I-TASSER results

I-TASSER results for job id Rv2166c

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

Input Sequence in FASTA format

>protein (143 residues)
MFLGTYTPKLDDKGRLTLPAKFRDALAGGLMVTKSQDHSLAVYPRAAFEQLARRASKAPR
SNPEARAFLRNLAAGTDEQHPDSQGRITLSADHRRYASLSKDCVVIGAVDYLEIWDAQAW
QNYQQIHEENFSAASDEALGDIF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFLGTYTPKLDDKGRLTLPAKFRDALAGGLMVTKSQDHSLAVYPRAAFEQLARRASKAPRSNPEARAFLRNLAAGTDEQHPDSQGRITLSADHRRYASLSKDCVVIGAVDYLEIWDAQAWQNYQQIHEENFSAASDEALGDIF
Prediction	CCCCEEHCCCCCCCCEHCCHHHHHHHCCEEEEEHCCCCEEEEHCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEHCCCCCEHCCHHHHHHHCCCCCEEEEHCCCEEEHCCHHHHHHHHHHCHHHHHHHHHHHHCCCC
Conf.Score	98656655667789855788899987997999978998599869999999999999899999999999999985867876579877668999999989999699996798899869999999999778769999999865769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFLGTYTPKLDDKGRLTLPAKFRDALAGGLMVTKSQDHSLAVYPRAAFEQLARRASKAPRSNPEARAFLRNLAAGTDEQHPDSQGRITLSADHRRYASLSKDCVVIGAVDYLEIWDAQAWQNYQQIHEENFSAASDEALGDIF
Prediction	63424252402542003002402740453000022332001014472054116206724544641330222021414514125413230164026307454300000133301012573056246644641452046326736
	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                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCEEHCCCCCCCCEHCCHHHHHHHCCEEEEEHCCCCEEEEHCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEHCCCCCEHCCHHHHHHHCCCCCEEEEHCCCEEEHCCHHHHHHHHHHCHHHHHHHHHHHHCCCC
MFLGTYTPKLDDKGRLTLPAKFRDALAGGLMVTKSQDHSLAVYPRAAFEQLARRASKAPRSNPEARAFLRNLAAGTDEQHPDSQGRITLSADHRRYASLSKDCVVIGAVDYLEIWDAQAWQNYQQIHEENFSAASDEALGDIF

1n0eB

0.28

0.27

0.96

3.78

MUSTER

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

8.26

dPPAS

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

6.76

wdPPAS

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

4.47

wMUSTER

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

5.25

wPPAS

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

18.57

dPPAS2

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

4.80

PPAS

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

1n0eB

0.28

0.27

0.96

5.53

Env-PPAS

MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANS-ESLETVAERM-----

3dp9C2

0.13

0.12

0.91

0.71

MUSTER

INTGS---GFDASGDVVISSEVRTAFGYEIGQMAGQPAAFKA-DEKLMTVAEQALAQLPVCTAERQQFIRQHFPSVVAVEMEASA-I---AQTCHQFKVP--VVVRAISDVAD--SPLSFEEFLPLAAKSSSAMVLKMVELL-

4alzA2

0.09

0.03

0.40

0.88

dPPAS

------------------------------------------------------------------------------------NQRKRLDALLEQFGLDSDFTVNVKGELIEL--RGQVNDEKLSSFNQLQQTFRQEFGNRP

(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=1.83

Estimated TM-score = 0.97±0.05

Estimated RMSD = 1.3±1.3Å

Download Model 2

C-score=-2.29

Download Model 3

C-score=-2.48

Download Model 4

C-score=-2.70

Download Model 5

C-score=-2.85

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	1n0eB	0.945	0.53	0.277	0.958
2	4hynA	0.503	3.76	0.088	0.699
3	1dlcA1	0.480	4.28	0.068	0.748
4	1xkrA	0.475	4.23	0.043	0.720
5	3qtaA	0.473	4.36	0.041	0.741
6	1m56A	0.473	4.42	0.047	0.783
7	4w8yA	0.472	4.21	0.063	0.734
8	3dwbA	0.471	4.59	0.049	0.748
9	3eb7A1	0.467	4.39	0.067	0.755
10	4dweA	0.466	4.40	0.047	0.706

