I-TASSER results

I-TASSER results for job id Rv1767

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

Input Sequence in FASTA format

>protein (119 residues)
MSDQPRHHQVLDDLLPQHRALRHQIPQVYQRFVALGDAALTDGALSRKVKELVALAIAVV
QGCDGCVASHAQAAVRAGATAQEAAEAIGVTILMHGGPATIHGARAYAAFCEFADTTPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSDQPRHHQVLDDLLPQHRALRHQIPQVYQRFVALGDAALTDGALSRKVKELVALAIAVVQGCDGCVASHAQAAVRAGATAQEAAEAIGVTILMHGGPATIHGARAYAAFCEFADTTPS
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCC
Conf.Score	99867899999889999999998698999999999999986799999999999999999989956899999999998999999999999999978858899999999999999975889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSDQPRHHQVLDDLLPQHRALRHQIPQVYQRFVALGDAALTDGALSRKVKELVALAIAVVQGCDGCVASHAQAAVRAGATAQEAAEAIGVTILMHGGPATIHGARAYAAFCEFADTTPS
Prediction	87647514531551363145027323500520340353037655045312200000000034144003300430373413550022003102332232113303401400441376478
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCC
MSDQPRHHQVLDDLLPQHRALRHQIPQVYQRFVALGDAALTDGALSRKVKELVALAIAVVQGCDGCVASHAQAAVRAGATAQEAAEAIGVTILMHGGPATIHGARAYAAFCEFADTTPS

5dikA

0.37

0.34

0.94

2.53

MUSTER

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

2.61

dPPAS

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

3.78

wdPPAS

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.93

3.02

wMUSTER

----DKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

4.19

wPPAS

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

6.66

dPPAS2

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

3.34

PPAS

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

5dikA

0.37

0.34

0.94

5.14

Env-PPAS

---SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK----

1p8cC

0.24

0.23

0.96

2.31

MUSTER

-----EYKKFVEARRELNEKVLSRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKN

1p8cC

0.24

0.23

0.96

2.40

dPPAS

-----EYKKFVEARRELNEKVLSRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKN

(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 1 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=1.28

Estimated TM-score = 0.89±0.07

Estimated RMSD = 1.9±1.6Å

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	5dikA	0.930	0.46	0.366	0.941
2	1p8cC	0.841	1.66	0.237	0.958
3	2qeuB	0.731	2.34	0.211	0.874
4	4g9qA	0.663	2.62	0.143	0.866
5	3d7iB	0.659	2.06	0.226	0.781
6	3beyD	0.635	1.26	0.269	0.689
7	2cwqA	0.613	1.89	0.181	0.706
8	2q0tA	0.588	2.28	0.174	0.689
9	2ouwB	0.587	2.30	0.189	0.681
10	3feyA	0.583	4.08	0.043	0.966

(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	0.08	4	2p06A	MG	Rep, Mult	51,54,70,73
2	0.06	3	2uxhA	QUE	Rep, Mult	14,15,32,36,63,67,94,97,101
3	0.06	3	4nilA	2O8	Rep, Mult	48,49,83,87
4	0.06	3	1m7r0	III	Rep, Mult	62,64,65,66,67,68,69,71,72,81
5	0.04	2	1h2u0	III	Rep, Mult	55,59,62,84
6	0.04	2	1wnoB	MG	Rep, Mult	62,67,102
7	0.04	2	1mz9B	VDY	Rep, Mult	52,55,59
8	0.02	1	5c6hA	III	Rep, Mult	72,116
9	0.02	1	4atkB	NUC	Rep, Mult	101,102,105
10	0.02	1	2fkwA	BCL	Rep, Mult	96,103
11	0.02	1	3c3yA	CA	Rep, Mult	83,86
12	0.02	1	1n52A	MG	Rep, Mult	53,88,90,91
13	0.02	1	2yxhA	MG	Rep, Mult	51,77

