0005524 GO:0005829 GO:0006164 GO:0006177 GO:0006541 GO:0016874
1	0.07	0.515	3.73	0.04	0.92	3dzvA	GO:0000166 GO:0000287 GO:0004417 GO:0005524 GO:0009228 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0046872
2	0.07	0.440	3.31	0.17	0.77	4ap9A	GO:0004647 GO:0006564 GO:0008152 GO:0016311 GO:0016791
3	0.07	0.557	3.13	0.05	0.83	3t33A	GO:0005886 GO:0009738 GO:0009787 GO:0010231 GO:0010427 GO:0019898 GO:0046872
4	0.07	0.458	3.97	0.04	0.90	4zdjA	GO:0000166 GO:0003883 GO:0005524 GO:0005886 GO:0006221 GO:0006541 GO:0016874 GO:0040007 GO:0044210
5	0.07	0.415	3.35	0.05	0.77	2vgeA	GO:0000122 GO:0003215 GO:0003229 GO:0003714 GO:0005634 GO:0005654 GO:0005737 GO:0005913 GO:0006351 GO:0006355 GO:0006915 GO:0008134 GO:0009791 GO:0030054 GO:0031076 GO:0035264 GO:0042633 GO:0042802 GO:0045171 GO:0045597 GO:0048871 GO:0060048 GO:0098609 GO:0098641 GO:1901796
6	0.07	0.385	4.21	0.08	0.87	1vjtA	GO:0000023 GO:0000166 GO:0003824 GO:0004553 GO:0004558 GO:0005975 GO:0008152 GO:0016616 GO:0016787 GO:0016798 GO:0032450 GO:0055114
7	0.07	0.413	3.10	0.07	0.68	4n5qB	GO:0005216 GO:0005261 GO:0005262 GO:0005887 GO:0006810 GO:0006811 GO:0006816 GO:0009266 GO:0009408 GO:0016020 GO:0016021 GO:0042636 GO:0043235 GO:0055085 GO:0070588 GO:0090280
8	0.07	0.435	4.14	0.10	0.86	3ct4A	GO:0004371 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0019563
9	0.07	0.453	3.70	0.06	0.92	3rssA	GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0016829 GO:0016853 GO:0046872 GO:0052855
10	0.07	0.395	3.46	0.11	0.69	4uucA	GO:0005622 GO:0016567 GO:0035556
11	0.07	0.435	3.68	0.09	0.89	3jrnA	GO:0005737 GO:0006952 GO:0007165 GO:0009506
12	0.07	0.381	3.83	0.04	0.72	3utmA	GO:0000139 GO:0000209 GO:0000775 GO:0000781 GO:0000784 GO:0000922 GO:0003950 GO:0005634 GO:0005643 GO:0005694 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0006471 GO:0006810 GO:0007049 GO:0007067 GO:0008270 GO:0015031 GO:0016020 GO:0016055 GO:0016740 GO:0016757 GO:0018105 GO:0018107 GO:0032212 GO:0042393 GO:0045944 GO:0046872 GO:0051028 GO:0051225 GO:0051301 GO:0051973 GO:0070198 GO:0070212 GO:0070213 GO:0090263 GO:1904355 GO:1904357 GO:1904743 GO:1904908
13	0.07	0.483	3.41	0.03	0.85	3nl2C	GO:0000166 GO:0003824 GO:0004417 GO:0004789 GO:0005829 GO:0009228 GO:0016310 GO:0046872
14	0.07	0.439	3.59	0.08	0.83	1n11A	GO:0005198 GO:0005200 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0006887 GO:0006888 GO:0007010 GO:0007165 GO:0008093 GO:0010638 GO:0014731 GO:0016020 GO:0016323 GO:0016529 GO:0019899 GO:0030018 GO:0030507 GO:0030673 GO:0031430 GO:0031672 GO:0042383 GO:0043005 GO:0045199 GO:0045211 GO:0051117 GO:0072661
15	0.07	0.451	3.63	0.03	0.83	2g02A
16	0.07	0.435	2.93	0.10	0.69	5iwrA	GO:0005216 GO:0005227 GO:0005262 GO:0005516 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006816 GO:0016020 GO:0016021 GO:0016324 GO:0055085 GO:0070509 GO:0070588
17	0.07	0.447	3.08	0.06	0.77	2etbA	GO:0005216 GO:0005262 GO:0005622 GO:0005737 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006816 GO:0008285 GO:0009408 GO:0012505 GO:0016020 GO:0016021 GO:0030027 GO:0042470 GO:0055085 GO:0070588
18	0.06	0.428	2.91	0.06	0.69	1k1aA	GO:0000060 GO:0002268 GO:0002315 GO:0002455 GO:0002467 GO:0003677 GO:0003700 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006974 GO:0007249 GO:0008134 GO:0009615 GO:0010225 GO:0019730 GO:0030198 GO:0030330 GO:0030674 GO:0032729 GO:0032996 GO:0033257 GO:0042088 GO:0042345 GO:0042536 GO:0042742 GO:0042771 GO:0042832 GO:0042981 GO:0043066 GO:0043234 GO:0045064 GO:0045082 GO:0045171 GO:0045415 GO:0045727 GO:0045892 GO:0045893 GO:0045944 GO:0048471 GO:0048536 GO:0051101 GO:0051457

Consensus prediction of GO terms

Molecular Function	GO:0032550	GO:0035639	GO:0032559
GO-Score	0.37	0.37	0.37
Biological Processes	GO:0006541	GO:0009787	GO:0006564	GO:0016310	GO:0009228	GO:0006177	GO:0016311	GO:0010231	GO:0009229	GO:0040007	GO:0044210
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0005886	GO:0019898	GO:0005829
GO-Score	0.13	0.07	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 Rv2395A

[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]