I-TASSER results

I-TASSER results for job id Rv3237c

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

Input Sequence in FASTA format

>protein (160 residues)
MDVKEVLLPGVGLRYEFTSYRGDRIGIVARRSGGFDVVLYGRDDPDEARPVLRLTDEEAE
AVAQILGAPRIAERFTELTREVPGLKAGQIHIRAGSLFVDRPLGDTRARTRTGASIVAIV
RDEDVLASPGPTDVLRAGDVLIVIGTEDGIAGVEQIVEKG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDVKEVLLPGVGLRYEFTSYRGDRIGIVARRSGGFDVVLYGRDDPDEARPVLRLTDEEAEAVAQILGAPRIAERFTELTREVPGLKAGQIHIRAGSLFVDRPLGDTRARTRTGASIVAIVRDEDVLASPGPTDVLRAGDVLIVIGTEDGIAGVEQIVEKG
Prediction	CEEEEEHCCCCCCEEEEEHCCCCEEEEEEHCCCCCEEEHCCCCCCCCCCEHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCHHHHHHHHHHCCEEEEEEHCCEEEHCCCCCEEHCCCEEEEEHCCHHHHHHHHHHHHCC
Conf.Score	9579985899885579997689889999955699589977888886543435789999999999875555545677777656787589999799986578688998678877968999998998986899985768997999986999999999999789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDVKEVLLPGVGLRYEFTSYRGDRIGIVARRSGGFDVVLYGRDDPDEARPVLRLTDEEAEAVAQILGAPRIAERFTELTREVPGLKAGQIHIRAGSLFVDRPLGDTRARTRTGASIVAIVRDEDVLASPGPTDVLRAGDVLIVIGTEDGIAGVEQIVEKG
Prediction	7616525045233423032465430000024434431222456446323421514562044015244344234314423442452222304145513113210411511652401000023675323205262404540100000457205302610788
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEHCCCCCCEEEEEHCCCCEEEEEEHCCCCCEEEHCCCCCCCCCCEHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCHHHHHHHHHHCCEEEEEEHCCEEEHCCCCCEEHCCCEEEEEHCCHHHHHHHHHHHHCC
MDVKEVLLPGVGLRYEFTSYRGDRIGIVARRSGGFDVVLYGRDDPDEARPVLRLTDEEAEAVAQILGAPRIAERFTELTREVPGLKAGQIHIRAGSLFVDRPLGDTRARTRTGASIVAIVRDEDVLASPGPTDVLRAGDVLIVIGTEDGIAGVEQIVEKG

2aemA

0.15

0.14

0.91

1.79

MUSTER

ETIHCILIRKIDESRIIAEAERYENIEQLRMAGADQVISPF--------------VISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISAL

2aemA2

0.20

0.11

0.57

2.69

dPPAS

--------------------------------------------------------------------GYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISAL

2aemA2

0.20

0.11

0.57

3.13

wdPPAS

--------------------------------------------------------------------GYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISAL

2aemA

0.15

0.14

0.89

2.18

wMUSTER

LGIRKID-ESV---RIIAEAERYENIEQLRMAGADQVISPF--------------VISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISAL

2aemA2

0.20

0.11

0.57

2.88

wPPAS

--------------------------------------------------------------------GYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYIS-A

2aemA2

0.20

0.11

0.57

6.55

dPPAS2

--------------------------------------------------------------------GYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISAL

2aemA2

0.20

0.11

0.57

2.63

PPAS

--------------------------------------------------------------------GYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYIS-A

4xttA

0.21

0.11

0.53

2.74

Env-PPAS

----------------------------------------------------------------------ASASVLDYLELADEHSIVELKA--TEKMAGQSIIDLDIRAQYGINIIAIKRGKEFIISPNPNINLEIGDILIMIGHDNDLNRFEKNI---

1lnqA

0.15

0.14

0.91

1.76

MUSTER

ETIHCILIRKIDESRIIAEAERYENIEQLRMAGADQVISPF--------------VISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISA-

4xttA

0.21

0.11

0.53

2.49

dPPAS

----------------------------------------------------------------------ASASVLDYLELADEHSIVELKA--TEKMAGQSIIDLDIRAQYGINIIAIKRGKEFIISPNPNINLEIGDILIMIGHDNDLNRFEKNI---

