I-TASSER results

I-TASSER results for job id Rv3717

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

Input Sequence in FASTA format

>protein (241 residues)
MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQAS
GTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNA
IVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGL
YGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQA
R

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQAR
Prediction	CHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHCCEEEEHCCCCCCCCCCHHHHHHHHHHHCCCEEEEEHCCCCCCCCCEEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCEEEEHCCCCCEEEEEHCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	5444445655677777788887778959998599999998887777778877777667788888998443588999999999999998998999779998788999999999999899999998758999999779999968998765455789999999999999855546666566657557878985899988999864689999999869999999999999999999999857889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQAR
Prediction	3100012123333345555445504410000000141613122244354444444444444444443130030014004301620573604020004504313230540052047360000000000034561300000012454544444504400530152037422552533454223532200002205020130210302266226324276004200400040025105645668
	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                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHCCEEEEHCCCCCCCCCCHHHHHHHHHHHCCCEEEEEHCCCCCCCCCEEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCEEEEHCCCCCEEEEEHCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQAR

4m6gA

1.00

0.89

4.03

MUSTER

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

7.60

dPPAS

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

7.02

wdPPAS

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.88

4.73

wMUSTER

------------------------AGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

5.39

wPPAS

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

9.98

dPPAS2

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

4.80

PPAS

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

4m6gA

1.00

0.89

6.36

Env-PPAS

-----------------------IAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQ----

5emiA

0.27

0.20

0.74

3.14

MUSTER

----------------------GSGKLLVVIDPGHGGKDSGAPG--------------------LGGLLEKDVILPIGKRVAAILEQHGVQAVLTRDADFFV--ELQGRVEIAERVNATAFVSIHANSVDPDVNGLEVYYYDS---------GYALAEVVRNTILQNI-----DTIKNRGTRKARFYVLRKSSMPSILVETGYMTGREDNPRLASREYQNQMAEAIARGILKYLQR-----

5emiA

0.27

0.20

0.74

5.43

dPPAS

----------------------GSGKLLVVIDPGHGGKDSGAPGL--------------------GGLLEKDVILPIGKRVAAILEQHGVQAVLTRDADFFV--ELQGRVEIAERVNATAFVSIHANSVDNDVNGLEVYYYDS---------GYALAEVVRNTILQNI-----DTIKNRGTRKARFYVLRKSSMPSILVETGYMTGREDNPRLASREYQNQMAEAIARGILKYLQR-----

(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=0.43

Estimated TM-score = 0.77±0.10

Estimated RMSD = 4.8±3.2Å

Download Model 2

C-score=-0.82

Download Model 3

C-score=-0.51

Download Model 4

C-score=-1.65

Download Model 5

C-score=-3.42

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	4m6gA	0.881	0.52	1.000	0.888
2	3ne8A	0.731	1.81	0.249	0.784
3	4binA2	0.718	2.37	0.196	0.784
4	4rn7A	0.710	1.45	0.232	0.747
5	5emiA	0.691	1.50	0.290	0.726
6	1jwqA	0.685	1.73	0.239	0.730
7	1xovA	0.640	2.30	0.173	0.714
8	3qayA	0.638	2.52	0.170	0.718
9	3czxA	0.622	2.21	0.146	0.697
10	4a37A	0.604	3.80	0.089	0.788

(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	0.79	21	1jwqA	ZN	Rep, Mult	35,70,125
2	0.03	1	4m6gA	III	Rep, Mult	35,55,58,59,70,106,125,186,187,188

	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	0.066	1iu8A	0.541	3.25	0.110	0.660	3.4.19.3	NA
2	0.060	1uwyA	0.596	3.76	0.119	0.772	3.4.17.12	NA
3	0.060	1obrA	0.564	4.35	0.086	0.780	3.4.17.18	117
4	0.060	3fedA	0.540	5.03	0.064	0.801	3.4.17.21	NA
5	0.060	3kl9A	0.586	4.25	0.084	0.805	3.4.11.7	106
6	0.060	1cpbB	0.448	4.65	0.092	0.647	3.4.17.2	NA
7	0.060	3h8eA	0.546	4.13	0.085	0.710	3.4.11.1	135
8	0.060	1kwmA	0.588	3.80	0.108	0.763	3.4.17.2	NA
9	0.060	1pcaA	0.587	3.61	0.103	0.751	3.4.17.1	NA
10	0.060	3ic1A	0.555	4.27	0.060	0.751	3.5.1.18	162,200
11	0.060	1jqgA	0.592	3.80	0.134	0.763	3.4.17.1	NA
12	0.060	3kzwA	0.586	4.46	0.081	0.788	3.4.11.1	74,138
13	0.060	1pytA	0.170	4.19	0.075	0.232	3.4.17.1	200
14	0.060	1gytJ	0.578	4.47	0.075	0.780	3.4.11.1	107
15	0.060	1xovA	0.640	2.30	0.173	0.714	3.5.1.28	229
16	0.060	1zg7A	0.586	3.57	0.101	0.747	3.4.17.2	NA
17	0.060	1ayeA	0.581	3.85	0.092	0.759	3.4.17.15	NA
18	0.060	1ampA	0.555	4.59	0.069	0.784	3.4.11.10	NA
19	0.060	1r3nA	0.571	4.26	0.074	0.780	3.5.1.6	70
20	0.060	2zofA	0.557	4.28	0.078	0.759	3.4.13.18	70

