I-TASSER results

I-TASSER results for job id Rv0699

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

Input Sequence in FASTA format

>protein (73 residues)
MGDRRVDLLAAKDSEIRRSMGAVPVGAGSSQVATSWASDRCIRCRAAILSADCANLARAN
SRGGLAVGGSAVS

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MGDRRVDLLAAKDSEIRRSMGAVPVGAGSSQVATSWASDRCIRCRAAILSADCANLARANSRGGLAVGGSAVS
Prediction	CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHCCCCCHHHHHHHHHCHHHHHHHHHHCCCCCEHCCCCCC
Conf.Score	9974555555546789987588556888654565346664467888886556788887656688555675469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MGDRRVDLLAAKDSEIRRSMGAVPVGAGSSQVATSWASDRCIRCRAAILSADCANLARANSRGGLAVGGSAVS
Prediction	8664424113354561454243233334444234423543014032212434134134346421213445448
	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

                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHCCCCCHHHHHHHHHCHHHHHHHHHHCCCCCEHCCCCCC
MGDRRVDLLAAKDSEIRRSMGAVPVGAGSSQVATSWASDRCIRCRAAILSADCANLARANSRGGLAVGGSAVS

3giqA1

0.21

0.97

0.79

MUSTER

MRDPQAAPTAAEQQAMQDMLQAA-LEAGAVGFSTGLAYQPGAVAQAAEL-EGLARVAAERRRLHTSHIRNEAD

1ry3A

0.17

0.15

0.88

0.67

dPPAS

MNS----VKELNVKEMKQLHGGVNYGNGVSCSKTKCSVNW-GQAFQERYTAGINSFVSGVASGAGSIGR----

1tvsA

0.23

0.21

0.89

0.63

wdPPAS

LEDRRI---GTAEENLQKSSGGVP-GTGGQEARPNY---HCQLCFLRSLGIDYLDASKNKQRL-IQQGRQPQY

3k07A

0.25

0.21

0.82

0.72

wMUSTER

SGT--LADIDAMAEQIEEVARTVP---GVASALAERLEGG-VREKAARYTADVQLFVTS-------VGGAMVG

2zadA3

0.29

0.22

0.75

0.59

wPPAS

---RRED--IEGLKFVRFH-SPFPVAADES-ARTKF--DRLVKEEAVVLKLAIVEIAESS---GLKL------

1yjtA

0.21

0.19

0.90

0.68

dPPAS2

MGDGVLELVASCVHKIESSLTKHR---GILYCSVALATNKAIKYDPEIIG--PRDIIHTIESLGFEP--SLVK

1yjtA

0.21

0.19

0.90

0.73

PPAS

MGDGVLELVASCVHKIESSLTKHR---GILYCSVALATNKAIKYDPEIIG--PRDIIHTIESLGFEP--SLVK

1v9pA1

0.19

0.16

0.88

0.89

Env-PPAS

MTEEARRRINELRDLIRYHNYRYYV-LADPEI--SDAEDRLLRELKELE-ERFPEFKSPDSQ----VGA-RPL

3giqA

0.21

0.97

0.76

MUSTER

MRDPQAAPTAAEQQAMQDMLQAA-LEAGAVGFSTGLAYQPGAVAQAAEL-EGLARVAAERRRLHTSHIRNEAD

4xkzA2

0.15

1.00

0.63

dPPAS

AAEGDIEWVKALMLGVRQIRGEMNISMAKRIDIILKNASPSDHRRLADNEPLLMKLAKLESEAGEEAPMSATA

(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=-2.33

Estimated TM-score = 0.44±0.14

Estimated RMSD = 8.2±4.5Å

Download Model 2

C-score=-4.00

Download Model 3

C-score=-4.82

Download Model 4

C-score=-3.44

Download Model 5

C-score=-3.57

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	4ichA	0.571	3.30	0.041	0.904
2	3ismC2	0.570	3.26	0.088	0.877
3	3cljA	0.565	2.91	0.129	0.863
4	3c0sA	0.562	3.13	0.060	0.849
5	5frpA4	0.561	2.66	0.083	0.822
6	2eh3A	0.560	3.00	0.027	0.877
7	4fldA	0.558	2.96	0.078	0.836
8	4r04A3	0.556	3.36	0.119	0.904
9	2nx4A	0.556	3.36	0.055	0.918
10	2g3bB	0.555	3.60	0.097	0.945

