I-TASSER results

I-TASSER results for job id Rv3851

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

Input Sequence in FASTA format

>protein (94 residues)
MTAIGMSHPPRVHRRVGGQRTALTAGIGLLLAALVLTTIANPPAAFAHTAQLSTATPAPA
VAATDANDVPTWPFVVGTVAAVAVAALWAVRRGR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MTAIGMSHPPRVHRRVGGQRTALTAGIGLLLAALVLTTIANPPAAFAHTAQLSTATPAPAVAATDANDVPTWPFVVGTVAAVAVAALWAVRRGR
Prediction	CCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHCC
Conf.Score	9866688997444334764445677799999999998747987555444345568888764456788899876555445678899998887679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MTAIGMSHPPRVHRRVGGQRTALTAGIGLLLAALVLTTIANPPAAFAHTAQLSTATPAPAVAATDANDVPTWPFVVGTVAAVAVAALWAVRRGR
Prediction	7432436334413542445432132212321132112223434332343341444443333334437533322212232222211112224568
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHCC
MTAIGMSHPPRVHRRVGGQRTALTAGIGLLLAALVLTTIANPPAAFAHTAQLSTATPAPAVAATDANDVPTWPFVVGTVAAVAVAALWAVRRGR

1z69A

0.20

0.17

0.84

0.71

MUSTER

MKEFVPSDPALKIAYYA--KLSEQQG----FDHVWITDHYNNRDVYSTLTVLALNTNGPGVTN-----SYTRP----AITASSIASIAEISGGR

5m1hA1

0.16

0.14

0.88

0.67

dPPAS

GTVIPIQHIRSVTGEPPRNPREIPIWLGRNAPAIDGVFPVTTPDLRCRIINILGGNIGLSLTPGDCLT-----------WDSAVATLFIRTHGT

3j2wQ

0.22

0.17

0.77

0.56

wdPPAS

-STNGTAH-PHLYYYELYPTMTVVIVSVASFVLLSMVGTA---VGMCVCARRRCITPTPG--AT----VPF-----------LLSLLCCVRTTK

4egfA1

0.26

0.21

0.82

0.63

wMUSTER

RYA-GVL---RLDGKRGATK-GIGADIARAFAAAVLS--RDVSELDAARRALGEQFGTDVHTAIDLAE-P---------DAPAELARRAAEAGG

3uvzA1

0.26

0.20

0.78

0.61

wPPAS

VSPI--LPGAWL---VGGQRMFCFAAQSM-YRVAVLDPDPASPAG-----AVADRH----RAADDEAEAVSTEF------NVPAASLDFLARTF

1yxmA1

0.22

0.18

0.83

0.56

dPPAS2

----GRSAPGLLQGQVGGAT-GIGKAIVKELLELVIASR-KLEAADELQANLPPTKQARVIPQCNIRN----------EEEVNNLVKSTLDTGK

1yxmA1

0.22

0.18

0.82

0.64

PPAS

----GRSAPGLLQGQVGGAT-GIGKAIVKELLELVIASR-KL-AADELQANLPPTKQARVIPQCN----------IRNEEEVNNLVKSTLDTGK

1lqmH

0.21

0.18

0.86

0.80

Env-PPAS

-----MTNLSDIIEKETGKQLVIQESI-LMLPEEVEEVIGNKPESLVHTAYDESTDENVMLLTSDAPEYKPWALVIQSNGENKIKML-------

2xepA

0.12

0.96

0.71

MUSTER

LAAAGHHDP-SLMRPFLTSHEVFELGWGD--PERRAEWVRQDEAGRRELLEMAGVMTVRDLGATVHQLGIDW-HMDAFDVVRVLEGLLQDSGRD

5cbfA

0.15

1.00

0.57

dPPAS

LMFKRFFGAVRTSWRDPSTRGAVLSLAIIVTAATIFYTLASVIDSLFYAVSGLPMGNGPLSPTLTLSKIFTLVYAVGLFVTVGGSLASAIVQNN

(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=-3.29

Estimated TM-score = 0.35±0.12

Estimated RMSD = 11.1±4.6Å

Download Model 2

C-score=-4.07

Download Model 3

C-score=-4.45

Download Model 4

C-score=-4.56

Download Model 5

C-score=-4.39

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	2ongA	0.572	3.47	0.054	0.904
2	3pyaA2	0.563	3.35	0.011	0.851
3	5c05A	0.556	3.68	0.011	0.904
4	3n0fA	0.552	3.82	0.022	0.904
5	1hxgA	0.550	3.76	0.033	0.904
6	4j72A	0.547	3.68	0.077	0.840
7	1h19A	0.545	4.18	0.078	0.915
8	5araW	0.545	4.01	0.087	0.904
9	1n1zA	0.544	3.66	0.057	0.872
10	4fjqA2	0.543	3.70	0.076	0.894