	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	3hf1B	0.429	4.79	0.060	0.807	1.17.4.1	NA
2	0.060	2qubA	0.552	3.96	0.067	0.874	3.1.1.3	64
3	0.060	1k7hA	0.514	4.38	0.075	0.882	3.1.3.1	105
4	0.060	2x38A	0.525	4.38	0.088	0.849	2.7.1.153	88
5	0.060	2fp0B	0.491	4.10	0.068	0.798	3.2.1.143	NA
6	0.060	2cqsA	0.481	4.57	0.075	0.840	2.4.1.20	NA
7	0.060	3cuzA	0.524	4.03	0.061	0.815	2.3.3.9	NA
8	0.060	2fiqC	0.510	4.12	0.074	0.840	2.7.1.144	62,68,106
9	0.060	3k1dA	0.536	4.30	0.071	0.882	2.4.1.18	NA
10	0.060	2a4aA	0.518	4.00	0.076	0.790	4.1.2.4	NA
11	0.060	1zefA	0.515	4.35	0.046	0.891	3.1.3.1	NA
12	0.060	1gaiA	0.514	4.44	0.070	0.840	3.2.1.3	86,112
13	0.060	1dwaM	0.507	4.34	0.037	0.899	3.2.1.147	NA
14	0.060	3a47A	0.508	4.30	0.067	0.874	3.2.1.10	NA
15	0.060	1gowA	0.540	3.95	0.067	0.824	3.2.1.23	NA
16	0.060	2bq1I	0.543	3.38	0.051	0.756	1.17.4.1	NA
17	0.060	3ebgA	0.509	3.94	0.019	0.824	3.4.11.-	NA
18	0.060	2vuxB	0.540	3.45	0.068	0.748	1.17.4.1	NA
19	0.060	2e3zA	0.523	3.57	0.048	0.748	3.2.1.21	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	0.55	0.930	0.46	0.37	0.94	5dikA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
1	0.45	0.635	1.26	0.27	0.69	3beyD	GO:0051920 GO:0055114 GO:0098869
2	0.45	0.841	1.66	0.24	0.96	1p8cC	GO:0004601 GO:0016209 GO:0016491 GO:0016829 GO:0051920 GO:0055114 GO:0098869
3	0.38	0.688	2.79	0.20	0.87	2af7D	GO:0051920 GO:0055114 GO:0098869
4	0.31	0.759	2.19	0.20	0.90	2qeuB	GO:0051920 GO:0055114 GO:0098869
5	0.31	0.686	2.08	0.22	0.82	3d7iB	GO:0051920 GO:0055114 GO:0098869
6	0.22	0.671	2.60	0.14	0.87	4g9qA	GO:0051920 GO:0055114 GO:0098869
7	0.22	0.623	1.79	0.18	0.71	2cwqA	GO:0051920 GO:0055114 GO:0098869
8	0.07	0.601	2.03	0.17	0.70	2q0tA	GO:0051920 GO:0055114 GO:0098869
9	0.07	0.564	3.61	0.17	0.78	2prrD	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
10	0.07	0.610	1.93	0.19	0.69	2ouwB	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
11	0.07	0.541	3.43	0.13	0.71	3lvyA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
12	0.07	0.546	3.42	0.19	0.76	2oyoA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
13	0.06	0.388	4.59	0.06	0.65	4b2ta	GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0006457 GO:0051082
14	0.06	0.366	4.81	0.05	0.68	3iygA	GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0006457 GO:0051082
15	0.06	0.371	5.50	0.08	0.76	4f7rD	GO:0019904
16	0.06	0.411	4.10	0.03	0.62	1ku1A	GO:0000137 GO:0005085 GO:0005086 GO:0005737 GO:0005829 GO:0006888 GO:0006890 GO:0006891 GO:0016020 GO:0016236 GO:0019898 GO:0030036 GO:0032012 GO:0033363 GO:0043547
17	0.06	0.362	4.90	0.06	0.65	1obgA	GO:0000166 GO:0004638 GO:0004639 GO:0005524 GO:0006164 GO:0006189 GO:0016874 GO:0046084
18	0.06	0.336	5.44	0.05	0.74	3skqA	GO:0005739 GO:0005743 GO:0006813 GO:0015992 GO:0016020 GO:0016021 GO:0030007 GO:0043022 GO:0051204 GO:0070131 GO:0097033 GO:0097034

Consensus prediction of GO terms

Molecular Function	GO:0051920	GO:0004601	GO:0016829
GO-Score	0.94	0.75	0.45
Biological Processes	GO:0098869	GO:0055114
GO-Score	0.94	0.94
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.