I-TASSER results

I-TASSER results for job id Rv0689c

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

Input Sequence in FASTA format

>protein (84 residues)
MLGWTVKPGRVADGWQAPGVHLMARCSGPQPASERRADMDGGDIDAAVARVRAAGALAEP
SRQPDDMSAECADDQGARCHLGQL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MLGWTVKPGRVADGWQAPGVHLMARCSGPQPASERRADMDGGDIDAAVARVRAAGALAEPSRQPDDMSAECADDQGARCHLGQL
Prediction	CCCEEEHCCCCCCCEEHCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCEEEEHCC
Conf.Score	976687566678876885888875555898888589998758789999999998898888778998588987899866876659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MLGWTVKPGRVADGWQAPGVHLMARCSGPQPASERRADMDGGDIDAAVARVRAAGALAEPSRQPDDMSAECADDQGARCHLGQL
Prediction	744141542537531415655142213244644222010306415401530473444542755624432504264415122455
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCEEEHCCCCCCCEEHCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCEEEEHCC
MLGWTVKPGRVADGWQAPGVHLMARCSGPQPASERRADMDGGDIDAAVARVRAAGALAEPSRQPDDMSAECADDQGARCHLGQL

3oxhA

0.26

0.25

0.96

1.81

MUSTER

VVGLTHSS---MYRVLKAGDAEVGGCMEPPMPNHWHVYFAVDDADATAAKAAAAGGIAEPADIPVGRFAVLSDPQGAIFSVLKA

2r6uD

0.14

1.00

1.96

dPPAS

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTRTPVGNMGFAAYFTDSEGNVVGLWET

2r6uD

0.14

1.00

2.41

wdPPAS

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTRTPVGNMGFAAYFTDSEGNVVGLWET

3oxhA

0.23

0.96

2.37

wMUSTER

VVGLTHSS---MYRVLKAGDAEVGGCMEPPMPNHWHVYFAVDDADATAAKAAAAGGQVEPDIPSVGRFAVLSDPQGAIFSVLKA

2r6uD

0.14

1.00

2.52

wPPAS

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTGRPVGNMGFAAYFTDSEGNVVGLWET

2r6uD

0.14

1.00

3.77

dPPAS2

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTRTPVGNMGFAAYFTDSEGNVVGLWET

2r6uD

0.14

1.00

2.37

PPAS

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTGRPVGNMGFAAYFTDSEGNVVGLWET

2r6uD1

0.18

0.10

0.52

2.51

Env-PPAS

----------------------------------------VESIESALERIESLGGKTGRPVGNMGFAAYFTDSEGNVVGLWET

2r6uD

0.14

1.00

1.57

MUSTER

AFGWAIAEPVGESGMPDEPGYINGGMMQRGEVTTPVVTVDVESIESALERIESLGGKTGRTPVGMGFAAYFTDSEGNVVGLWET

2r6uD1

0.18

0.10

0.52

1.89

dPPAS

----------------------------------------VESIESALERIESLGGKTRTPVGNMGFAAYFTDSEGNVVGLWET

(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=-0.54

Estimated TM-score = 0.64±0.13

Estimated RMSD = 4.7±3.1Å

Download Model 2

C-score=-0.85

Download Model 3

C-score=-2.87

Download Model 4

C-score=-1.00

Download Model 5

C-score=-3.56

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	2r6uD	0.783	2.59	0.119	0.976
2	3hdpA	0.674	2.98	0.099	0.917
3	3r6aA	0.672	3.17	0.114	0.929
4	3oxhA	0.664	3.11	0.235	0.941
5	3gm5A	0.659	3.16	0.152	0.929
6	2r5vA	0.641	3.58	0.123	0.952
7	1zswA	0.641	3.07	0.063	0.893
8	3oa4A	0.634	3.21	0.063	0.917
9	1jc5B	0.633	3.69	0.131	0.952
10	3oajA	0.628	2.98	0.036	0.869

(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	0.18	3	4nb0A	CYS	Rep, Mult	38,39,40,82
2	0.06	1	3hpyB	MCT	Rep, Mult	36,64,65,71,80
3	0.06	1	3oxhA	PMB	Rep, Mult	9,15,62,65
4	0.06	1	2ei3A	BPY	Rep, Mult	46,50,54
5	0.06	1	4x4qA	MG	Rep, Mult	38,80
6	0.06	1	2ehzA	MCT	Rep, Mult	72,77,78,79
7	0.06	1	3gm50	III	Rep, Mult	21,22,39,51,54,73,77

