I-TASSER results

I-TASSER results for job id Rv0079

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

Input Sequence in FASTA format

>protein (273 residues)
MEPKRSRLVVCAPEPSHAREFPDVAVFSGGRANASQAERLARAVGRVLADRGVTGGARVR
LTMANCADGPTLVQINLQVGDTPLRAQAATAGIDDLRPALIRLDRQIVRASAQWCPRPWP
DRPRRRLTTPAEALVTRRKPVVLRRATPLQAIAAMDAMDYDVHLFTDAETGEDAVVYRAG
PSGLRLARQHHVFPPGWSRCRAPAGPPVPLIVNSRPTPVLTEAAAVDRAREHGLPFLFFT
DQATGRGQLLYSRYDGNLGLITPTGDGVADGLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MEPKRSRLVVCAPEPSHAREFPDVAVFSGGRANASQAERLARAVGRVLADRGVTGGARVRLTMANCADGPTLVQINLQVGDTPLRAQAATAGIDDLRPALIRLDRQIVRASAQWCPRPWPDRPRRRLTTPAEALVTRRKPVVLRRATPLQAIAAMDAMDYDVHLFTDAETGEDAVVYRAGPSGLRLARQHHVFPPGWSRCRAPAGPPVPLIVNSRPTPVLTEAAAVDRAREHGLPFLFFTDQATGRGQLLYSRYDGNLGLITPTGDGVADGLA
Prediction	CCCCCCCEEEHCCCCCCCCCCCEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCCCEEEEEEEHCCCEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCCCCCEEEEEHCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCEEEEEHCCCCCEEEHCCCCCCCCCCCC
Conf.Score	987778656655788888777668999967888999999999999999755777489999998578898769999998599689988578758999999999999999998765545667777666778888768999997589999999999999859867888858899857999976998577755667788777667777776545654666888999999999999799879998588896899998578986898568888776789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MEPKRSRLVVCAPEPSHAREFPDVAVFSGGRANASQAERLARAVGRVLADRGVTGGARVRLTMANCADGPTLVQINLQVGDTPLRAQAATAGIDDLRPALIRLDRQIVRASAQWCPRPWPDRPRRRLTTPAEALVTRRKPVVLRRATPLQAIAAMDAMDYDVHLFTDAETGEDAVVYRAGPSGLRLARQHHVFPPGWSRCRAPAGPPVPLIVNSRPTPVLTEAAAVDRAREHGLPFLFFTDQATGRGQLLYSRYDGNLGLITPTGDGVADGLA
Prediction	855543313121244554443040302043502530252036202302533644350303033453574311000103074230101132621330251054035315424763554646554554356665241133241505203242003104214110100215637420000114634242044444444444645455554454445455354144730132042261300001137344130002045340000103354436528
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEHCCCCCCCCCCCEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCCCEEEEEEEHCCCEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCCCCCEEEEEHCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCEEEEEHCCCCCEEEHCCCCCCCCCCCC
MEPKRSRLVVCAPEPSHAREFPDVAVFSGGRANASQAERLARAVGRVLADRGVTGGARVRLTMANCADGPTLVQINLQVGDTPLRAQAATAGIDDLRPALIRLDRQIVRASAQWCPRPWPDRPRRRLTTPAEALVTRRKPVVLRRATPLQAIAAMDAMDYDVHLFTDAETGEDAVVYRAGPSGLRLARQHHVFPPGWSRCRAPAGPPVPLIVNSRPTPVLTEAAAVDRAREHGLPFLFFTDQATGRGQLLYSRYDGNLGLITPTGDGVADGLA

1n3gA

0.08

0.03

0.41

1.95

dPPAS

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.40

0.95

MUSTER

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ---GFVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEE-------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.41

2.60

wdPPAS

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.09

0.04

0.40

1.17

wMUSTER

----------------------TMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ---GFVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVDANFVEEVEEE-------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.41

2.05

wPPAS

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVE---------------EE---------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.41

5.18

dPPAS2

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.41

1.59

PPAS

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE------------------------------------------------------------------------------------------------------------------------------------------

1n3gA

0.08

0.03

0.41

1.95

Env-PPAS

---------------------MTMNITSKQEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQG---FVADATINTPNGVLVASGKHEDYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE------------------------------------------------------------------------------------------------------------------------------------------

1imuA

0.12

0.05

0.38

0.86

MUSTER

---------------------MTLNITSKQDITPAIREHLEERLAKLGKWQTQLISPHFVLNKVPN---GFSVEASIGTPLGNLLASATSDDYKAINEVEEKLERQLNKLQHKSESRRADERLKDSFEN------------------------------------------------------------------------------------------------------------------------------------------------

