I-TASSER results

I-TASSER results for job id Rv0856

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

Input Sequence in FASTA format

>protein (134 residues)
MEALADVGVLASWSPLHKQVEVIDYYPDGRPHHVRATVKILGLVDKEVLEYHWGPDWVCW
DADQTFQQHGQHIEYTVKPEGVDRARVRFDITVEPAGPIPGFIVKRASEHVLDAAAKGLQ
KLIAGAGDQGNAKS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEALADVGVLASWSPLHKQVEVIDYYPDGRPHHVRATVKILGLVDKEVLEYHWGPDWVCWDADQTFQQHGQHIEYTVKPEGVDRARVRFDITVEPAGPIPGFIVKRASEHVLDAAAKGLQKLIAGAGDQGNAKS
Prediction	CHHHHCHHHCCCCCCCCEEEEEEEHCCCCCEEEEEEEEEEEEEEEEEEEEEEHCCCEEEEEEEHCCEEEEHCEEEEEEHCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	85676477776555544589999858999878999999976578689999998598899999985546554658999985799589999999985787579999999999999999999999999865667889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEALADVGVLASWSPLHKQVEVIDYYPDGRPHHVRATVKILGLVDKEVLEYHWGPDWVCWDADQTFQQHGQHIEYTVKPEGVDRARVRFDITVEPAGPIPGFIVKRASEHVLDAAAKGLQKLIAGAGDQGNAKS
Prediction	65013416413523642460412352772304303030413424442114031466413033354632454614030365367403020303032514023103430463114301640352046366566468
	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

CHHHHCHHHCCCCCCCCEEEEEEEHCCCCCEEEEEEEEEEEEEEEEEEEEEEHCCCEEEEEEEHCCEEEEHCEEEEEEHCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MEALADVGVLASWSPLHKQVEVIDYYPDGRPHHVRATVKILGLVDKEVLEYHWGPDWVCWDADQTFQQHGQHIEYTVKPEGVDRARVRFDITVEPAGPIPGFIVKRASEHVLDAAAKGLQKLIAGAGDQGNAKS

1t17A

0.13

0.95

2.60

MUSTER

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKRSIDVSLLYG-PFKRLNNGWRFMPE-GDATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.14

0.13

0.96

3.66

dPPAS

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDDARSIDVSLLYGPFKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.15

0.14

0.95

4.50

wdPPAS

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKDSIDVSLLYGP-FKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.14

0.13

0.95

3.28

wMUSTER

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKRSIDVSLLYG-PFKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.15

0.14

0.95

4.16

wPPAS

LELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKDSIDVSLLYG-PFKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.14

0.13

0.95

6.54

dPPAS2

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKRSIDVSLLYG-PFKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.15

0.14

0.95

3.79

PPAS

FELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKDSIDVSLLYG-PFKRLNNGWRFMPEG-DATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

1t17A

0.14

0.13

0.95

3.25

Env-PPAS

LELVGDVDAYPKFVPWITGMRTWNGRVDGATVDAEAQVGFSFLREKFATRVRRDKDSIDVSLLYG-PFKRLNNGWRFMPEGD-ATRVEFVIEFAFKSALLDAMLAANVDRAAGKLIACFEARAQQLHGA-----

2d4rA

0.16

0.15

0.92

2.29

MUSTER

YRLAKDLEGLKPYLKEVESLEVVAREGA--RTRSRWVAVA-GKKVRWLEEEEWDDERNRFFSPEGD-FDRYEGTWVFLPE-GEGTRVVLTLTYELTIPIFLRKLVQKLQENVESLLKGLEERVLAASS------

2d4rA

0.16

0.15

0.94

3.28

dPPAS

YRLAKDLEGLKPYLKEVESLEVVAREGA---RTRSRWVAVAGKKVRWLEEEEWDDERNRFFSPEGD-FDRYEGTWVFLPEG-EGTRVVLTLTYELTIPIFGGLLRKLVQKLQENVESLLKGLEERVLAASS---

(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 3 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=0.81