	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	0.067	3hdpA	0.674	2.98	0.099	0.917	4.4.1.5	NA
2	0.066	1jc5B	0.633	3.69	0.131	0.952	5.1.99.1	NA
3	0.060	2b3lA	0.489	4.46	0.071	0.893	3.4.11.18	70
4	0.060	4matA	0.495	3.72	0.071	0.845	3.4.11.18	NA
5	0.060	3dbmA	0.531	4.30	0.086	0.952	4.2.1.92	81
6	0.060	3c66A	0.475	2.49	0.049	0.631	2.7.7.19	NA
7	0.060	1f9zA	0.543	2.35	0.095	0.679	4.4.1.5	NA
8	0.060	1egyA	0.500	4.30	0.107	0.869	1.14.-.-	NA
9	0.060	3a4gA	0.499	4.27	0.081	0.857	1.14.13.15	NA
10	0.060	1rp5A	0.491	3.74	0.024	0.786	3.4.-.-	NA
11	0.060	1sqdA	0.486	2.95	0.096	0.667	1.13.11.27	30
12	0.060	2ehzA	0.585	3.24	0.115	0.905	1.13.11.-	NA
13	0.060	2q0eA	0.488	2.66	0.048	0.655	2.7.7.52	NA
14	0.060	3ecjA	0.603	3.27	0.085	0.893	1.13.11.15	NA
15	0.060	1mpyA	0.600	3.06	0.084	0.893	1.13.11.2	NA
16	0.060	3dsiA	0.539	4.02	0.074	0.941	4.2.1.92	NA
17	0.060	1sqiA	0.614	3.90	0.072	0.964	1.13.11.27	43
18	0.060	3lm4D	0.606	3.03	0.105	0.869	1.13.11.2	55
19	0.060	1f1uA	0.598	3.31	0.110	0.893	1.13.11.15	NA
20	0.060	3iw0A	0.494	4.21	0.049	0.929	1.14.-.-	NA
21	0.060	2wm4A	0.520	4.33	0.060	0.917	1.14.-.-	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	0.11	0.674	2.98	0.10	0.92	3hdpA	GO:0016829 GO:0046872
1	0.10	0.683	3.28	0.10	0.95	3r6aB	GO:0004462 GO:0016829
2	0.10	0.633	3.69	0.13	0.95	1jc5B	GO:0004493 GO:0016853
3	0.09	0.609	3.39	0.16	0.93	3zgjB	GO:0003868 GO:0009072 GO:0016701 GO:0046872 GO:0051213 GO:0055114
4	0.09	0.664	3.11	0.23	0.94	3oxhA	GO:0005886
5	0.09	0.659	3.16	0.15	0.93	3gm5A	GO:0016829
6	0.07	0.599	3.35	0.15	0.92	3rmuA	GO:0004493 GO:0005739 GO:0005759 GO:0016853 GO:0019626 GO:0046491 GO:0046872
7	0.07	0.641	3.58	0.12	0.95	2r5vA	GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
8	0.07	0.624	3.24	0.17	0.92	1t47A	GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
9	0.07	0.615	3.09	0.17	0.90	1sp9B	GO:0003868 GO:0005737 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0042802 GO:0046872 GO:0051213 GO:0055114
10	0.07	0.634	3.21	0.06	0.92	3oa4A	GO:0046872
11	0.07	0.621	3.61	0.10	0.92	5d7zA	GO:0004462 GO:0016829 GO:0046872
12	0.07	0.620	3.59	0.09	0.94	5ec3A	GO:0003868 GO:0005829 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114 GO:0070062
13	0.07	0.469	3.43	0.08	0.69	1kmyA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
14	0.07	0.610	3.31	0.15	0.89	1sqiB	GO:0000139 GO:0003868 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0006559 GO:0006572 GO:0009072 GO:0016020 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
15	0.07	0.621	3.63	0.09	0.94	1cjxA	GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
16	0.07	0.512	2.57	0.11	0.65	2p25A
17	0.07	0.519	2.81	0.14	0.68	3l7tA	GO:0004462 GO:0046872
18	0.07	0.499	2.61	0.10	0.67	3ey7A	GO:0003824 GO:0051213 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.39
Biological Processes	GO:0055114	GO:0009072
GO-Score	0.09	0.09
Cellular Component	GO:0005886
GO-Score	0.09

(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.