I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MVAADHRALGSNKSYPASQTAEAIWPPARTLRYDRQSPWLATGFDRRMSQTVTGVGVQNC
AVSKRRCSAVDHSSRTPYRR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MVAADHRALGSNKSYPASQTAEAIWPPARTLRYDRQSPWLATGFDRRMSQTVTGVGVQNCAVSKRRCSAVDHSSRTPYRR
Prediction	CCCHHHHHHCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
Conf.Score	98655555467888875444444377643344567897444666444444455556664454444445566778897789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MVAADHRALGSNKSYPASQTAEAIWPPARTLRYDRQSPWLATGFDRRMSQTVTGVGVQNCAVSKRRCSAVDHSSRTPYRR
Prediction	74345353246655243553162213334324354733222332444245314233254132445415424476544468
	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                  80

                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
MVAADHRALGSNKSYPASQTAEAIWPPARTLRYDRQSPWLATGFDRRMSQTVTGVGVQNCAVSKRRCSAVDHSSRTPYRR

4ru4A1

0.23

0.97

0.69

MUSTER

VTPAQFGAVGDGASHPLSERAQTVYPHAVAL--SDEIDWAALAVDSGAPVHIPGDYQINRGISSTGSLQIAGDGATSIIR

1idiA

0.21

0.17

0.85

0.82

dPPAS

--------IVCHTTATSPISAVTC-PPGENLCYRKM--WCDAFCSSRGKVVELGCA-ATCPSKKPYCCSTDKCNPHPKQR

1idiA

0.22

0.17

0.80

wdPPAS

--------IVCHTTATSPISAVTC-PPGENLCYRKM--WCDAFCSSRGKVVELG-----CAKKPYTCCSTDKCNPHPKQR

1r43A

0.29

0.25

0.88

0.77

wMUSTER

SVYDSLKNIGYIGDTPASYKENEID--AHFELHIEQGPILDENKA-----IVTGVAYNWQKV---TVHGVGHAGTTPLRK

4a18B

0.36

0.20

0.55

0.64

wPPAS

---------GANKTLNMKKR-------GRKIKQNRPLPWY------RYK---SDTNIRN---SKRR-----NWRRT-Y--

2lzeA

0.20

0.15

0.75

0.93

dPPAS2

--------MGAPVPYPDPL------EPRGGKHINN-----AEDYKHDMDLTYTDRDYKNCESYHKKDLAI-HHQHHHGGS

2lzeA

0.20

0.15

0.75

0.80

PPAS

--------MGAPVPYPDPL------EPRGGKHINN-----AEDYKHDMDLTYTDRDYKNCESYHKKDLAIHHQ-HHHGGS

4rxhB4

0.25

0.19

0.75

0.72

Env-PPAS

ALPVLAKLVYSLD----DEVIDACW----AISY------LSDGSNDKI-QAVIEAGI--P---RRLVELLMHASQTPALR

1ya5T

0.25

0.24

0.95

0.59

MUSTER

MATSE---LSSEVSEENSERREAFWAEWKDLTLEGSS-LHEEDTQRHETQGQSQVLVQRSPWLMMRMGILGRGLQLPYQR

2lzeA

0.18

0.15

0.82

0.81

dPPAS

--------MGAPVPYPDPL------EPRGGKHICAICGNNAEDYKHDMDLTYTDRDYKNCESYHKKDLAIHHQHHHGGSM

(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=-2.98

Estimated TM-score = 0.38±0.13

Estimated RMSD = 10.0±4.6Å

Download Model 2

C-score=-3.82

Download Model 3

C-score=-4.08

Download Model 4

C-score=-3.75

Download Model 5

C-score=-4.58

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	1tffA	0.489	3.52	0.029	0.812
2	2zfyA	0.478	3.49	0.061	0.812
3	4ksjA	0.464	3.54	0.043	0.838
4	4j72A	0.454	4.09	0.063	0.863
5	1yguB	0.452	3.90	0.113	0.800
6	2qdpA	0.451	3.87	0.069	0.812
7	3kh5A	0.448	4.63	0.052	0.925
8	3owaA	0.446	4.45	0.027	0.887
9	4ruwA	0.445	4.18	0.072	0.838
10	4k6mA1	0.444	3.12	0.123	0.713

