I-TASSER results

I-TASSER results for job id Rv2132

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

Input Sequence in FASTA format

>protein (76 residues)
MRTTVSLADDVAAAVQRLRKERSIGLSEAVNELIRAGLTKRQVANRFQQQTYDMGEGIDY
SNIGDAIETLDGPASG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MRTTVSLADDVAAAVQRLRKERSIGLSEAVNELIRAGLTKRQVANRFQQQTYDMGEGIDYSNIGDAIETLDGPASG
Prediction	CCEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Conf.Score	9678986778999999999998998999999999996557899888876664468877866899999999767789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MRTTVSLADDVAAAVQRLRKERSIGLSEAVNELIRAGLTKRQVANRFQQQTYDMGEGIDYSNIGDAIETLDGPASG
Prediction	7534041374025204533665745245102400452255664575245443624352415303401532555578
	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

CCEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
MRTTVSLADDVAAAVQRLRKERSIGLSEAVNELIRAGLTKRQVANRFQQQTYDMGEGIDYSNIGDAIETLDGPASG

2bsqE

0.15

0.12

0.78

0.99

wPPAS

IR----LSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQ--------QTVRLG-----SMLASIGQEIGGVERG

2k5jA

0.17

0.14

0.87

1.00

PPAS

GRILLDLSNEVIKQLDDLEVQRNLPRADLLREAVDQYLINQSQTAR----TSVPGIGCEEDGVE------QRKLRE

2k5jA

0.19

0.14

0.76

0.95

wPPAS

MRILLDLSNEVIKQLDDLEVQRNLPRADLLREAVDQYLINQSQTA----RTSVPGI--------------GCEEDG

2k5jA

0.16

0.14

0.92

0.83

MUSTER

GRILLDLSNEVIKQLDDLEVQRNLPRADLLREAVDQYLINQSQTARTSVPGIWQGCEEDG------VEYQRKLREE

2k5jA

0.16

0.14

0.92

0.81

dPPAS

GRILLDLSNEVIKQLDDLEVQRNLPRADLLREAVDQYLINQSQTARTSVPGIWQGCEEDG------VEYQRKLREE

2bsqE

0.14

0.11

0.78

0.93

wdPPAS

IR----LSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTV--------RLG-----SMLASIGQEIGGVERG

2bj3C

0.14

1.00

0.85

wMUSTER

IRFSISIPSKLLEKFDQIIEEIGENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDDVVKALLDLQHEYLD

2adlA

0.26

0.21

0.80

0.88

wPPAS

MRITVTVDSD----SYQLLKAYDVNISGLVSTTMQNEA-RRLRAERWKVENQE-GMV----EVARFIE-----MNG

1ea4F

0.14

0.08

0.57

1.00

dPPAS2

KRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK---------------------------------

2bsqE

0.15

0.12

0.78

0.86

PPAS

IR----LSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQ--------TVRLG-----SMLASIGQEIGGVVRG

(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=-2.72

Estimated TM-score = 0.40±0.13

Estimated RMSD = 9.2±4.6Å

Download Model 2

C-score=-2.73

Download Model 3

C-score=-4.34

Download Model 4

C-score=-4.62

Download Model 5

C-score=-3.21

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	5c2iA	0.591	2.91	0.067	0.855
2	3lwjA	0.576	3.18	0.027	0.855
3	2dqbE1	0.568	3.57	0.082	0.934
4	4g2cA	0.560	3.18	0.108	0.855
5	2pgsA	0.557	3.35	0.069	0.921
6	4x9eA	0.550	3.50	0.133	0.947
7	4zpjA	0.549	3.70	0.068	0.934
8	3c07A	0.544	3.60	0.054	0.868
9	3vxgA	0.543	2.50	0.068	0.711
10	1qo0B	0.543	3.24	0.083	0.855

(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	0.30	15	3rbmA	B73	Rep, Mult	30,31,34
2	0.06	3	2bsqH	NUC	Rep, Mult	16,20,25,26,27,31
3	0.06	3	2istA	BCT	Rep, Mult	32,35
4	0.04	2	2hzvA	NUC	Rep, Mult	2,25,26,27,31
5	0.04	2	5ezmA	MPG	Rep, Mult	34,37
6	0.02	1	2vsfA	SF4	Rep, Mult	32,33,65
7	0.02	1	2hzaA	3CM	Rep, Mult	18,19,22,24,33