2rqlA

0.11

0.04

0.34

1.84

dPPAS

---------------------MQLNITGNNEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVT---HTSDATLHVNGGEIHASAEGQDYAAIDGLIDKLARQLTKHKDKLKQH------------------------------------------------------------------------------------------------------------------------------------------------------------

(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=-4.11

Estimated TM-score = 0.28±0.09

Estimated RMSD = 16.2±3.1Å

Download Model 2

C-score=-4.28

Download Model 3

C-score=-4.15

Download Model 4

C-score=-4.06

Download Model 5

C-score=-4.20

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	4ar8A	0.426	5.27	0.053	0.656
2	2y3uA	0.423	5.38	0.039	0.648
3	4ar1A	0.417	5.38	0.064	0.634
4	4k3cA	0.415	5.85	0.046	0.667
5	5c2vA	0.413	6.10	0.034	0.689
6	1q47B	0.413	6.35	0.088	0.729
7	3cf4A	0.412	6.39	0.045	0.725
8	3v4pA	0.406	6.13	0.030	0.681
9	1fwxA	0.405	5.93	0.053	0.670
10	3dx4A	0.404	6.35	0.056	0.678

(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	0.08	4	3dtuC	TRD	Rep, Mult	97,100,101,105
2	0.08	4	3v26X	NUC	Rep, Mult	46,50,64,66,70,85,86,87,102,106,109,111,112,113,115
3	0.04	2	3v2eY	NUC	Rep, Mult	25,26,27,28,30,37,43,46,49,50,53,55,56,60,65,69,76,78,80,85,86,87,94,97,102,105,106,108,109,111,112,113,115,118
4	0.04	2	3fwsA	ANP	Rep, Mult	159,178
5	0.04	2	3wmm5	CRT	Rep, Mult	93,96,103,107
6	0.02	1	4fylA	3CO	Rep, Mult	62,74
7	0.02	1	4fylA	3CO	Rep, Mult	78,83
8	0.02	1	3dtuC	DXC	Rep, Mult	150,153,154,157
9	0.02	1	1qgxA	MG	Rep, Mult	139,169
10	0.02	1	4iqdB	PYR	Rep, Mult	38,39
11	0.02	1	4fylA	3CO	Rep, Mult	74,85,87
12	0.02	1	3lyvE	III	Rep, Mult	134,136,137,138,139,140,141,142,143,161,162,164,175,177,187
13	0.02	1	2zy9A	MG	Rep, Mult	94,95,262,270
14	0.02	1	3svlB	CA	Rep, Mult	84,85
15	0.02	1	4tsmA	TMO	Rep, Mult	33,34
16	0.02	1	1vkxA	NUC	Rep, Mult	85,109

	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	1xmeA	0.394	5.59	0.056	0.634	1.9.3.1	NA
2	0.060	1fwxA	0.405	5.93	0.053	0.670	1.7.99.6	73
3	0.060	1eurA	0.366	6.49	0.072	0.652	3.2.1.18	85,89
4	0.060	1w6sC	0.368	6.37	0.051	0.656	1.1.99.8	NA
5	0.060	3h71B	0.382	6.30	0.069	0.670	3.2.1.18	NA
6	0.060	1lrwA	0.360	6.95	0.039	0.692	1.1.99.8	NA
7	0.060	3cf4A	0.412	6.39	0.045	0.725	1.2.99.2	NA
8	0.060	2occN	0.380	6.15	0.062	0.637	1.9.3.1	83
9	0.060	1st8A	0.377	6.64	0.033	0.703	3.2.1.80	NA
10	0.060	1simA	0.386	6.41	0.036	0.678	3.2.1.18	NA
11	0.060	3gm8A	0.374	5.86	0.044	0.615	3.2.1.-	NA
12	0.060	1m56A	0.400	5.94	0.053	0.656	1.9.3.1	NA
13	0.060	1s0kA	0.372	6.30	0.069	0.648	3.2.1.18	NA
14	0.060	2d0vA	0.377	6.57	0.053	0.678	1.1.99.8	NA
15	0.060	1c9uB	0.382	5.88	0.040	0.626	1.1.5.2,1.1.99.17	NA
16	0.060	1cruB	0.376	5.79	0.042	0.615	1.1.5.2	12,57
17	0.060	2vk6A	0.381	6.18	0.037	0.648	3.2.1.18	NA
18	0.060	2ow6A	0.404	6.40	0.052	0.681	3.2.1.114	156
19	0.060	1kv9A	0.395	5.95	0.025	0.652	1.1.99.-	NA

