I-TASSER results

I-TASSER results for job id Rv2844

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

Input Sequence in FASTA format

>protein (162 residues)
MTSSEPAHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALK
QHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEH
AETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSSEPAHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE
Prediction	CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Conf.Score	999888888888888888867999999999999999999999986588779999999999999999999999999899999998888899888999999999999999999999999997899889999999999999999999999788998888999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSSEPAHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE
Prediction	854364544544645455665134003401530220020111113224661252045126404411530252047365624445451524462743530240033005400310230044064561141004002400210131444165441334134478
	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

CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
MTSSEPAHGATPKRSPSEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE

2ib0A

1.00

0.88

2.41

MUSTER

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

2.16

dPPAS

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

3.49

wdPPAS

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.87

3.02

wMUSTER

-----------------EGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

4.44

wPPAS

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

4.74

dPPAS2

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

3.36

PPAS

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2ib0A

1.00

0.88

5.24

Env-PPAS

----------------SEGSADNAALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFP----

2fzfA

0.08

0.07

0.91

1.10

MUSTER

----------GLPIEKMADFSLEELLGMAIKAEIGAREFYKSLAEKIKEALKEKINWLAEEEKKHEALLRKLYSQMGKEVVFGPELQPVARELEKIIDLIRWAMKAEEIAAEFYLKLEEMVKEEEKKRLMRYLADMERGHYYTLRAEYELLLNWEMY-----

2clbA

0.16

0.15

0.95

0.92

dPPAS

-QEPKVVGVEILEKSGLDIKKLVDKLVKATAAEFTTYYYYTILRHLTGGEGLKEIAEDARLEDRLHFELTQRIYELGGGLPSACSDAYLPENWKDPKEILKVLLEAEQCAIRTWKEVCDTYKDPRTYDLAQRILQEEIEHEAWFLELLYGRPSGH-------

(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=0.75

Estimated TM-score = 0.81±0.09

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-2.65

Download Model 3

C-score=-3.56

Download Model 4

C-score=-4.10

Download Model 5

C-score=-4.29

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	2ib0A	0.858	0.88	0.993	0.876
2	2vzbA	0.815	2.44	0.097	0.926
3	2clbA	0.814	2.19	0.150	0.914
4	3fseB	0.789	2.54	0.081	0.914
5	2j2fA	0.785	2.52	0.089	0.951
6	4r42A	0.783	2.49	0.097	0.914
7	1veiA	0.778	2.85	0.118	0.932
8	1o9rA	0.774	2.48	0.102	0.895
9	4cy9A	0.773	2.52	0.138	0.889
10	1o9iA	0.768	2.50	0.098	0.907

(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	0.35	161	2o1zA	FE	Rep, Mult	58,62,107,137,140
2	0.29	134	2jd6O	FE	Rep, Mult	33,62,65,110,137
3	0.07	38	1nf6C	FEC	Rep, Mult	30,37,38,41,45,56,63,64,66,67
4	0.02	12	2v8tA	CL	Rep, Mult	62,65,136,137,140
5	0.01	4	3e2cB	EDO	Rep, Mult	29,32,33,69,110,114,133,137
6	0.01	9	4mn9A	FE	Rep, Mult	58,61,136,140,143
7	0.00	1	2c2fA	FE	Rep, Mult	31,34,62
8	0.00	2	2uw1B	GVM	Rep, Mult	33,39,58,62,87,102,103,106,107
9	0.00	1	2ib00	III	Rep, Mult	119,127,128,131,134,135,138,142,143,146
10	0.00	1	3u52A	XE	Rep, Mult	25,69,72,73,126,129
11	0.00	1	2vxiK	HEM	Rep, Mult	114,115,118,127,131,134,135
12	0.00	1	2iy4N	FE	Rep, Mult	68,71,72,129
13	0.00	2	5d8pD	FE2	Rep, Mult	21,25,120

