I-TASSER results

Input Sequence in FASTA format

>protein (111 residues)
MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGM
EGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKERLELIRSRRRG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKERLELIRSRRRG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCCCEEEHCCCCCCCCCCCHCCCCCCCEEHCCCCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCC
Conf.Score	987654455568866556679865785899999599968996577655799865579998556568999998889999898999998599999999999999999999759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKERLELIRSRRRG
Prediction	867341212233343244676243133340413057444141312541622740505334514247765566676533320241044224474045115511641375478
	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                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCCCEEEHCCCCCCCCCCCHCCCCCCCEEHCCCCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCC
MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKERLELIRSRRRG

2m4vA

1.00

0.71

3.91

MUSTER

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

8.80

dPPAS

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

7.62

wdPPAS

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

4.75

wMUSTER

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

4.51

wPPAS

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

14.35

dPPAS2

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

4.51

PPAS

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m4vA

1.00

0.71

3.74

Env-PPAS

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR--------------------------------

2m6oA

0.45

0.19

0.42

1.98

MUSTER

---------------------------QAVEYACEKGHRFEMPFSVEAEIPPEWECKCGAQALLVDGDGPEEKK-------------------------------------

2m6oA

0.45

0.19

0.42

4.84

dPPAS

---------------------------QAVEYACEKGHRFEMPFSVEAEIPPEWECKCGAQALLVDGDGPEEKK-------------------------------------

(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=-1.02

Estimated TM-score = 0.59±0.14

Estimated RMSD = 6.2±3.8Å

Download Model 2

C-score=-1.17

Download Model 3

C-score=-2.12

Download Model 4

C-score=-2.61

Download Model 5

C-score=-1.66

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	2m4vA	0.624	1.75	1.000	0.712
2	5g0iA	0.502	4.29	0.069	0.856
3	4bz5A	0.496	4.25	0.091	0.838
4	3cesA3	0.494	4.01	0.085	0.784
5	2vdcG1	0.494	3.93	0.042	0.793
6	3a7kA	0.491	4.08	0.032	0.793
7	2jafA	0.489	4.24	0.043	0.802
8	1e6eA2	0.485	3.77	0.077	0.757
9	3q5dA1	0.484	4.76	0.091	0.847
10	2yr4A	0.483	4.61	0.045	0.883

(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	0.08	4	1ocoB	HEA	Rep, Mult	97,98
2	0.06	3	3mnnG	MML	Rep, Mult	100,103,104
3	0.06	3	4reuD	MG	Rep, Mult	87,93
4	0.04	2	1sumB	FE	Rep, Mult	92,96
5	0.04	2	2h6bA	3C4	Rep, Mult	102,105
6	0.02	1	1urkA	FUC	Rep, Mult	8,12,18
7	0.02	1	3k7tA	GP7	Rep, Mult	51,52
8	0.02	1	3e27A	MG	Rep, Mult	47,57
9	0.02	1	1xupO	GOL	Rep, Mult	27,38,82
10	0.02	1	3lxvN	CO3	Rep, Mult	57,59
11	0.02	1	4rkuL	CLA	Rep, Mult	98,102
12	0.02	1	2zegB	IMD	Rep, Mult	19,49,83
13	0.02	1	1hotB	16G	Rep, Mult	84,88
14	0.02	1	2vdcG	SF4	Rep, Mult	9,10,11,101,102,106
15	0.02	1	1mbxA	YBT	Rep, Mult	84,95