(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	0.06	0.430	5.39	0.06	0.66	4ar9A	GO:0004252 GO:0005576 GO:0006508 GO:0008270 GO:0046872
1	0.06	0.417	5.38	0.06	0.63	4ar1A	GO:0004252 GO:0005576 GO:0006508 GO:0008270 GO:0046872
2	0.06	0.320	6.99	0.06	0.61	5bwiA	GO:0005975
3	0.06	0.251	7.10	0.07	0.47	4txeA	GO:0000272 GO:0000920 GO:0004553 GO:0004568 GO:0005576 GO:0005618 GO:0005935 GO:0005975 GO:0006032 GO:0008061 GO:0008152 GO:0008843 GO:0009277 GO:0016787 GO:0016798 GO:0071555
4	0.06	0.296	6.84	0.04	0.56	4dq2A	GO:0000166 GO:0003677 GO:0004077 GO:0005524 GO:0006351 GO:0006355 GO:0006464 GO:0009305 GO:0016874
5	0.06	0.319	6.23	0.05	0.55	4namA	GO:0000122 GO:0001933 GO:0005576 GO:0005615 GO:0005886 GO:0009405 GO:0010008 GO:0010629 GO:0035897 GO:0042802 GO:0043409 GO:0044533 GO:0046872 GO:0051260 GO:0061136 GO:0097300 GO:1903140
6	0.06	0.339	6.16	0.08	0.58	4pk1A	GO:0007155 GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0042802 GO:0043165 GO:0051205 GO:0071709 GO:1990063
7	0.06	0.274	6.24	0.07	0.47	4g4sG	GO:0000502 GO:0003729 GO:0004175 GO:0004298 GO:0005634 GO:0005737 GO:0005839 GO:0006508 GO:0006511 GO:0008233 GO:0010499 GO:0016787 GO:0019773 GO:0034515 GO:0042175 GO:0043161 GO:0051603
8	0.06	0.268	6.74	0.03	0.48	3h2yA	GO:0005525
9	0.06	0.427	5.30	0.06	0.64	2y3uA	GO:0004252 GO:0005576 GO:0006508 GO:0008270 GO:0046872
10	0.06	0.282	6.86	0.04	0.52	4l79A	GO:0000146 GO:0000166 GO:0003774 GO:0003779 GO:0005516 GO:0005524 GO:0005546 GO:0005547 GO:0005737 GO:0005769 GO:0005856 GO:0005884 GO:0005886 GO:0005903 GO:0006892 GO:0007015 GO:0007399 GO:0010008 GO:0016459 GO:0030048 GO:0030175 GO:0030898 GO:0032588 GO:0048471 GO:0051015 GO:0051017 GO:0070062 GO:0071944
11	0.06	0.417	5.94	0.06	0.68	5d0oA	GO:0007155 GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0043165 GO:0051205 GO:0071709 GO:1990063
12	0.06	0.251	6.29	0.02	0.43	4rykA	GO:0003677 GO:0043565
13	0.06	0.264	5.97	0.03	0.43	4q5qA	GO:0004364 GO:0005737 GO:0008152 GO:0016740
14	0.06	0.250	4.79	0.05	0.36	2x8xX	GO:0009279 GO:0016020 GO:0016021 GO:0019867
15	0.06	0.300	6.24	0.05	0.51	3gueA	GO:0003983 GO:0006011 GO:0008152 GO:0016740 GO:0016779 GO:0020015 GO:0046872 GO:0070569
16	0.06	0.244	6.84	0.03	0.45	4efjA	GO:0004519 GO:0005739 GO:0090305
17	0.06	0.415	5.85	0.05	0.67	4k3cA	GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0043165 GO:0051205 GO:0071709
18	0.06	0.392	6.24	0.05	0.66	4k3bA	GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0043165 GO:0051205 GO:0071709

Consensus prediction of GO terms

Molecular Function	GO:0004252	GO:0008270	GO:0003677	GO:0005524	GO:0008061	GO:0004077	GO:0008843
GO-Score	0.12	0.12	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0006508	GO:0071555	GO:0006032	GO:0000272	GO:0009305	GO:0000920	GO:0006355
GO-Score	0.12	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0005576	GO:0005935	GO:0009277
GO-Score	0.18	0.06	0.06

(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.