(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	0.14	6	1sn5A	T3	Rep, Mult	13,71
2	0.07	3	3l74P	AZI	Rep, Mult	15,32
3	0.07	3	1r2rB	DMS	Rep, Mult	29,30,71,73
4	0.05	2	2gezF	CL	Rep, Mult	2,29,56
5	0.02	1	2p3oA	GTA	Rep, Mult	20,24,31,34
6	0.02	1	1smyF	MG	Rep, Mult	63,65
7	0.02	1	2cjzA	PTR	Rep, Mult	13,14,15,16,17,18,19
8	0.02	1	5cuyB	MG	Rep, Mult	34,64
9	0.02	1	3mmzA	CA	Rep, Mult	10,21
10	0.02	1	3kh5A	AMP	Rep, Mult	32,59,60,61,67,69
11	0.02	1	2xbmB	RQA	Rep, Mult	20,21,23,24,25

	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	1yguB	0.452	3.90	0.113	0.800	3.1.3.48	52
2	0.060	2h6eA	0.414	3.93	0.043	0.762	1.1.1.1	29,30
3	0.060	2ebaA	0.440	3.94	0.096	0.825	1.3.99.7	NA
4	0.060	2hwkA	0.416	3.87	0.057	0.738	3.4.11.1,2.7.7.48	40
5	0.060	2fh7A	0.442	3.92	0.091	0.825	3.1.3.48	NA
6	0.060	2dewX	0.423	4.55	0.070	0.863	3.5.3.15	NA
7	0.060	1wd8A	0.338	4.65	0.075	0.738	3.5.3.15	34
8	0.060	1jlnA	0.441	4.42	0.067	0.863	3.1.3.48	34
9	0.060	3enoA	0.435	4.07	0.065	0.850	3.4.24.57	NA
10	0.060	1r6aA	0.437	3.17	0.088	0.713	2.7.7.48	51
11	0.060	1larA	0.425	4.02	0.039	0.812	3.1.3.48	NA
12	0.060	2ivpA	0.403	3.90	0.043	0.800	3.4.24.57	16
13	0.060	2a3kA	0.447	3.87	0.095	0.825	3.1.3.48	NA
14	0.060	2hc1A	0.442	4.09	0.054	0.838	3.1.3.48	36
15	0.060	2gp0A	0.471	3.76	0.068	0.812	3.1.3.48	34,60,66
16	0.060	3evfA	0.434	3.21	0.123	0.713	2.7.7.48	10,54
17	0.060	2bijA	0.440	3.96	0.028	0.812	3.1.3.48	20
18	0.060	2r7oA	0.416	3.97	0.093	0.800	2.7.7.48	NA
19	0.060	2pbnA	0.425	4.21	0.080	0.787	3.1.3.48	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	0.443	4.09	0.06	0.82	3o4sA	GO:0004721 GO:0004725 GO:0005737 GO:0005829 GO:0005856 GO:0006470 GO:0009898 GO:0016311 GO:0016787 GO:0016791 GO:0035335
1	0.07	0.380	4.40	0.05	0.81	2ooqB	GO:0004721 GO:0004725 GO:0005886 GO:0006470 GO:0007155 GO:0007156 GO:0007165 GO:0007169 GO:0008013 GO:0009986 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0045294 GO:0045295 GO:0045296 GO:0070097
2	0.07	0.300	4.66	0.03	0.64	2c7sA	GO:0001750 GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0005911 GO:0005912 GO:0006470 GO:0007155 GO:0007165 GO:0007179 GO:0008013 GO:0008285 GO:0009986 GO:0010839 GO:0016020 GO:0016021 GO:0016311 GO:0016477 GO:0016787 GO:0016791 GO:0019901 GO:0030054 GO:0030336 GO:0030424 GO:0030425 GO:0031175 GO:0031256 GO:0034394 GO:0034614 GO:0034644 GO:0035335 GO:0043025 GO:0045295 GO:0045786 GO:0045892 GO:0048041
3	0.07	0.311	4.60	0.06	0.69	2nlkA	GO:0004721 GO:0004725 GO:0005001 GO:0005887 GO:0006470 GO:0007169 GO:0010633 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0042802 GO:0070062 GO:1903385
