I-TASSER results

I-TASSER results for job id Rv3208A

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

Input Sequence in FASTA format

>protein (90 residues)
MEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYV
EIGVADARRVGFGVGVDAAAGSAGKVATSG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRVGFGVGVDAAAGSAGKVATSG
Prediction	CEEEEEEHCCCCEEEEHCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCEEEEHCCCEEEEEHCCCCCCCEEEEEHCCCCCCCCCCCCCCC
Conf.Score	978999756996799986999999999999999859987999978999999978858999985899986567764444567777666689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRVGFGVGVDAAAGSAGKVATSG
Prediction	761401244143403042744364035304511677542030316543421032631010201477633000011343344444434578
	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

CEEEEEEHCCCCEEEEHCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCEEEEHCCCEEEEEHCCCCCCCEEEEEHCCCCCCCCCCCCCCC
MEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRVGFGVGVDAAAGSAGKVATSG

4nx9A2

0.26

0.23

0.90

0.74

MUSTER

VDIAIDITGSAVNVKVDGNETAEQAAAKIAAAVNDNVGIGAFTD--G-------AQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAG

4nx9A2

0.24

0.21

0.89

0.87

dPPAS

VDIAIDITGGS-AVNVKVDKTAEQAAAKIAAAVNDNVGIGAFTDG---------AQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAG

4nx9A2

0.26

0.22

0.86

0.74

wdPPAS

VDIAIDITGGS-NVKVDKNETAEQAAAKIAAAVNDNVGIGAFTD--G-------AQISYVSASADTTSAVSGVAITDT--GSTG-AGTAA

4nx9A2

0.26

0.23

0.90

0.82

wMUSTER

VDIAIDITGSAVNVKVDGNETAEQAAAKIAAAVNDNVGIGAFTD--G-------AQISYVSASADTTSAVSGVAITDTGSTGAGTAATTT

4nx9A2

0.28

0.24

0.87

0.75

wPPAS

VDIAIDITGSAVNVKVDKNETAEQAAAKIAAAVNDANGIGAFTD--G-------AQISYVSASADTTSAVSGVAITDT--GSTG-AGTAG

4nx9A2

0.24

0.21

0.89

1.14

dPPAS2

VDIAIDITGGS-AVNVKVDKTAEQAAAKIAAAVNDNVGIGAFTDG---------AQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAG

4nx9A2

0.26

0.23

0.90

0.84

PPAS

VDIAIDITGSAVNVKVDKNETAEQAAAKIAAAVNDANGIGAFTD--G-------AQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAG

1isnA2

0.14

0.12

0.84

0.82

Env-PPAS

FTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLAKF--------------

4hcfA

0.13

0.12

0.92

0.69

MUSTER

KVIEVELNDNPNVITIPINES---TTLLLKN--KGKSEHTFTIKKLGIDVVVESGKEKNITVKPKSAGTYELICRYHLLKGE-GKVIVK-

1zxhA

0.09

0.06

0.60

0.80

dPPAS

MYYLVVNKGQNAETLTKAVDAETARNAFIQSLKDDGVQGVWTYDDATKTFTVQA------------------------------------

(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=-1.73

Estimated TM-score = 0.50±0.15

Estimated RMSD = 7.3±4.2Å

Download Model 2

C-score=-2.12

Download Model 3

C-score=-2.32

Download Model 4

C-score=-3.38

Download Model 5

C-score=-4.16

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	1cbyA	0.524	3.92	0.070	0.900
2	1z7mB	0.521	4.12	0.035	0.889
3	1pp0B	0.520	3.82	0.071	0.878
4	2xwxA3	0.520	3.09	0.052	0.822
5	4nx9A2	0.518	3.53	0.188	0.878
6	3bigA1	0.518	3.86	0.025	0.900
7	3rojA2	0.515	3.98	0.047	0.922
8	2a8iA	0.514	3.91	0.103	0.878
9	3ronA	0.512	3.71	0.082	0.856
10	1ddtA3	0.510	4.00	0.047	0.844

(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	0.09	5	4qvpK	MG	Rep, Mult	29,33
2	0.07	4	1jm0D	MN	Rep, Mult	24,27
3	0.05	3	1usy0	III	Rep, Mult	42,45,46,47,49
4	0.03	2	3krdC	FEB	Rep, Mult	4,5,13,59,60
5	0.03	2	3d5bF	MG	Rep, Mult	57,58,59
6	0.03	2	2e0aA	MG	Rep, Mult	27,31
7	0.03	2	1j4pA	III	Rep, Mult	37,38,39,40,41,62,70
8	0.03	2	2jqiA	III	Rep, Mult	30,37,41,50,62,63
9	0.02	1	2yvxA	MG	Rep, Mult	32,35
10	0.02	1	1j4qA	III	Rep, Mult	8,39,62,63
11	0.02	1	2vi7C	AZI	Rep, Mult	56,57
12	0.02	1	2porA	CA	Rep, Mult	13,44
13	0.02	1	1lt6P	GAA	Rep, Mult	58,63
14	0.02	1	1k3nA	III	Rep, Mult	30,53,57,58
15	0.02	1	1sofD	MG	Rep, Mult	20,24

