I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MMDVLAAGIAAGALTLAAWGAWRPHYRAASYLVAGAVELALIGLLVVTGQTLMAISVAFL
VALGGPLVVVNHRRAERSRG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MMDVLAAGIAAGALTLAAWGAWRPHYRAASYLVAGAVELALIGLLVVTGQTLMAISVAFLVALGGPLVVVNHRRAERSRG
Prediction	CCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHEEHCCCEEEHHHHHHHHHCCCEEEEEEEEHHHCCC
Conf.Score	85699999998789999977788544676665545445576644545478444467888998779789997443455479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MMDVLAAGIAAGALTLAAWGAWRPHYRAASYLVAGAVELALIGLLVVTGQTLMAISVAFLVALGGPLVVVNHRRAERSRG
Prediction	74422432333223312222323332421322123313131211111334332213213333341221013344365768
	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

CCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHEEHCCCEEEHHHHHHHHHCCCEEEEEEEEHHHCCC
MMDVLAAGIAAGALTLAAWGAWRPHYRAASYLVAGAVELALIGLLVVTGQTLMAISVAFLVALGGPLVVVNHRRAERSRG

5ezmA3

0.23

1.00

0.95

MUSTER

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTVLGHETVGRPAS

5ezmA3

0.21

1.00

0.65

dPPAS

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTVALLGHETVGRP

5ezmA3

0.25

0.24

0.95

0.71

wdPPAS

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTVLGHRPAS----

5ezmA3

0.25

0.24

0.94

0.90

wMUSTER

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTV-GHRPAS----

5ezmA3

0.27

0.25

0.93

0.73

wPPAS

MAIVAACGLLASPVVATL-NANHPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTV-GHRPAS----

5ezmA3

0.23

0.21

0.94

0.70

dPPAS2

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTV-----ALLGHE

5ezmA3

0.23

1.00

0.94

PPAS

MAIVAACGLLASPVVATLNANHIPNYRAYAVWVAVAFVVMLLGIAVLLRRGVLPSVAVYAMGMYLGFTVLGHETVGRPAS

1ku9A1

0.16

0.15

0.94

0.89

Env-PPAS

IEEAKKLIIELFSELAKIHGLNKSVGAVYAILYLKPLTISDIEELKIS-KGNV-SSLKKLEELG--FVRKVWIKGER-KN

4x5mA

0.19

0.17

0.91

0.86

MUSTER

LTGLFAAFFTTFAFAPQSIKTIR--TRNTSVVMYIMFLTGVISWIA--GRSDFAVLIANIVTLFLAAPVL--LINRRKK-

3on2A2

0.17

0.14

0.81

0.62

dPPAS

---DLTVRIVTEAQAAGDIGPGDA-SRIALVAFATFHGIATLAAGGLDGAPVDEVVTAASDTFWRGLAQ-----------

(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=-1.93

Estimated TM-score = 0.48±0.15

Estimated RMSD = 7.5±4.3Å

Download Model 2

C-score=-2.37

Download Model 3

C-score=-2.48

Download Model 4

C-score=-4.06

Download Model 5

C-score=-4.57

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	0.675	2.58	0.101	0.912
2	1w07B	0.663	2.50	0.068	0.912
3	5ezmA	0.660	2.71	0.208	0.887
4	3ay5A2	0.652	3.31	0.038	0.975
5	1r8iA	0.649	2.25	0.076	0.850
6	5cwiA	0.648	2.86	0.128	0.900
7	4he8N3	0.646	2.38	0.206	0.850
8	2yn7A	0.642	2.52	0.043	0.863
9	3i04A	0.638	2.13	0.026	0.825
10	4rnbA	0.636	3.37	0.039	0.912

(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	0.22	48	1sofH	HEM	Rep, Mult	34,37,38,41,59,63,66,67
2	0.08	17	3qvdA	FE	Rep, Mult	33,36,65
3	0.05	10	4uxzC	79M	Rep, Mult	37,40,41,44
4	0.04	10	2xquE	CVM	Rep, Mult	29,32,33,36
5	0.03	7	3wmn2	BCL	Rep, Mult	42,46
6	0.03	7	4fbyX	CLA	Rep, Mult	31,32,35,39
7	0.03	7	1brrC	ARC	Rep, Mult	2,9,10,41
8	0.03	6	3dk4A	GSH	Rep, Mult	39,42,43
9	0.01	2	4zzcA	XE	Rep, Mult	2,5,41,44
10	0.01	3	3ze3A	78N	Rep, Mult	13,17,26
11	0.00	1	2q9eB	MTN	Rep, Mult	9,13,16,31,38
12	0.00	1	3dezA	SO4	Rep, Mult	69,73
13	0.00	1	1u8vC	FAD	Rep, Mult	32,64,65,67
14	0.00	1	3a7kA	CL	Rep, Mult	24,27
15	0.00	1	3d1lB	MPR	Rep, Mult	32,51,65
16	0.00	1	1izlB	CLA	Rep, Mult	4,6,10
17	0.00	1	1oroA	SO4	Rep, Mult	73,77

