I-TASSER results

I-TASSER results for job id Rv3686c

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

Input Sequence in FASTA format

>protein (110 residues)
MVYTGSDAGDHASAPQPSGSGSVPASVNVPGLVVAAVWAVGLVAGLVALTIGHLAVAAAA
LVVAVMAPWCRVAYIAHGQHRVCGETLRGTPAGETASFPTGWRGLRFSTR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MVYTGSDAGDHASAPQPSGSGSVPASVNVPGLVVAAVWAVGLVAGLVALTIGHLAVAAAALVVAVMAPWCRVAYIAHGQHRVCGETLRGTPAGETASFPTGWRGLRFSTR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCEEEHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCCCCCCCCCCCCEEHCCC
Conf.Score	97668887765568898988766665555765555789999999999999775678888999999766678888876787656777658999988778887665554579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MVYTGSDAGDHASAPQPSGSGSVPASVNVPGLVVAAVWAVGLVAGLVALTIGHLAVAAAALVVAVMAPWCRVAYIAHGQHRVCGETLRGTPAGETASFPTGWRGLRFSTR
Prediction	63234553354434444564453444341311212333331212111221343411221212213323222112244454433444144445444542443244243558
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCEEEHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCCCCCCCCCCCCEEHCCC
MVYTGSDAGDHASAPQPSGSGSVPASVNVPGLVVAAVWAVGLVAGLVALTIGHLAVAAAALVVAVMAPWCRVAYIAHGQHRVCGETLRGTPAGETASFPTGWRGLRFSTR

3jbhA1

0.18

0.17

0.96

1.25

wMUSTER

LVQEEDHPGLGAEEKGGGGKGGGGRKKGASFQTVSALYREQLNRLMASLHSTQPHFVRCIIPNELKQPGVIDSGLVMHQLTCNGEGIRICRKG----FPNRMVYPDFKQR

1g8xA

0.17

0.16

0.94

1.23

wMUSTER

FKDSSDNVVTKLFNDPNIASRAKKGA---NFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGEGIRITRKG----FPNRIIYADFVKR

5cwiA1

0.12

1.00

0.78

MUSTER

KLCKKESEAREARSKAEELRQRHPDSQAARDAQKLASQAEEAVKLACELAQEHPDIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQE

5d92D2

0.13

0.09

0.69

0.80

dPPAS

----SGSLNKYARGLLPIARLLADWGVS-PDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFRE-----------------------------

5d92D2

0.13

0.09

0.68

0.77

wdPPAS

-----SGSLNKYARGLPIARLLADWGVS-PDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFRE-----------------------------

2ycuA

0.13

0.95

1.22

wMUSTER

LLHSTDRLTAEIWKDVEGIVGLEQRRGMFR--TVGQLYKESLSRLMATLSNTNPSFVRCIVPNHEKRAGKLEPRLVLDQLRCNGEGIRICRQG----FPNRILFQEFRQR

1opoC2

0.29

0.22

0.75

0.68

wPPAS

KI---SQASNDKVSDGP--TYVVP-SVN--GVVAAGKWCI-IVRGTVE---G--GFTKPTL----IGP--GIS---ESARPIAVCELVTQMEGQSAEQPLQW--VVY--R

5d92D2

0.13

0.09

0.68

0.87

dPPAS2

----SGSLNKYARGLLPIARLLADWGVS-PDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLFRE------------------------------

5d92D2

0.13

0.09

0.68

0.71

PPAS

----SGSLNKYARGLLPIARLLADWGVS-PDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLFRE------------------------------

4fd0A3

0.13

0.10

0.75

0.72

Env-PPAS

IL--GQGLLGG----NRKTQLTIPANVTQINFSA--FNNTGI------KEV----------VEGITPPQVFEKVWYGFPDDITVIRVP-AESVEKYKNANGWK--DFTNK

(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=-2.74

Estimated TM-score = 0.40±0.13

Estimated RMSD = 10.2±4.6Å

Download Model 2

C-score=-3.45

Download Model 3

C-score=-4.31

Download Model 4

C-score=-4.43

Download Model 5

C-score=-4.29

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	5d92D	0.699	3.15	0.107	0.900
2	4o6mA2	0.666	2.93	0.071	0.882
3	4mndA	0.648	2.55	0.082	0.836
4	4xhjA	0.613	3.39	0.031	0.882
5	4ybqA	0.596	3.74	0.056	0.891
6	5c65A	0.589	3.78	0.105	0.891
7	4pypA	0.582	3.73	0.076	0.882
8	2cjeA	0.582	4.00	0.097	0.891
9	3o7pA	0.581	3.85	0.084	0.873
10	5aymA1	0.579	3.89	0.104	0.864