4	0.07	0.447	3.87	0.10	0.82	2a3kA	GO:0004721 GO:0004725 GO:0005737 GO:0005829 GO:0005856 GO:0006470 GO:0009898 GO:0016311 GO:0016787 GO:0016791 GO:0035335
5	0.07	0.440	3.96	0.03	0.81	2bijA	GO:0001784 GO:0001934 GO:0001975 GO:0002092 GO:0004721 GO:0004725 GO:0005783 GO:0005789 GO:0005829 GO:0006470 GO:0010976 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0030424 GO:0033160 GO:0035254 GO:0035335 GO:0035640 GO:0035902 GO:0042493 GO:0043025 GO:0043204 GO:0043407 GO:0051019 GO:1900273 GO:1901216 GO:1903492 GO:1903955 GO:1990635 GO:2001025
6	0.06	0.374	4.26	0.03	0.72	4ri5A	GO:0001784 GO:0004721 GO:0004725 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0008092 GO:0009898 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0017080 GO:0035335 GO:0045930 GO:0051045 GO:0051117 GO:0097421 GO:0098902 GO:2000649
7	0.06	0.315	4.95	0.04	0.75	5j8rA	GO:0002102 GO:0004721 GO:0004725 GO:0004726 GO:0005737 GO:0005829 GO:0005886 GO:0005925 GO:0006470 GO:0016311 GO:0016787 GO:0016791 GO:0017124 GO:0030054 GO:0035335 GO:0042058 GO:0042246 GO:0042995 GO:0071364
8	0.06	0.303	4.68	0.03	0.65	1rpmA	GO:0001937 GO:0004721 GO:0004725 GO:0005001 GO:0005737 GO:0005887 GO:0005911 GO:0005913 GO:0006470 GO:0007155 GO:0007156 GO:0007165 GO:0010596 GO:0010842 GO:0016020 GO:0016021 GO:0016311 GO:0016525 GO:0016787 GO:0016791 GO:0030027 GO:0031175 GO:0031290 GO:0035335 GO:0042493 GO:0042802 GO:0045296 GO:0045909 GO:0048471
9	0.06	0.425	4.02	0.04	0.81	1larA	GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0006470 GO:0007155 GO:0007185 GO:0007268 GO:0008201 GO:0010975 GO:0016020 GO:0016021 GO:0016311 GO:0016477 GO:0016787 GO:0016791 GO:0031102 GO:0032403 GO:0035335 GO:0035373 GO:0043005 GO:0043025 GO:0048679 GO:0070062 GO:1900121
10	0.06	0.442	4.34	0.05	0.85	3s3eA	GO:0004721 GO:0004725 GO:0004728 GO:0005001 GO:0005886 GO:0006470 GO:0007275 GO:0007399 GO:0007411 GO:0007417 GO:0007424 GO:0007616 GO:0008045 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0023014 GO:0030154 GO:0030424 GO:0035335 GO:0045177
11	0.06	0.325	4.60	0.00	0.69	4ikcA	GO:0004721 GO:0004725 GO:0006470 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0030154 GO:0035335 GO:0042472 GO:0045598 GO:0046856
12	0.06	0.301	4.99	0.05	0.68	2i75A	GO:0004721 GO:0004725 GO:0004726 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0008092 GO:0009898 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0035335