Estimated TM-score = 0.82±0.08

Estimated RMSD = 3.0±2.1Å

Download Model 2

C-score=0.58

Download Model 3

C-score=-2.79

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	1t17A	0.877	1.41	0.126	0.948
2	1em2A	0.781	2.17	0.081	0.925
3	2r55A	0.771	2.33	0.096	0.933
4	3tfzA	0.762	2.52	0.159	0.955
5	2rezA	0.757	2.58	0.102	0.940
6	2mouA	0.756	2.87	0.053	0.978
7	1jssA	0.750	2.39	0.138	0.918
8	3p0lA	0.749	2.50	0.130	0.918
9	2d4rA	0.748	2.23	0.172	0.910
10	2e3mA	0.740	2.76	0.083	0.955

(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	0.30	14	3h3tB	16H	Rep, Mult	6,14,36,38,41,42,49,60,71,73,89,93,107,111,112,115
2	0.04	2	3tl1A	JRO	Rep, Mult	36,39,45,47,62,68,71,91,103,104,107,108,111
3	0.02	1	2vk6A	MG	Rep, Mult	27,28
4	0.02	1	3gkeA	FES	Rep, Mult	20,34,36,47,48,49
5	0.02	1	2qimA	ZEA	Rep, Mult	60,73,89,108
6	0.02	1	3e85A	BSU	Rep, Mult	75,89,112,115,118
7	0.02	1	3e85A	BSU	Rep, Mult	73,75,77,87,89,119
8	0.02	1	3qszA	MN	Rep, Mult	80,86
9	0.02	1	3gb4A	FES	Rep, Mult	49,60,72,74

	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	1n63B	0.536	4.54	0.092	0.910	1.2.99.2	NA
2	0.060	2j1pB	0.555	3.98	0.059	0.828	2.5.1.1,2.5.1.10,2.5.1.29	NA
3	0.060	3m9uA	0.532	4.14	0.056	0.858	2.5.1.10	NA
4	0.060	1jrpB	0.534	4.69	0.054	0.925	1.17.1.4	112,118
5	0.060	1eg9A	0.574	4.10	0.072	0.910	1.14.12.12	NA
6	0.060	1jroB	0.531	4.64	0.054	0.918	1.1.1.204	NA
7	0.060	3kvnX	0.533	4.37	0.074	0.866	3.1.1.1	4,6,10
8	0.060	2azkA	0.524	4.52	0.049	0.873	2.5.1.1,2.5.1.29,2.5.1.10	NA
9	0.060	2f8zF	0.514	4.46	0.074	0.873	2.5.1.10,2.5.1.1	NA
10	0.060	2azjA	0.529	4.39	0.041	0.866	2.5.1.1	NA
11	0.060	2f89F	0.518	4.54	0.083	0.873	2.5.1.1,2.5.1.10	NA
12	0.060	1im0A	0.538	3.97	0.026	0.806	3.1.1.32,3.1.1.4	NA
13	0.060	2b1xA	0.556	4.06	0.083	0.873	1.14.12.12	NA
14	0.060	1rqiA	0.559	3.88	0.039	0.873	2.5.1.10	NA
15	0.060	1z01A	0.563	4.16	0.038	0.866	1.14.13.61	17
16	0.060	3lk5A	0.544	4.13	0.056	0.866	2.5.1.1	105
17	0.060	2vq5A	0.619	3.65	0.117	0.895	4.2.1.78	21,23
18	0.060	2eabA	0.512	4.11	0.053	0.776	3.2.1.63	NA
19	0.060	3en1A	0.594	4.00	0.080	0.910	1.14.12.11	17