	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	0.220	2gpeD	0.519	1.55	0.109	0.592	1.5.1.12,1.5.99.8	5,7
2	0.060	1dgpA	0.487	4.11	0.087	0.882	4.2.3.9,4.1.99.7	NA
3	0.060	2epoB	0.445	4.24	0.056	0.895	3.2.1.52	28
4	0.060	2ptwA	0.435	4.23	0.060	0.829	4.2.1.11	NA
5	0.060	3h0gA	0.490	3.99	0.056	0.934	2.7.7.6	35,38
6	0.060	1igwA	0.510	3.67	0.045	0.842	4.1.3.1	NA
7	0.060	2iw5A	0.417	3.99	0.087	0.789	1.-.-.-	NA
8	0.060	3eolA	0.431	3.70	0.083	0.724	4.1.3.1	NA
9	0.060	2dqbA	0.581	3.24	0.069	0.921	3.1.5.1	4
10	0.060	2hi4A	0.491	3.64	0.028	0.842	1.14.14.1	NA
11	0.060	153lA	0.489	4.54	0.039	1.000	3.2.1.17	60
12	0.060	2epoA	0.495	4.22	0.055	0.908	3.2.1.52	28
13	0.060	3lggA	0.500	3.69	0.119	0.868	3.5.4.4	NA
14	0.060	1z82A	0.493	3.61	0.014	0.789	1.1.1.8	NA
15	0.060	1x42A	0.511	3.52	0.062	0.855	3.8.1.-	NA
16	0.060	2vsfA	0.540	3.37	0.110	0.842	3.6.4.12	9,30
17	0.060	1is2A	0.492	3.62	0.041	0.789	1.3.3.6	NA
18	0.060	1og6C	0.477	2.50	0.086	0.658	1.-.-.-	NA
19	0.060	2e1pA	0.487	3.83	0.088	0.842	3.4.21.62	NA
20	0.060	2bghA	0.496	3.61	0.088	0.803	2.3.1.160	15,69

(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	0.24	0.519	1.55	0.11	0.59	2gpeD	GO:0000986 GO:0001141 GO:0003677 GO:0003700 GO:0003824 GO:0003842 GO:0004029 GO:0004657 GO:0006351 GO:0006355 GO:0006560 GO:0006561 GO:0008152 GO:0009898 GO:0010133 GO:0016491 GO:0016620 GO:0043565 GO:0045892 GO:0050660 GO:0055114
1	0.22	0.474	2.11	0.14	0.57	2cpgB	GO:0003677 GO:0006276 GO:0006351 GO:0006355
2	0.16	0.491	3.94	0.05	0.83	3qkxA	GO:0003677 GO:0006351 GO:0006355
3	0.15	0.464	3.72	0.06	0.74	2np5A	GO:0003677 GO:0006351 GO:0006355
4	0.08	0.591	2.91	0.07	0.86	5c2iA	GO:0004601 GO:0020037 GO:0055114 GO:0098869
5	0.07	0.578	3.30	0.04	0.87	3lwjA	GO:0003677 GO:0006351 GO:0006355
6	0.07	0.516	3.48	0.04	0.86	3whcA	GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
7	0.07	0.484	3.65	0.03	0.87	2iu5A	GO:0003677 GO:0006351 GO:0006355
8	0.07	0.430	3.35	0.04	0.72	3lhqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
9	0.07	0.529	3.90	0.05	0.89	3vibC	GO:0003677 GO:0006351 GO:0006355
10	0.07	0.417	4.27	0.07	0.79	4au9A	GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
11	0.07	0.487	3.92	0.04	0.82	3nnrA	GO:0003677 GO:0006351 GO:0006355
12	0.07	0.429	3.50	0.03	0.74	4w97A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010468 GO:0019217
13	0.07	0.506	3.65	0.06	0.82	3kkcA	GO:0003677 GO:0006351 GO:0006355
14	0.07	0.471	3.90	0.06	0.83	2qibA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
15	0.07	0.492	3.95	0.10	0.80	3vprA	GO:0003677 GO:0006351 GO:0006355 GO:0042802
16	0.07	0.459	3.21	0.07	0.71	2zcnD	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.469	3.68	0.04	0.78	3rh2A	GO:0003677 GO:0006351 GO:0006355
18	0.07	0.421	3.17	0.07	0.64	2raeA	GO:0003677 GO:0006351 GO:0006355
19	0.07	0.449	4.14	0.08	0.84	2fbqA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714
20	0.07	0.492	3.83	0.07	0.79	2iaiA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0016646	GO:0000987	GO:0001217	GO:0000984	GO:0016903	GO:0000166	GO:0050662	GO:0001131
GO-Score	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48
Biological Processes	GO:0006355	GO:1903507	GO:0008652	GO:0009084	GO:2000113	GO:0010629	GO:0006562	GO:0006536
GO-Score	0.57	0.48	0.48	0.48	0.48	0.48	0.48	0.48
Cellular Component	GO:0098562	GO:0044459
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.