	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	1pzhA	0.459	4.75	0.038	0.874	1.1.1.27	NA
2	0.060	2zbwB	0.460	4.32	0.043	0.775	1.18.1.2	97
3	0.060	1llcA	0.459	4.47	0.029	0.820	1.1.1.27	NA
4	0.060	1gq7E	0.439	4.76	0.063	0.775	3.5.3.22	NA
5	0.060	1f8rA	0.479	4.16	0.061	0.802	1.4.3.2	NA
6	0.060	1jnrA	0.480	4.37	0.040	0.838	1.8.99.2	NA
7	0.060	1sowB	0.448	4.54	0.062	0.820	1.1.1.27	NA
8	0.060	1uxiA	0.463	4.55	0.040	0.847	1.1.1.37	NA
9	0.060	1d4cA	0.470	4.42	0.030	0.829	1.3.99.1	NA
10	0.060	1xfkA	0.468	4.55	0.038	0.820	3.5.3.8	68
11	0.060	1smkA	0.468	4.76	0.028	0.874	1.1.1.37	NA
12	0.060	2dfdA	0.459	4.98	0.038	0.901	1.1.1.37	88
13	0.060	2jaeA	0.464	4.11	0.071	0.784	1.4.3.2	NA
14	0.060	1ldnA	0.460	4.75	0.038	0.856	1.1.1.27	NA
15	0.060	1uxgA	0.423	4.92	0.046	0.811	1.1.1.37	31
16	0.060	2ztgA	0.462	4.78	0.056	0.892	6.1.1.7	NA
17	0.060	1sevA	0.464	4.94	0.047	0.901	1.1.1.37	88
18	0.060	2jb2A	0.465	4.11	0.071	0.784	1.4.3.2	NA
19	0.060	2a0mA	0.469	4.46	0.068	0.802	3.5.3.8	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	0.58	0.624	1.75	1.00	0.71	2m4vA	GO:0001000 GO:0006351 GO:0006355 GO:0045893
1	0.07	0.494	4.01	0.09	0.78	3cesA	GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0016491 GO:0030488 GO:0050660 GO:0055114
2	0.07	0.378	5.06	0.06	0.72	2vqqA	GO:0000118 GO:0000122 GO:0001025 GO:0001047 GO:0001501 GO:0002076 GO:0003677 GO:0003682 GO:0003714 GO:0004407 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006338 GO:0006351 GO:0006355 GO:0006954 GO:0007399 GO:0008134 GO:0008270 GO:0008284 GO:0008285 GO:0010592 GO:0010832 GO:0010882 GO:0014894 GO:0014898 GO:0014911 GO:0016568 GO:0016575 GO:0016787 GO:0017053 GO:0019901 GO:0030017 GO:0030018 GO:0030183 GO:0030955 GO:0031594 GO:0031672 GO:0032041 GO:0033235 GO:0033558 GO:0033613 GO:0034983 GO:0040029 GO:0042113 GO:0042493 GO:0042641 GO:0042826 GO:0043234 GO:0043393 GO:0043433 GO:0043525 GO:0043565 GO:0044212 GO:0045668 GO:0045820 GO:0045892 GO:0045893 GO:0045944 GO:0046872 GO:0048661 GO:0048742 GO:0051091 GO:0051153 GO:0070491 GO:0070555 GO:0070932 GO:0070933 GO:0071260 GO:0071356 GO:0071374 GO:1903428
3	0.07	0.372	4.78	0.07	0.69	3c0zC	GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
4	0.07	0.426	4.91	0.03	0.82	2vvmA	GO:0005777 GO:0016491 GO:0055114
5	0.07	0.358	4.92	0.01	0.72	3q9bA	GO:0016787 GO:0046872
6	0.07	0.416	4.70	0.06	0.77	3bdvA	GO:0016787 GO:0046872
7	0.07	0.332	4.54	0.04	0.61	3nepX	GO:0003824 GO:0005975 GO:0006099 GO:0016491 GO:0016616 GO:0019752 GO:0030060 GO:0055114
8	0.07	0.396	4.86	0.08	0.72	3g5sA	GO:0005737 GO:0008033 GO:0008168 GO:0016491 GO:0016740 GO:0030698 GO:0032259 GO:0047151 GO:0050660 GO:0055114
9	0.07	0.463	4.09	0.05	0.77	4jn9A	GO:0000166 GO:0016491 GO:0055114
10	0.06	0.461	4.36	0.05	0.78	5ikkA	GO:0000122 GO:0000183 GO:0000775 GO:0000781 GO:0000790 GO:0004407 GO:0005634 GO:0005694 GO:0006348 GO:0006351 GO:0006355 GO:0016568 GO:0016575 GO:0016584 GO:0016787 GO:0030466 GO:0030702 GO:0030874 GO:0031078 GO:0031618 GO:0031934 GO:0032041 GO:0033553 GO:0035391 GO:0070824 GO:0070932 GO:1990707
11	0.06	0.422	4.77	0.08	0.79	2vhyB	GO:0000166 GO:0000286 GO:0001666 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0006524 GO:0016491 GO:0042853 GO:0046872 GO:0055114
12	0.06	0.349	5.08	0.05	0.71	3menB	GO:0016787 GO:0046872
13	0.06	0.425	4.69	0.03	0.80	1rp0A	GO:0005739 GO:0005829 GO:0006950 GO:0006974 GO:0008270 GO:0009228 GO:0009409 GO:0009507 GO:0009536 GO:0009570 GO:0009579 GO:0009941 GO:0010319 GO:0016491 GO:0018131 GO:0042803 GO:0046872 GO:0052837 GO:0055114
14	0.06	0.328	5.22	0.04	0.69	4bz5B	GO:0016787 GO:0046872
15	0.06	0.363	4.84	0.03	0.67	2apoA	GO:0000495 GO:0001522 GO:0003723 GO:0006396 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0031118 GO:0031119 GO:0031120 GO:0031429 GO:1990481
16	0.06	0.406	3.99	0.08	0.67	3wnbA	GO:0003746 GO:0006414
17	0.06	0.483	4.32	0.06	0.82	3c0yA	GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
18	0.06	0.308	4.64	0.03	0.59	3sfhA	GO:0000118 GO:0000122 GO:0000228 GO:0004407 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006333 GO:0006351 GO:0006355 GO:0007062 GO:0008134 GO:0016568 GO:0016575 GO:0016787 GO:0030544 GO:0031397 GO:0031647 GO:0032041 GO:0032204 GO:0046872 GO:0051879 GO:0070932 GO:0071922

Consensus prediction of GO terms

Molecular Function	GO:0001000
GO-Score	0.58
Biological Processes	GO:0045893
GO-Score	0.60
Cellular Component	GO:0044424
GO-Score	0.37

(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 Rv2050

[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]