I-TASSER results

Input Sequence in FASTA format

>protein (93 residues)
MPKSKVRKKNDFTVSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIGSQA
PTALNWMAQLGPWNYAIAFAFMITGLLLTMRWH

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MPKSKVRKKNDFTVSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIGSQAPTALNWMAQLGPWNYAIAFAFMITGLLLTMRWH
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHCCC
Conf.Score	987556676667888776777544689997558999999999999999999874899988765654665586568899999999999986779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MPKSKVRKKNDFTVSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIGSQAPTALNWMAQLGPWNYAIAFAFMITGLLLTMRWH
Prediction	766445554765546556554464766533401202232233333312200011435344454343145333210111323333223323428
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHCCC
MPKSKVRKKNDFTVSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIGSQAPTALNWMAQLGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

2.47

MUSTER

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

2.73

dPPAS

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

4.33

wdPPAS

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.51

3.03

wMUSTER

------------------------------VWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

4.29

wPPAS

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

8.28

dPPAS2

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

3.84

PPAS

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2mmuA

1.00

0.52

2.56

Env-PPAS

-----------------------------SVWFVSLFIGLMLIGLIWLMVFQL----------------LGPWNYAIAFAFMITGLLLTMRWH

2kseA

0.21

0.16

0.75

0.91

MUSTER

------------MGKFTQRLSLRVRL---------TLIFLILASVTWLLSSFVAWKQTEYREDMALAIVAGPWLVALPIMLIIMMVLLGRE--

2kseA

0.15

0.12

0.77

1.06

dPPAS

------------MGKFTQRLSLRVRL---------TLIFLILASVTWLLSSFVATDNWEYREDMALAIVAGQIPWLVALPIMLIIMMVLLGRE

(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=-0.82

Estimated TM-score = 0.61±0.14

Estimated RMSD = 5.5±3.5Å

Download Model 2

C-score=-1.68

Download Model 3

C-score=-1.85

Download Model 4

C-score=-1.42

Download Model 5

C-score=-1.13

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	5lp2B	0.689	2.93	0.141	0.903
2	2yfaA	0.689	2.75	0.060	0.892
3	2l7nA	0.683	2.53	0.071	0.860
4	2y44A	0.674	3.15	0.036	0.903
5	3i9wA	0.672	2.77	0.080	0.892
6	4e40A	0.670	2.86	0.071	0.882
7	1sumB	0.669	2.64	0.068	0.871
8	4dvyP4	0.669	2.79	0.022	0.903
9	3ug9A	0.667	3.13	0.103	0.903
10	4jioA	0.667	2.70	0.059	0.850

(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	0.30	113	2htnA	HEM	Rep, Mult	43,46,47,50,71,75,78,79,81,82
2	0.07	25	2yf3A	MN	Rep, Mult	42,45,77,80
3	0.05	17	4ryrA	MPG	Rep, Mult	43,46,47,50,74,78,81,85
4	0.04	13	3rifD	IVM	Rep, Mult	50,53,57,67,70,71,74,75,78
5	0.02	6	3re7A	CU	Rep, Mult	53,67,71
6	0.02	7	3aecD	HEM	Rep, Mult	43,46,47,50,78,81,85,86
7	0.01	4	3fyiA	DMU	Rep, Mult	30,34,83,87
8	0.01	4	3qblD	22B	Rep, Mult	38,42,76,80,83,84,87
9	0.01	3	3asoP	CDL	Rep, Mult	33,36,37,40,44
10	0.01	3	3lnmB	PGW	Rep, Mult	29,30,31,46
11	0.01	4	3ag3A	PEK	Rep, Mult	39,43,88
12	0.01	3	4d2eC	78N	Rep, Mult	89,92,93
13	0.01	4	1ow6A	III	Rep, Mult	73,76,77,80,83
14	0.00	2	3abkA	PEK	Rep, Mult	39,43,88,93
15	0.00	1	3k7tA	GP7	Rep, Mult	28,29
16	0.00	1	2wsc4	CLA	Rep, Mult	43,46,61
17	0.00	1	2o011	CLA	Rep, Mult	50,51