	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	0.260	2htnG	0.754	2.01	0.131	0.846	1.16.3.1	37,70
2	0.255	2wlaA	0.735	2.44	0.125	0.827	1.16.3.1	59,133
3	0.238	1r03A	0.735	2.67	0.106	0.889	1.16.3.1	38
4	0.237	3es3A	0.732	2.68	0.106	0.889	1.16.3.1	38
5	0.203	3bvlF	0.719	2.73	0.119	0.883	1.16.3.1	129
6	0.202	3a68R	0.720	2.67	0.138	0.883	1.16.3.1	NA
7	0.155	1eumE	0.697	2.53	0.104	0.840	1.16.3.1	NA
8	0.116	2g2dA	0.603	3.00	0.089	0.728	2.5.1.17	NA
9	0.060	1jkuA	0.767	2.41	0.099	0.901	1.11.1.6	NA
10	0.060	2v8tA	0.733	2.64	0.131	0.864	1.11.1.6	NA
11	0.060	1ygeA	0.568	4.66	0.057	0.926	1.13.11.12	NA
12	0.060	1mhyB	0.723	3.36	0.106	0.938	1.14.13.25	30,129,135
13	0.060	1mfrW	0.735	2.62	0.139	0.889	1.16.3.1	38
14	0.060	2iukA	0.567	4.76	0.087	0.932	1.13.11.12	NA
15	0.060	3e6sF	0.714	2.45	0.097	0.846	1.16.3.1	NA
16	0.060	1krqA	0.694	2.51	0.105	0.833	1.16.3.1	NA
17	0.060	1no3A	0.565	4.86	0.075	0.938	1.13.11.12	NA
18	0.060	1smsA	0.717	3.56	0.062	0.951	1.17.4.1	NA
19	0.060	1biqB	0.723	3.53	0.062	0.963	1.17.4.1	NA
20	0.060	1bg7A	0.593	3.36	0.050	0.821	1.16.3.1	38
21	0.060	2iukB	0.566	4.65	0.063	0.932	1.13.11.12	NA
22	0.060	2bq1I	0.729	3.43	0.062	0.957	1.17.4.1	NA
23	0.060	1h0nA	0.719	3.44	0.043	0.944	1.17.4.1	NA
24	0.060	1otwA	0.629	3.68	0.050	0.876	1.3.3.11	111,134
25	0.060	1jk0A	0.728	3.30	0.025	0.932	1.17.4.1	NA
26	0.060	3hf1B	0.727	3.42	0.037	0.938	1.17.4.1	NA
27	0.060	1uzrB	0.730	3.46	0.037	0.957	1.17.4.1	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	0.47	0.316	5.59	0.07	0.57	3pyzA	GO:0000166 GO:0004326 GO:0005524 GO:0009058 GO:0009396 GO:0016874 GO:0046901
1	0.34	0.751	2.10	0.11	0.85	4e6kA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0046872 GO:0055114
2	0.31	0.815	2.44	0.10	0.93	2vzbA	GO:0005623 GO:0006879 GO:0008199 GO:0046872
3	0.29	0.750	2.08	0.10	0.85	3gvyB	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872 GO:0055114
4	0.29	0.762	2.03	0.10	0.86	3fvbA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872 GO:0055114
5	0.29	0.830	2.04	0.14	0.92	2clbA	GO:0005737 GO:0006879 GO:0008199 GO:0009295 GO:0016491 GO:0046872 GO:0055114
6	0.28	0.754	2.03	0.11	0.84	3r2hA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0016491 GO:0046872 GO:0055114
7	0.26	0.741	2.60	0.09	0.86	2c41C	GO:0003677 GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0055114
8	0.25	0.733	1.90	0.13	0.81	2qqyA	GO:0005623 GO:0006879 GO:0008199
9	0.25	0.752	2.02	0.10	0.85	1jgcA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
10	0.24	0.723	2.47	0.13	0.83	2gyqA	GO:0046872
11	0.24	0.756	2.03	0.06	0.85	4am2A	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
12	0.23	0.681	2.53	0.10	0.80	4eveA	GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0055114
13	0.20	0.767	2.76	0.09	0.90	2vxxB	GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0046872 GO:0055114
14	0.16	0.801	2.53	0.08	0.93	3fseB	GO:0016798
15	0.13	0.693	2.20	0.10	0.80	1ji5A	GO:0003677 GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0016722 GO:0046872 GO:0055114
16	0.06	0.350	6.02	0.09	0.70	1ox0A	GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817 GO:0046872
17	0.06	0.350	5.31	0.03	0.63	4lruA	GO:0016829 GO:0019172 GO:0019243 GO:0019249
18	0.06	0.282	5.22	0.06	0.51	4e08A	GO:0003713 GO:0005634 GO:0005739 GO:0005829 GO:0006357 GO:0006979 GO:0008344 GO:0019172 GO:0019243 GO:0019249 GO:0042775 GO:0046626 GO:0048640 GO:0070301

Consensus prediction of GO terms

Molecular Function	GO:0008199	GO:0004322	GO:0005524	GO:0004326
GO-Score	0.77	0.67	0.47	0.47
Biological Processes	GO:0055114	GO:0006826	GO:0046901	GO:0006880
GO-Score	0.67	0.67	0.47	0.34
Cellular Component	GO:0005623
GO-Score	0.77

(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.