(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	0.13	4	5e7cD	CLA	Rep, Mult	27,33,34,52
2	0.09	3	3fu0A	22F	Rep, Mult	35,37,42,45,46,53
3	0.03	1	3ftwA	IMD	Rep, Mult	22,23,27,30,57,59
4	0.03	1	2bf0X	CA	Rep, Mult	52,55
5	0.03	1	2j8rB	AZI	Rep, Mult	35,80
6	0.03	1	4n6hA	OLA	Rep, Mult	25,28,29,32
7	0.03	1	1n9bA	MA4	Rep, Mult	15,84,85
8	0.03	1	4l6v0	CLA	Rep, Mult	24,27,31,84
9	0.03	1	5ezmA	MPG	Rep, Mult	44,47
10	0.03	1	3fueA	11S	Rep, Mult	12,15,29,31,80
11	0.03	1	3zk1E	DMU	Rep, Mult	78,82

	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	1ohcA	0.486	4.13	0.055	0.862	3.1.3.48,3.1.3.16	91
2	0.060	3lomA	0.535	4.00	0.098	0.915	2.5.1.10	NA
3	0.060	3f7mA	0.503	3.94	0.071	0.862	3.4.21.-	NA
4	0.060	3cwfB	0.515	2.95	0.108	0.734	2.7.13.3	NA
5	0.060	1z1wA	0.541	3.94	0.044	0.894	3.4.11.-	NA
6	0.060	2i2xA	0.518	4.23	0.056	0.883	2.1.1.90	18,54,55
7	0.060	3fvyA	0.499	4.35	0.022	0.904	3.4.14.4	NA
8	0.060	3enhA	0.404	4.10	0.125	0.713	3.4.24.57	37,41
9	0.060	3g4dA	0.511	4.00	0.078	0.883	4.2.3.13	NA
10	0.060	1dbiA	0.504	3.86	0.034	0.915	3.4.21.-	NA
11	0.060	2j1pB	0.511	3.84	0.121	0.894	2.5.1.1,2.5.1.10,2.5.1.29	NA
12	0.060	1n1zA	0.544	3.66	0.057	0.872	5.5.1.8	NA
13	0.060	3ebgA	0.506	4.03	0.102	0.862	3.4.11.-	NA
14	0.060	3f7oA	0.498	3.93	0.082	0.872	3.4.21.-	NA
15	0.060	1gw6A	0.544	4.18	0.078	0.915	3.3.2.6	NA
16	0.060	2pnqB	0.501	3.68	0.054	0.787	3.1.3.43	72
17	0.060	2oa6D	0.513	3.67	0.108	0.872	4.2.3.9	NA
18	0.060	1d8hA	0.524	3.90	0.035	0.904	3.1.3.33	11
19	0.060	1o58A	0.504	3.88	0.108	0.830	2.5.1.47	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	0.13	0.544	3.66	0.06	0.87	1n1zA	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046211 GO:0046872 GO:0047926
1	0.09	0.572	3.47	0.05	0.90	2ongA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
2	0.07	0.383	3.90	0.06	0.64	4gaxA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0034006 GO:0046872
3	0.07	0.434	4.39	0.04	0.78	4jhlA	GO:0000272 GO:0005737 GO:0005975 GO:0016787 GO:0045493 GO:0046555 GO:0052689
4	0.07	0.416	4.45	0.07	0.81	4c2dD	GO:0006508 GO:0006518 GO:0007165 GO:0008233 GO:0008236 GO:0016787 GO:0030435 GO:0042277 GO:0042802 GO:0042803
5	0.06	0.390	4.11	0.06	0.67	4ce5A	GO:0003824 GO:0008152
6	0.06	0.367	4.01	0.06	0.63	5c05B	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
7	0.06	0.410	4.76	0.05	0.81	3pr3A	GO:0004347 GO:0006094 GO:0006096 GO:0006098 GO:0016853
8	0.06	0.332	4.63	0.02	0.64	3hqtB	GO:0003824 GO:0008483 GO:0009058 GO:0016740 GO:0016746 GO:0030170
9	0.06	0.423	3.51	0.12	0.71	2cu2A	GO:0009058 GO:0016740 GO:0016779 GO:0016853
10	0.06	0.369	4.44	0.05	0.70	3pybB	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0009686 GO:0009740 GO:0009905 GO:0010333 GO:0016829 GO:0016853
11	0.06	0.495	4.22	0.09	0.87	3p5rA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0042617 GO:0046872 GO:0050553
12	0.06	0.432	4.42	0.09	0.80	4rpaA	GO:0004427 GO:0005737 GO:0016462 GO:0016787 GO:0030145 GO:0046872
13	0.06	0.404	4.52	0.04	0.78	3saeA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016829 GO:0046872 GO:0052681
14	0.06	0.479	4.37	0.01	0.84	3ffzA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
15	0.06	0.493	3.97	0.07	0.87	5dhiA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872
16	0.06	0.413	4.48	0.02	0.73	2j5cB	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
17	0.06	0.511	4.00	0.08	0.88	3g4dA	GO:0000287 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872 GO:0047461
18	0.06	0.325	4.35	0.02	0.62	3ff7C	GO:0002376 GO:0004872 GO:0005886 GO:0006954 GO:0006968 GO:0007166 GO:0016020 GO:0016021 GO:0030246 GO:0045087

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0016838
GO-Score	0.52	0.52
Biological Processes	GO:0046211	GO:0045493	GO:0006518	GO:0006508	GO:0007165	GO:0030435
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0009507
GO-Score	0.13

(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.