I-TASSER results

I-TASSER results for job id Rv3067

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

Input Sequence in FASTA format

>protein (136 residues)
MLTVGVGIGAAILLGWFTLAHRHPDQPGAAATPPPAGLTTRSAPTAAPPSTLQSPDLDSV
FLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPALGDRTTAYVAVS
IRTYCPKYDAVLPPGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLTVGVGIGAAILLGWFTLAHRHPDQPGAAATPPPAGLTTRSAPTAAPPSTLQSPDLDSVFLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPALGDRTTAYVAVSIRTYCPKYDAVLPPGS
Prediction	CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCHHHHCCCCCCC
Conf.Score	9753488999999988875799988887766665456666555457888889999757999999999799999999999999999999977999999999999959999567768999999985946655899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLTVGVGIGAAILLGWFTLAHRHPDQPGAAATPPPAGLTTRSAPTAAPPSTLQSPDLDSVFLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPALGDRTTAYVAVSIRTYCPKYDAVLPPGS
Prediction	5221023322011102121345446444443333333200232323242453646741430043057441527337301420330053066454244004203753524453013000000321124247636768
	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

CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCHHHHCCCCCCC
MLTVGVGIGAAILLGWFTLAHRHPDQPGAAATPPPAGLTTRSAPTAAPPSTLQSPDLDSVFLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPALGDRTTAYVAVSIRTYCPKYDAVLPPGS

5ed7A2

0.17

0.15

0.93

0.84

MUSTER

LFALAAGTTAEQLLMFDLLPPKDVPVGSDVQADSTALLRFIESQRLAVPGGVISPE-HVAYLGAFLSV-AGRGRMSAATHTARLT-------TSLVLAVGDVDRLSAFDRGAAGAASRTRAAGYLDVLLTVRLARS

5ed7A2

0.07

0.99

0.76

dPPAS

GLFRDALAAGTTAEQLLMFDLLPPKDVPVGSDVQADSTALLRFIESQRLAVPGGVISPEHVAYLGAFLSVLYA--GRGRMSAATHTARLTGVTSLVLAVGDVDRLSAFDRGAAGAASRTRAAGYLDVLLTVRLARS

2q5tA3

0.20

0.16

0.82

0.79

wdPPAS

M--SALAAHRVCGVPLETLARSR--KPRDLTDDLSCAYQAQNIVSLFVATRILFSHLDSVFTLNLDEQ-----EPEVAERLSDLRRINENNGMVARQIYNDYVTHHPGLTPEQTSAGAQAA---------------

5ed7A2

0.21

0.18

0.86

0.82

wMUSTER

LFALAAGTTAEQLLMFDLLPPKDVPVGSDVQADSTALLRFIESQRLAVPGGVISPEYLGAFLSVLYARG----RMSAATHTARLT-------TSLVLAVGDVDRLS-AFRTRAAGYLDVLLTVRLARSQ-------

5ed7A2

0.18

0.15

0.87

0.83

wPPAS

LFALAAGTTAEQLLMFDLLPPKDVPVGSDVQADSTALLRFIESQRLAVPGGVISPE-HVAYLGAFLSV---YAGMSAATHTARLT-------TSLVLAVGDVDRLSAASRTRAAGYLDVLLTVRLARSQ-------

4ke2A

0.12

0.10

0.88

0.98

dPPAS2

AAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP----------------

5ed7A2

0.17

0.15

0.93

0.87

PPAS

LFALAAGTTAEQLLMFDLLPPKDVPVGSDVQADSTALLRFIESQRLAVPGGVISPE-HVAYLGAFLSV-AGRGRMSAATHTARLT-------TSLVLAVGDVDRLSAFDRGAAGAASRTRAAGYLDVLLTVRLARS

2gqbA

0.16

0.15

0.91

0.72

Env-PPAS

-----MSIFGKIMSAIFGDSAAASPGGAQAPATTGAAG---TAPTAPQPTAAPSIDVAPILDKAVKAKGLEWRT--SIVDLMKALD--IDSSLSARKELAKELGYSGDMNDSASMNIWLHKQVMSVANGGKLPPEI

