I-TASSER results

I-TASSER results for job id Rv3412

[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)
MRDHLPPGLPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKG
IRGLVVCCDECQQDHYHDWDMLRSNLLQLLIDGTVRPHEPAYDPEPDSYVTWDYCRGYAD
ASLNEAAPDADRFRRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRDHLPPGLPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKGIRGLVVCCDECQQDHYHDWDMLRSNLLQLLIDGTVRPHEPAYDPEPDSYVTWDYCRGYADASLNEAAPDADRFRRR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	9878999999999999999965546778899999999999999999999999999867788579998789999876678999999999998699999999999995668998898888877766655777777789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRDHLPPGLPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKGIRGLVVCCDECQQDHYHDWDMLRSNLLQLLIDGTVRPHEPAYDPEPDSYVTWDYCRGYADASLNEAAPDADRFRRR
Prediction	7555347713532165337422541574764641467315403620540530451154440300001055076611231410343034116774343343635253732130310201020124444675564558
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCC
MRDHLPPGLPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKGIRGLVVCCDECQQDHYHDWDMLRSNLLQLLIDGTVRPHEPAYDPEPDSYVTWDYCRGYADASLNEAAPDADRFRRR

4uuzC

0.19

0.07

0.35

1.51

dPPAS2

IGDGMERDYRAIP-ELDAYEAEGLALDDEDVEELTASQREAAERAMRD----------------------------------------------------------------------------------------

5frfA

0.12

0.07

0.59

1.16

dPPAS2

---------------------GSHMSAGEPHETMPDSDAVKFEHHFEE-------------------SSPCLE-KYG----LEQAVKKLVKRAAGQDDVPG-----------DLRAKVMGRLDLIRSGQSVPEHDV

3tsaA

0.17

0.15

0.90

0.72

MUSTER

LQATAHGGLTTAGILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAWRPSVLLVDVCA-----------LIGRVLGGLLDLPVVLHRWGVDPTAGPF--SDRAHELLDPVCRHHGLTGLPTPEL

4bkxA

0.10

0.09

0.93

0.83

dPPAS

IRADITDLLKEGE-EDGRDQSRLETQVWEAHNPLTDKQIDQFLVVARSVGTFARALD---------SLHMSAAAASRDITLFHAMDTLHKNIYDVPQGGPVLCRDEMEEWSASEANLFEEALEKYGKDQQDFLPWK

2n5dA

0.29

0.15

0.51

0.71

wdPPAS

-------------------GPGSYTGAGEP----SQADLDALLSAVRDIEQAVTLLTPRGGSG------DAKE--FKDGGLDRAAAQALLAGRT-----PAAAPRP------------------------------

4ozvA1

0.13

0.12

0.96

0.87

wMUSTER

ERKAGSPAVPP-PYTGSLVFTSKYEGSDSARATLNVKAEKTFRSQIKDITDMERGAT-SG-RDGDLACDDFNHTGKSKWALGSLSGAYMRLK-FSSSRPLAAHAEQSREI-EDWFARLGTQVVRDWSSFRLGGEVT

2n5dA

0.27

0.15

0.54

0.64

wPPAS

-------------------GPGSYTGA---GEP-SQADLDALLSAVRDIEQAVTLLTPRGSGG----SMDAKETRFKDGGLDRAAAQALLA-GRT----PAAAPRP------------------------------

1q0vA

0.11

0.04

0.40

1.03

dPPAS2

NSASSEPIVPV---VESKNEVKRQEIEEEE----DPDLKAAIQESLREAEEAKLRSERQKA---------------------------------------------------------------------------

4bkxA

0.08

0.96

0.81

PPAS

IR-DITDLLKEGE-EDGRDQSRLETQVWEAHNPLTDKQIDQFLVVARSVGTFARALDSLHM-SAAAASRDITLFHAM-DTLHKNDISKAISALVPQ-GGPVLCRDEMEEWSASEANLFEEALEKYGKDQQDFLPWK

4wd2A2

0.20

0.16

0.82

0.80

Env-PPAS

MFEHIDAY-PGDPFQKDPRDQIGIYFDAEGRIPRIARMRQSIHDGLRDHVALTRYVKQRGM----FTYTGLTESQ---VDALREVHGYILRSGRMCV--AGLNDS-----NVGIVADAIGKVLKSGA---------

