I-TASSER results

I-TASSER results for job id Rv0390

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

Input Sequence in FASTA format

>protein (140 residues)
MSYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTH
NDNFLAELRDRIPADADQHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLD
AEGHRGATGWRAVGLPWRQG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRIPADADQHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG
Prediction	CCCCCCCCHHHHHHHHHHCCCEEEEHCCCHHHHHHHCCCCCCCCCCCCEEHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCHHHHHHHHHHHHHCCCCEEHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC
Conf.Score	99865699999999999899979998799899987498885447876467544678887885899999999876578999879998799989999999999989997576468755555547887655478879998779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRIPADADQHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG
Prediction	67344703163035106756501001343464164242241442445113132443643434611540474167554556220000021231033004204734164023033014124556455434104647134658
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHCCCEEEEHCCCHHHHHHHCCCCCCCCCCCCEEHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCHHHHHHHHHHHHHCCCCEEHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC
MSYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRIPADADQHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

3.84

MUSTER

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

4.17

dPPAS

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

4.61

wdPPAS

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.93

0.94

4.52

wMUSTER

--YAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

4.91

wPPAS

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

6.89

dPPAS2

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

4.51

PPAS

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2fsxA

0.99

0.94

4.61

Env-PPAS

-SYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRI-------PRPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG

2dcqA

0.29

0.26

0.89

2.79

MUSTER

GSSGSSGSAKNAYTKLGTDDNAQLLDIRATADFRQVGSPNIKGLGKKAVSTVY---NGEDKPGFLKKLSLKF---KDPENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAEGP---------RGWLNSSLPWIEP

2dcqA

0.29

0.26

0.89

2.96

dPPAS

GSSGSSGSAKNAYTKLGTDDNAQLLDIRATADFRQVGSPNIKGLGKKAVSTVYN---GEDKPGFLKKLSLK---FKDPENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAEGP---------RGWLNSSLPWIEP

(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 1 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=1.61

Estimated TM-score = 0.94±0.05

Estimated RMSD = 1.6±1.4Å

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	2fsxA	0.922	0.80	0.992	0.943
2	2dcqA	0.773	1.78	0.274	0.864
3	3ippB	0.679	2.88	0.182	0.864
4	1qxnA	0.676	2.15	0.257	0.779
5	3fs5A	0.670	2.62	0.181	0.829
6	2hhgA	0.666	1.94	0.245	0.757
7	1gn0A	0.664	2.12	0.264	0.757
8	2j6pA	0.662	2.45	0.161	0.800
9	3tp9A	0.659	1.78	0.260	0.743
10	3i2vA	0.655	2.62	0.162	0.786

(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	0.28	4	1qxnA	PS5	Rep, Mult	28,87,113,114,115
2	0.13	2	1h4kX	PO2	Rep, Mult	87,88,89,91,92
3	0.06	1	2yjfA	MG	Rep, Mult	26,115
4	0.06	1	1siwA	SF4	Rep, Mult	26,27,87,89,93,94,111
5	0.06	1	3icsB	ADP	Rep, Mult	11,24,25,26,110,111

	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	0.218	2jtqA	0.548	1.59	0.200	0.607	2.8.1.1	87,90,110
2	0.163	1cwsA	0.636	3.02	0.179	0.800	3.1.3.48	49,87
3	0.089	1c25A	0.630	2.90	0.161	0.793	3.1.3.48	49,92
4	0.067	2gwfC	0.621	2.89	0.144	0.793	3.1.2.15	NA
5	0.066	1t3kA	0.503	3.92	0.147	0.771	3.1.3.48	27,92,115
6	0.060	3ippB	0.679	2.88	0.182	0.864	2.8.1.1	9,128
7	0.060	1q16A	0.572	4.59	0.051	0.950	1.7.99.4	NA
8	0.060	1ivyA	0.561	3.91	0.066	0.843	3.4.16.5	NA
9	0.060	1qo9A	0.565	3.66	0.052	0.821	3.1.1.7	NA
10	0.060	1tyaE	0.561	4.34	0.086	0.893	6.1.1.1	NA
11	0.060	1e0cA	0.651	2.78	0.147	0.821	2.8.1.1	87,92
12	0.060	1bohA	0.655	2.71	0.197	0.814	2.8.1.1	88,90
13	0.060	3f4aB	0.652	2.76	0.193	0.814	3.1.3.16	92,97
14	0.060	2qjoB	0.563	4.28	0.108	0.864	2.7.7.1	NA
15	0.060	1f6wA	0.559	3.69	0.081	0.821	3.1.1.13,3.1.1.3	NA
16	0.060	2veoB	0.596	3.77	0.093	0.879	3.1.1.3	NA
17	0.060	1pq3A	0.560	3.83	0.092	0.807	3.5.3.1	NA
18	0.060	1y42X	0.565	4.13	0.093	0.879	6.1.1.1	NA
19	0.060	1gn0A	0.664	2.12	0.264	0.757	2.8.1.1	96,115
20	0.060	3d1pA	0.626	2.76	0.191	0.771	2.8.1.1	24,84,89
21	0.060	2oucB	0.640	2.53	0.108	0.786	3.1.3.16,3.1.3.48	32,49
22	0.060	2w22A	0.577	3.79	0.090	0.829	3.1.1.3	135
23	0.060	2vswB	0.653	2.73	0.114	0.814	3.1.3.16,3.1.3.48	24,32,89
24	0.060	3bfjT	0.582	3.67	0.098	0.857	1.1.1.202	8

