I-TASSER results

I-TASSER results for job id Rv2271

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

Input Sequence in FASTA format

>protein (99 residues)
MTTPPDKARRRFLRDAYKNAERVARTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQ
RWAQSHRIEWETLAEGLQEFGGYCDCEIVMNVEPEAIFG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MTTPPDKARRRFLRDAYKNAERVARTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLAEGLQEFGGYCDCEIVMNVEPEAIFG
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEEEEEHCCHHHCCC
Conf.Score	998656899999999999999999999789999999999999999986579987478999999997999899999999989988657877456565579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MTTPPDKARRRFLRDAYKNAERVARTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLAEGLQEFGGYCDCEIVMNVEPEAIFG
Prediction	865565664254136314654366255614254730440052036517754142325204410564715264015103742130101002404564268
	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

CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEEEEEHCCHHHCCC
MTTPPDKARRRFLRDAYKNAERVARTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLAEGLQEFGGYCDCEIVMNVEPEAIFG

4aurA

0.12

0.97

0.67

MUSTER

VTSLTDQALFDEQAAIKKANLKGKLQRAADLTAQECEQLIVCVASNPNGRGLTYWFTKPEHYESRSRINKNAATEILKTNVPE---VLLVKTGDVVKDI

1z3yA1

0.14

0.12

0.85

0.74

dPPAS

MVTPALADLQEQLYNGNEKSQLAAMSTLSTAGTEGYHLLQEFLKDSATFSPPPAPWIRGQAYRLLFHSPEASVQAFLQQHYPQG---------------

1z3yA1

0.16

0.13

0.82

0.68

wdPPAS

MVTPALADLQEQLYNGNEKSQLAAMSTLSTAGTEGYHLLQEFLKDSATFSPPPAPWIRGQAYRLLFHSPEASVQAFLQQH-G-----------------

3rc3A1

0.12

0.11

0.89

0.72

wMUSTER

KPQPLDKNEVKKVLDKFYKKEIQKLGADYGLDARLFHQAFISFRNYIQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHA-----QIFPVLD------

2vl7A3

0.23

0.19

0.85

0.72

wPPAS

-----RKISRKMLERALKEIEIVERLNRIDAKKDYINLLIDYMSKLIKDGRC-HEIVVTRAYLNIDEVKLKSLLKFVEMKG---DCNSLVKVP------

4k12B

0.07

0.05

0.76

0.88

dPPAS2

ARKEVEEYVKKIVGESYAKSTKKRHTITVALVNELNNIKNEYLNKIVEST----SESELQILMMESRSKVDEAVSKFEK--------------------

3k5bG

0.16

0.98

0.77

PPAS

IKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAARLD-EAVALVLKEVLP-

4q2uB

0.15

0.11

0.75

Env-PPAS

QRDEYSGQYSKDVKLAQKRH-----------KDNKLKYLTLLINLPLPAVYKDHPL--QGSWKGYRDAHVEP------------DWILIYKLTDKLLRG

3um9A

0.13

0.98

0.66

MUSTER

IFPGQGEMVSKMWRQKQLEYTWMRTLMGQYQDESATLDALRYTCGSLGLALDADGEAHLCSEYLSLTPDVPQALQQLRAAG--LKTAILSNGSRHSIRQ

3k5bG

0.12

0.98

0.61

dPPAS

IKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAARLDEAVALVLKEVLP--

(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=-3.02

Estimated TM-score = 0.37±0.13

Estimated RMSD = 10.6±4.6Å

Download Model 2

C-score=-3.45

Download Model 3

C-score=-3.62

Download Model 4

C-score=-4.76

Download Model 5

C-score=-4.52

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	3fewX	0.635	2.97	0.067	0.909
2	1rh1A	0.635	2.88	0.044	0.919
3	1a87A	0.622	3.24	0.053	0.960
4	5cwpA2	0.616	2.77	0.090	0.849
5	3ay5A	0.612	3.56	0.061	0.990
6	5cwoA	0.604	3.05	0.081	0.869
7	4o6mA	0.599	3.12	0.054	0.859
8	3rkoL	0.595	3.59	0.063	0.939
9	1r0dA	0.590	3.57	0.073	0.970
10	4btfA1	0.590	3.28	0.088	0.909

(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	0.12	6	4aycA	ZN	Rep, Mult	52,54,84,86
2	0.06	3	1nr5B	CO	Rep, Mult	46,82
3	0.04	2	3edvB	MG	Rep, Mult	11,15
4	0.04	2	2agvA	PTY	Rep, Mult	38,42,46,47
5	0.04	2	3et2A	1BO	Rep, Mult	21,36
6	0.04	2	3h2zA	PO4	Rep, Mult	10,14,41
7	0.02	1	5hxcA	MYC	Rep, Mult	13,17,40
8	0.02	1	4zzcA	XE	Rep, Mult	13,44,47
9	0.02	1	2anuA	ZN	Rep, Mult	45,54
10	0.02	1	3ar4A	PTY	Rep, Mult	32,39,44,74,77
11	0.02	1	3u39C	CA	Rep, Mult	9,53
12	0.02	1	2uuhA	GSH	Rep, Mult	18,41,42,62,66,73,77
13	0.02	1	2vzbA	FE	Rep, Mult	37,71,92,95
14	0.02	1	4toaA	FE2	Rep, Mult	7,11

