I-TASSER results

Input Sequence in FASTA format

>protein (136 residues)
MRYLPVSTRRIWVNPLCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDR
LDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRL
RITKPEAGRRSAEAKP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRYLPVSTRRIWVNPLCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP
Prediction	CCCCCCCCCEEEEEHCCCCCCCEEEEEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCC
Conf.Score	9888876556776544445654555678887654346778876899999999999999998755433368999999999999999867886467888888758978858874678888766897677775777589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRYLPVSTRRIWVNPLCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP
Prediction	7543434344220221243324333331212134334403243343024004204520530161304011134013004302424441413624202304742467314230342015314224652643356468
	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                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCEEEEEHCCCCCCCEEEEEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCC
MRYLPVSTRRIWVNPLCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP

1ltqA1

0.16

0.15

0.94

0.60

MUSTER

TIGCPGSGKSTWAREFINPGFYNINRDYRQSIAHEERDYTKKKEGIVTGQFDTAKSILYGGDSVKGVIISTNLNPERRLAWETFAKEYGW-KVEHK--FD--VPWTEL---VKRNSKRGTKAVPIDVLRSYKSREP

3koyE

0.19

0.15

0.76

0.68

dPPAS

--------------------------DDFQQRRAHLANL---SDEELQTRFWEMAEKIVDPLLDLGKKNTTPSIERSVLLRMGFS---SLEAKAIVDKTMDRGLMGKGAGHIVYKIAKEKNISVREAGLALSEGKY

3jszA1

0.30

0.20

0.65

0.77

wdPPAS

------------------------SNEL--KLRRFFSALNHTSEIDLHTLFDNLKSNL------------T---LGSIEHLQ------GSVTYAIIQELLKGADQKKIESFLKGAIKNVIHLTPNEINWNVAKAYP

1ygmA

0.26

0.20

0.77

0.62

wMUSTER

T-FFEKHHRK-W-DILLEKSTGVME------AMKVTS----EEKEQLSTAIDRMNEGLDAFIQLYNE--SEIDE--------------PLIQAELMKQARDMYGQEKLNEKLNTIIKQILSISVSEEGEK--ELVP

3jszA1

0.27

0.18

0.65

wPPAS

----------------------------------------SNELSKLRRFFSALNSEID-LHTL-FDNLKSNLTLGSIEHLQ------GSVTYAIIQELLKGADQKKIESFLKGAIKNVIHLTPNEINWNVAKAYP

3jszA1

0.26

0.18

0.67

0.91

dPPAS2

-------------------------SNELSKLRRFFSALNHTSEIDLHTLFDNLKSNLT---------------LGSIEHLQ-----EGSVTYAIIQELLKGADQKKIESFLKGAIKNVIHLTPNEINWNVAKAYP

3jszA1

0.27

0.18

0.65

0.60

PPAS

----------------------------------------SNELSKLRRFFSALNSEID-LHTL-FDNLKSNLTLGSIEHLQ-----EGSVTYAIIQELLKGADQKKIESFLKGAIKNVIHLTPNEINWNVAKAYP

4e5kA1

0.14

0.12

0.88

0.76

Env-PPAS

MLP------KLVITRVHEEILQLLAPHCELITNQTDSTL---TREEILRRCRDAQAMMAF---MPDRV--DADFLQACPELRVIGCALKGFDNFDVDACTARVPVRAVRLEIERCAAQNI--LQALAGERPINAVP

4e5kA1

0.14

0.12

0.88

0.60

MUSTER

MLP------KLVIHRVHEEILQLLAPHCELITNQTDSTL---TREEILRRCRDAQAMMAF---MPDRV--DADFLQACPELRVIGCALKGFDNFDVDACTARVPVRAVRLEIERCAAQNI--LQALAGERPINAVP

5d2sA

0.13

0.09

0.67

dPPAS

-----------------------------------------ETSEERAARLAKMSAYAAQRLANESPEQRATRLKRMSEYAAKRLSSETREQRAIRLARMSAYAARRLANETPAQRQARLLRMSAYAAKRQA----

(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=-4.12

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.3±3.8Å

Download Model 2

C-score=-4.72

Download Model 3

C-score=-4.74

Download Model 4

C-score=-4.88

Download Model 5

C-score=-4.64

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	5cwoA	0.554	4.26	0.088	0.904
2	3k7dA	0.553	3.93	0.076	0.846
3	5dn6A	0.549	4.04	0.090	0.809
4	5cwcA	0.539	4.18	0.083	0.868
5	5cwpA	0.529	4.49	0.117	0.875
6	5cwiA	0.528	4.35	0.098	0.890
7	4oojA	0.527	3.65	0.078	0.757
8	5cwfA	0.525	4.26	0.110	0.831
9	2wssA	0.524	3.93	0.081	0.809
10	1obrA	0.522	4.33	0.082	0.816

(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	0.11	7	1ji5A	FE	Rep, Mult	59,63
2	0.05	3	4il6H	CLA	Rep, Mult	54,58,61
3	0.05	3	2dqmA	BES	Rep, Mult	55,74,77,78,81,112,113
4	0.03	2	1mabA	ATP	Rep, Mult	75,76,77,78,79,80,119,128,129
5	0.03	2	1zzhB	ZN	Rep, Mult	79,82
6	0.03	2	1bqbA	CA	Rep, Mult	59,61,79
7	0.03	2	1h8eC	ADP	Rep, Mult	93,94,95,96,97,98,132,135
8	0.03	2	4evdA	CD	Rep, Mult	45,46,49
9	0.02	1	1obrA	CA	Rep, Mult	100,101,103,105,107
10	0.02	1	1aopA	SF4	Rep, Mult	61,64,66,114
11	0.02	1	2h1iB	CA	Rep, Mult	49,52
12	0.02	1	2wpdC	ATP	Rep, Mult	49,51,54,55,56
13	0.02	1	1tdiA	GSH	Rep, Mult	59,86
14	0.02	1	1fbmD	RTL	Rep, Mult	47,54
15	0.02	1	1ybaD	AKG	Rep, Mult	60,65
16	0.02	1	3m7kA	MG	Rep, Mult	100,118

