I-TASSER results

I-TASSER results for job id Rv1744c

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

Input Sequence in FASTA format

>protein (133 residues)
MVINRSIASIDSIAVAGSAATTGAVAVAGSVATAGSVAVAGSVATAGSVAIAGAAATAGS
VGIIGSLLTVLCVAVRQCVACLACITCTRCVACIGCVRCTDCVGCLWCVNCSGLRNVVGA
RNLRVGNLGRVSN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVINRSIASIDSIAVAGSAATTGAVAVAGSVATAGSVAVAGSVATAGSVAIAGAAATAGSVGIIGSLLTVLCVAVRQCVACLACITCTRCVACIGCVRCTDCVGCLWCVNCSGLRNVVGARNLRVGNLGRVSN
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCC
Conf.Score	9877888888988888987788888788887788888888887778888788988888988889987668887778887777888788887777887778898888898888888888887555456776689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVINRSIASIDSIAVAGSAATTGAVAVAGSVATAGSVAVAGSVATAGSVAIAGAAATAGSVGIIGSLLTVLCVAVRQCVACLACITCTRCVACIGCVRCTDCVGCLWCVNCSGLRNVVGARNLRVGNLGRVSN
Prediction	4323334434334424333334233434343424243334333333233334333424233434233333333424333323223424433323123423434323123414233323324524145446468
	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                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCC
MVINRSIASIDSIAVAGSAATTGAVAVAGSVATAGSVAVAGSVATAGSVAIAGAAATAGSVGIIGSLLTVLCVAVRQCVACLACITCTRCVACIGCVRCTDCVGCLWCVNCSGLRNVVGARNLRVGNLGRVSN

3boiA

0.22

0.14

0.61

2.00

MUSTER

--------------CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------------------

3boiA

0.16

0.10

0.61

2.34

dPPAS

-----CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP---------------------------------------------

3boiA

0.16

0.10

0.61

3.51

wdPPAS

-----CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP---------------------------------------------

3boiA

0.23

0.14

0.60

3.98

wMUSTER

---------------KGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------------------

3boiA

0.19

0.11

0.61

3.67

wPPAS

--CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------------------------------

3boiA

0.16

0.10

0.61

5.44

dPPAS2

-----CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP---------------------------------------------

3boiA

0.19

0.11

0.61

3.40

PPAS

--CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------------------------------

4e75A2

0.14

0.97

0.86

Env-PPAS

TARIHPSAVISETAYIGHYVVIGENCVVGDNTVIQSHTKLDDNVEVGKDCFIDSYVTITGSSKLRDRVRIHSSTVIGGEG-FGFAPYQGKWHRIAQLGSVGNDVRIG-SNCSIDRGALD--NTILEDGVIIDN

3bogA

0.24

0.14

0.60

1.81

MUSTER

--------------CKGADGAHG-VGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAG--GASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------------------

3bogA

0.19

0.11

0.60

2.10

dPPAS

--------------------------CKGADGAHG-VGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAG--GASGGTGVGGRGGKGGSGTPKGADGAPGAP------------------------

(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=-1.98

Estimated TM-score = 0.48±0.15

Estimated RMSD = 8.8±4.6Å

Download Model 2

C-score=-2.51

Download Model 3

C-score=-2.84

Download Model 4

C-score=-2.77

Download Model 5

C-score=-2.90

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	3pffA2	0.555	4.18	0.067	0.895
2	3mwdA	0.535	4.18	0.051	0.880
3	4oifA	0.529	4.20	0.086	0.872
4	3civA	0.526	4.09	0.050	0.842
5	3mbfA	0.526	4.21	0.073	0.857
6	4rm6A	0.521	4.54	0.057	0.895
7	4dn7A	0.517	3.92	0.039	0.842
8	4i84A	0.515	3.91	0.076	0.789
9	2zu0A	0.514	4.17	0.070	0.880
10	5cskA4	0.511	4.47	0.074	0.842

(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	6	3srfC	PYR	Rep, Mult	19,21,48,50,52,82
2	0.08	4	2quvB	PO4	Rep, Mult	19,20,21,48,51
3	0.04	2	2quvA	PO4	Rep, Mult	13,14,40,41
4	0.04	2	1rwvA	5PH	Rep, Mult	58,59,60,85,87
5	0.04	2	4oa5A	IOD	Rep, Mult	48,80,118
6	0.02	1	2wse1	CLA	Rep, Mult	20,23
7	0.02	1	5elcC	GAL	Rep, Mult	47,49
8	0.02	1	1zalC	PO4	Rep, Mult	16,17,45,46,47
9	0.02	1	1zalB	PO4	Rep, Mult	68,69,70,95,96,97,98
10	0.02	1	4b3eJ	CO3	Rep, Mult	119,121
11	0.02	1	3iylA	MYR	Rep, Mult	41,51
12	0.02	1	3mi1B	FE	Rep, Mult	33,35
13	0.02	1	1c9uA	CA	Rep, Mult	10,15
14	0.02	1	3nvjA	NEN	Rep, Mult	77,102