(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	0.19	0.742	2.64	0.10	0.94	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
1	0.15	0.771	2.33	0.10	0.93	2r55A	GO:0005829 GO:0006700 GO:0006810 GO:0006869 GO:0008289 GO:0032052
2	0.15	0.756	2.87	0.05	0.98	2mouA	GO:0006810 GO:0006869 GO:0008289
3	0.15	0.800	2.23	0.08	0.95	1em2A	GO:0005737 GO:0005739 GO:0005765 GO:0005768 GO:0006629 GO:0006694 GO:0006701 GO:0006810 GO:0006839 GO:0006869 GO:0008202 GO:0008203 GO:0008289 GO:0015485 GO:0016020 GO:0016021 GO:0031902
4	0.14	0.749	2.50	0.13	0.92	3p0lA	GO:0005739 GO:0005758 GO:0005829 GO:0006082 GO:0006694 GO:0006699 GO:0006700 GO:0006701 GO:0006703 GO:0006810 GO:0006869 GO:0007420 GO:0007584 GO:0007623 GO:0008203 GO:0008211 GO:0008289 GO:0008584 GO:0009635 GO:0009636 GO:0010033 GO:0010212 GO:0010288 GO:0010628 GO:0014070 GO:0014823 GO:0015485 GO:0016101 GO:0017085 GO:0017127 GO:0017143 GO:0018879 GO:0018894 GO:0018958 GO:0018963 GO:0030061 GO:0031667 GO:0032367 GO:0032869 GO:0034698 GO:0035094 GO:0035457 GO:0042493 GO:0042542 GO:0042747 GO:0043005 GO:0043025 GO:0043434 GO:0043524 GO:0043627 GO:0044255 GO:0044321 GO:0044344 GO:0045471 GO:0046677 GO:0048168 GO:0048545 GO:0050769 GO:0050810 GO:0051412 GO:0060992 GO:0061370 GO:0071222 GO:0071236 GO:0071248 GO:0071276 GO:0071312 GO:0071320 GO:0071333 GO:0071346 GO:0071371 GO:0071372 GO:0071373 GO:0071378 GO:0071407 GO:0071549 GO:0071560 GO:0071872
5	0.14	0.703	3.00	0.12	0.93	3qszB	GO:0008289
6	0.14	0.746	2.50	0.15	0.92	5brlA	GO:0005739 GO:0005783 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0015485 GO:0016023 GO:0034435
7	0.07	0.643	3.04	0.09	0.87	3cnwA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
8	0.07	0.548	3.96	0.03	0.81	2kewA	GO:0006950
9	0.06	0.428	4.85	0.04	0.75	3frkA	GO:0003824
10	0.06	0.387	3.85	0.06	0.59	3l2nA	GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0046872
11	0.06	0.334	5.54	0.08	0.65	1a71A	GO:0004022 GO:0005737 GO:0008270 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.354	5.26	0.04	0.69	1yc0A	GO:0004252 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008236 GO:0016787
13	0.06	0.697	2.86	0.12	0.91	3fo5A	GO:0005737 GO:0005829 GO:0006631 GO:0008289 GO:0009266 GO:0009409 GO:0016787 GO:0035338 GO:0035556 GO:0047617 GO:0052689 GO:0070062
14	0.06	0.325	5.44	0.06	0.63	1agnA	GO:0001523 GO:0004022 GO:0004024 GO:0004031 GO:0004745 GO:0005576 GO:0005622 GO:0005737 GO:0005829 GO:0006068 GO:0006069 GO:0008270 GO:0009617 GO:0010430 GO:0016491 GO:0019841 GO:0035276 GO:0042572 GO:0042573 GO:0045471 GO:0046872 GO:0048019 GO:0055114 GO:1900116
15	0.06	0.336	5.36	0.07	0.64	1dehA	GO:0004022 GO:0004024 GO:0005737 GO:0005829 GO:0006069 GO:0008270 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.304	5.28	0.04	0.56	4v6wAI	GO:0000462 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022008 GO:0022627 GO:0030529 GO:0035167
17	0.06	0.367	5.36	0.08	0.72	2qk4B	GO:0000166 GO:0003360 GO:0003824 GO:0004637 GO:0004641 GO:0004644 GO:0005524 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006544 GO:0008152 GO:0009058 GO:0009113 GO:0009156 GO:0009168 GO:0010033 GO:0010035 GO:0016740 GO:0016742 GO:0016874 GO:0021549 GO:0021987 GO:0046654 GO:0046872 GO:0070062
18	0.06	0.433	4.45	0.04	0.69	4n4nA	GO:0016491 GO:0019331 GO:0042597 GO:0046872 GO:0047991 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0032934	GO:0043178	GO:0008168
GO-Score	0.54	0.54	0.38
Biological Processes	GO:0006694	GO:0042446	GO:0042448	GO:0016125	GO:1902652	GO:0042181	GO:0006869	GO:0016999
GO-Score	0.54	0.54	0.54	0.54	0.54	0.54	0.47	0.38
Cellular Component	GO:0044444	GO:0043231
GO-Score	0.54	0.54

(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.