(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=-0.69

Estimated TM-score = 0.63±0.14

Estimated RMSD = 6.3±3.9Å

Download Model 2

C-score=-1.81

Download Model 3

C-score=-1.47

Download Model 4

C-score=-4.38

Download Model 5

C-score=-0.89

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	2aemA	0.822	1.80	0.144	0.912
2	1lnqA	0.817	1.69	0.145	0.906
3	4hpfA	0.679	3.02	0.125	0.887
4	5a6eC	0.656	2.85	0.126	0.831
5	3mt5A2	0.643	2.90	0.120	0.825
6	4gvlA	0.530	4.65	0.154	0.812
7	4g65A	0.528	4.15	0.194	0.775
8	2bkpA	0.511	3.83	0.182	0.675
9	4j8lA	0.489	4.83	0.077	0.819
10	3loyA	0.487	4.97	0.073	0.850

(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	0.28	5	3kxdA	CD	Rep, Mult	85,113,149
2	0.15	3	3rbxD	CA	Rep, Mult	111,149,152
3	0.07	1	1vctA	NA	Rep, Mult	91,122,138,139
4	0.05	1	3rbxC	CA	Rep, Mult	128,129
5	0.05	1	2y73A	IMD	Rep, Mult	117,118,119,141,143

	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	1z7dA	0.461	4.96	0.068	0.781	2.6.1.13	NA
2	0.060	3hz3A	0.452	4.46	0.030	0.713	2.4.1.5	145
3	0.060	2hk3A	0.454	4.45	0.081	0.706	4.1.1.33	NA
4	0.060	1n8pA	0.469	4.85	0.062	0.794	4.4.1.1	NA
5	0.060	1eqbB	0.459	5.08	0.057	0.794	2.1.2.1	113
6	0.060	1mdwA	0.306	6.01	0.046	0.594	3.4.22.53	NA
7	0.060	2dkcA	0.461	4.84	0.069	0.756	5.4.2.3	145,147
8	0.060	1y4iA	0.468	5.16	0.080	0.819	4.4.1.11	NA
9	0.060	1kfxL	0.411	5.22	0.046	0.731	3.4.22.53	NA
10	0.060	2j1qA	0.400	4.25	0.041	0.619	2.7.3.3	NA
11	0.060	1pg8A	0.464	5.04	0.097	0.800	4.4.1.11	NA
12	0.060	3jzlA	0.466	5.02	0.063	0.794	4.4.1.8	133
13	0.060	3nztA	0.457	4.91	0.036	0.756	6.3.2.2	NA
14	0.060	2c10B	0.463	5.88	0.052	0.919	1.4.3.21,1.4.3.6	NA
15	0.060	1n8pC	0.469	4.84	0.062	0.794	4.4.1.1	98,115
16	0.060	1p3wB	0.455	4.96	0.088	0.769	2.8.1.7	NA
17	0.060	1n16B	0.477	4.26	0.074	0.738	2.7.3.2	93,121
18	0.060	1ibjA	0.460	4.99	0.076	0.800	4.4.1.8	NA
19	0.060	3gbxA	0.465	5.39	0.082	0.806	2.1.2.1	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	0.35	0.817	1.69	0.14	0.91	1lnqA	GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0042802 GO:0046872 GO:0098655
1	0.17	0.511	3.83	0.18	0.68	2bkpA	GO:0006813 GO:0008324 GO:0098655
2	0.07	0.541	4.98	0.20	0.85	4gx2B	GO:0000166 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0046872 GO:0098655
3	0.07	0.449	2.62	0.12	0.53	4j7cB	GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0008324 GO:0016020 GO:0098655
4	0.06	0.402	5.08	0.07	0.67	3l9xA	GO:0000166 GO:0003955 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006812 GO:0006813 GO:0006885 GO:0008324 GO:0009055 GO:0009636 GO:0010181 GO:0015079 GO:0015297 GO:0015299 GO:0015503 GO:0015643 GO:0016020 GO:0016021 GO:0016491 GO:0019899 GO:0032414 GO:0051595 GO:0055085 GO:0055114 GO:0071805 GO:0098655 GO:1901381 GO:1902600
5	0.06	0.400	5.03	0.07	0.67	3l9wB	GO:0000166 GO:0003955 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006812 GO:0006813 GO:0006885 GO:0008324 GO:0009055 GO:0009636 GO:0010181 GO:0015079 GO:0015297 GO:0015299 GO:0015503 GO:0015643 GO:0016020 GO:0016021 GO:0016491 GO:0019899 GO:0032414 GO:0051595 GO:0055085 GO:0055114 GO:0071805 GO:0098655 GO:1901381 GO:1902600
6	0.06	0.366	5.16	0.06	0.64	3wo8B	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0009254 GO:0016787 GO:0016798
