I-TASSER results

I-TASSER results for job id Rv0309

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

Input Sequence in FASTA format

>protein (218 residues)
MSRLLALLCAAVCTGCVAVVLAPVSLAVVNPWFANSVGNATQVVSVVGTGGSTAKMDVYQ
RTAAGWQPLKTGITTHIGSAGMAPEAKSGYPATPMGVYSLDSAFGTAPNPGGGLPYTQVG
PNHWWSGDDNSPTFNSMQVCQKSQCPFSTADSENLQIPQYKHSVVMGVNKAKVPGKGSAF
FFHTTDGGPTAGCVAIDDATLVQIIRWLRPGAVIAIAK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRLLALLCAAVCTGCVAVVLAPVSLAVVNPWFANSVGNATQVVSVVGTGGSTAKMDVYQRTAAGWQPLKTGITTHIGSAGMAPEAKSGYPATPMGVYSLDSAFGTAPNPGGGLPYTQVGPNHWWSGDDNSPTFNSMQVCQKSQCPFSTADSENLQIPQYKHSVVMGVNKAKVPGKGSAFFFHTTDGGPTAGCVAIDDATLVQIIRWLRPGAVIAIAK
Prediction	CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCEEEEEHCCCCCEEEEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEHCCHCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCHHHHCCCCCCCCEEEHCCCCCCCCCCCCCEEEEHCCCCCCCCCEEHCCHHHHHHHHHHCCCCCCEEHCC
Conf.Score	97579999999998765566677677888857876579985899999599987899999985985688654567887678998776678899985899864444677899889985885788865578898778867866777788765566566677776899958988878898867999757999876568778999999999969998689869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRLLALLCAAVCTGCVAVVLAPVSLAVVNPWFANSVGNATQVVSVVGTGGSTAKMDVYQRTAAGWQPLKTGITTHIGSAGMAPEAKSGYPATPMGVYSLDSAFGTAPNPGGGLPYTQVGPNHWWSGDDNSPTFNSMQVCQKSQCPFSTADSENLQIPQYKHSVVMGVNKAKVPGKGSAFFFHTTDGGPTAGCVAIDDATLVQIIRWLRPGAVIAIAK
Prediction	63312001001111332333333353443434225425603000000156434020200124662044124402020033113442454241003010303302222452515031440465210022242531011132543644343344242344102000002124642554100000003474111000103472034005304573303028
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCEEEEEHCCCCCEEEEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEHCCHCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCHHHHCCCCCCCCEEEHCCCCCCCCCCCCCEEEEHCCCCCCCCCEEHCCHHHHHHHHHHCCCCCCEEHCC
MSRLLALLCAAVCTGCVAVVLAPVSLAVVNPWFANSVGNATQVVSVVGTGGSTAKMDVYQRTAAGWQPLKTGITTHIGSAGMAPEAKSGYPATPMGVYSLDSAFGTAPNPGGGLPYTQVGPNHWWSGDDNSPTFNSMQVCQKSQCPFSTADSENLQIPQYKHSVVMGVNKAKVPGKGSAFFFHTTDGGPTAGCVAIDDATLVQIIRWLRPGAVIAIAK

4xzzA3

0.17

0.11

0.63

1.34

MUSTER

------------------------------DTDFGYYQNKQFLFVAN---KSKPSLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKLERLDQYYGVL---------------------AFVTNYPNLY----DTLKKRT--------------------GHGIWVHGMPLNNTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.17

0.11

0.63

1.92

dPPAS

------------------------------DTDFGYYQNKQFLFVANKSKP---SLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKLERLDQYYGVL---------------------AFVTNYPNLYDTLKK------------------------RTGHGIWVHGMPLNGTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.16

0.10

0.62

3.31

wdPPAS

------------------------------DTDFGYYQNKQFLFVAN---KSKPSLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKL------------------------RLDQYYGAFVTNYPNLYDTLKKR------------------------TGHGIWVHGMPLNNTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA

0.17

0.13

0.76

1.42

wMUSTER

SDRLLEIMRLYQKQGLEMVGQKLDSYLADKSFWAEELQNKQFLFVAN---KSKPSLEFYEIE-NNMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKL---ERL--------------------DQYYGAFVTNYPNL----YDTLKKRT--------------------GHGIWVHGMPLNNTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.17

0.10

0.60

2.97

wPPAS

-----------------------------------DTQNKQFLFVAN---KSKPSLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKL---ERL--------------------DQYYGAFVTNYPNLYDTLKKR------------------------TGHGIWVHGMPLNNTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.18