(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	0.68	0.922	0.80	0.99	0.94	2fsxA	GO:0016740
1	0.35	0.664	2.12	0.26	0.76	1gn0A	GO:0004792 GO:0005737 GO:0006071 GO:0016740
2	0.34	0.773	1.78	0.27	0.86	2dcqA	GO:0004568 GO:0005576 GO:0006032 GO:0008061 GO:0009507 GO:0009534 GO:0009535 GO:0009536 GO:0009579 GO:0009772 GO:0009941 GO:0016020 GO:0016021 GO:0042742
3	0.21	0.582	2.56	0.21	0.74	2moiA	GO:0004792 GO:0005886 GO:0005887 GO:0016020 GO:0016021
4	0.21	0.626	2.44	0.16	0.75	3g5jA	GO:0016785 GO:0043828 GO:0070329
5	0.20	0.661	2.61	0.16	0.79	3i2vA	GO:0000166 GO:0002098 GO:0002143 GO:0003824 GO:0004792 GO:0005524 GO:0005737 GO:0005829 GO:0006777 GO:0008033 GO:0008152 GO:0008641 GO:0016740 GO:0016779 GO:0016783 GO:0018117 GO:0018192 GO:0032324 GO:0032447 GO:0034227 GO:0042292 GO:0046872 GO:0061604 GO:0061605 GO:0070733
6	0.19	0.639	2.75	0.19	0.79	3d1pA	GO:0004792 GO:0005739 GO:0016740
7	0.18	0.611	2.68	0.25	0.75	2eg4A	GO:0004792 GO:0016740 GO:0046872
8	0.10	0.548	1.59	0.20	0.61	2jtqA	GO:0004792 GO:0016740 GO:0030288 GO:0042597
9	0.08	0.646	2.82	0.12	0.82	3utnX	GO:0002098 GO:0002143 GO:0004792 GO:0005737 GO:0005739 GO:0016740
10	0.08	0.645	2.19	0.19	0.77	1yt8A	GO:0004792 GO:0016740
11	0.08	0.606	3.26	0.11	0.79	1okgA	GO:0005829 GO:0016740 GO:0016784 GO:0019343 GO:0019499
12	0.07	0.652	2.79	0.20	0.81	1orbA	GO:0003723 GO:0004792 GO:0005615 GO:0005739 GO:0005743 GO:0005759 GO:0008097 GO:0016740 GO:0030855 GO:0035928 GO:0051029 GO:0070062
13	0.07	0.540	3.43	0.11	0.72	1urhA	GO:0004792 GO:0005737 GO:0005829 GO:0016740 GO:0016784 GO:0046677
14	0.07	0.634	3.16	0.19	0.81	3hzuA	GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
15	0.07	0.679	2.88	0.18	0.86	3ippB	GO:0004792 GO:0016740 GO:0016783 GO:0042597
16	0.07	0.642	3.09	0.20	0.84	1uarA	GO:0004792 GO:0016740
17	0.07	0.647	2.81	0.15	0.82	1h4kX	GO:0004792 GO:0005737 GO:0016740
18	0.07	0.631	2.84	0.21	0.79	3p3aA	GO:0004792 GO:0016740
19	0.07	0.619	3.02	0.12	0.81	3aaxB	GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
20	0.07	0.636	3.13	0.10	0.83	4jgtA	GO:0001822 GO:0001889 GO:0004792 GO:0005737 GO:0005739 GO:0005829 GO:0009440 GO:0009636 GO:0016740 GO:0016784 GO:0019346 GO:0021510 GO:0030054 GO:0042802 GO:0043005 GO:0045202 GO:0070062 GO:0070814
21	0.07	0.666	1.77	0.26	0.75	3tp9A	GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0004792	GO:0016785	GO:0008061	GO:0004568
GO-Score	0.49	0.41	0.34	0.34
Biological Processes	GO:0001887	GO:0006400	GO:0006071	GO:0006032	GO:0042742	GO:0009772
GO-Score	0.41	0.41	0.35	0.34	0.34	0.34
Cellular Component	GO:0016021	GO:0031226	GO:0009535	GO:0009941	GO:0005576
GO-Score	0.48	0.42	0.34	0.34	0.34

(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.