	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	1adoA	0.524	4.35	0.040	0.865	4.1.2.13	NA
2	0.060	2wdpD	0.503	4.22	0.065	0.804	3.4.22.59	NA
3	0.060	1bglA	0.473	4.35	0.017	0.789	3.2.1.23	NA
4	0.060	1b4eA	0.484	4.57	0.024	0.789	4.2.1.24	NA
5	0.060	1fdjA	0.508	4.54	0.049	0.865	4.1.2.13	NA
6	0.060	1e5jA	0.488	4.13	0.050	0.789	3.2.1.4	NA
7	0.060	3cyvA	0.484	4.22	0.065	0.782	4.1.1.37	NA
8	0.060	2nn3D	0.496	4.43	0.056	0.827	3.4.22.36	NA
9	0.060	1xfbA	0.487	4.60	0.062	0.820	4.1.2.13	NA
10	0.060	3e4cA	0.499	4.12	0.079	0.804	3.4.22.36	NA
11	0.060	1pclA	0.489	4.34	0.084	0.812	4.2.2.2	NA
12	0.060	3kx6A	0.491	4.62	0.071	0.820	4.1.2.13	NA
13	0.060	1f2jA	0.487	4.65	0.046	0.835	4.1.2.13	NA
14	0.060	1hjuC	0.479	4.42	0.049	0.789	3.2.1.89	NA
15	0.060	1aldA	0.501	5.05	0.038	0.910	4.1.2.13	80,106
16	0.060	1kcdA	0.487	4.58	0.073	0.842	3.2.1.15	NA
17	0.060	1bqcA	0.494	4.22	0.041	0.804	3.2.1.78	NA
18	0.060	3fn9C	0.485	4.38	0.066	0.804	3.2.1.23	NA
19	0.060	1xc6A	0.503	4.22	0.036	0.827	3.2.1.23	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	0.07	0.462	4.61	0.04	0.80	3amdB	GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
1	0.07	0.434	4.49	0.06	0.74	1eucB	GO:0000166 GO:0003824 GO:0004776 GO:0005524 GO:0005525 GO:0005739 GO:0006099 GO:0008152 GO:0016874
2	0.07	0.374	4.72	0.07	0.68	1jkjA	GO:0000166 GO:0003824 GO:0004775 GO:0005524 GO:0005737 GO:0005829 GO:0006099 GO:0006104 GO:0006105 GO:0008152 GO:0009142 GO:0009361 GO:0016874 GO:0046777 GO:0048037
3	0.07	0.465	4.69	0.05	0.81	3amgB	GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
4	0.07	0.382	4.92	0.07	0.69	3ufxA	GO:0000166 GO:0003824 GO:0004775 GO:0005524 GO:0006099 GO:0008152 GO:0016874 GO:0048037
5	0.06	0.430	4.54	0.08	0.73	2yv1A	GO:0000166 GO:0003824 GO:0004775 GO:0005524 GO:0005829 GO:0006099 GO:0006104 GO:0006105 GO:0008152 GO:0009142 GO:0016874 GO:0048037
6	0.06	0.494	4.22	0.04	0.80	1bqcA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
7	0.06	0.399	5.21	0.08	0.77	3k2kA	GO:0004181 GO:0006508 GO:0008270
8	0.06	0.429	4.86	0.04	0.75	1eucA	GO:0000166 GO:0003824 GO:0004775 GO:0004776 GO:0005525 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006104 GO:0006105 GO:0008152 GO:0009142 GO:0016874 GO:0048037
9	0.06	0.435	4.58	0.10	0.73	2yv2A	GO:0000166 GO:0003824 GO:0004775 GO:0005524 GO:0008152 GO:0016874 GO:0048037
10	0.06	0.553	4.02	0.06	0.88	3pffA	GO:0000166 GO:0003824 GO:0003878 GO:0005524 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006084 GO:0006085 GO:0006101 GO:0006107 GO:0006629 GO:0006633 GO:0006695 GO:0008152 GO:0008610 GO:0016020 GO:0016740 GO:0031325 GO:0035338 GO:0046872 GO:0046912 GO:0048037 GO:0070062
11	0.06	0.395	5.27	0.08	0.77	4b6zB	GO:0004181 GO:0006508 GO:0008270 GO:0046872
12	0.06	0.364	4.53	0.06	0.62	2anuA	GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0046872 GO:0071897
13	0.06	0.276	5.38	0.05	0.54	4mpoB	GO:0016787
14	0.06	0.313	4.92	0.02	0.53	1eapB
15	0.06	0.303	5.90	0.02	0.65	1autC	GO:0004252 GO:0005509 GO:0005576 GO:0005615 GO:0005783 GO:0005788 GO:0005794 GO:0005796 GO:0006465 GO:0006508 GO:0006888 GO:0007596 GO:0007599 GO:0008233 GO:0008236 GO:0016787 GO:0017187 GO:0030195 GO:0043066 GO:0050728 GO:0050819 GO:0050900 GO:1903142
16	0.06	0.239	4.81	0.06	0.44	3dbjB	GO:0015979 GO:0018298 GO:0030089 GO:0055114
17	0.06	0.445	4.39	0.07	0.72	1jkjB	GO:0000166 GO:0000287 GO:0003824 GO:0004775 GO:0005524 GO:0005737 GO:0005829 GO:0006099 GO:0008152 GO:0009361 GO:0016874 GO:0030145 GO:0046872
18	0.06	0.272	5.02	0.03	0.50	1ie5A	GO:0005886 GO:0007155 GO:0016020 GO:0016021 GO:0030198 GO:0031175 GO:0048167

Consensus prediction of GO terms

Molecular Function	GO:0032550	GO:0035639	GO:0032559
GO-Score	0.37	0.37	0.37
Biological Processes	GO:0009060	GO:0006082	GO:0044238
GO-Score	0.37	0.37	0.32
Cellular Component	GO:0009986	GO:0005576	GO:0009361	GO:0005829	GO:0005739
GO-Score	0.13	0.13	0.07	0.07	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.