I-TASSER results

I-TASSER results for job id Rv2085

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

Input Sequence in FASTA format

>protein (101 residues)
MSDMCDVVSFVGAAERVLRARFRPSPESGPPVHARRCGWSLGISAETLRRWAGQAEVDSG
VVAGVSASRSGSVKTSELEQTIEILKVATSFFARKCDPRHR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSDMCDVVSFVGAAERVLRARFRPSPESGPPVHARRCGWSLGISAETLRRWAGQAEVDSGVVAGVSASRSGSVKTSELEQTIEILKVATSFFARKCDPRHR
Prediction	CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	98566677778889999998864467888479999999988999999999999986556888898978999999999999999999999999998689999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSDMCDVVSFVGAAERVLRARFRPSPESGPPVHARRCGWSLGISAETLRRWAGQAEVDSGVVAGVSASRSGSVKTSELEQTIEILKVATSFFARKCDPRHR
Prediction	75412412434433430323324556745433104400762613350024015415476465554556544534445255435204300321044345668
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
MSDMCDVVSFVGAAERVLRARFRPSPESGPPVHARRCGWSLGISAETLRRWAGQAEVDSGVVAGVSASRSGSVKTSELEQTIEILKVATSFFARKCDPRHR

2jn6A

0.18

0.17

0.91

1.43

MUSTER

MPTKTYSEEFKRDAVALYE---------SDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGTTPAAVSEAEQIRQLKKENALQRARTRHPAESCLEHHH

2rn7A

0.23

0.98

1.45

dPPAS

MT--KNTRFSPEVRQRAVRMVLESQGEYDSWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGGLTTAEPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.23

0.98

3.00

wdPPAS

MTK--NTRFSPEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGGQRLKEPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.23

0.22

0.96

1.85

wMUSTER

KNTRFS----PEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGGQRLKEPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.23

0.98

3.04

wPPAS

MT--KNTRFSPEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGRQRLKEPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.23

0.98

4.22

dPPAS2

MT--KNTRFSPEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDGGLTTAERPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.25

0.23

0.92

1.99

PPAS

MT--------PEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDGGLTTAERPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.23

0.98

2.95

Env-PPAS

MT--KNTRFSPEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDGGLTTAERPERENRELRRSNDILRLASAYFAKEFDRLWK

2rn7A

0.24

0.23

0.93

1.41

MUSTER

MTK-------PEVRQRAVRMVLESQGEYSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGGLRLKEPERENRELRRSNDILRLASAYFAKEFDRLWK

2jn6A

0.16

0.15

0.92

1.42

dPPAS

---MPTKTYSEEFKRDAVALYEN-----SDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGTTPAAVSEAEQIRQLKKENALQRARTRHPAESCLEHHH

(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=-1.28

Estimated TM-score = 0.56±0.15

Estimated RMSD = 6.6±4.0Å

Download Model 2

C-score=-2.35

Download Model 3

C-score=-2.87

Download Model 4

C-score=-2.69

Download Model 5

C-score=-3.65

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	2jn6A	0.620	3.06	0.136	0.871
2	3r5eA	0.526	3.37	0.067	0.762
3	2q6hA	0.510	4.09	0.078	0.861
4	3ayfA	0.507	3.86	0.069	0.782
5	3zuzA	0.502	3.89	0.051	0.842
6	1dgjA2	0.501	4.30	0.072	0.911
7	1kqgA	0.501	4.35	0.043	0.802
8	5cehA	0.500	3.20	0.071	0.703
9	1ru3A	0.500	3.78	0.064	0.802
10	5azbA	0.497	2.73	0.070	0.673

(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	0.16	9	1ku7A	NUC	Rep, Mult	16,43,44,46,47,50
2	0.12	7	2h27A	NUC	Rep, Mult	11,44,46,47,49,50,51,54
3	0.04	2	1dgjA	FES	Rep, Mult	17,21,35,36,37,38,41,44,48
4	0.04	2	2qeiA	CXX	Rep, Mult	76,80,81,84,85,87
5	0.02	1	1kv8A	PO4	Rep, Mult	42,64,69
6	0.02	1	2h27A	NUC	Rep, Mult	21,33,34,49,53,54,56
7	0.02	1	1kqfA	SF4	Rep, Mult	5,7,11,89,91,92
8	0.02	1	1zg1B	NUC	Rep, Mult	11,12,13,43,44,46,47,51
9	0.02	1	3keoA	MG	Rep, Mult	41,42
10	0.02	1	2x4hB	ZN	Rep, Mult	15,51
11	0.02	1	1m1yA	CA	Rep, Mult	91,95
12	0.02	1	3i4u0	III	Rep, Mult	66,67,71,72,74,75,78,82,88,89,92