7	0.06	0.255	5.50	0.02	0.47	4xdlA	GO:0005244 GO:0005267 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0007165 GO:0007613 GO:0016020 GO:0016021 GO:0022841 GO:0030322 GO:0034765 GO:0071805
8	0.06	0.322	4.82	0.08	0.53	4chvA	GO:0000166 GO:0005249 GO:0005267 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0008076 GO:0016020 GO:0016021 GO:0030552 GO:0071805
9	0.06	0.302	6.07	0.10	0.61	4gx0D	GO:0000166 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0046872 GO:0098655
10	0.06	0.244	6.08	0.05	0.49	4xdkD	GO:0005244 GO:0005267 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0007165 GO:0007613 GO:0016020 GO:0016021 GO:0022841 GO:0030322 GO:0034765 GO:0071805
11	0.06	0.286	5.86	0.09	0.57	2wlkA	GO:0005242 GO:0005244 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0034765 GO:0071805
12	0.06	0.334	4.95	0.06	0.56	3ukmA	GO:0005242 GO:0005249 GO:0005267 GO:0005272 GO:0005737 GO:0005768 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0008076 GO:0016020 GO:0016021 GO:0016023 GO:0016324 GO:0022841 GO:0030054 GO:0030322 GO:0030425 GO:0031410 GO:0031526 GO:0034705 GO:0035094 GO:0035725 GO:0042995 GO:0043204 GO:0045202 GO:0055037 GO:0060075 GO:0061337 GO:0071805 GO:1902937
13	0.06	0.251	6.12	0.05	0.53	3um7A	GO:0005244 GO:0005267 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0007613 GO:0016020 GO:0016021 GO:0019233 GO:0022841 GO:0030322 GO:0034705 GO:0034765 GO:0050951 GO:0050976 GO:0071260 GO:0071398 GO:0071469 GO:0071502 GO:0071805 GO:0097604 GO:0098782
14	0.06	0.306	4.76	0.09	0.52	4jtaQ	GO:0000149 GO:0001508 GO:0005216 GO:0005244 GO:0005249 GO:0005251 GO:0005267 GO:0005622 GO:0005768 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006887 GO:0006904 GO:0007215 GO:0008076 GO:0010701 GO:0014059 GO:0015271 GO:0016020 GO:0016021 GO:0016328 GO:0019228 GO:0019233 GO:0019894 GO:0030027 GO:0030054 GO:0030424 GO:0030425 GO:0031258 GO:0031669 GO:0032590 GO:0032809 GO:0033605 GO:0034705 GO:0034765 GO:0042383 GO:0042593 GO:0042734 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043679 GO:0044224 GO:0044325 GO:0045202 GO:0045211 GO:0045956 GO:0046676 GO:0046982 GO:0047485 GO:0051259 GO:0051260 GO:0055085 GO:0071333 GO:0071805 GO:0072661 GO:0090314 GO:0098900 GO:1900454 GO:2000671
15	0.06	0.258	6.19	0.04	0.53	3f8pD	GO:0000166 GO:0003954 GO:0004791 GO:0005737 GO:0016491 GO:0019430 GO:0055114
16	0.06	0.260	5.40	0.04	0.48	1id1A	GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0042802 GO:0051289
17	0.06	0.252	5.70	0.08	0.46	1orqC	GO:0005216 GO:0005244 GO:0005249 GO:0005267 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0008076 GO:0016020 GO:0016021 GO:0034765 GO:0055085 GO:0071805
18	0.06	0.307	5.96	0.07	0.63	2qksA	GO:0005242 GO:0005244 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0009897 GO:0009986 GO:0010107 GO:0015467 GO:0016020 GO:0016021 GO:0030315 GO:0034765 GO:0051602 GO:0071805

Consensus prediction of GO terms

Molecular Function	GO:0008324	GO:0046872	GO:0042802
GO-Score	0.56	0.39	0.35
Biological Processes	GO:0006813	GO:0098655
GO-Score	0.56	0.56
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.43	0.43

(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.