I-TASSER results

I-TASSER results for job id Rv2422

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

Input Sequence in FASTA format

>protein (90 residues)
MPASVSTVLVDTSVAVAPVVADHDHHEDTFQALRGRTLGLAGHAAFERRTLATVAKLLAH
TFPATRFLGAGAAMSLLPELAPAEIAGGAV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MPASVSTVLVDTSVAVAPVVADHDHHEDTFQALRGRTLGLAGHAAFERRTLATVAKLLAHTFPATRFLGAGAAMSLLPELAPAEIAGGAV
Prediction	CCCCCCCEEEEHCHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEHCCCHHHHHHHHHHHHHCCCCCCC
Conf.Score	998898578875434445556788999999999868766546789999999999999998678856758567999999999877888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MPASVSTVLVDTSVAVAPVVADHDHHEDTFQALRGRTLGLAGHAAFERRTLATVAKLLAHTFPATRFLGAGAAMSLLPELAPAEIAGGAV
Prediction	754744322132212133135635315303520574521231322343331020031245514443314464145024402734154358
	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

CCCCCCCEEEEHCHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEHCCCHHHHHHHHHHHHHCCCCCCC
MPASVSTVLVDTSVAVAPVVADHDHHEDTFQALRGRTLGLAGHAAFERRTLATVAKLLAHTFPATRFLGAGAAMSLLPELAPAEIAGGAV

4pe5A2

0.12

0.98

0.79

MUSTER

MPFQSCLSVHVVAVMLYLLDRSAMWFSWGVLLNAPRSFSARILGMVWAGFAMIIVASYTANLAA--FLVTCENMAGVFMLVAGGIVAGIF

1gpjA2

0.20

0.16

0.77

0.61

dPPAS

-------------VADVAKSLHEIKDRELERALRRLKTVLQDFAEAYTKRLINVLTSAIMELPDEYRRAASRALRRASELNG--------

4xgqA

0.12

0.11

0.92

0.71

wdPPAS

M------MVIDTSALVAMLSDEPDAERFEAAVEADHIRLMSTASYLETALVIEARFGEPGG-VDLVAVHADQADAARAAYRTYGKGRHRA

4chgA

0.13

0.12

0.91

0.65

wMUSTER

-------AIVDTSVWIAYLSTSESLASRWLADRIAADSTVIVPEVVELLI-EDTAALRRRLLQRFAIEPAEDAAAIHRRCRRGGDTVRSL

2fe1A

0.23

0.19

0.82

0.81

wPPAS

ME-----LVVDASAIAALYVPE-ERSEQAERAVSQAQELHTDLAAYEVANDLWKHARRGL-------LREDEASNMLEELWEFFK---AL

4xgqA

0.11

0.10

0.93

0.78

dPPAS2

------MMVIDTSALVAMLSDEPDAERFEAAVEADHIRLMSTASYLETALVIEARFGEPGGRVDLVAVHADQADAARAAYRTYGKGRHRA

4xgqA

0.12

0.11

0.92

0.83

PPAS

M------MVIDTSALVAMLSDEPDAERFEAAVEADHIRLMSTASYLETALVIEARFGEPGG-VDLVAVHADQADAARAAYRTYGKGRHRA

3wsvA2

0.19

0.17

0.87

0.75

Env-PPAS

TGT-----TLDTTKEIALKLAVDPRSV------HGYILGEHGDSEVAAWSHTTVGGKIMEYVEKDHRLEENDLTVLADKVKNAAIDRKA-

4bqnA1

0.11

0.98

0.72

MUSTER

MA-QRKKYSVYGSCQAPALAKMLNSCPTFARDWELVEMEPC-FVASEEQIDRHLAETIPKLLYQPVSEGYRGEKYSSVFLRNSMPPGGNA

4xgqA

0.11

0.10

0.93

0.57

dPPAS

------MMVIDTSALVAMLSDEPDAERFEAAVEADHIRLMSTASYLETALVIEARFGEPGGRVDLVAVHADQADAARAAYRTYGKGRHRA

(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=-2.56

Estimated TM-score = 0.42±0.14

Estimated RMSD = 9.3±4.6Å

Download Model 2

C-score=-3.18

Download Model 3

C-score=-3.39

Download Model 4

C-score=-3.98

Download Model 5

C-score=-4.92

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	4xgqA	0.594	3.35	0.125	0.878
2	3c9fB	0.569	3.15	0.062	0.856
3	2yeqA2	0.554	3.34	0.049	0.878
4	1ur2A	0.551	3.32	0.036	0.878
5	1w8iA	0.551	3.50	0.125	0.889
6	3tndA	0.547	3.61	0.098	0.911
7	3zvkA	0.545	3.71	0.099	0.889
8	5a8mA	0.545	3.74	0.098	0.911
9	1nq6A	0.545	3.36	0.024	0.889
10	4dhlA	0.544	3.52	0.060	0.889