(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	0.11	9	4to9X	HEM	Rep, Mult	34,37,38,41,61,65,68,75
2	0.07	5	4qi1B	MPG	Rep, Mult	33,36,67,74
3	0.04	3	2gdcA	III	Rep, Mult	61,68,72,75,76,79
4	0.04	3	3a5cI	ADP	Rep, Mult	17,18,19,20,21,22
5	0.03	2	5c65B	37X	Rep, Mult	21,32,63,66
6	0.03	2	5ix6A	AU	Rep, Mult	45,57,61
7	0.02	2	1zw2A	III	Rep, Mult	34,41,61,65,68,72,75,79
8	0.02	2	1cwqA	UND	Rep, Mult	29,33,72
9	0.02	2	2gk1B	UUU	Rep, Mult	15,29,30,32
10	0.01	1	3rkoM	LFA	Rep, Mult	31,38,42,46
11	0.01	1	2ibfA	III	Rep, Mult	59,66,70
12	0.01	1	3kviA	FAH	Rep, Mult	58,59
13	0.01	1	2o012	CLA	Rep, Mult	45,46
14	0.01	1	4dhaF	MG	Rep, Mult	73,74
15	0.01	1	5jreD	ADE	Rep, Mult	42,103
16	0.01	1	3rkoC	LFA	Rep, Mult	39,42,46
17	0.01	1	3nq1B	ZN	Rep, Mult	4,77
18	0.01	1	4ryoA	MPG	Rep, Mult	39,56,63
19	0.01	1	1ydiA	III	Rep, Mult	7,61,62,65,72,79
20	0.01	1	2ww2A	NA	Rep, Mult	3,4,5,6,7

	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	1l2aE	0.440	4.68	0.076	0.791	3.2.1.4	7
2	0.060	1syyA	0.529	4.34	0.037	0.818	1.17.4.1	NA
3	0.060	1ly8A	0.512	4.23	0.049	0.864	1.11.1.7	NA
4	0.060	3btaA	0.522	4.15	0.061	0.891	3.4.24.69	103
5	0.060	2vuaA	0.314	5.52	0.041	0.682	3.4.24.69	NA
6	0.060	1uzrB	0.528	4.38	0.037	0.836	1.17.4.1	NA
7	0.060	1biqB	0.519	3.94	0.065	0.800	1.17.4.1	NA
8	0.060	1qpaA	0.498	3.93	0.101	0.809	1.11.1.14,1.11.1.-	NA
9	0.060	1wcrA	0.524	3.32	0.094	0.700	2.7.1.69	77,79
10	0.060	1khoA	0.516	4.23	0.068	0.836	3.1.4.3	NA
11	0.060	1n2lA	0.541	4.15	0.115	0.864	3.1.6.8	35,77
12	0.060	2pfdB	0.513	3.67	0.082	0.773	2.1.2.5,4.3.1.4	NA
13	0.060	3iayA	0.518	4.37	0.103	0.891	2.7.7.7	NA
14	0.060	1ca1A	0.512	4.46	0.067	0.882	3.1.4.3	NA
15	0.060	1s5jA	0.538	4.02	0.036	0.846	2.7.7.7	61
16	0.060	1i1iP	0.521	3.66	0.115	0.800	3.4.24.16	NA
17	0.060	1ah7A	0.516	4.38	0.069	0.873	3.1.4.3	NA
18	0.060	1tgoA	0.535	3.89	0.028	0.818	2.7.7.7	38
19	0.060	3n2oA	0.522	3.52	0.048	0.746	4.1.1.19	74

(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	0.12	0.702	3.09	0.11	0.90	5d92B	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
1	0.10	0.665	3.07	0.08	0.89	4o6mB	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
2	0.08	0.613	3.39	0.03	0.88	4xhjA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
3	0.07	0.648	2.55	0.08	0.84	4mndA	GO:0003824 GO:0008152 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0016780 GO:0046872
4	0.07	0.537	3.77	0.11	0.83	2xqyA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
5	0.07	0.515	4.39	0.06	0.92	3phf1	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
6	0.07	0.510	4.21	0.11	0.89	3m1cA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
7	0.06	0.371	4.35	0.02	0.62	3kjeA	GO:0000166 GO:0019415
8	0.06	0.420	3.93	0.06	0.69	2ah6B
9	0.06	0.368	3.60	0.03	0.55	1rhgB	GO:0005125 GO:0005130 GO:0005576 GO:0005615 GO:0006955 GO:0007275 GO:0008083 GO:0008284 GO:0014068 GO:0019221 GO:0019899 GO:0030838 GO:0030851 GO:0032092 GO:0033138 GO:0042993 GO:0045639 GO:0045944 GO:0050731 GO:0051897 GO:0071222 GO:0071345 GO:1901215 GO:2000251
10	0.06	0.364	4.70	0.03	0.71	1v5vA	GO:0004047 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259
11	0.06	0.310	5.05	0.06	0.62	3beyD	GO:0051920 GO:0055114 GO:0098869
12	0.06	0.335	3.26	0.07	0.47	2vmaA	GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
13	0.06	0.340	5.15	0.03	0.68	1wvcA	GO:0000166 GO:0009058 GO:0009103 GO:0009243 GO:0016740 GO:0016779 GO:0046872 GO:0047343
14	0.06	0.333	4.48	0.02	0.60	4jd0A	GO:0009058 GO:0016740 GO:0016779
15	0.06	0.337	3.29	0.05	0.47	2vmbA	GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
16	0.06	0.336	4.73	0.03	0.63	3aj3A	GO:0016787 GO:0042820 GO:0046872 GO:0047585
17	0.06	0.328	4.98	0.05	0.65	3ayxB	GO:0008901 GO:0009375 GO:0046872 GO:0051536 GO:0051538 GO:0051539 GO:0055114
18	0.06	0.371	4.50	0.02	0.65	4wj3M	GO:0000166 GO:0003676 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874 GO:0050560

Consensus prediction of GO terms

Molecular Function	GO:0016772	GO:0043169	GO:1901265	GO:0036094
GO-Score	0.52	0.52	0.40	0.40
Biological Processes	GO:0008610	GO:0006644	GO:0044249	GO:0090407
GO-Score	0.52	0.52	0.52	0.52
Cellular Component	GO:0016021
GO-Score	0.36

(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.