4tvxU2

0.18

0.15

0.84

0.78

MUSTER

IVTVGLGYKTALRKALYTFAFKNKDFKGAGVSVHETAERHFYRQS------------ELLIPDVLAN--VNFSQADEVIADLRDKLHQLCEML-FNQSVA------PYAHHPKLISTLALARATLYKHLRELKPQ-

5k7vA1

0.08

0.07

0.86

0.73

dPPAS

EMIDILAESSKKSIEELARAADNKTTEKAVAEAIEEIARLATAAIQLIEALAKNLASEEFMARAISAI------AELAKKAIEAIYRLADNHTTDTFMARAIAAIANLAVTAILAIAALASNH-------------

(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=-1.85

Estimated TM-score = 0.49±0.15

Estimated RMSD = 8.6±4.5Å

Download Model 2

C-score=-3.94

Download Model 3

C-score=-4.10

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	5ed7A2	0.739	2.73	0.162	0.956
2	2nyfA2	0.544	4.15	0.084	0.846
3	1w27A3	0.540	4.15	0.063	0.860
4	4xgtA	0.527	3.48	0.059	0.735
5	3u1nA	0.519	4.55	0.078	0.831
6	3g45A	0.517	4.70	0.045	0.838
7	1sojL	0.516	4.76	0.059	0.853
8	3ibjA3	0.516	4.41	0.044	0.824
9	1t9sA	0.516	4.73	0.038	0.838
10	2hekA1	0.512	4.31	0.071	0.809

(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	0.10	7	1xn0A	ROL	Rep, Mult	105,113,114,117,118,121
2	0.06	4	1y2bB	DEE	Rep, Mult	65,74,80,99,102
3	0.04	3	1mz9B	VDY	Rep, Mult	114,117,121
4	0.04	3	3g58A	988	Rep, Mult	71,78,81,85
5	0.04	3	3fa4A	MG	Rep, Mult	56,58
6	0.03	2	4x23P	III	Rep, Mult	119,122
7	0.03	2	2e75E	OPC	Rep, Mult	112,113,116,117
8	0.03	2	1y66B	DIO	Rep, Mult	121,124,128
9	0.01	1	1s5ld	CLA	Rep, Mult	102,125
10	0.01	1	1q9mC	ROL	Rep, Mult	79,82,83,97
11	0.01	1	1m32A	PLP	Rep, Mult	72,73
12	0.01	1	3eerA	ZN	Rep, Mult	86,125,126
13	0.01	1	1xrmA	III	Rep, Mult	99,102
14	0.01	1	3lezA	CA	Rep, Mult	56,76
15	0.01	1	2qykA	NPV	Rep, Mult	82,86,93
16	0.01	1	4ecgA	CA	Rep, Mult	106,111

	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	1e6yA	0.485	4.56	0.058	0.831	2.8.4.1	99
2	0.060	1w27A	0.525	4.81	0.032	0.897	4.3.1.24	NA
3	0.060	1iv8A	0.490	4.48	0.040	0.779	5.4.99.15	76
4	0.060	1mc0A	0.374	4.93	0.065	0.669	3.1.4.17	57
5	0.060	1tazA	0.477	4.86	0.044	0.846	3.1.4.17	NA
6	0.060	2ouyA	0.488	4.76	0.066	0.853	3.1.4.17	NA
7	0.060	1t2eA	0.479	3.42	0.032	0.684	1.1.1.27	7
8	0.060	2o48X	0.493	3.95	0.054	0.750	1.1.1.179,1.3.1.20	NA
9	0.060	2r72A	0.477	4.51	0.083	0.801	2.7.7.48	NA
10	0.060	1b8fA	0.506	4.45	0.032	0.824	4.3.1.3	NA
11	0.060	1zklA	0.483	4.73	0.076	0.846	3.1.4.17	25
12	0.060	2qykB	0.516	4.58	0.060	0.824	3.1.4.17	NA
13	0.060	1q11A	0.489	4.34	0.038	0.809	6.1.1.1	97
14	0.060	1e6vA	0.475	5.16	0.039	0.868	2.8.4.1	NA
15	0.060	1lldB	0.474	3.74	0.084	0.691	1.1.1.27	11,101
16	0.060	2nyfA	0.544	4.15	0.084	0.846	4.3.1.5	NA
17	0.060	2ohyB	0.517	4.42	0.025	0.846	5.4.3.6	NA
18	0.060	3czoB	0.455	4.98	0.060	0.824	4.3.1.3	NA
19	0.060	3ecnB	0.480	4.82	0.052	0.838	3.1.4.17	34,124