	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	2e9fB	0.580	2.73	0.203	0.850	4.3.2.1	NA
2	0.060	3i9wA	0.574	2.32	0.039	0.775	2.7.13.3	7,30,38
3	0.060	1k04A	0.592	2.37	0.117	0.838	2.7.10.2	58,61,67,69
4	0.060	3jz4A	0.574	3.78	0.075	0.925	1.2.1.16	65
5	0.060	3d4sA	0.611	3.56	0.104	0.925	3.2.1.17	58
6	0.060	1t90D	0.579	3.72	0.103	0.912	1.2.1.27	6
7	0.060	1jswB	0.584	2.76	0.063	0.825	4.3.1.1	NA
8	0.060	3djlA	0.581	3.55	0.063	0.975	1.3.99.-	NA
9	0.060	3gtdA	0.585	2.72	0.038	0.825	4.2.1.2	NA
10	0.060	1jtnA	0.356	4.61	0.087	0.750	3.2.1.17	NA
11	0.060	3cf4A	0.608	2.68	0.091	0.850	1.2.99.2	NA
12	0.060	1siqA	0.574	2.75	0.063	0.850	1.3.99.7	36
13	0.060	3ii9C	0.588	2.84	0.075	0.863	1.3.99.7	38
14	0.060	2fenD	0.583	2.64	0.076	0.825	5.5.1.2	NA
15	0.060	3c20B	0.603	2.74	0.090	0.875	2.7.2.4	11
16	0.060	2g2dA	0.593	2.33	0.080	0.800	2.5.1.17	NA
17	0.060	3ek1A	0.573	3.73	0.101	0.925	1.2.1.16	NA
18	0.060	2z8yD	0.637	2.14	0.026	0.825	1.2.7.4,1.2.99.2	61
19	0.060	2wpnB	0.577	3.09	0.038	0.838	1.12.7.2	67

(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	0.461	3.35	0.10	0.76	4iwbA	GO:0044780
1	0.10	0.550	3.38	0.11	0.84	1jqiA	GO:0000062 GO:0003995 GO:0004085 GO:0005739 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0031966 GO:0033539 GO:0042594 GO:0046359 GO:0050660 GO:0051289 GO:0051384 GO:0055088 GO:0055114
2	0.09	0.559	2.73	0.04	0.85	3pfdC	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
3	0.07	0.481	3.70	0.08	0.81	2ebaA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
4	0.07	0.604	2.57	0.06	0.85	5iduC	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
5	0.07	0.565	2.49	0.09	0.80	2z1qB	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
6	0.07	0.525	3.58	0.08	0.90	2uxwA	GO:0000062 GO:0001659 GO:0003995 GO:0004466 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0015980 GO:0016020 GO:0016491 GO:0016627 GO:0017099 GO:0030855 GO:0033539 GO:0036498 GO:0042645 GO:0042760 GO:0045717 GO:0046322 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0090181
7	0.07	0.556	2.70	0.11	0.82	4irnA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
8	0.07	0.546	2.78	0.13	0.84	3r7kA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
9	0.07	0.533	2.92	0.10	0.84	3mddA	GO:0000062 GO:0001889 GO:0003995 GO:0005739 GO:0005759 GO:0005777 GO:0005978 GO:0006082 GO:0006111 GO:0006629 GO:0006631 GO:0006635 GO:0007507 GO:0008152 GO:0009055 GO:0009409 GO:0009437 GO:0009791 GO:0016491 GO:0016627 GO:0019254 GO:0033539 GO:0042594 GO:0050660 GO:0051791 GO:0052890 GO:0055007 GO:0055088 GO:0055114 GO:0070991
10	0.07	0.486	3.65	0.04	0.85	3owaC	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
11	0.07	0.548	2.55	0.09	0.82	1ukwA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
12	0.07	0.593	2.68	0.14	0.84	3nf4A	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
13	0.07	0.601	2.60	0.07	0.85	5jscA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
14	0.07	0.574	2.70	0.04	0.84	2ix6A	GO:0000062 GO:0003995 GO:0003997 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0009514 GO:0009793 GO:0016491 GO:0016627 GO:0033539 GO:0046459 GO:0050660 GO:0052890 GO:0055088 GO:0055114
15	0.07	0.545	2.68	0.09	0.82	2pg0A	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
16	0.07	0.545	2.80	0.14	0.82	4m9aB	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
17	0.07	0.516	3.28	0.14	0.82	3mpiC	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0019439 GO:0050660 GO:0055114
18	0.07	0.571	2.77	0.06	0.85	2r0mA	GO:0000062 GO:0003995 GO:0004361 GO:0005739 GO:0005759 GO:0006554 GO:0006568 GO:0006637 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0019395 GO:0033539 GO:0046949 GO:0050660 GO:0052890 GO:0055088 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016627	GO:0050662	GO:0000166
GO-Score	0.59	0.59	0.59
Biological Processes	GO:0044710
GO-Score	0.59
Cellular Component	GO:0005759	GO:0031966
GO-Score	0.10	0.10

(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 Rv0615

[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]