(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	7	2dnjA	QNA	Rep, Mult	12,15,16,17,48,50
2	0.06	3	4riqV	III	Rep, Mult	68,73,77,80,81
3	0.06	3	2h1cA	MG	Rep, Mult	9,10,40,41,44
4	0.06	3	2bf0X	CA	Rep, Mult	80,83
5	0.04	2	4fyqA	ZN	Rep, Mult	26,30,47
6	0.04	2	2j5tD	GLU	Rep, Mult	11,13,14,17,27
7	0.04	2	4xgqE	MG	Rep, Mult	10,12,47,88
8	0.02	1	3clhB	ZN	Rep, Mult	26,43
9	0.02	1	1g42A	CA	Rep, Mult	28,31
10	0.02	1	1w5cB	CLA	Rep, Mult	70,77
11	0.02	1	2j5vA	PCA	Rep, Mult	12,45,46,47

	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	1ur2A	0.551	3.32	0.036	0.878	3.2.1.8	NA
2	0.060	1xyzA	0.527	3.37	0.048	0.878	3.2.1.8	NA
3	0.060	2depA	0.529	3.60	0.036	0.911	3.2.1.4,3.2.1.8	NA
4	0.060	3cufA	0.546	3.39	0.048	0.878	3.2.1.91,3.2.1.8	43
5	0.060	4kbpA	0.543	3.65	0.060	0.911	3.1.3.2	NA
6	0.060	2zunB	0.519	3.85	0.060	0.900	3.2.1.4	NA
7	0.060	1n82A	0.541	3.54	0.048	0.889	3.2.1.8	43
8	0.060	1xzwB	0.543	3.48	0.024	0.900	3.1.3.2	NA
9	0.060	2z1aA	0.542	3.54	0.085	0.878	3.1.3.5	NA
10	0.060	1b30A	0.539	3.38	0.036	0.889	3.2.1.8	47
11	0.060	1pz3A	0.536	3.57	0.060	0.889	3.2.1.55	NA
12	0.060	2c8nA	0.526	3.80	0.069	0.922	3.2.1.55	41
13	0.060	2cksB	0.535	3.92	0.048	0.911	3.2.1.4	43,79
14	0.060	3emqA	0.542	3.47	0.060	0.889	3.2.1.8	NA
15	0.060	1oc5A	0.523	3.93	0.071	0.911	3.2.1.91	NA
16	0.060	1isvA	0.550	3.29	0.024	0.878	3.2.1.8	43
17	0.060	3bpwA	0.523	3.80	0.051	0.844	4.1.1.23	NA
18	0.060	2bs9E	0.499	3.97	0.035	0.922	3.2.1.37	39
19	0.060	1ceoA	0.542	3.76	0.082	0.911	3.2.1.4	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	0.15	0.487	3.89	0.05	0.87	1w3hA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248 GO:0031176 GO:0045493
1	0.14	0.448	4.25	0.10	0.84	2fglA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493 GO:0046872
2	0.08	0.594	3.35	0.12	0.88	4xgqA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0045926 GO:0046872 GO:0090305 GO:0090501
3	0.07	0.569	3.15	0.06	0.86	3c9fB	GO:0009166 GO:0016787 GO:0046872
4	0.07	0.539	3.41	0.05	0.88	1tuxA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
5	0.07	0.545	3.36	0.02	0.89	1nq6A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0031176
6	0.07	0.477	4.57	0.07	0.92	5eqvA	GO:0000166 GO:0008663 GO:0009117 GO:0009166 GO:0016787 GO:0016788 GO:0046872
7	0.07	0.474	4.03	0.06	0.86	3jyfA	GO:0000166 GO:0008663 GO:0009117 GO:0009166 GO:0016787 GO:0016788 GO:0046872
8	0.07	0.541	3.49	0.05	0.89	3o2lA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
9	0.07	0.504	3.73	0.03	0.82	4l4oA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
10	0.07	0.472	4.02	0.05	0.88	2wysB	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0043263 GO:0045493
11	0.07	0.540	3.36	0.04	0.89	4xuyA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
12	0.07	0.542	3.54	0.09	0.88	2z1aA	GO:0000166 GO:0009166 GO:0016787 GO:0016788 GO:0046872
13	0.07	0.536	3.73	0.08	0.92	4pmvA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
14	0.07	0.444	3.66	0.04	0.78	3gveA	GO:0000166 GO:0003824 GO:0005576 GO:0005618 GO:0008152 GO:0008253 GO:0008254 GO:0008663 GO:0009166 GO:0016311 GO:0016787 GO:0016788 GO:0046872
15	0.07	0.403	4.02	0.08	0.73	4pmxA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493 GO:0046872
16	0.07	0.539	3.38	0.04	0.89	1b30A	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
17	0.07	0.536	3.64	0.02	0.91	4w8lA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016052 GO:0016787 GO:0016798 GO:0030246 GO:0031176 GO:0045493
18	0.07	0.443	4.75	0.05	0.92	2uwfA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0031176	GO:0001871
GO-Score	0.51	0.32	0.31
Biological Processes	GO:0045493
GO-Score	0.32
Cellular Component
GO-Score

(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.