(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	0.13	0.739	2.73	0.16	0.96	5ed7A	GO:0019012 GO:0019033 GO:0030430 GO:0042025
1	0.07	0.435	4.76	0.02	0.74	3mkmA	GO:0005509 GO:0006206 GO:0008152 GO:0016787 GO:0016798 GO:0016799 GO:0046133 GO:0046872 GO:0050263
2	0.06	0.525	4.81	0.03	0.90	1w27A	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548
3	0.06	0.378	5.46	0.04	0.76	1y2mB	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0052883
4	0.06	0.544	4.15	0.08	0.85	2nyfA	GO:0003824 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
5	0.06	0.522	4.21	0.07	0.84	4v2rB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
6	0.06	0.376	4.82	0.06	0.65	3ojcA	GO:0006520 GO:0006807 GO:0008152 GO:0009252 GO:0016853 GO:0016855 GO:0036361 GO:0046872 GO:0047661 GO:0047689
7	0.06	0.310	5.02	0.03	0.52	3nojA	GO:0008948 GO:0016829 GO:0046872 GO:0047443
8	0.06	0.486	5.00	0.05	0.86	1gk2A	GO:0003824 GO:0004397 GO:0005737 GO:0006547 GO:0006548 GO:0016829 GO:0016841 GO:0019556 GO:0019557
9	0.06	0.443	4.55	0.06	0.76	2qb6A	GO:0004309 GO:0005737 GO:0005759 GO:0005829 GO:0005886 GO:0006798 GO:0016462 GO:0016787 GO:0046872
10	0.06	0.372	5.27	0.07	0.65	2x79A	GO:0005215 GO:0016020 GO:0016021 GO:0055085
11	0.06	0.461	4.26	0.07	0.74	3unvA	GO:0003824
12	0.06	0.341	5.28	0.08	0.62	4bhhF	GO:0003723 GO:0016032 GO:0019012 GO:0019013 GO:0019028 GO:0019029 GO:0039657
13	0.06	0.495	4.34	0.07	0.79	4c6gB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
14	0.06	0.321	5.09	0.07	0.59	1ef9A	GO:0003824 GO:0004300 GO:0004492 GO:0005829 GO:0006635 GO:0008152 GO:0016829 GO:0016831
15	0.06	0.392	3.35	0.05	0.56	3nz4B	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
16	0.06	0.409	5.20	0.03	0.78	3kdyA	GO:0003824 GO:0009403 GO:0016829 GO:0016841 GO:0016853 GO:0017000 GO:0050368 GO:0052883
17	0.06	0.354	5.12	0.09	0.64	3zizA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
18	0.06	0.394	5.41	0.04	0.76	2o6yA	GO:0003824 GO:0006572 GO:0009698 GO:0009699 GO:0016829 GO:0016841 GO:0042802 GO:0051289 GO:0052883

Consensus prediction of GO terms

Molecular Function	GO:0016840
GO-Score	0.36
Biological Processes	GO:0009803	GO:0009699	GO:0072330
GO-Score	0.36	0.36	0.36
Cellular Component	GO:0044424
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.