I-TASSER results

I-TASSER results for job id Rv3364c

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

Input Sequence in FASTA format

>protein (130 residues)
MKARLPDSPLDWLVSKFAREVPGVAHALLVSVDGLPVAASEHLPRERADQLAAVTSGLAS
LAGGAAQLFDGGQVLQSVVEMQNGYLLLMQVGDGSALAALAATGCDIGQIGYEMAILVER
VGGVVQSCRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKARLPDSPLDWLVSKFAREVPGVAHALLVSVDGLPVAASEHLPRERADQLAAVTSGLASLAGGAAQLFDGGQVLQSVVEMQNGYLLLMQVGDGSALAALAATGCDIGQIGYEMAILVERVGGVVQSCRR
Prediction	CCCCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCCEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCEEEEEEHCCCCEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	9988885568999999999788846999995899767774899856789999999999999999999988899569999989969999985899799999789998579999999999999999667899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKARLPDSPLDWLVSKFAREVPGVAHALLVSVDGLPVAASEHLPRERADQLAAVTSGLASLAGGAAQLFDGGQVLQSVVEMQNGYLLLMQVGDGSALAALAATGCDIGQIGYEMAILVERVGGVVQSCRR
Prediction	8656466740330054027525403100001333030132571556403300000011221043005317635042000215412000011343100000036704112023204410630273245668
	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

CCCCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCCEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCEEEEEEHCCCCEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
MKARLPDSPLDWLVSKFAREVPGVAHALLVSVDGLPVAASEHLPRERADQLAAVTSGLASLAGGAAQLFDGGQVLQSVVEMQNGYLLLMQVGDGSALAALAATGCDIGQIGYEMAILVERVGGVVQSCRR

3kyeB

0.39

0.35

0.89

2.36

MUSTER

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVH-GLD-PDSADHAALASGLYSLGRSAGIRFDGGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.36

0.32

0.89

3.43

dPPAS

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVHGLD--PDSADHAALASGLYSLGRSAGIRFGDGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.36

0.32

0.89

3.83

wdPPAS

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVHGLD--PDSADHAALASGLYSLGRSAGIRFGDGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.38

0.34

0.88

2.80

wMUSTER

VS------DLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVH-GLD-PDSADHAALASGLYSLGRSAGIRFDGGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.37

0.33

0.89

3.68

wPPAS

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVH-GLD-PDSADHAALASGLYSLGRSAGIRFGDGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.36

0.32

0.89

9.39

dPPAS2

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVHGLD--PDSADHAALASGLYSLGRSAGIRFGDGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.37

0.33

0.89

3.34

PPAS

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVH-GLD-PDSADHAALASGLYSLGRSAGIRFGDGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3kyeB

0.38

0.34

0.89

4.35

Env-PPAS

-----HVSDLDW-LSGLVQRVPHTTSAVLLSCDGLVKSVH-GLD-PDSADHAALASGLYSLGRSAGIRFGGGDVRQVVVELDSTLLFVSTAGSGTCLAVLAGREADAAVLGYEA--LVKSVRPYLT----

3leqA

0.39

0.29

0.75

2.00

MUSTER

------HSQLDQLLTGLVDRVAEVDHAVVLSEDGLVVSKSTGFLRDDAERLAATASGL---------------LRQALIE-GKGYLILTAAGPGAHLVVLTRQGADVGVVAYQN--LVKKI---------

3leqA

0.39

0.29

0.75

3.04

dPPAS

------HSQLDQLLTGLVDRVAEVDHAVVLSEDGLVVSKSTGFLRDDAERLAATASGLS--------------LRQALIE-GKGYLILTAAGPGAHLVVLTRQGADVGVVAYQN--LVKKI---------

(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=1.26

Estimated TM-score = 0.89±0.07

Estimated RMSD = 2.1±1.7Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=0.58

Download Model 5

C-score=-4.51

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	3kyeB	0.852	1.01	0.397	0.892
2	1j3wB	0.847	2.07	0.173	0.977
3	3r7wB	0.735	2.19	0.148	0.885
4	1skoA	0.735	2.40	0.136	0.900
5	2o9aA	0.720	2.93	0.103	0.954
6	4bwiA1	0.705	3.19	0.146	0.923
7	4zmuA	0.699	2.59	0.158	0.877
8	3eeaA	0.698	2.93	0.117	0.900
9	2qybA	0.697	2.70	0.121	0.877
10	3leqA	0.697	1.37	0.408	0.754

