I-TASSER results

I-TASSER results for job id Rv2556c

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

Input Sequence in FASTA format

>protein (129 residues)
MLDVDTARRRIVDLTDAVRAFCTAHDDGLCNVFVPHATAGVAIIETGAGSDEDLVDTLVR
LLPRDDRYRHAHGSYGHGADHLLPAFVAPSVTVPVSGGQPLLGTWQSIVLVDLNQDNPRR
SVRLSFVEG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLDVDTARRRIVDLTDAVRAFCTAHDDGLCNVFVPHATAGVAIIETGAGSDEDLVDTLVRLLPRDDRYRHAHGSYGHGADHLLPAFVAPSVTVPVSGGQPLLGTWQSIVLVDLNQDNPRRSVRLSFVEG
Prediction	CEEEEHCCCEEEHCHHHHHHHHHHCCCCEEEEHCCCCCCEEEEEHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCEEEEEHCCCEHCCCCEEEEEEEHCCCCCCCEEEEEEEHCC
Conf.Score	989996996577458999999997699679998799763456664589858999999999889999976688999985777665546885799975987656755589999889999985899999689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLDVDTARRRIVDLTDAVRAFCTAHDDGLCNVFVPHATAGVAIIETGAGSDEDLVDTLVRLLPRDDRYRHAHGSYGHGADHLLPAFVAPSVTVPVSGGQPLLGTWQSIVLVDLNQDNPRRSVRLSFVEG
Prediction	714061564321301640461057353000000013200000000335413610251045013573504245446410200023132433110104634230212010000005445350402032278
	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

CEEEEHCCCEEEHCHHHHHHHHHHCCCCEEEEHCCCCCCEEEEEHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCEEEEEHCCCEHCCCCEEEEEEEHCCCCCCCEEEEEEEHCC
MLDVDTARRRIVDLTDAVRAFCTAHDDGLCNVFVPHATAGVAIIETGAGSDEDLVDTLVRLLPRDDRYRHAHGSYGHGADHLLPAFVAPSVTVPVSGGQPLLGTWQSIVLVDLNQDNPRRSVRLSFVEG

2p6hA

0.35

0.34

0.97

3.12

MUSTER

MFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLVD-VNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPRRTVNLLYL-G

1vmfA

0.23

0.22

0.98

7.31

dPPAS

TFHLTTSRDEMVDITSQIETWIRETGNGVAIVSSLHTTAGITVNENAPDVKRDMIMRLDEVYPWHHE--NDRHMEGNTAAHLKTSTVGHAQTLIISEGRLVLGTWQGVYFCEFDGPRTNRKFVVKLLTD

2p6hA

0.34

0.33

0.97

4.76

wdPPAS

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLVD-VNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPRRTVNLLYL-G

2p6hA

0.34

0.33

0.97

3.32

wMUSTER

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLVD-VNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPRRTVNLLYL-G

2p6hA

0.34

0.33

0.97

3.12

wPPAS

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLV-DVNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPERTVNLLYL-G

2p6hA

0.33

0.32

0.98

7.88

dPPAS2

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLV-DVNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVE--MDGPERTVNLLYLGE

2p6hA

0.34

0.33

0.97

3.21

PPAS

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLV-DVNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPERTVNLLYL-G

2p6hA

0.34

0.33

0.97

3.76

Env-PPAS

SFTVKTRRLQVLDVTGKVEEWLSTVGNGLLVVYVPHTTAAVAVNEAEPRLMEDIVEFIRELTKPGGPWKHNLV-DVNAHAHLGNTIIGDSRVIPVVGGRLSLGTWQRILFVEM--DGPERTVNLLYL-G

2p6cA

0.29

0.98

3.07

MUSTER

YLTFNTKRRELIRITDEVKKAVEESKEGLCLVSSMHLTSSVIIQDDEEGLHEDIWEWLEKLAPYRPDYKHHRTGEDNGDAHLKNLLTHLQVVLPITNGKLDLGPWQEIFYAEFDGQRP-KRVVIKII-G

2p6cA

0.28

0.99

7.26

dPPAS

YLTFNTKRRELIRITDEVKKAVEESEEGLCLVSSMHLTSSVIIQDDEEGLHEDIWEWLEKLAPYRPDYKHHRTGEDNGDAHLKNLLTHLQVVLPITNGKLDLGPWQEIFYAEFDGQRP-KRVVIKIIGE

(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 1 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=1.53

Estimated TM-score = 0.93±0.06

Estimated RMSD = 1.6±1.4Å

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	1vphC	0.931	1.22	0.281	0.992
2	2p6hA	0.929	1.12	0.307	0.985
3	1vmfA	0.906	1.40	0.220	0.985
4	1vmjA	0.902	1.45	0.203	0.992
5	2p6cA	0.895	1.50	0.273	0.992
6	1xbfA	0.889	1.31	0.242	0.961
7	1ve0A	0.886	1.42	0.272	0.969
8	2cu5A	0.854	1.63	0.268	0.954
9	4mguA	0.528	4.09	0.117	0.822
10	2wff1	0.521	4.17	0.061	0.837