(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=-3.92

Estimated TM-score = 0.29±0.09

Estimated RMSD = 13.7±4.0Å

Download Model 2

C-score=-3.66

Download Model 3

C-score=-4.49

Download Model 4

C-score=-3.91

Download Model 5

C-score=-3.49

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	3wajA1	0.532	3.89	0.048	0.824
2	5e6pA	0.502	4.33	0.069	0.794
3	4m6zA	0.501	4.66	0.073	0.897
4	2fa0A	0.500	4.29	0.034	0.794
5	3ig3A	0.498	4.60	0.055	0.824
6	1nthA	0.498	4.45	0.053	0.824
7	4p1tA	0.498	4.28	0.032	0.816
8	1iduA	0.498	4.31	0.027	0.809
9	4m8mA	0.496	4.51	0.067	0.801
10	2p8uA	0.493	4.41	0.049	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	0.05	3	2iegB	FRY	Rep, Mult	85,86,87,118,122
2	0.05	3	4r7cC	GLY	Rep, Mult	49,50,53
3	0.05	3	3oyzA	MG	Rep, Mult	99,120
4	0.03	2	2atiA	IHU	Rep, Mult	15,17,19,20
5	0.03	2	5ezmA	MPG	Rep, Mult	81,119
6	0.03	2	2wsfB	CLA	Rep, Mult	46,61
7	0.03	2	1iw7P	MG	Rep, Mult	42,46
8	0.02	1	3r4iB	CA	Rep, Mult	99,113
9	0.02	1	4ev6E	MG	Rep, Mult	64,110
10	0.02	1	3pugA	MG	Rep, Mult	3,99,113
11	0.02	1	1jcsA	FII	Rep, Mult	76,109
12	0.02	1	3leeD	MG	Rep, Mult	12,16
13	0.02	1	5d57D	78M	Rep, Mult	24,38,42
14	0.02	1	2kq9A	ZN	Rep, Mult	68,71,115,118
15	0.02	1	2h1iB	CA	Rep, Mult	45,48
16	0.02	1	4n4wA	ZN	Rep, Mult	77,80
17	0.02	1	1exvB	700	Rep, Mult	22,40,44
18	0.02	1	4rku3	CLA	Rep, Mult	34,38
19	0.02	1	1p2bA	GLC	Rep, Mult	44,45,47,48,62,90,92
20	0.02	1	1gfzA	CFF	Rep, Mult	115,117,118