0.11

0.61

4.05

dPPAS2

-----------------------------------DTQNKQFLFVAN---KSKPSLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKLERLDQYYGVL---------------------AFVTNYPNLYDTLKK------------------------RTGHGIWVHGMPLNGTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.18

0.11

0.60

2.11

PPAS

-----------------------------------DTQNKQFLFVAN---KSKPSLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKLE-----------------------RLDQYYG-------------------------VLAFVTNYNLTLKKRTGHGIWVHGMPELNTKGCIAIENPLLSSYDKVLKGEKAFLITY

4xzzA3

0.16

0.10

0.63

2.77

Env-PPAS

------------------------------DTDFGYYQNKQFLFVAN---KSKPSLEFYEI-ENNMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKL---ERL-----------DQYY-------GVLAFVTNYPNLYDTLKK------------------------RTGHGIWVHGMPLNNTKGCIAIENPLLSSYDKVLKGEKAFLITY

1zatA2

0.10

0.06

0.65

0.95

MUSTER

---------------------DTKFKSTKRGEVTVPVGTYDTYIEVD---LENQHMWYYKDG-----KVALETDIVSGKPT---------TPTPAGVFYVWN------------KEEDA----------------TLKGTNGTPYESPVNYWMPIDWTGV---GIHDSDWQPEYGGD------LWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF-

4xzzA

0.15

0.11

0.75

1.19

dPPAS

LEMVGQKLDSYLADKSFWAEELQNKDTDFG-----YYQNKQFLFVANKSKP---SLEFYEIEN-NMLKKINSSKALVGSKK-GDKTLEGDLATPIGVYRITQKLERLDQYYGVL---------------------AFVTNYPNL----YDTLKKRT--------------------GHGIWVHGMPLNGTKGCIAIENPLLSSYDKVLKGEKAFLITY

(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=-1.50

Estimated TM-score = 0.53±0.15

Estimated RMSD = 8.8±4.6Å

Download Model 2

C-score=-2.07

Download Model 3

C-score=-3.23

Download Model 4

C-score=-2.68

Download Model 5

C-score=-2.18

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	4xzzA	0.651	2.50	0.156	0.729
2	1zatA	0.484	3.99	0.099	0.628
3	4xxtA	0.478	2.53	0.084	0.546
4	4jmnA	0.470	3.42	0.095	0.583
5	3turA	0.466	3.18	0.111	0.564
6	4z7aA	0.465	3.44	0.100	0.573
7	4k73A	0.459	2.97	0.099	0.541
8	4xvoA	0.451	3.42	0.078	0.550
9	5bmqA2	0.448	2.41	0.150	0.514
10	3vaeA2	0.442	2.82	0.132	0.523

(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	0.06	3	1xmeC	HAS	Rep, Mult	4,8
2	0.04	2	1dgjA	FES	Rep, Mult	77,78,80,84
3	0.04	2	3bkfA	ZN	Rep, Mult	183,193
4	0.04	2	3kc2B	MG	Rep, Mult	113,114,118
5	0.04	2	1l0vO	MQ7	Rep, Mult	20,22
6	0.04	2	4y4vA	DAL	Rep, Mult	85,88,89,177,178
7	0.02	1	5fseC	HQE	Rep, Mult	12,13
8	0.02	1	1i95K	WO2	Rep, Mult	94,98
9	0.02	1	2zuvA	NO3	Rep, Mult	74,75,137,185,196
10	0.02	1	1s44B	GOL	Rep, Mult	116,180,182
11	0.02	1	3fahA	GOL	Rep, Mult	56,72,73,74
12	0.02	1	2o014	CLA	Rep, Mult	96,100,116
13	0.02	1	3zk1B	DMU	Rep, Mult	5,12
14	0.02	1	1ztzB	CB5	Rep, Mult	78,93,94,97
15	0.02	1	1sijA	FES	Rep, Mult	80,81,82,83,85,86,87,91,94
16	0.02	1	3mz8A	ZN	Rep, Mult	123,183
17	0.02	1	4w8cB	GLY	Rep, Mult	57,201
18	0.02	1	1somA	UNX	Rep, Mult	48,49,218