(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	0.07	4	2jfrA	MG	Rep, Mult	33,34
2	0.05	3	3jcuX	CLA	Rep, Mult	53,57
3	0.05	3	3ungC	CA	Rep, Mult	33,34,93
4	0.04	2	1ocoB	HEA	Rep, Mult	116,117
5	0.04	2	2w3dA	HEM	Rep, Mult	25,26,27,38,40,41,43,53,54,98,100
6	0.04	2	2o9aD	PYR	Rep, Mult	51,55,87,98,100
7	0.04	2	5ey1A	GTP	Rep, Mult	10,31,32,33,35,37,124,125,127,128,129
8	0.02	1	2xquB	CVM	Rep, Mult	111,114
9	0.02	1	3ak1D	EDO	Rep, Mult	61,68
10	0.02	1	3cr3A	MG	Rep, Mult	33,49
11	0.02	1	1y10C	CA	Rep, Mult	92,93
12	0.02	1	3necB	DTV	Rep, Mult	4,5,9,123,124,127
13	0.02	1	2h9dD	CA	Rep, Mult	46,49
14	0.02	1	4m70A	III	Rep, Mult	55,58,88,98
15	0.02	1	2jkgA	III	Rep, Mult	8,12,36,118
16	0.02	1	3t1rA	MG	Rep, Mult	76,89
17	0.02	1	3r7wD	GNP	Rep, Mult	16,18,20,110

	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	1zkjA	0.587	3.95	0.084	0.915	3.5.2.6	16
2	0.060	2e8iA	0.595	3.89	0.081	0.923	3.5.1.46	61
3	0.060	2qmiA	0.571	3.86	0.092	0.869	3.5.2.6	16
4	0.060	2rcxB	0.639	3.17	0.061	0.885	3.5.2.6	NA
5	0.060	1mc0A	0.644	3.34	0.043	0.892	3.1.4.17	NA
6	0.060	3dbaB	0.642	3.47	0.051	0.877	3.1.4.35	100
7	0.060	1z6fA	0.585	3.96	0.119	0.885	3.4.16.4	90
8	0.060	2veaA	0.643	3.30	0.107	0.900	2.7.13.3	33,62
9	0.060	3eqvA	0.687	3.59	0.092	0.969	3.4.16.4	NA
10	0.060	3ci6B	0.646	3.18	0.164	0.869	2.7.3.9	63,97,117,123
11	0.060	3fwmA	0.633	3.61	0.086	0.923	2.4.1.129,	NA
12	0.060	2zc7A	0.617	3.66	0.085	0.908	3.5.2.6	16,113
13	0.060	2k2nA	0.659	3.27	0.128	0.900	2.7.13.3	87
14	0.060	2jc7A	0.619	3.54	0.075	0.908	3.5.2.6	15
15	0.060	2j9oD	0.583	4.37	0.070	0.954	3.4.16.4	18,52,106
16	0.060	2rl3B	0.571	3.40	0.045	0.808	3.5.2.6	NA
17	0.060	3fwlA	0.597	4.02	0.055	0.946	2.4.1.129	NA
18	0.060	1c3bA	0.638	3.19	0.052	0.885	3.5.2.6	16
19	0.060	2qz6A	0.623	3.26	0.045	0.854	3.5.2.6	16

