I-TASSER results

Input Sequence in FASTA format

>protein (53 residues)
MLYLLLVLILATLIYLGWRAARAQMNRPKTRVIGPDDDPEFLRRLGHGDNNRS

Predicted Secondary Structure

Sequence	20 40 \| \| MLYLLLVLILATLIYLGWRAARAQMNRPKTRVIGPDDDPEFLRRLGHGDNNRS
Prediction	HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCC
Conf.Score	68999999999999999999984788998877799999899998778998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MLYLLLVLILATLIYLGWRAARAQMNRPKTRVIGPDDDPEFLRRLGHGDNNRS
Prediction	43313233333233322232244457445443334763351144236577778
	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

                   |                   |

Sec.Str
Seq

HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCC
MLYLLLVLILATLIYLGWRAARAQMNRPKTRVIGPDDDPEFLRRLGHGDNNRS

2ptfA2

0.30

0.28

0.94

1.09

MUSTER

IYAVIESLIAYTRAPLVLRERIAEMNRVARKVGGPR-EKEAMRRIIQALES--

2micA

0.07

0.04

0.55

0.99

dPPAS

YCSILAAVVVGLVAYIAFKRWNSSKQNKQ------------------------

2micA

0.07

0.04

0.55

1.07

wdPPAS

YCSILAAVVVGLVAYIAFKRWNSSKQNKQ------------------------

5a1uD9

0.13

0.11

0.87

1.22

wMUSTER

EAAFLART-QVSRVVKLWRENLSKVNQKAAESLAPTEYENLFPGLKE------

4u4cB

0.26

0.17

0.66

0.81

wPPAS

-----------TAPFV------TAPTTPPDKLVAPNSNPNELRAL-SDDDNDD

2micA

0.07

0.04

0.55

1.29

dPPAS2

YCSILAAVVVGLVAYIAFKRWNSSKQNKQ------------------------

2m20A

0.26

0.25

0.94

1.03

PPAS

GLVGALLLLLVVALGIGLFIRRRHIVRKRTRLL---QERELVEPLTPGEKLWS

2lzrA

0.11

0.09

0.83

1.30

Env-PPAS

IWQLLIIAVIVVLLFGPKKLGSIGSDLGAS--I-----KGFKKAMSDDEPK--

5a1uD9

0.13

0.11

0.87

1.07

MUSTER

EAAFLART-QVSRVVKLWRENLSKVNQKAAESLAPTEYENLFPGLKE------

2kncA

0.21

0.15

0.72

0.91

dPPAS

VGVLGGLLLLTILVLAMWKVGFFKRNRPPLEEDDEEGE---------------

(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=-1.68

Estimated TM-score = 0.51±0.15

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-2.23

Download Model 3

C-score=-4.82

Download Model 4

C-score=-5.00

Download Model 5

C-score=-1.64

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	3vvnA	0.658	2.90	0.077	0.943
2	1dowA	0.643	2.57	0.077	0.868
3	4z3nA	0.642	2.62	0.038	0.924
4	5cwoA1	0.642	2.96	0.075	0.943
5	4hkaA	0.642	2.23	0.041	0.868
6	2yyjA	0.642	2.93	0.096	0.981
7	4onsA1	0.641	2.18	0.058	0.830
8	5cwpA2	0.639	2.51	0.077	0.906
9	1u8vA	0.633	2.13	0.120	0.906
10	3fz7F	0.631	2.76	0.098	0.924

(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	0.12	75	3wmmW	CRT	Rep, Mult	15,16,19,20
2	0.11	63	4pj0I	CLA	Rep, Mult	9,10,12,13,16,17
3	0.11	68	4m32A	FE2	Rep, Mult	19,22,23
4	0.09	54	3wmn9	CRT	Rep, Mult	4,7,10,11,14
5	0.06	38	3jcuR	CLA	Rep, Mult	2,5,6,9,10,13
6	0.05	30	4r8hA	SP1	Rep, Mult	14,15,18
7	0.02	11	4ogqE	3WM	Rep, Mult	1,2,5,6
8	0.01	4	1z1nX	ZN	Rep, Mult	40,43
9	0.01	4	3af7X	PLL	Rep, Mult	18,22,27,30
10	0.01	8	1fz8C	2BM	Rep, Mult	17,20,21
11	0.00	2	3glnA	XE	Rep, Mult	13,14,32
12	0.00	2	1pmoF	TRS	Rep, Mult	17,18,21,30,31
13	0.00	3	3sphA	PIO	Rep, Mult	34,38,39,42

