I-TASSER results

I-TASSER results for job id Rv3521

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

Input Sequence in FASTA format

>protein (303 residues)
MGPTLSRFFTALRARRIVGVRGSDGRVHVPPVEYDPVTYEPLSEMVPVSSVGTVASWTWQ
PEPLAGQPLDRPFAWALIKLDGADTLLMHAVDVGTAGPSAIHTGARVHAHWADQPVGAIT
DIACFALGETAEPVAAHKTEDARDPVTMIVTPIQLEIQHTASHEESAYLRAIAQGKLVGA
RTGKTGKVYFPPHGADPATGKPTSEFVELPDKGTVTTFAIVNIPFLGQRIKPPYVAAYVL
LDGADIPFLHLVSDVDAHQVRMGMRVEAVWKPRERWGLGIDNIEYFRPTGEPDANYDTYK
HHL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MGPTLSRFFTALRARRIVGVRGSDGRVHVPPVEYDPVTYEPLSEMVPVSSVGTVASWTWQPEPLAGQPLDRPFAWALIKLDGADTLLMHAVDVGTAGPSAIHTGARVHAHWADQPVGAITDIACFALGETAEPVAAHKTEDARDPVTMIVTPIQLEIQHTASHEESAYLRAIAQGKLVGARTGKTGKVYFPPHGADPATGKPTSEFVELPDKGTVTTFAIVNIPFLGQRIKPPYVAAYVLLDGADIPFLHLVSDVDAHQVRMGMRVEAVWKPRERWGLGIDNIEYFRPTGEPDANYDTYKHHL
Prediction	CCCCHHHHHHHHHHCCEEEEHCCCCEEEHCCCCCCCCCCCCCCCEEHCCCCEEEEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCCEEEEEEHCCCCCHHHCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEHCCCCCEEEHCCCCCCCCCCCCCCEEEHCCCEEEEEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCEEEEEEHCCCCHHHCCCCEEEEEEEEHCCCCCCCCCCEEEEHCCCCCCCCCHHHHHCC
Conf.Score	998578999999989689996799859858855688778888758984897799999997578998877898799999968998757888757888856656786799999857777766654445677777777777777788876555777777777899668999999998968999858998699588667987888876688759958999999986689988888987999999589885788765688988777886789999986778888655677765788888746666559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MGPTLSRFFTALRARRIVGVRGSDGRVHVPPVEYDPVTYEPLSEMVPVSSVGTVASWTWQPEPLAGQPLDRPFAWALIKLDGADTLLMHAVDVGTAGPSAIHTGARVHAHWADQPVGAITDIACFALGETAEPVAAHKTEDARDPVTMIVTPIQLEIQHTASHEESAYLRAIAQGKLVGARTGKTGKVYFPPHGADPATGKPTSEFVELPDKGTVTTFAIVNIPFLGQRIKPPYVAAYVLLDGADIPFLHLVSDVDAHQVRMGMRVEAVWKPRERWGLGIDNIEYFRPTGEPDANYDTYKHHL
Prediction	735523400500473301032042022100013102403166231150445010000000123254353420000000104425310010020444416312142403020354444303203213335344445444465445533122232515242214561340050046230103215510321010230125031541431536440101000000132552634210000001035031200010250427404232502020243464544242020010112274527416726
	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                 280                 300

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

Sec.Str
Seq

CCCCHHHHHHHHHHCCEEEEHCCCCEEEHCCCCCCCCCCCCCCCEEHCCCCEEEEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCCEEEEEEHCCCCCHHHCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEHCCCCCEEEHCCCCCCCCCCCCCCEEEHCCCEEEEEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCEEEEEEHCCCCHHHCCCCEEEEEEEEHCCCCCCCCCCEEEEHCCCCCCCCCHHHHHCC
MGPTLSRFFTALRARRIVGVRGSDGRVHVPPVEYDPVTYEPLSEMVPVSSVGTVASWTWQPEPLAGQPLDRPFAWALIKLDGADTLLMHAVDVGTAGPSAIHTGARVHAHWADQPVGAITDIACFALGETAEPVAAHKTEDARDPVTMIVTPIQLEIQHTASHEESAYLRAIAQGKLVGARTGKTGKVYFPPHGADPATGKPTSEFVELPDKGTVTTFAIVNIPFLGQRIKPPYVAAYVLLDGADIPFLHLVSDVDAHQVRMGMRVEAVWKPRERWGLGIDNIEYFRPTGEPDANYDTYKHHL

