I-TASSER results

I-TASSER results for job id Rv3224A

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (62 residues)
MRRSASTCGWKTPTRRGTSRPSDSKTLILELPDERAVAIVPVPSKLSLKAAGGPRGAQSG
HG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MRRSASTCGWKTPTRRGTSRPSDSKTLILELPDERAVAIVPVPSKLSLKAAGGPRGAQSGHG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCEEEEEHCCCCEEEEHCCCCCCCCCCCC
Conf.Score	98665667777777778888888866898858987689985787555654578766566889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MRRSASTCGWKTPTRRGTSRPSDSKTLILELPDERAVAIVPVPSKLSLKAAGGPRGAQSGHG
Prediction	85554642425334554464456443011413563111123135514243444454366668
	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

CCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCEEEEEHCCCCEEEEHCCCCCCCCCCCC
MRRSASTCGWKTPTRRGTSRPSDSKTLILELPDERAVAIVPVPSKLSLKAAGGPRGAQSGHG

1vw4V

0.20

0.19

0.98

0.95

MUSTER

TRITLPRRPAKK-IQLGKSRPAIYHNVKMELSDGSVVIRRSQYPKGEIRLIQDQRNNPLWNP

1vw4V

0.21

0.19

0.94

0.88

dPPAS

-TRITLPRRPAKKIQLGKSRPAIYHNVKMELSDGSVVIRRSQYPKGEIRLIQDQRNNPS---

1vrqC1

0.29

0.27

0.94

0.69

wdPPAS

LRAVPGS-GVGLPAAVGEVAGDVSGTAVLWLPDE-FLLAAEENPALTLQGAGQEPGQ-SAN-

1vrqC1

0.31

0.29

0.95

0.93

wMUSTER

VPGSAAATGVGLPAAVGEVAGDVSGTAVLWLPDE-FLLAAEENPALTLQGAGQEPGQ-SAN-

1vrqC1

0.31

0.29

0.95

0.69

wPPAS

LRGSTAATGVGLPAAVGEVAGDVSGTAVLWLPDE-FLLAAEENPALTLQGAGQEPGQ-SAN-

1vrqC1

0.30

0.29

0.97

0.76

dPPAS2

VPGSAAATGVGLPAAVGEVAGDVSGTAVLWLPDE-FLLAAEENPALTLQGALGQEPGQSAN-

1sqqI

0.29

0.24

0.82

0.80

PPAS

MLSVAARSGPFAPVLSATSRAGALRPLV-----QAAVPATSESPVLDLK----SRESLRG--

2aemA1

0.29

0.27

0.95

0.90

Env-PPAS

KSRHVVICGWSESTLECLRELRGSEVFVLA-EDENANFVHGDPTRVSLEKA-NVRGARAVI-

1vrqC1

0.31

0.29

0.95

0.84

MUSTER

VPGSAAATGVGLPAAVGEVAGDVSGTAVLWLPDE-FLLAAEENPALTLQGAGQEPGQ-SAN-

1maeH2

0.15

0.11

0.77

0.81

dPPAS

PRFDVGPYSWMN-----ANTPNNADLLFFQFAAGPAVGLVVQGGSSDDQLLSS---------

(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=-2.47

Estimated TM-score = 0.43±0.14

Estimated RMSD = 8.2±4.5Å

Download Model 2

C-score=-2.81

Download Model 3

C-score=-3.35

Download Model 4

C-score=-4.68

Download Model 5

C-score=-2.74

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	1vrqC1	0.557	2.92	0.250	0.903
2	3qslA1	0.477	3.96	0.065	0.984
3	3eeqA1	0.474	3.31	0.000	0.887
4	3holA	0.472	3.50	0.121	0.919
5	4ix8A2	0.469	3.48	0.049	0.839
6	3pqsA	0.467	3.45	0.133	0.919
7	3m8wA	0.463	3.40	0.034	0.935
8	1hynQ	0.462	3.13	0.049	0.806
9	1ak6A	0.460	3.99	0.102	0.935
10	4j15A2	0.460	3.83	0.049	0.903

(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	0.09	4	1fq9A	SGN	Rep, Mult	11,25
2	0.07	3	2gxaA	MG	Rep, Mult	1,33
3	0.07	3	5gxpA	CA	Rep, Mult	25,41
4	0.07	3	3et2A	1BO	Rep, Mult	12,36
5	0.07	3	2gr7A	C8E	Rep, Mult	37,39
6	0.04	2	4j6wF	CTP	Rep, Mult	29,37
7	0.02	1	4rqiD	MG	Rep, Mult	15,17
8	0.02	1	1q5hA	DUD	Rep, Mult	55,59,60
9	0.02	1	2a5hA	UUU	Rep, Mult	6,9
10	0.02	1	3rbhC	C8E	Rep, Mult	27,40,41,46
11	0.02	1	1n7vA	CA	Rep, Mult	23,25,56