	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	1js6A	0.592	3.14	0.094	0.924	4.1.1.28	NA
2	0.060	1iayA	0.597	2.68	0.063	0.868	4.4.1.14	NA
3	0.060	1b8aA	0.589	2.96	0.000	0.924	6.1.1.12	NA
4	0.060	3b8eA	0.553	2.98	0.021	0.868	3.6.3.9	NA
5	0.060	1u8vA	0.633	2.13	0.120	0.906	5.3.3.3	NA
6	0.060	1fbvA	0.622	2.41	0.096	0.943	6.3.2.19	29
7	0.060	1d8yA	0.595	2.65	0.085	0.830	2.7.7.7	NA
8	0.060	1fiuA	0.599	2.72	0.040	0.943	3.1.21.4	NA
9	0.060	2bwjA	0.609	2.71	0.104	0.868	2.7.4.3	NA
10	0.060	1n1zA	0.588	3.62	0.059	0.962	5.5.1.8	18
11	0.060	1unbA	0.601	3.28	0.100	0.943	1.14.20.1	NA
12	0.060	3mebA	0.591	2.60	0.038	0.924	2.6.1.1	NA
13	0.060	1g12A	0.608	2.58	0.020	0.924	3.4.24.20	NA
14	0.060	1uofA	0.603	2.98	0.118	0.887	1.14.20.1	19
15	0.060	1ge7A	0.619	2.59	0.020	0.924	3.4.24.20	NA
16	0.060	1mo7A	0.377	3.36	0.095	0.623	3.6.3.9	31
17	0.060	1dmtA	0.593	2.68	0.042	0.887	3.4.24.11	NA
18	0.060	3bwnB	0.602	2.78	0.000	0.906	2.6.1.27	NA
19	0.060	1dc1B	0.605	2.78	0.143	0.924	3.1.21.4	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	0.12	0.664	2.96	0.08	0.94	3vvpA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
1	0.08	0.642	2.23	0.04	0.87	4hkaA	GO:0004833 GO:0006569 GO:0006727 GO:0016491 GO:0019441 GO:0019442 GO:0020037 GO:0046872 GO:0048072 GO:0051213 GO:0055114 GO:0070189 GO:1901216
2	0.07	0.642	2.62	0.04	0.92	4z3nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
3	0.07	0.518	2.45	0.06	0.85	1dowA	GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
4	0.07	0.562	2.38	0.04	0.83	1bbuA	GO:0000166 GO:0000287 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006430 GO:0016020 GO:0016874 GO:0046872
5	0.07	0.591	2.78	0.08	0.91	4iggB	GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034332 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0051015 GO:0051149 GO:0051291 GO:0071681 GO:0090136 GO:0098641 GO:2000146 GO:2001045 GO:2001240 GO:2001241
6	0.07	0.603	2.48	0.04	0.96	5c6nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
7	0.07	0.535	2.35	0.09	0.74	3bk9B	GO:0004833 GO:0006569 GO:0016491 GO:0019441 GO:0019442 GO:0020037 GO:0046872 GO:0051213 GO:0051289 GO:0055114
8	0.07	0.555	3.09	0.08	0.89	1e1tA	GO:0000166 GO:0000287 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006430 GO:0016020 GO:0016874 GO:0046872
9	0.07	0.527	3.01	0.12	0.85	4ffcA	GO:0003824 GO:0003867 GO:0008483 GO:0009448 GO:0016740 GO:0030170
10	0.07	0.516	2.93	0.06	0.87	4pw8E	GO:0004833 GO:0005829 GO:0006568 GO:0006569 GO:0016491 GO:0016597 GO:0019441 GO:0019442 GO:0019825 GO:0020037 GO:0046872 GO:0051213 GO:0055114
11	0.07	0.651	2.95	0.08	0.94	4mlbB	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
12	0.07	0.481	2.22	0.06	0.72	2noxB	GO:0004833 GO:0006569 GO:0009435 GO:0016491 GO:0019441 GO:0019805 GO:0020037 GO:0046872 GO:0051213 GO:0051260 GO:0055114
13	0.07	0.517	2.56	0.04	0.74	4p9tA	GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
14	0.07	0.615	2.53	0.04	0.89	4pw8C	GO:0004833 GO:0005829 GO:0006568 GO:0006569 GO:0016491 GO:0016597 GO:0019441 GO:0019442 GO:0019825 GO:0020037 GO:0046872 GO:0051213 GO:0055114
15	0.07	0.587	2.39	0.12	0.89	4k1nA	GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
16	0.07	0.533	2.86	0.02	0.77	3mktA
17	0.07	0.485	3.10	0.04	0.77	3cjmA	GO:0016020 GO:0016021
18	0.07	0.438	3.72	0.08	0.89	4boqA	GO:0004843 GO:0006508 GO:0006986 GO:0008233 GO:0008234 GO:0016787 GO:0030433 GO:0030968 GO:0031625 GO:0035523 GO:0035871 GO:0036459 GO:0046872 GO:0061578 GO:0070536 GO:0071108 GO:1904153 GO:1904265 GO:1990167 GO:1990168 GO:1990380

Consensus prediction of GO terms

Molecular Function	GO:0090484	GO:0015291
GO-Score	0.37	0.37
Biological Processes	GO:0044763	GO:0015893
GO-Score	0.37	0.37
Cellular Component	GO:0016021	GO:0005829	GO:0005915	GO:0014704	GO:0015629	GO:0005925	GO:0016342	GO:0001669	GO:0005794	GO:0016600	GO:0030027
GO-Score	0.18	0.13	0.07	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 Rv0530A

[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]