I-TASSER results

Input Sequence in FASTA format

>protein (79 residues)
MVEIVAGKQRAPVAAGVYNVYTGELADTATPTAARMGLEPPRFCAQCGRRMVVQVRPDGW
WARCSRHGQVDSADLATQR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MVEIVAGKQRAPVAAGVYNVYTGELADTATPTAARMGLEPPRFCAQCGRRMVVQVRPDGWWARCSRHGQVDSADLATQR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHCHHHCCEEEEEEHCCCEEEEEHCCCCCCHHHHHCCC
Conf.Score	9887778888876567778988976788999678768999874477698789999668769998567875567754579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MVEIVAGKQRAPVAAGVYNVYTGELADTATPTAARMGLEPPRFCAQCGRRMVVQVRPDGWWARCSRHGQVDSADLATQR
Prediction	7444444635543433313331354366642442436151242064044403030324314241453352437525668
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHCHHHCCEEEEEEHCCCEEEEEHCCCCCCHHHHHCCC
MVEIVAGKQRAPVAAGVYNVYTGELADTATPTAARMGLEPPRFCAQCGRRMVVQVRPDGWWARCSRHGQVDSADLATQR

2kqpA

0.13

0.08

0.57

1.19

dPPAS2

FFYTKPTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRYCN----------------------------------

2l4zA

0.15

0.13

0.86

1.06

dPPAS2

VTVIDTKDGSQSKLGGGGSGGHMGSGGLSWKR-----------CAGCGGRFLLYAMDSYWHSRCLKCSSCQAQLGDIGT

2p3fN

0.15

0.14

0.91

0.84

MUSTER

YPECGENEWLDDCGTQKPCAKCNEEPPEEEDPICRSGCLLPPAC-VCKDGF-YRDTVIG---DCVREEECDQHEIIH--

2jraA

0.09

0.08

0.82

1.00

dPPAS

TASDRLGADPTQAASSPGGARAVSIVGNQIDSRELFTV---------DREIVIAHGDDRYRLRLTSQNKLILTK-----

2odxA

0.27

0.16

0.62

0.77

wdPPAS

--------MKDPIIIESYDDYTGSPAGSHTIMWLKPTVNEVARCWECGS--VYKLNPVG--------------------

5d5hA3

0.18

0.16

0.94

0.80

wMUSTER

FYFGGDHGVPDSVRSGGLKKLVGINLEGIDAREVNS---IKLFDDTHGRPIYVRVGKNGPYLERLVAG--DTGEPTPQR

2cr8A

0.24

0.14

0.57

0.80

wPPAS

------GSSGSSGSEDEWCTECKK-------------FNSPRYCFRC-RK--------DWYSDCSKHSGPSSG------

1y43A

0.19

0.08

0.41

1.06

dPPAS2

-EEYSSNWAGAVLIGDGYTKVTGEFTVPSVSAG----------------------------------------------

2jtnA2

0.17

0.15

0.87

0.93

PPAS

LIT---ENTQFDAANGI-----DDEGGSGGHMGSGGTPEIPM-CAGCDQRFILKALDRHWHSKCLKCSDCHVP-LAERC

1k9aB1

0.15

0.11

0.76

0.99

Env-PPAS

IQASWP---SGTECIAKY-NFHGTAEQD---------LP---FCK--GDVLTIVAVTKDYKAKNKREGIIPANYVQKR-

(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=-3.11

Estimated TM-score = 0.36±0.12

Estimated RMSD = 10.3±4.6Å

Download Model 2

C-score=-3.25

Download Model 3

C-score=-3.36

Download Model 4

C-score=-4.41

Download Model 5

C-score=-4.33

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	4nn2A	0.489	3.79	0.013	0.911
2	2irpA	0.473	4.02	0.107	0.861
3	3pl2A	0.471	3.87	0.026	0.823
4	3ie7A	0.469	4.02	0.025	0.861
5	3nokA	0.467	3.99	0.074	0.861
6	3mbrX	0.465	4.03	0.057	0.873
7	2f02A	0.464	4.28	0.152	0.886
8	4agiA	0.460	4.19	0.082	0.899
9	2fz0A	0.460	3.96	0.027	0.873
10	4c24A	0.459	4.08	0.027	0.823

(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	0.19	11	2vjeB	ZN	Rep, Mult	44,47,64,65
2	0.11	6	3raeD	NUC	Rep, Mult	71,72
3	0.07	4	1ofzA	FUL	Rep, Mult	65,67,68,69,73
4	0.07	4	1iucA	FUL	Rep, Mult	19,37,38,55,61
5	0.02	1	2cvxA	DGT	Rep, Mult	1,2,18,56
6	0.02	1	1zzdA	III	Rep, Mult	20,21,44,62
7	0.02	1	2ajrA	MG	Rep, Mult	33,37,39