	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	3lssB	0.437	3.60	0.048	0.887	6.1.1.11	26
2	0.060	2jkvA	0.448	3.56	0.055	0.855	1.1.1.44	NA
3	0.060	3ialB	0.447	3.78	0.085	0.871	6.1.1.15	NA
4	0.060	2rhsC	0.442	3.85	0.097	0.935	6.1.1.20	NA
5	0.060	1e6vA	0.437	3.79	0.052	0.903	2.8.4.1	NA
6	0.060	1hn0A	0.449	3.80	0.050	0.935	4.2.2.20	35
7	0.060	3hrkA	0.332	4.54	0.000	0.823	6.1.1.21	NA
8	0.060	12asA	0.438	3.88	0.067	0.919	6.3.1.1	NA
9	0.060	1httA	0.316	4.49	0.096	0.790	6.1.1.21	NA
10	0.060	2ogsA	0.450	3.95	0.050	0.919	3.1.1.1	NA
11	0.060	1eiyA	0.445	3.86	0.082	0.919	6.1.1.20	NA
12	0.060	2amfE	0.459	3.79	0.088	0.919	1.5.1.2	NA
13	0.060	1wdlA	0.440	3.65	0.073	0.855	5.3.3.8,5.1.2.3,4.2.1.17,1.1.1.35	60
14	0.060	1wopA	0.445	3.51	0.161	0.871	2.1.2.10	2,27
15	0.060	1t7nA	0.439	3.33	0.018	0.806	2.3.1.7	NA
16	0.060	1yx2B	0.446	3.44	0.148	0.839	2.1.2.10	NA
17	0.060	3hdoA	0.437	3.75	0.049	0.871	2.6.1.9	NA
18	0.060	1i72B	0.246	3.75	0.029	0.452	4.1.1.50	NA
19	0.060	1a8tA	0.368	4.05	0.109	0.742	3.5.2.6	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	0.06	0.345	3.86	0.06	0.73	4eswA	GO:0009228 GO:0009229
1	0.06	0.374	4.10	0.05	0.84	4oenB	GO:0004970 GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0035235
2	0.06	0.335	3.97	0.02	0.74	4nmyA	GO:0009228
3	0.06	0.333	3.82	0.04	0.68	4h6dE	GO:0009228 GO:0009229
4	0.06	0.354	4.23	0.06	0.81	2i4bA	GO:0005215 GO:0005886 GO:0006810 GO:0006811 GO:0016020
5	0.06	0.370	2.89	0.13	0.65	4emjA	GO:0005623 GO:0008860 GO:0016491 GO:0019439 GO:0042203 GO:0045454 GO:0050660 GO:0055114
6	0.06	0.269	4.48	0.02	0.71	1ls9A	GO:0005506 GO:0009055 GO:0009507 GO:0009536 GO:0009543 GO:0009579 GO:0015979 GO:0020037 GO:0046872 GO:0055114
7	0.06	0.384	4.24	0.12	0.90	3dm5A	GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005737 GO:0006612 GO:0006614 GO:0008312 GO:0030529 GO:0048500
8	0.06	0.274	4.29	0.04	0.68	4i62A	GO:0004970 GO:0016020 GO:0035235
9	0.06	0.300	4.48	0.14	0.74	4g36B	GO:0000166 GO:0003824 GO:0004497 GO:0005524 GO:0005777 GO:0008152 GO:0008218 GO:0016491 GO:0046872 GO:0047077 GO:0055114
10	0.06	0.307	4.40	0.10	0.68	4df2A	GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0055114
11	0.06	0.378	4.39	0.07	0.90	1t90A	GO:0004029 GO:0004491 GO:0008152 GO:0016491 GO:0016620 GO:0018478 GO:0019310 GO:0055114
12	0.06	0.363	4.15	0.04	0.81	2g29A	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0042128
13	0.06	0.472	3.31	0.02	0.90	3eeqA	GO:0009236
14	0.06	0.339	4.10	0.02	0.74	4h65B	GO:0009228 GO:0009229
15	0.06	0.327	4.60	0.09	0.82	3e4rA	GO:0006790 GO:0006810 GO:0016020
16	0.06	0.350	4.23	0.05	0.84	4h67C	GO:0009228 GO:0009229
17	0.06	0.328	4.62	0.10	0.89	4pabB	GO:0005542 GO:0005739 GO:0006579 GO:0016491 GO:0019695 GO:0035999 GO:0042426 GO:0047865 GO:0050660 GO:0055114
18	0.06	0.295	4.31	0.04	0.71	3j3vT	GO:0000027 GO:0000166 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0022625 GO:0030529

Consensus prediction of GO terms

Molecular Function	GO:0004970
GO-Score	0.07
Biological Processes	GO:0006772	GO:0042724
GO-Score	0.36	0.36
Cellular Component	GO:0005886	GO:0016021
GO-Score	0.12	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.