(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	4	1ve0A	ZN	Rep, Mult	70,77,81
2	0.12	4	4xk8K	CLA	Rep, Mult	55,62
3	0.12	4	4p5hA	III	Rep, Mult	1,33,34,36,38,39,118,121,123
4	0.09	3	4il6H	CLA	Rep, Mult	54,58,61
5	0.03	1	2xg5A	EC5	Rep, Mult	28,29,92,94,127,128,129
6	0.03	1	1nlqE	MG	Rep, Mult	1,124

	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	1sdwA	0.438	4.27	0.059	0.690	4.3.2.5,1.14.17.3	NA
2	0.060	1h8tA	0.503	4.20	0.063	0.791	3.4.22.28	32,89,108,120
3	0.060	1qgc1	0.444	4.59	0.087	0.744	3.4.22.28	128
4	0.060	1c8m1	0.495	4.24	0.018	0.791	3.4.22.28	123
5	0.060	1bev1	0.503	4.37	0.080	0.806	2.7.7.48	29,123
6	0.060	2nqaB	0.334	4.54	0.082	0.558	3.4.22.53,3.4.22.52	70
7	0.060	1pnfA	0.440	4.86	0.049	0.760	3.5.1.52	3
8	0.060	1bbuA	0.439	4.74	0.047	0.752	6.1.1.6	NA
9	0.060	1yjlA	0.439	4.39	0.067	0.713	1.14.17.3,4.3.2.5	NA
10	0.060	1piv1	0.503	4.12	0.036	0.791	3.4.22.29	111
11	0.060	1d4m1	0.478	4.45	0.046	0.798	3.6.1.15	89
12	0.060	1v9u1	0.500	4.04	0.028	0.775	3.6.1.15	87,94,101,110
13	0.060	1pov0	0.499	4.13	0.105	0.814	3.4.22.29	39,82,113
14	0.060	2mev1	0.504	3.89	0.090	0.760	3.6.1.15	95,127
15	0.060	1wd8A	0.312	5.09	0.039	0.581	3.5.3.15	112
16	0.060	1ddgB	0.431	4.63	0.077	0.713	1.8.1.2	14
17	0.060	1mdwA	0.339	4.75	0.081	0.574	3.4.22.53	70
18	0.060	1a65A	0.438	3.15	0.123	0.589	1.10.3.2	NA
19	0.060	1wd9A	0.330	4.68	0.056	0.566	3.5.3.15	13

(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	0.48	0.901	1.41	0.27	0.98	1ve0A	GO:0046872
1	0.15	0.929	1.12	0.31	0.98	2p6hA
2	0.06	0.335	5.27	0.03	0.67	5eviB	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
3	0.06	0.364	5.23	0.08	0.65	4cmnA	GO:0001701 GO:0001750 GO:0004439 GO:0005096 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005795 GO:0005798 GO:0005802 GO:0005829 GO:0005886 GO:0005905 GO:0005929 GO:0006629 GO:0006661 GO:0007165 GO:0016020 GO:0016023 GO:0016787 GO:0030030 GO:0030136 GO:0030670 GO:0031410 GO:0031901 GO:0042384 GO:0042995 GO:0043087 GO:0043547 GO:0043647 GO:0046856 GO:0048365 GO:0051056 GO:0052658 GO:0052659 GO:0052745 GO:0070062
4	0.06	0.300	4.65	0.08	0.50	1d5cA	GO:0005525 GO:0005622 GO:0007264
5	0.06	0.349	3.41	0.08	0.51	2v5dA	GO:0004563 GO:0005975 GO:0006517 GO:0008152 GO:0016231 GO:0016787 GO:0016798 GO:0030246
6	0.06	0.178	4.95	0.05	0.33	1uhcA	GO:0005085 GO:0005089 GO:0005737 GO:0005794 GO:0005795 GO:0005856 GO:0030054 GO:0035023 GO:0035556 GO:0043547 GO:0045202
7	0.06	0.297	4.55	0.03	0.53	3f1tB
8	0.06	0.906	1.40	0.22	0.98	1vmfA
9	0.06	0.889	1.31	0.24	0.96	1xbfA
10	0.06	0.902	1.45	0.20	0.99	1vmjA
11	0.06	0.931	1.22	0.28	0.99	1vphC
12	0.06	0.895	1.50	0.27	0.99	2p6cA

Consensus prediction of GO terms

Molecular Function	GO:0046872
GO-Score	0.48
Biological Processes	GO:0046677	GO:0017001	GO:0043547	GO:0046856	GO:0006661	GO:0043647	GO:0042384	GO:0051056	GO:0001701
GO-Score	0.07	0.07	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0030288	GO:0005802	GO:0005634	GO:0070062	GO:0031901	GO:0005795	GO:0005905	GO:0005798	GO:0030670	GO:0030136	GO:0001750	GO:0005886	GO:0005829
GO-Score	0.07	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06

(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.