(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	0.41	0.866	1.98	0.16	0.98	3t1rC	GO:0042802
1	0.26	0.735	2.40	0.14	0.90	1skoA	GO:0000165 GO:0005085 GO:0005765 GO:0005768 GO:0005925 GO:0007050 GO:0010008 GO:0016020 GO:0016236 GO:0031902 GO:0032006 GO:0032008 GO:0032947 GO:0034613 GO:0043547 GO:0070062 GO:0071230 GO:0071986
2	0.25	0.596	1.91	0.18	0.68	3ms6A	GO:0005085 GO:0005737 GO:0005764 GO:0005765 GO:0005829 GO:0007050 GO:0008361 GO:0009615 GO:0016236 GO:0019079 GO:0032008 GO:0032947 GO:0043066 GO:0043154 GO:0043547 GO:0061462 GO:0071230 GO:0071986
3	0.20	0.740	2.64	0.13	0.92	1vetA	GO:0000186 GO:0005085 GO:0005768 GO:0005770 GO:0005925 GO:0016020 GO:0019209 GO:0031902 GO:0032006 GO:0032008 GO:0032947 GO:0034613 GO:0043547 GO:0070062 GO:0071230 GO:0071986
4	0.19	0.671	3.13	0.16	0.89	3ci6B	GO:0003824 GO:0008965 GO:0009401 GO:0016310 GO:0016740 GO:0016772
5	0.12	0.697	3.20	0.14	0.95	2o99C	GO:0003677 GO:0003700 GO:0005829 GO:0006097 GO:0006351 GO:0006355 GO:0045892
6	0.12	0.699	3.32	0.12	0.95	2ia2A	GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
7	0.12	0.744	2.60	0.14	0.92	4arzB	GO:0000166 GO:0000329 GO:0000790 GO:0003924 GO:0005525 GO:0005634 GO:0005737 GO:0005764 GO:0005773 GO:0005774 GO:0006810 GO:0006914 GO:0009267 GO:0010507 GO:0015031 GO:0016020 GO:0016237 GO:0031902 GO:0034448 GO:0043547 GO:0045944 GO:0071230 GO:1903778 GO:1904263 GO:1990131
8	0.11	0.691	3.35	0.09	0.95	1ysqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
9	0.11	0.675	3.46	0.07	0.93	3obfA	GO:0003677 GO:0006351 GO:0006355
10	0.11	0.669	3.42	0.07	0.94	1tf1A	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0006974 GO:0042802 GO:0045892
11	0.10	0.659	3.33	0.06	0.91	5akpB	GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0018298
12	0.10	0.653	3.27	0.09	0.89	1yspA	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
13	0.10	0.658	2.83	0.10	0.88	3p01A	GO:0000160 GO:0005622
14	0.10	0.629	3.94	0.06	0.93	3mq0B	GO:0003677 GO:0006351 GO:0006355
15	0.10	0.669	3.56	0.10	0.95	2o0yC	GO:0003677 GO:0006351 GO:0006355
16	0.09	0.685	2.54	0.10	0.86	4r70A	GO:0000155 GO:0000160 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0016301 GO:0016310 GO:0018298 GO:0023014
17	0.09	0.671	3.34	0.11	0.92	3w2zA	GO:0004871 GO:0006935 GO:0007165 GO:0016020 GO:0016021 GO:0018298
18	0.09	0.672	3.25	0.13	0.92	4fofA	GO:0004871 GO:0007165 GO:0016020 GO:0016021 GO:0018298
19	0.08	0.661	2.82	0.08	0.86	4arzA	GO:0000166 GO:0000329 GO:0000781 GO:0003924 GO:0005525 GO:0005634 GO:0005737 GO:0005764 GO:0005773 GO:0005774 GO:0006348 GO:0006360 GO:0006383 GO:0006810 GO:0006817 GO:0009267 GO:0010507 GO:0015031 GO:0016020 GO:0031902 GO:0034448 GO:0071230 GO:1903778 GO:1904263 GO:1990131

Consensus prediction of GO terms

Molecular Function	GO:0032947	GO:0005085	GO:0042802	GO:0019207	GO:0008047	GO:0016775
GO-Score	0.56	0.56	0.41	0.41	0.41	0.38
Biological Processes	GO:0071230	GO:0032008	GO:0043547	GO:0043281	GO:0043069	GO:0032535	GO:0051707	GO:0019058	GO:2000117	GO:0072665	GO:0007050	GO:0016236	GO:0043405	GO:0043410	GO:0032147	GO:0008643
GO-Score	0.56	0.56	0.56	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.44	0.44	0.41	0.41	0.41	0.38
Cellular Component	GO:0071986	GO:0005765	GO:0070062	GO:0005925
GO-Score	0.56	0.44	0.41	0.41

(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.