(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	0.67	0.881	0.52	1.00	0.89	4m6gA	GO:0008745 GO:0009253 GO:0046872
1	0.45	0.635	2.26	0.13	0.71	3czxA	GO:0008745 GO:0009253 GO:0046872
2	0.43	0.685	1.73	0.24	0.73	1jwqA	GO:0008745 GO:0009253 GO:0046872
3	0.40	0.734	1.80	0.25	0.79	3ne8A	GO:0008745 GO:0009253 GO:0016020 GO:0016021
4	0.40	0.640	2.30	0.17	0.71	1xovA	GO:0004386 GO:0008168 GO:0008745 GO:0009253 GO:0032259 GO:0046872
5	0.30	0.691	1.50	0.29	0.73	5emiA	GO:0008745 GO:0009253 GO:0016787
6	0.28	0.715	1.45	0.23	0.75	4rn7A	GO:0008745 GO:0009253 GO:0016020 GO:0016021 GO:0016787 GO:0046872
7	0.26	0.638	2.52	0.17	0.72	3qayA	GO:0008745 GO:0009253 GO:0046872
8	0.20	0.718	1.97	0.19	0.78	4binA	GO:0008745 GO:0009253 GO:0016787 GO:0030288 GO:0042597 GO:0043093 GO:0071555
9	0.06	0.328	5.94	0.06	0.58	3irsA	GO:0016787
10	0.06	0.325	5.71	0.04	0.54	3rbnA	GO:0000289 GO:0000712 GO:0000793 GO:0000794 GO:0000795 GO:0001673 GO:0002204 GO:0003682 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005712 GO:0006281 GO:0006298 GO:0006303 GO:0006974 GO:0007049 GO:0007060 GO:0007126 GO:0007129 GO:0007131 GO:0007140 GO:0007283 GO:0008630 GO:0016020 GO:0016321 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032389 GO:0032407 GO:0043060 GO:0045132 GO:0045141 GO:0045143 GO:0045190 GO:0045950 GO:0048477 GO:0051257
11	0.06	0.310	4.58	0.09	0.44	5fddA	GO:0003723 GO:0003968 GO:0005576 GO:0005654 GO:0005829 GO:0006351 GO:0016032 GO:0019061 GO:0019062 GO:0019064 GO:0019065 GO:0019070 GO:0019072 GO:0019076 GO:0019083 GO:0030430 GO:0031904 GO:0039523 GO:0039657 GO:0042025 GO:0046761 GO:0075526 GO:0075733
12	0.06	0.341	4.50	0.06	0.49	4dgsA	GO:0008152 GO:0016616 GO:0051287 GO:0055114
13	0.06	0.311	6.21	0.05	0.56	3pukA	GO:0005737 GO:0005829 GO:0005886 GO:0006810 GO:0006887 GO:0006904 GO:0007420 GO:0015031 GO:0015758 GO:0016020 GO:0016192 GO:0016323 GO:0016324 GO:0017075 GO:0019905 GO:0022615 GO:0030073 GO:0031091 GO:0032868 GO:0042581 GO:0043312 GO:0045955 GO:0051291 GO:0061024 GO:0070062 GO:0070527 GO:0070820
14	0.06	0.328	5.41	0.05	0.51	3jzlA	GO:0003824 GO:0030170
15	0.06	0.274	6.32	0.04	0.49	3mt1B	GO:0003824 GO:0005737 GO:0006596 GO:0008295 GO:0016829 GO:0016831
16	0.06	0.248	5.39	0.04	0.39	3j7aK	GO:0003735 GO:0005840 GO:0006412 GO:0022627 GO:0030529
17	0.06	0.220	4.81	0.08	0.32	2jzyA	GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355
18	0.06	0.202	4.34	0.06	0.28	3mayC	GO:0005576 GO:0015886 GO:0020037
19	0.06	0.180	4.49	0.06	0.25	2csjA	GO:0005634 GO:0005737 GO:0005886 GO:0005921 GO:0005923 GO:0008022 GO:0009986 GO:0010033 GO:0016020 GO:0019904 GO:0030054 GO:0030674 GO:0050892 GO:0071847 GO:0090557 GO:0090559 GO:2001205

Consensus prediction of GO terms

Molecular Function	GO:0008745	GO:0046872	GO:0008168	GO:0004386
GO-Score	0.96	0.94	0.40	0.40
Biological Processes	GO:0009253	GO:0032259
GO-Score	0.96	0.40
Cellular Component	GO:0016021
GO-Score	0.40

(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.