I-TASSER results

I-TASSER results for job id Rv3353c

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

Input Sequence in FASTA format

>protein (86 residues)
MSRQTFLRGAVGAPATSAVFPTILARATPGDGWASLASSIGGQVLLPANGRAFTSGKQIF
NSNYSGLNPAAVVTVASQADVRKAVS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSRQTFLRGAVGAPATSAVFPTILARATPGDGWASLASSIGGQVLLPANGRAFTSGKQIFNSNYSGLNPAAVVTVASQADVRKAVS
Prediction	CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCEEHCCCCCCCHHHHHHHHHCCCCCCCEEEEEHCCHHHHHHHHC
Conf.Score	97899998776666665445777777888887899998769959957999986678888765578888758999889999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSRQTFLRGAVGAPATSAVFPTILARATPGDGWASLASSIGGQVLLPANGRAFTSGKQIFNSNYSGLNPAAVVTVASQADVRKAVS
Prediction	86343224223434333342344444464454154036516141122354551530341234415634120103134474145138
	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

CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCEEHCCCCCCCHHHHHHHHHCCCCCCCEEEEEHCCHHHHHHHHC
MSRQTFLRGAVGAPATSAVFPTILARATPGDGWASLASSIGGQVLLPANGRAFTSGKQIFNSNYSGLNPAAVVTVASQADVRKAVS

3w8wA1

0.21

0.15

0.71

1.24

MUSTER

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

1.11

dPPAS

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

1.64

wdPPAS

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.22

0.15

0.70

1.43

wMUSTER

------------------------FPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

2.04

wPPAS

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

1.96

dPPAS2

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

1.89

PPAS

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

3w8wA1

0.21

0.15

0.71

1.61

Env-PPAS

-----------------------QFPQLDPATLAAFSAAFRGELIWPSD-ADYDEARRIWNGTID-RRPALIARCTSTPDVVAAVS

2bvgA1

0.30

0.17

0.58

0.86

MUSTER

----------------------------------KLATSIQGEVIYPDD-SGFDAIANIWDGRHL-QRPSLIARCLSAGDVAKSVR

2bvgA1

0.25

0.15

0.60

0.74

dPPAS

--------------------------------KLATPLSIQGEVIYPDD-SGFDAIANIWDGRHL-QRPSLIARCLSAGDVAKSVR

(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=-1.10

Estimated TM-score = 0.58±0.14

Estimated RMSD = 5.9±3.7Å

Download Model 2

C-score=-2.76

Download Model 3

C-score=-3.21

Download Model 4

C-score=-3.96

Download Model 5

C-score=-4.49

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	3w8wA1	0.626	1.30	0.213	0.709
2	3d2dA1	0.538	2.47	0.131	0.709
3	5d79A	0.525	2.15	0.123	0.663
4	3tshA	0.525	2.11	0.161	0.651
5	4urpA	0.520	3.07	0.063	0.779
6	3aczA	0.517	2.93	0.013	0.756
7	3vteA	0.517	2.59	0.083	0.686
8	1bkjA	0.516	2.85	0.067	0.756
9	1e5eA2	0.516	3.16	0.025	0.767
10	1zchA1	0.516	2.79	0.027	0.744

(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	0.12	4	3rbxA	CA	Rep, Mult	41,80
2	0.06	2	1jfiA	NUC	Rep, Mult	79,83
3	0.06	2	2z6iB	CA	Rep, Mult	37,40
4	0.03	1	3nbtA	HEM	Rep, Mult	20,36,40
5	0.03	1	4f8hA	LMD	Rep, Mult	15,18
6	0.03	1	2hj6L	PS2	Rep, Mult	6,40
7	0.03	1	1ykiB	NFZ	Rep, Mult	49,50,54,55,58
8	0.03	1	1bjeA	AZI	Rep, Mult	11,75
9	0.03	1	2d41B	SNH	Rep, Mult	37,44,45
10	0.03	1	1fxrB	SO4	Rep, Mult	9,77,78
11	0.03	1	3rjaA	ABL	Rep, Mult	43,44,45,46,49,52,74