3irbA

0.13

0.06

0.45

1.19

MUSTER

---------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEAERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYAEG----NVKVGAKAKILSF-------QWPLRVKVD----------------

5ay6A

0.08

0.07

0.87

1.01

dPPAS

---------------KGVNANLRSEQPVAAAVSYKVGTAGSPSKTNVVDSATNSHNYDVVYSSTGIANPVSGNNEYLVDIKENGVIVATGKVAYDAA----TNELVSSTIDYKGASPVTGSMTTTRINAAGTTVNLADLGIVNASGADDAEVVAGKLYDPSTWSMSDYAKDNSKGVVQIPLSDSKGGQRT-----------VTLSMLKGPGPNQWYAELRAKPGDLANNGNGQISTGIIEFTDGKLKNTGSLFGTTSPT--------AITIKSSGYIAPTVTPPAVQPPTPPTWADALGIDEQ

3irbA

0.13

0.06

0.45

2.75

dPPAS

---------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEAERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYAEG----NVKVGAKAKILSFQWPLRVKVD-----------------------

2m1hA

0.06

0.02

0.32

1.76

dPPAS2

---------------------------------------------------------------MLQERVFHINDRVWLKTGANTWWPAKVTSVTGVEGVDETGTSTVTVLTYPGTQNKATYKNVDSHSSAITFFEPSSEKAVTANEDLLKESNALRFEPT-----------------------------------------------------------------------------------------------------------------------------------------------

3irbA

0.14

0.06

0.43

3.90

wdPPAS

---------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEAERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYA----EGNVKVGAKAKILSFQWPD----------------------------

3irbA

0.14

0.06

0.43

1.45

wMUSTER

----------------------------------------------------------------------------------------------------------------------------------------------EGSLLRWYDVEAERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYAEG----NVKVGAKAKILSFQWPD----------------------------

3irbA

0.14

0.06

0.43

2.85

wPPAS

--------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEA-ERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYA----EGNVKVGAKAKILSFQWPD----------------------------

3irbA

0.14

0.06

0.43

10.25

dPPAS2

---------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEAERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYAEG----NVKVGAKAKILSFQWPD----------------------------

3irbA

0.14

0.06

0.43

2.26

PPAS

--------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEA-ERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYA----EGNVKVGAKAKILSFQWPD----------------------------

3irbA

0.13

0.06

0.45

3.69

Env-PPAS

--------------------------------------------------------------------------------------------------------------------------------------------KEGSLLRWYDVEA-ERYEYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKIENYVEINDEAYVDSYTIIYNDDEGNKLAQPVYIALIRFPNIEGGLLCYA----EGNVKVGAKAKILSF-------QWPLRVKVD----------------

(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=-3.75

Estimated TM-score = 0.31±0.10

Estimated RMSD = 15.5±3.4Å

Download Model 2

C-score=-3.90

Download Model 3

C-score=-3.76

Download Model 4

C-score=-4.21

Download Model 5

C-score=-4.63

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	3ldkA	0.424	6.29	0.071	0.723
2	3irbA	0.415	2.12	0.141	0.446
3	1b25A	0.408	6.27	0.047	0.693
4	4lgnA1	0.398	5.92	0.032	0.640
5	2x2hA	0.396	6.40	0.049	0.670
6	5fkqA	0.396	6.89	0.040	0.700
7	5dotA	0.394	6.55	0.044	0.683
8	1faeA	0.394	6.72	0.028	0.696
9	3azoA	0.394	6.24	0.066	0.663
10	4wjsA	0.394	6.66	0.041	0.670

(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	0.09	4	2wscK	CLA	Rep, Mult	167,171
2	0.05	2	2j0tC	CA	Rep, Mult	244,245,277,279,281
3	0.05	2	3frpA	CA	Rep, Mult	233,254,255,257
4	0.02	1	2h2gA	ZN	Rep, Mult	163,165
5	0.02	1	3unxA	CA	Rep, Mult	233,234
6	0.02	1	4f6xA	MG	Rep, Mult	91,158
7	0.02	1	1cg0A	MG	Rep, Mult	242,263
8	0.02	1	2d2mB	HEM	Rep, Mult	170,174
9	0.02	1	3dasA	ARA	Rep, Mult	242,261,263,264,265,297
10	0.02	1	2hcnA	CA	Rep, Mult	24,242
11	0.02	1	1j6xB	MET	Rep, Mult	215,218
12	0.02	1	1qezA	MG	Rep, Mult	242,281
13	0.02	1	3lfiA	BGC	Rep, Mult	13,219,238
14	0.02	1	3irbA	ZN	Rep, Mult	182,185,196,199
15	0.02	1	3fyeD	HEA	Rep, Mult	152,155
16	0.02	1	1b25A	SF4	Rep, Mult	188,240,241,244,246,247,248
17	0.02	1	4g7hD	NUC	Rep, Mult	26,300