	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	1u8vA	0.462	4.28	0.053	0.735	5.3.3.3	NA
2	0.060	2z1qB	0.479	4.94	0.045	0.868	1.3.99.3	NA
3	0.060	1auoA	0.463	4.26	0.046	0.735	3.1.1.1	92
4	0.060	1e1yA	0.488	4.26	0.111	0.750	2.4.1.1	NA
5	0.060	1jqiA	0.464	4.92	0.070	0.853	1.3.99.2	NA
6	0.060	3gpbA	0.488	4.14	0.103	0.750	2.4.1.1	NA
7	0.060	2h1iA	0.463	4.04	0.090	0.721	3.1.1.1	55,84
8	0.060	1ivhA	0.477	4.73	0.031	0.838	1.3.99.10	NA
9	0.060	2qllA	0.459	4.36	0.045	0.721	2.4.1.1	NA
10	0.060	1rx0A	0.461	4.93	0.053	0.868	1.3.99.-	NA
11	0.060	3d9dA	0.462	5.11	0.075	0.875	1.7.3.1	NA
12	0.060	2r72A	0.471	5.20	0.031	0.868	2.7.7.48	83
13	0.060	3fmrB	0.468	4.79	0.015	0.787	3.4.11.18	NA
14	0.060	1vgpA	0.455	4.37	0.045	0.772	4.1.3.7	22,80
15	0.060	1iduA	0.498	4.31	0.027	0.809	1.11.1.10	NA
16	0.060	2pg0A	0.462	4.89	0.038	0.853	1.3.99.3	NA
17	0.060	2uxwA	0.481	4.85	0.078	0.868	1.3.99.-	NA
18	0.060	2ix6E	0.460	5.24	0.045	0.882	1.3.3.6	114
19	0.060	1ig8A	0.395	4.76	0.065	0.676	2.7.1.1	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	0.07	0.535	3.95	0.06	0.85	3wakA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
1	0.07	0.417	5.56	0.05	0.82	4m8nA	GO:0007165 GO:0016020 GO:0016021 GO:0017154 GO:0043087 GO:0071526
2	0.07	0.487	4.40	0.06	0.79	3suaF	GO:0002116 GO:0004872 GO:0004888 GO:0005096 GO:0005576 GO:0005622 GO:0005886 GO:0005887 GO:0007162 GO:0007165 GO:0008360 GO:0014068 GO:0016020 GO:0016021 GO:0016477 GO:0017154 GO:0030215 GO:0030334 GO:0032794 GO:0033689 GO:0035556 GO:0043087 GO:0043547 GO:0043931 GO:0048675 GO:0048812 GO:0050772 GO:0051493 GO:0071526 GO:1900220 GO:1902287
3	0.07	0.459	5.20	0.09	0.84	3su8X	GO:0002116 GO:0004872 GO:0004888 GO:0005096 GO:0005576 GO:0005622 GO:0005886 GO:0005887 GO:0007162 GO:0007165 GO:0008360 GO:0014068 GO:0016020 GO:0016021 GO:0016477 GO:0017154 GO:0030215 GO:0030334 GO:0032794 GO:0033689 GO:0035556 GO:0043087 GO:0043547 GO:0043931 GO:0048675 GO:0048812 GO:0050772 GO:0051493 GO:0071526 GO:1900220 GO:1902287
4	0.06	0.448	5.18	0.06	0.76	3rytA	GO:0002116 GO:0005634 GO:0005737 GO:0005886 GO:0005887 GO:0007165 GO:0014910 GO:0016020 GO:0016021 GO:0017154 GO:0021785 GO:0048841 GO:0060666 GO:0070062 GO:0071526 GO:0097485 GO:1902287 GO:1990138
5	0.06	0.502	4.33	0.07	0.79	5e6pA	GO:0001843 GO:0001932 GO:0002116 GO:0005886 GO:0005887 GO:0007162 GO:0007165 GO:0007275 GO:0007405 GO:0007420 GO:0008360 GO:0009986 GO:0016020 GO:0016021 GO:0017154 GO:0043087 GO:0050772 GO:0070062 GO:0071526 GO:1902287 GO:2001222
6	0.06	0.408	4.85	0.03	0.71	1lshA	GO:0005319 GO:0006869 GO:0045735
7	0.06	0.416	4.93	0.03	0.75	2amxA	GO:0009168 GO:0019239
8	0.06	0.498	4.60	0.06	0.82	3ig3A	GO:0002116 GO:0005634 GO:0005886 GO:0005887 GO:0007165 GO:0007411 GO:0016020 GO:0016021 GO:0017154 GO:0021612 GO:0021637 GO:0021766 GO:0021785 GO:0021860 GO:0030054 GO:0030334 GO:0043231 GO:0048843 GO:0050919 GO:0051495 GO:0071526 GO:0097485 GO:1902287 GO:1990138
9	0.06	0.355	4.11	0.06	0.56	3beoA	GO:0000166 GO:0008761 GO:0016853
10	0.06	0.532	3.89	0.05	0.82	3wajA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
11	0.06	0.323	5.70	0.06	0.65	3vgpA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740
12	0.06	0.460	4.25	0.06	0.75	4m8mB	GO:0007165 GO:0016020 GO:0016021 GO:0017154 GO:0043087 GO:0071526
13	0.06	0.330	5.92	0.05	0.69	3vu0B	GO:0004576 GO:0006486 GO:0016020 GO:0016021
14	0.06	0.318	5.58	0.08	0.65	3wovA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
15	0.06	0.326	4.89	0.05	0.57	1qo3C	GO:0004871 GO:0005886 GO:0007155 GO:0007165 GO:0009897 GO:0016020 GO:0016021 GO:0030246
16	0.06	0.372	5.26	0.07	0.70	3waiA	GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0046872 GO:0055052 GO:0060326 GO:1901982 GO:1990060
17	0.06	0.311	5.29	0.06	0.62	3g8lB	GO:0005886 GO:0016020 GO:0016021
18	0.06	0.307	5.30	0.02	0.57	3e20B	GO:0002184 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006415 GO:0016149 GO:0018444

Consensus prediction of GO terms

Molecular Function	GO:0004888
GO-Score	0.47
Biological Processes	GO:0051336	GO:0007411	GO:1902285
GO-Score	0.37	0.37	0.37
Cellular Component	GO:0043235	GO:0031226
GO-Score	0.37	0.37

(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.