	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	1xvgC	0.501	3.90	0.072	0.849	1.14.13.25	41
2	0.060	2ouyA	0.545	3.71	0.073	0.909	3.1.4.17	NA
3	0.060	1txgB	0.543	3.00	0.104	0.778	1.1.1.94	NA
4	0.060	3b8cA	0.536	3.74	0.044	0.859	3.6.3.6	NA
5	0.060	1ynnJ	0.372	4.46	0.051	0.667	2.7.7.6	NA
6	0.060	3iydD	0.543	3.70	0.075	0.879	2.7.7.6	NA
7	0.060	1tazA	0.551	3.74	0.134	0.929	3.1.4.17	NA
8	0.060	2htnG	0.540	3.81	0.043	0.828	1.16.3.1	NA
9	0.060	2j1qA	0.528	3.48	0.082	0.849	2.7.3.3	37
10	0.060	3ecnB	0.557	3.69	0.104	0.929	3.1.4.17	41
11	0.060	1bg0A	0.535	3.30	0.107	0.838	2.7.3.3	21
12	0.060	1mc0A	0.370	4.26	0.013	0.646	3.1.4.17	NA
13	0.060	1ynnD	0.451	3.45	0.036	0.717	2.7.7.6	45
14	0.060	2qcxB	0.539	3.83	0.084	0.869	3.5.99.2	13,18
15	0.060	3c20B	0.536	3.42	0.085	0.788	2.7.2.4	NA
16	0.060	2qymA	0.553	3.74	0.105	0.929	3.1.4.17	63,77
17	0.060	1is2A	0.582	3.74	0.099	0.919	1.3.3.6	NA
18	0.060	3b8cB	0.536	3.74	0.044	0.859	3.6.3.6	NA
19	0.060	2bffA	0.542	3.72	0.054	0.859	1.2.4.4	66

(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	0.616	3.07	0.07	0.90	1colA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
1	0.07	0.516	3.61	0.06	0.84	3g06A	GO:0003824 GO:0004842 GO:0005576 GO:0009405 GO:0016020 GO:0016567 GO:0016874 GO:0020002 GO:0030254 GO:0030430 GO:0033644 GO:0034052 GO:0061630 GO:0070430 GO:2000484
2	0.07	0.540	3.20	0.11	0.82	2i88A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
3	0.07	0.635	2.97	0.07	0.91	3fewX	GO:0016020 GO:0016021 GO:0019835 GO:0050829
4	0.07	0.394	4.29	0.06	0.66	1y1oA	GO:0000287 GO:0003676 GO:0004518 GO:0004519 GO:0005737 GO:0006281 GO:0006310 GO:0006974 GO:0007059 GO:0016787 GO:0046872 GO:0090305
5	0.07	0.622	3.24	0.05	0.96	1a87A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
6	0.06	0.407	4.19	0.08	0.64	3ldzA	GO:0005070 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0007165 GO:0009967 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:1903543 GO:1903551
7	0.06	0.360	3.73	0.04	0.55	2w8dB	GO:0003824 GO:0005576 GO:0005886 GO:0008152 GO:0008484 GO:0016020 GO:0016021 GO:0016740 GO:0046872 GO:0070395 GO:0071555
8	0.06	0.635	2.88	0.04	0.92	1rh1A	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
9	0.06	0.412	4.24	0.04	0.72	4i99B	GO:0000166 GO:0003677 GO:0005524 GO:0005694 GO:0005737 GO:0006260 GO:0007059 GO:0007062 GO:0030261 GO:0051276
10	0.06	0.351	4.34	0.11	0.60	2fcoA	GO:0000287 GO:0003676 GO:0004518 GO:0004519 GO:0005737 GO:0006281 GO:0006310 GO:0006974 GO:0007059 GO:0016787 GO:0046872 GO:0090305
11	0.06	0.319	4.33	0.01	0.54	2w3zA	GO:0003824 GO:0005975 GO:0016810 GO:0046872
12	0.06	0.463	4.11	0.09	0.77	1e6yA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
13	0.06	0.493	3.78	0.03	0.85	1ciiA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
14	0.06	0.330	3.24	0.03	0.48	2b5uA	GO:0003723 GO:0004518 GO:0004519 GO:0005727 GO:0009405 GO:0016787 GO:0016788 GO:0019835 GO:0042742 GO:0043022 GO:0090305
15	0.06	0.439	3.30	0.06	0.64	3ksuA
16	0.06	0.337	4.56	0.03	0.61	2axcA	GO:0004518 GO:0004519 GO:0005727 GO:0009405 GO:0016787 GO:0019835 GO:0042742 GO:0046872 GO:0090305
17	0.06	0.356	4.83	0.02	0.71	3bobA	GO:0046872
18	0.06	0.259	4.42	0.04	0.46	3jaqR	GO:0003735 GO:0005622 GO:0005840 GO:0006412

Consensus prediction of GO terms

Molecular Function	GO:0003676	GO:0004519	GO:0000287	GO:0061630	GO:0016874
GO-Score	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0042742
GO-Score	0.37
Cellular Component	GO:0016021	GO:0005886	GO:0005737	GO:0005576	GO:0030430	GO:0020002
GO-Score	0.19	0.13	0.07	0.07	0.07	0.07

(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.