I-TASSER results

I-TASSER results for job id Rv3897c

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

Input Sequence in FASTA format

>protein (210 residues)
MMQQAVSGITGALGGAVGGVMGPLTQLPQQAMQAGQGAMQPLMSALQQTYGAEGLDVADG
ARLVDSIEGEPGLGGEPGAGDVGAGGGGGGTTPTGYLGPPPVPTSSPPTTPAGAPAKSVT
PDPVSGTPRASGPAGMTGMPMVPPGALGAGAEGANKDKPVEKRVTGCAEWSTGQGPLNST
AECSGEICRRQAGGHQVDATDPCCAERRQG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMQQAVSGITGALGGAVGGVMGPLTQLPQQAMQAGQGAMQPLMSALQQTYGAEGLDVADGARLVDSIEGEPGLGGEPGAGDVGAGGGGGGTTPTGYLGPPPVPTSSPPTTPAGAPAKSVTPDPVSGTPRASGPAGMTGMPMVPPGALGAGAEGANKDKPVEKRVTGCAEWSTGQGPLNSTAECSGEICRRQAGGHQVDATDPCCAERRQG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCC
Conf.Score	988654566677778888889998888888888888888999888888888888888899987788999999999989888899999999999888999999999999999999999999999999999999988899999999888999999999999888888999888888999988877776555667876667788764444579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMQQAVSGITGALGGAVGGVMGPLTQLPQQAMQAGQGAMQPLMSALQQTYGAEGLDVADGARLVDSIEGEPGLGGEPGAGDVGAGGGGGGTTPTGYLGPPPVPTSSPPTTPAGAPAKSVTPDPVSGTPRASGPAGMTGMPMVPPGALGAGAEGANKDKPVEKRVTGCAEWSTGQGPLNSTAECSGEICRRQAGGHQVDATDPCCAERRQG
Prediction	735422542433332343343432451354145345443444343254544544253274352144345444242452544443444573433434343442445443544444446644442444444443432344242323234235454367653466424324446455243344350424104443444515244412364678
	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                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCC
MMQQAVSGITGALGGAVGGVMGPLTQLPQQAMQAGQGAMQPLMSALQQTYGAEGLDVADGARLVDSIEGEPGLGGEPGAGDVGAGGGGGGTTPTGYLGPPPVPTSSPPTTPAGAPAKSVTPDPVSGTPRASGPAGMTGMPMVPPGALGAGAEGANKDKPVEKRVTGCAEWSTGQGPLNSTAECSGEICRRQAGGHQVDATDPCCAERRQG

2pffA

0.20

1.00

2.24

MUSTER

GGGGGGGGGGGGGG-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

1vt4I4

0.21

0.17

0.78

1.72

dPPAS

-----------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG----------------------------

3boiA

0.22

0.09

0.39

2.44

wdPPAS

---------------------------------CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGA-----SGGTGVGGRGGKGGSGTPKGADGAPGAP-----------------------------------------------------------------------------------------

1vt4I3

0.20

1.00

3.50

wMUSTER

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3boiA

0.22

0.09

0.39

2.43

wPPAS

---------------CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVG--GAGGASGGTGVGGRGGKGGSGT-----PKGADGAPGAP-----------------------------------------------------------------------------------------------------------

3boiA

0.19

0.07

0.39

3.64

dPPAS2

------------------------------------CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAG-------GASGGTGVGGRGGKGGSGTPKGADGAPGAP--------------------------------------------------------------------------------------

1vt4I4

0.21

0.17

0.78

2.67

PPAS

-----------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG----------------------

1kx5B

0.13

0.06

0.45

0.71

Env-PPAS

---------------------------------------------------------------------------------------------------------------SGRGKGGKGLGKGGAKRHRK--VLRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH-AKRKTVTAMDVVYALKRQG

2pffB

0.21

0.20

0.99

2.21

MUSTER

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--GGGGGG

3boiA

0.19

0.07

0.39

1.66

dPPAS

------------------------------------CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAG-------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=-2.90

Estimated TM-score = 0.38±0.13

Estimated RMSD = 12.2±4.4Å

Download Model 2

C-score=-3.74

Download Model 3

C-score=-4.10

Download Model 4

C-score=-3.76

Download Model 5

C-score=-4.72

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	4aahA	0.618	4.67	0.063	0.933
2	4maeA	0.610	4.77	0.058	0.938
3	1kv9A	0.608	4.82	0.063	0.933
4	4zn4A	0.608	4.26	0.055	0.886
5	1kb0A1	0.605	4.87	0.063	0.933
6	1hj5A	0.601	4.63	0.041	0.914
7	4pk1A	0.598	4.76	0.041	0.919
8	2uzyB1	0.596	4.86	0.048	0.933
9	3nvnB	0.596	4.99	0.068	0.948
10	4cvbA	0.594	4.72	0.030	0.909