	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	2h6jH	0.370	4.14	0.130	0.667	3.4.25.1	NA
2	0.060	1o0xA	0.500	3.81	0.072	0.822	3.4.11.18	NA
3	0.060	3mr1A	0.488	3.77	0.059	0.833	3.4.11.18	3
4	0.060	1vlpB	0.510	4.41	0.045	0.911	2.4.2.11	63,85
5	0.060	3hriF	0.495	4.40	0.057	0.911	6.1.1.21	NA
6	0.060	1cjyA	0.488	4.31	0.071	0.922	3.1.1.4,3.1.1.5	NA
7	0.060	3hrkA	0.496	4.64	0.069	0.933	6.1.1.21	NA
8	0.060	2im5A	0.487	4.15	0.069	0.889	2.4.2.11	17
9	0.060	2a8iA	0.514	3.91	0.103	0.878	3.4.25.-	NA
10	0.060	3hfaV	0.381	3.71	0.092	0.633	3.4.25.1	NA
11	0.060	1x54A	0.489	4.40	0.071	0.900	6.1.1.22	NA
12	0.060	1wleB	0.500	3.87	0.105	0.800	6.1.1.11	26
13	0.060	1nj1A	0.487	4.10	0.129	0.811	6.1.1.15	NA
14	0.060	1asyA	0.501	4.09	0.061	0.867	6.1.1.12	NA
15	0.060	1m5hC	0.493	4.05	0.034	0.833	2.3.1.101	41,90
16	0.060	3ivcA	0.487	3.64	0.068	0.789	6.3.2.1	NA
17	0.060	1wu7A	0.494	4.25	0.069	0.889	6.1.1.21	NA
18	0.060	1qxwA	0.478	3.75	0.076	0.833	3.4.11.18	6
19	0.060	1q5rN	0.498	3.82	0.037	0.900	3.4.25.1	21,27

(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	0.09	0.497	4.32	0.08	0.89	1usyA	GO:0000105 GO:0005737 GO:0008652
1	0.07	0.522	3.99	0.07	0.90	2rciA	GO:0005576 GO:0009405 GO:0030435
2	0.07	0.490	4.35	0.06	0.91	4phcA	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0005739 GO:0005829 GO:0006412 GO:0006418 GO:0006427 GO:0016874 GO:0032543
3	0.07	0.520	3.82	0.07	0.88	1pp0B	GO:0005576 GO:0009405
4	0.07	0.480	4.39	0.07	0.89	5e3iB	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
5	0.07	0.494	4.25	0.07	0.89	1wu7A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
6	0.07	0.524	3.92	0.07	0.90	1cbyA	GO:0005576 GO:0009405 GO:0030435
7	0.07	0.480	4.34	0.08	0.89	1qe0B	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
8	0.07	0.480	4.40	0.08	0.90	1qe0A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
9	0.07	0.421	4.01	0.09	0.71	1httA	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006427 GO:0016874
10	0.07	0.364	4.49	0.08	0.72	2dfjA	GO:0008803 GO:0016787
11	0.06	0.480	4.32	0.05	0.86	3racA	GO:0004821 GO:0005737 GO:0016874
12	0.06	0.362	4.95	0.08	0.76	4e51A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
13	0.06	0.397	4.50	0.11	0.81	2mlwA	GO:0005576 GO:0009405
14	0.06	0.429	3.85	0.07	0.77	3g04B
15	0.06	0.495	4.40	0.06	0.91	3hriF	GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006418 GO:0006427 GO:0016874
16	0.06	0.520	3.86	0.14	0.90	3ronB	GO:0005576 GO:0009405 GO:0030435
17	0.06	0.395	4.69	0.04	0.76	5bv5D	GO:0004497 GO:0004601 GO:0005506 GO:0005737 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0098869
18	0.06	0.496	4.53	0.05	0.92	4yrcA	GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006418 GO:0006427 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0004821
GO-Score	0.13	0.13
Biological Processes	GO:0006427	GO:0009405	GO:0000105	GO:0030435	GO:0032543
GO-Score	0.13	0.13	0.09	0.07	0.07
Cellular Component	GO:0044424
GO-Score	0.42

(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.