	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	0.090	1urfA	0.569	2.40	0.043	0.699	2.7.11.13	NA
2	0.060	2rf7D	0.611	2.92	0.047	0.871	1.7.2.2	32,85
3	0.060	3cxhN	0.609	2.95	0.106	0.828	1.10.2.2	36
4	0.060	1w27A	0.603	3.60	0.056	0.957	4.3.1.24	NA
5	0.060	3no9A	0.625	3.25	0.059	0.903	4.2.1.2	80
6	0.060	1t9gC	0.569	2.63	0.056	0.753	1.3.99.3	NA
7	0.060	1yfeA	0.624	3.27	0.035	0.903	4.2.1.2	NA
8	0.060	1occA	0.622	3.18	0.054	0.892	1.9.3.1	NA
9	0.060	3gtdA	0.623	3.29	0.035	0.903	4.2.1.2	NA
10	0.060	2uxwA	0.632	3.35	0.077	0.914	1.3.99.-	NA
11	0.060	1is2A	0.611	2.52	0.067	0.796	1.3.3.6	39
12	0.060	3d9dA	0.606	3.07	0.048	0.860	1.7.3.1	NA
13	0.060	3e04D	0.622	3.31	0.058	0.914	4.2.1.2	NA
14	0.060	3a68R	0.607	2.24	0.011	0.720	1.16.3.1	NA
15	0.060	1yfmA	0.623	3.30	0.035	0.903	4.2.1.2	NA
16	0.060	2ix6A	0.603	3.24	0.108	0.850	1.3.3.6	NA
17	0.060	3ipiA	0.606	3.01	0.080	0.828	2.5.1.-	NA
18	0.060	3gm1B	0.610	3.12	0.084	0.882	2.7.10.2	45
19	0.060	2fenD	0.634	3.14	0.072	0.882	5.5.1.2	NA
20	0.060	2ix6E	0.603	3.24	0.108	0.850	1.3.3.6	72

(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	0.25	0.669	2.64	0.07	0.87	1sumB	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
1	0.18	0.491	2.43	0.05	0.60	1zw0D	GO:0009405
2	0.17	0.518	2.12	0.11	0.67	3k9aA
3	0.17	0.560	2.16	0.10	0.66	3p30A
4	0.13	0.567	2.52	0.03	0.70	3cp1A	GO:0005198 GO:0019031
5	0.09	0.674	2.96	0.07	0.89	5jdoA	GO:0016020 GO:0016021
6	0.09	0.668	2.95	0.07	0.94	3dyjA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
7	0.08	0.566	2.49	0.04	0.70	3wfvA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
8	0.08	0.629	2.85	0.08	0.86	1t72A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
9	0.07	0.625	2.67	0.08	0.82	3i9yA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
10	0.07	0.672	2.77	0.08	0.89	3i9wA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006470 GO:0007165 GO:0009061 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016868 GO:0018106 GO:0023014 GO:0046777 GO:0071310
11	0.07	0.529	3.72	0.04	0.82	3o1jA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
12	0.07	0.623	3.13	0.10	0.92	5ic0A	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
13	0.07	0.587	3.06	0.04	0.84	4qiwA	GO:0003677 GO:0003899 GO:0006351 GO:0008270 GO:0016740 GO:0016779 GO:0046872
14	0.07	0.704	2.66	0.04	0.90	2yfbB	GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0016020 GO:0016021
15	0.07	0.552	2.35	0.09	0.69	2i0mA	GO:0005737 GO:0006810 GO:0006817 GO:0030643 GO:0042803 GO:0045936 GO:2000186
16	0.07	0.683	2.53	0.07	0.86	2l7nA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
17	0.07	0.458	3.69	0.08	0.73	4n56A	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
18	0.07	0.468	3.55	0.04	0.71	2ejtA	GO:0000049 GO:0003723 GO:0004809 GO:0008033 GO:0008168 GO:0016740 GO:0030488 GO:0032259
19	0.07	0.528	3.51	0.06	0.85	4dvyP	GO:0019534 GO:1901998
20	0.07	0.587	3.53	0.08	0.86	4q25A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0006935 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0050922 GO:0050928 GO:0055085 GO:0060326 GO:2000186
21	0.06	0.445	4.50	0.05	0.78	1k30A	GO:0004366 GO:0006629 GO:0006650 GO:0008152 GO:0008654 GO:0009507 GO:0009536 GO:0009570 GO:0016024 GO:0016740 GO:0016746
22	0.06	0.442	3.63	0.00	0.69	2o2dB	GO:0004347 GO:0005777 GO:0006094 GO:0006096 GO:0016853 GO:0020015
23	0.06	0.415	2.96	0.05	0.56	5e5wB	GO:0016020 GO:0016021 GO:0016032 GO:0016788 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036

Consensus prediction of GO terms

Molecular Function	GO:1901677	GO:0015081	GO:0015296	GO:0015114	GO:0042802	GO:0046983
GO-Score	0.51	0.51	0.51	0.51	0.51	0.51
Biological Processes	GO:0019220	GO:0006814	GO:0072502	GO:0055062	GO:2000185	GO:1903796	GO:0098662	GO:0010563	GO:0051704
GO-Score	0.51	0.51	0.51	0.51	0.51	0.51	0.51	0.51	0.35
Cellular Component	GO:0044424	GO:0071944	GO:0016020
GO-Score	0.51	0.51	0.38

(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 Rv0011c

[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]