	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	1gt7A	0.450	4.24	0.027	0.873	4.1.2.19	NA
2	0.060	1wyeA	0.442	3.99	0.081	0.848	2.7.1.45	NA
3	0.060	3dr2A	0.449	3.92	0.028	0.861	3.1.1.17	NA
4	0.060	3e7wA	0.415	4.32	0.064	0.861	6.1.1.13	50
5	0.060	2cu0A	0.438	3.84	0.103	0.810	1.1.1.205	NA
6	0.060	2z7bA	0.426	4.14	0.081	0.810	4.1.1.51	NA
7	0.060	1k9yA	0.439	4.00	0.055	0.785	3.1.3.7	NA
8	0.060	1utwF	0.445	4.06	0.056	0.886	3.2.1.26	70
9	0.060	2jg1A	0.451	3.83	0.063	0.835	2.7.1.144	NA
10	0.060	1zyzA	0.455	4.26	0.053	0.861	1.17.4.1	NA
11	0.060	2o6yA	0.438	3.61	0.045	0.747	4.3.1.-	NA
12	0.060	1oygA	0.397	3.82	0.043	0.797	2.4.1.10	NA
13	0.060	3cqdB	0.454	3.69	0.038	0.835	2.7.1.11	NA
14	0.060	3ec3A	0.444	4.05	0.070	0.835	5.3.4.1	NA
15	0.060	1e5eA	0.439	3.90	0.027	0.810	4.4.1.11	NA
16	0.060	1ebfA	0.424	3.74	0.043	0.759	1.1.1.3	NA
17	0.060	2wghB	0.430	4.23	0.042	0.861	1.17.4.1	NA
18	0.060	3ie7A	0.469	4.02	0.025	0.861	2.7.1.-	NA
19	0.060	3go6A	0.430	3.97	0.077	0.835	2.7.1.15	37

(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	0.10	0.436	3.94	0.18	0.85	1gqtB	GO:0000166 GO:0004747 GO:0005524 GO:0005737 GO:0005829 GO:0005975 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835 GO:0046872
1	0.07	0.489	3.79	0.01	0.91	4nn2A	GO:0000775 GO:0000776 GO:0000777 GO:0003677 GO:0005634 GO:0005654 GO:0005694 GO:0005730 GO:0006351 GO:0006355 GO:0008270 GO:0015631 GO:0019899 GO:0042393 GO:0042826 GO:0043021 GO:0044822 GO:0046872 GO:0051219 GO:0097110
2	0.07	0.476	3.81	0.03	0.82	3pl2A	GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0046835
3	0.07	0.449	3.74	0.10	0.84	3kzhA	GO:0016301 GO:0016310 GO:0016740
4	0.07	0.320	4.42	0.06	0.62	2qcvA	GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019310 GO:0047590
5	0.07	0.455	3.58	0.08	0.82	2c49A	GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
6	0.07	0.328	4.46	0.06	0.63	3n1cA	GO:0000166 GO:0000287 GO:0003872 GO:0005524 GO:0005829 GO:0005975 GO:0006096 GO:0006974 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0042802 GO:0046872 GO:0061615
7	0.07	0.474	4.02	0.11	0.86	2irpA	GO:0005737 GO:0008270 GO:0008652 GO:0009086 GO:0016829 GO:0019284 GO:0019509 GO:0046570 GO:0046872
8	0.07	0.331	4.22	0.03	0.65	3ljsB	GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773
9	0.07	0.442	3.99	0.08	0.85	1wyeA	GO:0000166 GO:0008673 GO:0016301 GO:0016310 GO:0016740 GO:0046835
10	0.07	0.363	4.72	0.06	0.73	4m6rA	GO:0005737 GO:0006915 GO:0008270 GO:0008652 GO:0009086 GO:0016829 GO:0019284 GO:0019509 GO:0042802 GO:0043066 GO:0046570 GO:0046872 GO:0070372
11	0.07	0.309	4.80	0.01	0.65	1vm7A	GO:0004747 GO:0005524 GO:0005737 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835
12	0.07	0.468	4.03	0.03	0.85	3q1yA	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:2001059
13	0.07	0.446	3.31	0.03	0.78	3in1A	GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
14	0.07	0.313	4.54	0.09	0.63	4gm6C	GO:0016301 GO:0016310 GO:0016740
15	0.07	0.445	4.19	0.03	0.85	2opiB	GO:0008738 GO:0016829
16	0.07	0.466	3.87	0.09	0.85	2f02A	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019512 GO:2001059
17	0.07	0.364	4.04	0.04	0.71	1pvtA	GO:0005829 GO:0008994 GO:0016829 GO:0016832 GO:0019323
18	0.07	0.431	4.27	0.08	0.85	2fk5A

Consensus prediction of GO terms

Molecular Function	GO:0016772	GO:0043169	GO:0032550	GO:0032559	GO:0035639
GO-Score	0.54	0.33	0.33	0.33	0.33
Biological Processes	GO:0006796	GO:0044262
GO-Score	0.54	0.33
Cellular Component	GO:0005829	GO:0005730	GO:0000777	GO:0005654
GO-Score	0.10	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 Rv1590

[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]