(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	0.08	4	2eh9A	ZN	Rep, Mult	13,86
2	0.06	3	3fyeA	DMU	Rep, Mult	34,36,67,68,71,72,75
3	0.06	3	4dfdA	MG	Rep, Mult	11,14,141
4	0.04	2	2ab4A	ZN	Rep, Mult	6,103
5	0.04	2	5hxcA	MYC	Rep, Mult	48,52,72
6	0.04	2	2efgA	III	Rep, Mult	10,103
7	0.02	1	1fx4A	MG	Rep, Mult	11,37
8	0.02	1	3k57A	MG	Rep, Mult	11,110
9	0.02	1	1cl6A	NO	Rep, Mult	74,75
10	0.02	1	1crxB	NUC	Rep, Mult	66,70
11	0.02	1	3sn0A	MG	Rep, Mult	82,113,137
12	0.02	1	3dtuC	DMU	Rep, Mult	69,72,73,76
13	0.02	1	2wpdF	ATP	Rep, Mult	35,48
14	0.02	1	3rj8A	ZN	Rep, Mult	37,38
15	0.02	1	3fyeC	UNX	Rep, Mult	14,15,89,91

	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	3flkA	0.435	5.43	0.031	0.832	1.1.1.83,1.1.1.93	83
2	0.060	1t09B	0.444	5.01	0.059	0.797	1.1.1.42	20
3	0.060	1mhyD	0.397	4.66	0.070	0.650	1.14.13.25	NA
4	0.060	1p8fA	0.417	5.18	0.044	0.783	1.1.1.42	NA
5	0.060	2oodA	0.451	5.02	0.113	0.783	3.5.4.3	NA
6	0.060	2iv0B	0.436	5.06	0.056	0.797	1.1.1.42	28,30
7	0.060	3dwbA	0.471	4.59	0.049	0.748	3.4.24.71	NA
8	0.060	2d4vA	0.454	5.13	0.061	0.832	1.1.1.42	NA
9	0.060	1ug9A	0.439	4.92	0.040	0.748	3.2.1.70	NA
10	0.060	2d1cA	0.438	5.09	0.046	0.804	1.1.1.42	34
11	0.060	1pb3A	0.438	5.11	0.062	0.804	1.1.1.42	NA
12	0.060	1r1jA	0.464	4.93	0.089	0.790	3.4.24.11	69
13	0.060	2iv0A	0.450	4.97	0.046	0.825	1.1.1.42	NA
14	0.060	2v27B	0.450	4.63	0.080	0.727	1.14.16.1	127
15	0.060	2pnrB	0.448	4.45	0.049	0.713	2.7.11.2	NA
16	0.060	1x0lA	0.442	4.84	0.068	0.783	1.1.1.87	NA
17	0.060	1fziA	0.372	5.21	0.039	0.671	1.14.13.25	NA
18	0.060	2zdxA	0.459	4.49	0.040	0.734	2.7.11.2	NA
19	0.060	1y8pA	0.452	4.54	0.049	0.727	2.7.11.2	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	0.48	0.945	0.53	0.28	0.96	1n0eB	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0009295
1	0.07	0.514	3.69	0.09	0.71	4hynA	GO:0003774 GO:0006935 GO:0009288 GO:0009425 GO:0016020 GO:0016787 GO:0071973
2	0.07	0.424	4.74	0.07	0.72	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
3	0.07	0.467	4.39	0.07	0.76	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
4	0.07	0.460	4.68	0.08	0.76	1ji6A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
5	0.07	0.475	4.23	0.04	0.72	1xkrA	GO:0006935 GO:0016787
6	0.07	0.442	4.45	0.05	0.73	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
7	0.07	0.429	4.73	0.09	0.72	1ciyA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
8	0.07	0.452	4.47	0.07	0.74	3x0uA	GO:0009405
9	0.06	0.484	4.07	0.06	0.73	3qtaA	GO:0046872
10	0.06	0.406	4.95	0.07	0.71	1i5pA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
11	0.06	0.370	5.43	0.09	0.74	2c9kA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
12	0.06	0.423	3.98	0.03	0.60	1xkoB	GO:0006935 GO:0016787
13	0.06	0.392	4.07	0.01	0.54	3hzhB
14	0.06	0.372	5.03	0.03	0.67	4d8mA	GO:0009405 GO:0030435
15	0.06	0.328	4.79	0.07	0.54	1v8pF	GO:0004518 GO:0004527 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
16	0.06	0.337	5.07	0.10	0.61	1q7tA	GO:0005886 GO:0008270 GO:0010125 GO:0016787 GO:0016811 GO:0019213 GO:0035595 GO:0046872
17	0.06	0.300	5.13	0.03	0.53	4k3zA	GO:0016491 GO:0055114
18	0.06	0.322	5.41	0.04	0.59	5cdhC	GO:0003993 GO:0016311

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003700	GO:0005515
GO-Score	0.48	0.48	0.37
Biological Processes	GO:0006355	GO:0006950	GO:0030154	GO:0051704	GO:0043934	GO:0048646
GO-Score	0.48	0.37	0.37	0.37	0.37	0.37
Cellular Component	GO:0009295	GO:0005737
GO-Score	0.48	0.48

(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.