	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	1espA	0.498	4.50	0.067	0.772	3.4.24.28	NA
2	0.060	1fx0A	0.504	4.16	0.073	0.787	3.6.3.14	NA
3	0.060	2v4jE	0.502	4.66	0.057	0.875	1.8.99.3	14,30
4	0.060	2z38A	0.494	4.31	0.044	0.765	3.2.1.14	NA
5	0.060	2gepA	0.510	4.58	0.067	0.853	1.8.1.2	NA
6	0.060	1uwyA	0.496	4.61	0.087	0.831	3.4.17.12	NA
7	0.060	1j36A	0.493	4.71	0.051	0.853	3.4.15.1	82
8	0.060	2qe7A	0.517	3.80	0.073	0.779	3.6.1.34	34
9	0.060	3cqlA	0.497	4.16	0.053	0.765	3.2.1.14	NA
10	0.060	1zg7A	0.486	4.55	0.035	0.801	3.4.17.2	NA
11	0.060	3bkkA	0.492	4.54	0.067	0.838	3.4.15.1	82
12	0.060	1s4bP	0.512	4.80	0.057	0.897	3.4.24.15	NA
13	0.060	1cnsA	0.489	4.29	0.053	0.757	3.2.1.14	73,79
14	0.060	1z8lA	0.491	4.35	0.016	0.772	3.4.17.21	73
15	0.060	2dqmA	0.509	4.22	0.061	0.765	3.4.11.2	NA
16	0.060	1nsaA	0.456	4.62	0.095	0.801	3.4.17.2	NA
17	0.060	1y791	0.512	4.48	0.072	0.890	3.4.15.5	NA
18	0.060	1ayeA	0.498	4.55	0.068	0.801	3.4.17.15	NA
19	0.060	1j38A	0.496	4.75	0.051	0.868	3.4.15.1	111

(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	0.22	0.511	4.05	0.08	0.79	2hldK	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005754 GO:0005758 GO:0005829 GO:0006626 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016820 GO:0016887 GO:0033178 GO:0042645 GO:0045261 GO:0046034 GO:0046933 GO:0046961
1	0.16	0.524	3.93	0.08	0.81	2wssA	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005753 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016820 GO:0033178 GO:0045261 GO:0046034 GO:0046933 GO:0046961
2	0.07	0.553	3.93	0.08	0.85	3k7dA	GO:0000166 GO:0000287 GO:0000820 GO:0005524 GO:0005829 GO:0008882 GO:0016740 GO:0016779
3	0.07	0.515	4.26	0.06	0.81	3oaaA	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961
4	0.07	0.504	4.16	0.07	0.79	1fx0A	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0045261 GO:0046034 GO:0046933 GO:0046961
5	0.07	0.513	4.18	0.08	0.81	2r9vA	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961
6	0.07	0.465	4.84	0.05	0.80	5bn4A	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
7	0.07	0.447	5.35	0.06	0.85	5d80B	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
8	0.07	0.442	5.23	0.09	0.85	3qiaA	GO:0000166 GO:0004518 GO:0004519 GO:0005524 GO:0006314 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016539 GO:0016787 GO:0016820 GO:0033178 GO:0046034 GO:0090305
9	0.07	0.457	5.18	0.10	0.83	3gqbA	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
10	0.07	0.427	4.87	0.06	0.77	1mabB	GO:0000166 GO:0000275 GO:0005509 GO:0005524 GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0006898 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0016887 GO:0030228 GO:0033178 GO:0045261 GO:0046034 GO:0046933
11	0.06	0.524	4.23	0.07	0.81	1skyB	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961
12	0.06	0.440	5.20	0.07	0.84	3vr4B	GO:0000166 GO:0005524 GO:0006810 GO:0006811 GO:0006814 GO:0015991 GO:0015992 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
13	0.06	0.377	5.66	0.04	0.78	3vr4F	GO:0005524 GO:0006810 GO:0006811 GO:0006814 GO:0015991 GO:0015992 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
14	0.06	0.420	4.57	0.08	0.69	1fx0B	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0045261 GO:0046034 GO:0046933
15	0.06	0.549	4.04	0.09	0.81	5dn6A	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961
16	0.06	0.394	4.75	0.05	0.68	3gqbB	GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
17	0.06	0.400	5.07	0.07	0.71	4nphA	GO:0000166 GO:0005524 GO:0005737 GO:0006754 GO:0006810 GO:0006811 GO:0009058 GO:0009405 GO:0015031 GO:0015992 GO:0016787 GO:0016887 GO:0030254 GO:0030257 GO:0030430 GO:0033644 GO:0043621 GO:0044128 GO:0046961 GO:0050714 GO:0051087 GO:1902600
18	0.06	0.517	3.80	0.07	0.78	2qe7A	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0046961	GO:0046933
GO-Score	0.47	0.43	0.43
Biological Processes	GO:0006605	GO:0072655	GO:0006839	GO:0007005	GO:0015986	GO:0015991
GO-Score	0.44	0.44	0.44	0.44	0.43	0.43
Cellular Component	GO:0045267	GO:0000275	GO:0009295	GO:0043232	GO:0031970	GO:0005759	GO:0071944
GO-Score	0.44	0.44	0.44	0.44	0.44	0.44	0.43

(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 Rv0095c

[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]