	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	1gpiA	0.333	5.95	0.055	0.601	3.2.1.91	NA
2	0.060	1t3qB	0.380	5.84	0.062	0.656	1.3.99.17	NA
3	0.060	1l1lA	0.408	6.02	0.049	0.743	1.17.4.2	NA
4	0.060	2wj2A	0.386	5.64	0.052	0.647	3.5.1.99	187
5	0.060	1c9uB	0.319	6.13	0.062	0.583	1.1.5.2,1.1.99.17	NA
6	0.060	2pffB	0.400	5.81	0.095	0.716	2.3.1.86	51,112
7	0.060	1t3tA	0.390	5.98	0.037	0.688	6.3.5.3	198
8	0.060	1mosA	0.355	6.01	0.052	0.633	2.6.1.16	NA
9	0.060	1moqA	0.355	5.98	0.053	0.633	2.6.1.16	NA
10	0.060	2wgdA	0.392	5.79	0.032	0.693	2.3.1.41	181
11	0.060	2iobB	0.394	5.71	0.029	0.670	3.5.1.78,6.3.1.8	123
12	0.060	1h16A	0.404	6.08	0.047	0.743	2.3.1.54	NA
13	0.060	3kzuA	0.398	5.83	0.051	0.693	2.3.1.41	NA
14	0.060	1dgjA	0.407	5.58	0.032	0.679	1.2.-.-	NA
15	0.060	2pflA	0.403	6.17	0.019	0.739	2.3.1.54	201
16	0.060	3cjcA	0.311	5.60	0.062	0.532	3.1.21.1	55,77
17	0.060	3fr8B	0.383	6.18	0.060	0.702	1.1.1.86	NA
18	0.060	1s0kA	0.386	5.55	0.028	0.647	3.2.1.18	NA
19	0.060	2vkzG	0.381	5.90	0.077	0.679	2.3.1.38,3.1.2.14	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	0.12	0.480	2.55	0.09	0.55	4xxtA	GO:0004180 GO:0006508 GO:0016740 GO:0016787
1	0.07	0.651	2.50	0.16	0.73	4xzzA	GO:0016740
2	0.07	0.459	2.97	0.10	0.54	4k73A	GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0071555
3	0.07	0.470	3.05	0.11	0.56	4qr7A	GO:0005886 GO:0008360 GO:0009252 GO:0016020 GO:0016740 GO:0016746 GO:0046872 GO:0071555
4	0.07	0.483	4.04	0.09	0.63	2hklA	GO:0016020 GO:0016021 GO:0016740
5	0.07	0.470	3.42	0.10	0.58	4jmnA	GO:0005576 GO:0006508 GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0018104 GO:0042597 GO:0071555 GO:0071972
6	0.07	0.452	3.44	0.09	0.55	4lpqA	GO:0016740
7	0.07	0.465	3.43	0.07	0.56	4xvoA	GO:0016740
8	0.07	0.457	2.78	0.13	0.53	5bmqA	GO:0016020 GO:0016021 GO:0016740
9	0.06	0.410	3.01	0.08	0.50	4a52A	GO:0008360 GO:0009252 GO:0016740 GO:0016757 GO:0016787 GO:0030435 GO:0031160 GO:0071555
10	0.06	0.352	6.06	0.04	0.63	4tlvA	GO:0003950 GO:0005576 GO:0005886 GO:0009405 GO:0016020 GO:0016740 GO:0016757
11	0.06	0.279	6.49	0.03	0.56	2jieA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
12	0.06	0.273	6.68	0.02	0.54	4lzhA	GO:0016740
13	0.06	0.269	6.21	0.04	0.50	4pz0A	GO:0008643 GO:0015608 GO:0034219 GO:0043190
14	0.06	0.266	6.00	0.04	0.46	2ws2A	GO:0016740
15	0.06	0.275	5.99	0.07	0.49	4gf6B	GO:0006091 GO:0008218 GO:0018298
16	0.06	0.257	5.73	0.05	0.46	1lbuA	GO:0004180 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009046 GO:0016787 GO:0046872 GO:0071555
17	0.06	0.234	4.52	0.00	0.34	2ux0A	GO:0000082 GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0004723 GO:0005088 GO:0005516 GO:0005524 GO:0005654 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006816 GO:0007275 GO:0007399 GO:0014733 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0030073 GO:0030154 GO:0030666 GO:0033017 GO:0042803 GO:0043547 GO:0046777 GO:0051259 GO:0051924 GO:0060333 GO:0097481 GO:1900034 GO:1901897
18	0.06	0.231	5.24	0.03	0.37	1nyeD	GO:0004601 GO:0005737 GO:0005829 GO:0006972 GO:0006979 GO:0016209 GO:0016491 GO:0033194 GO:0051920 GO:0055114 GO:0098869

Consensus prediction of GO terms

Molecular Function	GO:0016740
GO-Score	0.33
Biological Processes	GO:0008360	GO:0071555	GO:0009252	GO:0006508
GO-Score	0.13	0.13	0.13	0.12
Cellular Component	GO:0005886	GO:0016021
GO-Score	0.07	0.07

(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.