	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	1t3tA	0.469	3.97	0.089	0.872	6.3.5.3	66
2	0.060	1ds7A	0.515	3.07	0.051	0.791	1.5.1.34,1.6.99.7	NA
3	0.060	1qgnA	0.490	3.19	0.075	0.767	2.5.1.48	NA
4	0.060	3cogD	0.516	2.93	0.025	0.756	4.4.1.1	NA
5	0.060	1cliA	0.472	4.13	0.068	0.849	6.3.3.1	NA
6	0.060	2dgmC	0.471	3.56	0.069	0.767	4.1.1.15	NA
7	0.060	3d2jA	0.517	2.54	0.102	0.686	1.21.3.3	41,42
8	0.060	1v5yA	0.485	3.42	0.075	0.791	1.6.99.-	NA
9	0.060	2btuA	0.477	3.98	0.145	0.872	6.3.3.1	NA
10	0.060	2v9yA	0.507	3.88	0.118	0.872	6.3.3.1	42
11	0.060	3fd5B	0.473	3.98	0.093	0.826	2.7.9.3	NA
12	0.060	1bjoA	0.466	3.73	0.045	0.779	2.6.1.52	23
13	0.060	1e5eA	0.516	3.16	0.025	0.767	4.4.1.11	NA
14	0.060	1m5hC	0.467	4.00	0.082	0.837	2.3.1.101	12,72
15	0.060	1n8pC	0.485	3.58	0.050	0.791	4.4.1.1	5,42
16	0.060	1diiA	0.490	2.70	0.153	0.686	1.17.99.1	NA
17	0.060	1bjnA	0.465	3.57	0.045	0.767	2.6.1.52	NA
18	0.060	3gh8A	0.487	3.24	0.050	0.791	1.-.-.-	NA
19	0.060	1cl1B	0.453	3.80	0.038	0.802	4.4.1.8	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	0.08	0.632	1.24	0.21	0.71	3w8wB	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
1	0.07	0.523	2.12	0.16	0.65	4pveA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
2	0.07	0.517	2.54	0.10	0.69	3d2jA	GO:0003824 GO:0009820 GO:0016023 GO:0016491 GO:0016614 GO:0031410 GO:0050468 GO:0050660 GO:0055114
3	0.07	0.517	2.15	0.16	0.64	4dnsA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
4	0.07	0.525	2.15	0.12	0.66	5d79A	GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
5	0.07	0.496	2.23	0.12	0.66	3pm9A	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
6	0.07	0.510	1.92	0.25	0.60	2bvfA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0018530 GO:0050660 GO:0055114
7	0.07	0.517	2.59	0.08	0.69	3vteA	GO:0003824 GO:0005576 GO:0016491 GO:0016614 GO:0048046 GO:0050660 GO:0055114
8	0.07	0.503	2.51	0.18	0.69	4ud8A	GO:0000166 GO:0003824 GO:0005618 GO:0009506 GO:0009793 GO:0010197 GO:0016491 GO:0016614 GO:0045551 GO:0050660 GO:0055114
9	0.07	0.435	3.88	0.06	0.78	5adzA	GO:0003824 GO:0005730 GO:0005739 GO:0005777 GO:0005778 GO:0006629 GO:0008609 GO:0008610 GO:0008611 GO:0016020 GO:0016491 GO:0016614 GO:0016740 GO:0043231 GO:0050660 GO:0055114 GO:0071949
10	0.07	0.418	3.62	0.03	0.76	3s1eA	GO:0003824 GO:0005576 GO:0005615 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
11	0.07	0.409	4.11	0.08	0.77	4mlaB	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
12	0.07	0.418	4.07	0.07	0.78	4ml8A	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
13	0.07	0.445	1.91	0.16	0.52	2y08B	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
14	0.07	0.467	2.57	0.17	0.64	2axrA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0046872 GO:0050660 GO:0055114
15	0.07	0.425	3.85	0.11	0.77	2ipiA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0017000 GO:0050660 GO:0055114
16	0.06	0.457	2.37	0.19	0.62	3rj8A	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0046562 GO:0046872 GO:0050660 GO:0055114
17	0.06	0.381	3.03	0.04	0.58	4ncrA	GO:0003824 GO:0003885 GO:0005737 GO:0005886 GO:0016020 GO:0016491 GO:0016614 GO:0035884 GO:0040007 GO:0045227 GO:0050660 GO:0055114 GO:0070592 GO:0071555
18	0.06	0.444	3.48	0.07	0.74	3popA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016614	GO:0050660
GO-Score	0.30	0.30
Biological Processes	GO:0055114
GO-Score	0.30
Cellular Component	GO:0016023
GO-Score	0.07

(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.