(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	0.13	6	2ovrB	III	Rep, Mult	24,41,62,78,109,145,204
2	0.07	3	1e1aA	CA	Rep, Mult	24,109,146,204
3	0.02	1	1qniA	CUA	Rep, Mult	39,41,63
4	0.02	1	1cq1B	CA	Rep, Mult	87,88
5	0.02	1	3fbyC	CA	Rep, Mult	146,148,150,152,153,155
6	0.02	1	1yklA	DHB	Rep, Mult	98,99,190
7	0.02	1	3lw5H	CLA	Rep, Mult	28,30
8	0.02	1	3sbrF	IMD	Rep, Mult	119,174,182
9	0.02	1	4v0nF	HG	Rep, Mult	61,62,107
10	0.02	1	1flgA	CA	Rep, Mult	56,59,81
11	0.02	1	3t6xB	CBS	Rep, Mult	92,178,180
12	0.02	1	2rhpA	CA	Rep, Mult	70,72,74,76
13	0.02	1	1yo8A	CA	Rep, Mult	169,171,173,175,178
14	0.02	1	1yo8A	CA	Rep, Mult	150,152,155,157,160,161,162
15	0.02	1	1yklG	DHB	Rep, Mult	98,99
16	0.02	1	3fbyC	CA	Rep, Mult	52,53,54,56,58,60,64,67

	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	2f10A	0.565	4.79	0.035	0.871	3.2.1.18	NA
2	0.060	2gc7A	0.555	4.98	0.057	0.876	1.4.99.3	69
3	0.060	1nn2A	0.550	4.50	0.054	0.829	3.2.1.18	NA
4	0.060	1gjqA	0.589	4.91	0.071	0.933	1.7.99.1,1.7.2.1	NA
5	0.060	2aepA	0.549	4.41	0.059	0.824	3.2.1.18	NA
6	0.060	1madH	0.554	4.98	0.079	0.876	1.4.99.3	69,114
7	0.060	2g8sA	0.557	4.57	0.047	0.843	1.1.5.-	NA
8	0.060	1aomB	0.596	4.91	0.050	0.948	1.7.99.1,1.7.2.1	NA
9	0.060	1qksB	0.598	4.89	0.055	0.948	1.7.2.1	79
10	0.060	1cvmA	0.558	4.95	0.051	0.876	3.1.3.8	38,208
11	0.060	1vcuB	0.566	4.96	0.041	0.895	3.2.1.18	NA
12	0.060	1kv9A	0.608	4.82	0.063	0.933	1.1.99.-	NA
13	0.060	1s0kA	0.552	4.90	0.041	0.881	3.2.1.18	NA
14	0.060	1fwxA	0.570	4.87	0.068	0.881	1.7.99.6	81
15	0.060	1kb0A	0.605	4.87	0.063	0.933	1.1.99.-	NA
16	0.060	1jofA	0.574	4.96	0.076	0.890	5.5.1.5	NA
17	0.060	2h47H	0.560	5.07	0.036	0.900	1.4.99.4	111,115
18	0.060	2bixA	0.556	5.26	0.036	0.909	1.14.99.-	144
19	0.060	1ri6A	0.573	4.77	0.048	0.871	3.1.1.31	62

(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	0.605	4.86	0.06	0.93	1kb0A	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114
1	0.07	0.608	4.82	0.06	0.93	1kv9A	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114 GO:0070968
2	0.07	0.610	4.77	0.06	0.94	4maeA	GO:0005509 GO:0016020 GO:0016491 GO:0016614 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0052934 GO:0052935 GO:0052936 GO:0055114
3	0.07	0.540	5.17	0.06	0.88	4hdjA	GO:0009279 GO:0016020 GO:0043165 GO:0051205
4	0.07	0.560	4.49	0.05	0.83	4immA	GO:0009279 GO:0016020 GO:0043165 GO:0046872 GO:0051205
5	0.07	0.514	4.94	0.05	0.81	1lrwA	GO:0005509 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0042597 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
6	0.07	0.618	4.67	0.06	0.93	4aahA	GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
7	0.07	0.598	4.76	0.04	0.92	4pk1A	GO:0007155 GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0042802 GO:0043165 GO:0051205 GO:0071709 GO:1990063
8	0.07	0.518	4.87	0.03	0.80	2d0vA	GO:0005509 GO:0016020 GO:0016614 GO:0030288 GO:0046872 GO:0055114
9	0.07	0.588	4.71	0.01	0.90	1yiqA	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0042597 GO:0046872 GO:0055114 GO:0070968
10	0.07	0.590	4.68	0.04	0.90	1flgA	GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
11	0.07	0.594	4.72	0.03	0.91	4cvbA	GO:0046872
12	0.07	0.617	4.67	0.04	0.93	4tqoA	GO:0005509 GO:0015946 GO:0016020 GO:0016614 GO:0018468 GO:0030288 GO:0046872 GO:0055114
13	0.07	0.507	4.99	0.04	0.80	1w6sC	GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
14	0.06	0.337	5.94	0.07	0.61	3tkkA	GO:0016811 GO:0046872
15	0.06	0.316	6.06	0.05	0.57	3rd5A
16	0.06	0.289	6.69	0.04	0.58	3q58A	GO:0003824 GO:0005975 GO:0006051 GO:0008152 GO:0016853 GO:0016857 GO:0019262 GO:0047465
17	0.06	0.300	5.73	0.01	0.52	3clrD	GO:0009055 GO:0050660 GO:0055114
18	0.06	0.287	5.70	0.02	0.50	3p2lA	GO:0004252 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0046872
GO-Score	0.37
Biological Processes	GO:0044710
GO-Score	0.37
Cellular Component	GO:0030288	GO:0009279
GO-Score	0.13	0.13

(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.