	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	3dc8A	0.368	6.62	0.058	0.634	3.5.2.2	196
2	0.060	2aepA	0.365	6.14	0.045	0.591	3.2.1.18	NA
3	0.060	2vr2A	0.372	6.61	0.058	0.644	3.5.2.2	NA
4	0.060	1yiqA	0.383	6.19	0.026	0.640	1.1.99.-	NA
5	0.060	2ebsB	0.392	5.90	0.041	0.634	3.2.1.150	NA
6	0.060	1n2lA	0.367	6.74	0.051	0.670	3.1.6.8	NA
7	0.060	1nn2A	0.363	6.14	0.045	0.591	3.2.1.18	NA
8	0.060	2ftwA	0.373	6.68	0.035	0.650	3.5.2.2	254
9	0.060	1oqzB	0.382	6.12	0.064	0.630	3.5.1.93	NA
10	0.060	2w68C	0.221	5.40	0.014	0.327	3.2.1.18	242
11	0.060	1kv9A	0.364	6.07	0.071	0.594	1.1.99.-	NA
12	0.060	1v0zA	0.335	6.96	0.057	0.614	3.2.1.18	NA
13	0.060	1euuA	0.341	6.71	0.058	0.604	3.2.1.18	239,243
14	0.060	1xmeA	0.368	6.64	0.043	0.647	1.9.3.1	190
15	0.060	2cmlC	0.364	6.09	0.066	0.588	3.2.1.18	NA
16	0.060	2aeyA	0.382	6.71	0.062	0.673	3.2.1.80	NA
17	0.060	1bxrA	0.374	7.06	0.042	0.693	6.3.5.5	NA
18	0.060	2qnoA	0.394	6.72	0.028	0.696	3.2.1.4	214
19	0.060	2ac1A	0.385	6.63	0.045	0.673	3.2.1.26	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	0.424	6.29	0.07	0.72	3ldkA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
1	0.06	0.396	6.89	0.04	0.70	5fkqA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248
2	0.06	0.395	6.04	0.03	0.64	5jwzA	GO:0004553 GO:0005975 GO:0030246 GO:0030247
3	0.06	0.415	1.94	0.14	0.44	3irbA	GO:0046872
4	0.06	0.388	6.34	0.05	0.66	4z3wC	GO:0009055 GO:0016491 GO:0016625 GO:0051536 GO:0055114
5	0.06	0.387	5.81	0.06	0.62	2cn3A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
6	0.06	0.380	6.69	0.07	0.66	1y4wA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051669
7	0.06	0.393	5.76	0.04	0.62	2cn2A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
8	0.06	0.391	6.14	0.04	0.65	4amwA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016829 GO:0030246 GO:0047457
9	0.06	0.408	6.27	0.05	0.69	1b25A	GO:0009055 GO:0016491 GO:0016625 GO:0046872 GO:0051536 GO:0051539 GO:0055114
10	0.06	0.374	5.95	0.07	0.61	4kwuA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0046872
11	0.06	0.317	6.79	0.04	0.57	5aedA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
12	0.06	0.338	7.04	0.04	0.62	1uypA	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0005987 GO:0008152 GO:0016787 GO:0016798
13	0.06	0.391	6.86	0.04	0.70	4lgnA	GO:0004553 GO:0005975 GO:0030246 GO:0030247 GO:0030248
14	0.06	0.334	6.43	0.04	0.57	3b7fA	GO:0016787
15	0.06	0.354	6.33	0.07	0.59	2berA	GO:0004308 GO:0005576 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
16	0.06	0.359	6.77	0.06	0.64	5annA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
17	0.06	0.392	5.90	0.04	0.63	2ebsB	GO:0000272 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033945
18	0.06	0.347	6.84	0.03	0.61	3kf5A	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0008152 GO:0016787 GO:0016798

Consensus prediction of GO terms

Molecular Function	GO:0016798
GO-Score	0.36
Biological Processes	GO:0044238
GO-Score	0.31
Cellular Component
GO-Score

(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.