	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	1bgwA	0.485	4.12	0.030	0.822	5.99.1.3	NA
2	0.060	2aj4A	0.474	4.06	0.046	0.792	2.7.1.6	12
3	0.060	2uz9A	0.462	4.50	0.065	0.881	3.5.4.3	NA
4	0.060	1b8gB	0.473	4.63	0.074	0.802	4.4.1.14	13
5	0.060	2b3lA	0.477	4.24	0.082	0.792	3.4.11.18	NA
6	0.060	1b02A	0.480	4.23	0.044	0.802	2.1.1.45	NA
7	0.060	1iayA	0.472	4.42	0.053	0.782	4.4.1.14	NA
8	0.060	2rgrA	0.485	4.21	0.050	0.832	5.99.1.3	NA
9	0.060	1f28A	0.482	3.70	0.034	0.752	2.1.1.45	NA
10	0.060	2c0hA	0.469	3.95	0.035	0.812	3.2.1.78	NA
11	0.060	2df4A	0.474	3.43	0.011	0.733	6.3.5.-	NA
12	0.060	2ztgA	0.480	2.93	0.059	0.644	6.1.1.7	NA
13	0.060	2hk2A	0.481	4.24	0.093	0.822	4.1.1.33	74
14	0.060	3mebA	0.479	4.76	0.061	0.871	2.6.1.1	NA
15	0.060	2a3lA	0.475	3.31	0.065	0.723	3.5.4.6	78
16	0.060	1f28B	0.480	3.64	0.036	0.752	2.1.1.45	NA
17	0.060	3e0lA	0.484	4.27	0.086	0.871	3.5.4.3	NA
18	0.060	1prhA	0.369	5.19	0.053	0.792	1.14.99.1	NA
19	0.060	1bgpA	0.488	3.21	0.093	0.723	1.11.1.7	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	0.19	0.620	3.06	0.14	0.87	2jn6A	GO:0003677 GO:0004803 GO:0006313
1	0.11	0.392	4.24	0.03	0.68	3o0rB	GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
2	0.07	0.467	3.79	0.04	0.77	4xp9C	GO:0005328 GO:0005329 GO:0005330 GO:0005886 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0015872 GO:0016020 GO:0016021 GO:0019811 GO:0030431 GO:0042745 GO:0043005 GO:0046872 GO:0051583 GO:0055085 GO:0072488 GO:0098793 GO:0099509 GO:1990834
3	0.07	0.442	4.66	0.05	0.87	3kruA	GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0055114
4	0.07	0.469	3.91	0.05	0.80	4us3A	GO:0005328 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
5	0.07	0.510	4.09	0.08	0.86	2q6hA	GO:0005215 GO:0005328 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
6	0.07	0.417	4.53	0.06	0.80	3e49A	GO:0003824 GO:0016740 GO:0019475 GO:0046872
7	0.06	0.419	4.06	0.08	0.73	1wx0A	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
8	0.06	0.395	4.50	0.04	0.74	2vcvA	GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687
9	0.06	0.396	3.92	0.07	0.67	3s0cC	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
10	0.06	0.411	4.17	0.09	0.69	5djqA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
11	0.06	0.397	4.92	0.01	0.76	4xydA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
12	0.06	0.394	4.12	0.01	0.71	3r8rA	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740 GO:0042802
13	0.06	0.350	2.82	0.04	0.49	3igxA	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
14	0.06	0.526	3.37	0.07	0.76	3r5eA	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
15	0.06	0.399	3.94	0.07	0.69	1vpxE	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
16	0.06	0.376	4.70	0.02	0.72	3m16A	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
17	0.06	0.404	4.34	0.12	0.77	1f05A	GO:0003824 GO:0004801 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0005999 GO:0006002 GO:0006098 GO:0009052 GO:0016740 GO:0019682 GO:0030246 GO:0043231 GO:0048029 GO:0070062
18	0.06	0.401	4.23	0.04	0.74	3cq0A	GO:0001300 GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740 GO:0034599

Consensus prediction of GO terms

Molecular Function	GO:0003676	GO:0043169
GO-Score	0.39	0.34
Biological Processes	GO:0032196	GO:0006310	GO:0044710
GO-Score	0.39	0.39	0.39
Cellular Component	GO:0031224	GO:0071944
GO-Score	0.36	0.34

(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.