13	0.06	0.397	4.50	0.03	0.79	2i1yB	GO:0000302 GO:0001553 GO:0004725 GO:0005768 GO:0005794 GO:0005886 GO:0008021 GO:0009749 GO:0016020 GO:0016021 GO:0019221 GO:0030054 GO:0030073 GO:0030141 GO:0030424 GO:0030507 GO:0030658 GO:0031410 GO:0032868 GO:0035773 GO:0042995 GO:0043025 GO:0043204 GO:0043627 GO:0043679 GO:0045202 GO:0051020 GO:0051591 GO:1990502
14	0.06	0.397	4.16	0.04	0.75	5awxA	GO:0002244 GO:0004721 GO:0004725 GO:0005001 GO:0005576 GO:0005578 GO:0005615 GO:0005737 GO:0005886 GO:0005887 GO:0006470 GO:0007409 GO:0007413 GO:0007417 GO:0007420 GO:0007611 GO:0008285 GO:0008542 GO:0010812 GO:0010976 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0017134 GO:0021766 GO:0030027 GO:0030175 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0031226 GO:0032587 GO:0035335 GO:0043025 GO:0043197 GO:0045211 GO:0048146 GO:0048666 GO:0048709 GO:0048814 GO:0050731 GO:0070445 GO:0072534 GO:1900006 GO:1900149 GO:1901216 GO:2000171 GO:2001224
15	0.06	0.309	4.80	0.07	0.70	1l8kA	GO:0004721 GO:0004725 GO:0004726 GO:0005178 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005793 GO:0005886 GO:0006470 GO:0008285 GO:0008286 GO:0010804 GO:0010888 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0019905 GO:0030183 GO:0030217 GO:0030218 GO:0030971 GO:0035335 GO:0042059 GO:0042512 GO:0042518 GO:0042524 GO:0042527 GO:0042593 GO:0045650 GO:0045722 GO:0046627 GO:0050728 GO:0050860 GO:0050922 GO:0060334 GO:0060336 GO:0060339 GO:0061099 GO:0070104 GO:0070373 GO:1902202 GO:1902206 GO:1902212 GO:1902215 GO:1902227 GO:1902233 GO:1902237 GO:1903899 GO:2000587
16	0.06	0.438	4.22	0.03	0.82	1yguB	GO:0001915 GO:0001960 GO:0002244 GO:0002378 GO:0004721 GO:0004725 GO:0005001 GO:0005622 GO:0005886 GO:0005887 GO:0005925 GO:0006469 GO:0006470 GO:0006933 GO:0007166 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0030217 GO:0030890 GO:0035335 GO:0042100 GO:0042102 GO:0044770 GO:0045121 GO:0045860 GO:0048539 GO:0048864 GO:0050852 GO:0050853 GO:0050857 GO:0051209 GO:0051607 GO:0051726 GO:0070062 GO:2000473 GO:2000648
17	0.06	0.432	4.00	0.01	0.84	4fjvA	GO:0004843 GO:0005634 GO:0006508 GO:0008233 GO:0008234 GO:0016579 GO:0016787 GO:0019784 GO:0035871 GO:0036459 GO:0043130 GO:0070536 GO:0071108
18	0.06	0.435	3.76	0.07	0.79	2nv5A

Consensus prediction of GO terms

Molecular Function	GO:0042578
GO-Score	0.57
Biological Processes	GO:0006470
GO-Score	0.57
Cellular Component	GO:0005829	GO:0005856	GO:0009986	GO:0009898	GO:0005887	GO:0031256	GO:0043025	GO:0030425	GO:0070062	GO:0030424	GO:0001750	GO:0005912	GO:0005911
GO-Score	0.13	0.13	0.13	0.13	0.13	0.07	0.07	0.07	0.07	0.07	0.07	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 Rv2635

[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]