(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	0.10	11	1f6nM	BPH	Rep, Mult	4,7,8,11,12,36,38
2	0.07	8	4zzcA	XE	Rep, Mult	6,9,10
3	0.07	8	2iy4S	FE	Rep, Mult	10,13,14
4	0.04	4	2wssX	III	Rep, Mult	1,5
5	0.04	5	2h9dD	CA	Rep, Mult	4,7
6	0.03	3	3bqzA	IMD	Rep, Mult	12,13,36,60
7	0.03	3	5sv1F	III	Rep, Mult	6,9,16
8	0.02	2	1sumB	FE	Rep, Mult	15,19
9	0.02	3	1h78A	DCP	Rep, Mult	49,50,52,55,56,59
10	0.02	3	3r5cB	COA	Rep, Mult	8,10,11,23,26,27,58,59,60,61
11	0.02	2	4nslC	N2P	Rep, Mult	17,20,21
12	0.02	2	3d8aA	III	Rep, Mult	12,16
13	0.02	2	3d9lB	III	Rep, Mult	10,13,14,17,55,56,59
14	0.01	1	1jtyA	ET	Rep, Mult	42,43,54,57
15	0.01	1	3p2yA	CA	Rep, Mult	1,39
16	0.01	1	2vl1B	III	Rep, Mult	38,39
17	0.01	1	3d9mA	III	Rep, Mult	35,39,42,66,70
18	0.01	1	2eerA	ZN	Rep, Mult	39,41,44,53
19	0.01	1	3lsmA	SO3	Rep, Mult	58,63

	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	1ffyA	0.534	2.80	0.046	0.836	6.1.1.5	NA
2	0.060	3dsxA	0.445	3.48	0.058	0.767	2.5.1.60	NA
3	0.060	1h7aA	0.539	3.68	0.043	0.904	1.17.4.2	NA
4	0.060	1gaxA	0.526	2.69	0.083	0.781	6.1.1.9	NA
5	0.060	3gr6D	0.522	2.78	0.155	0.781	1.3.1.9	NA
6	0.060	1pdyA	0.509	3.09	0.092	0.822	4.2.1.11	NA
7	0.060	1e9iD	0.517	3.02	0.111	0.794	4.2.1.11	NA
8	0.060	1e6wD	0.528	2.98	0.141	0.849	1.1.1.35,1.1.1.178	34,51
9	0.060	2zzgA	0.521	3.49	0.063	0.836	6.1.1.7	NA
10	0.060	1k87A	0.521	3.06	0.125	0.863	1.5.99.8	NA
11	0.060	3ismC	0.570	3.16	0.085	0.863	3.6.1.3	45,49,52
12	0.060	2dyvA	0.543	3.10	0.046	0.849	3.5.1.49	17
13	0.060	1zl9B	0.503	3.65	0.106	0.836	2.5.1.18	37,57
14	0.060	1k2wA	0.531	2.67	0.138	0.794	1.1.1.14	NA
15	0.060	2c7vC	0.518	2.98	0.078	0.822	1.5.1.33	11
16	0.060	1dgpA	0.550	3.13	0.042	0.836	4.2.3.9,4.1.99.7	NA
17	0.060	2psnC	0.516	3.04	0.078	0.808	4.2.1.11	NA
18	0.060	1bt1A	0.383	4.01	0.031	0.726	1.10.3.1	NA
19	0.060	2akzA	0.523	3.23	0.077	0.836	4.2.1.11	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	0.14	0.514	3.37	0.05	0.84	3egqA	GO:0003677 GO:0006351 GO:0006355
1	0.07	0.441	3.56	0.04	0.75	4g12A	GO:0003677 GO:0006351 GO:0006355
2	0.07	0.545	2.81	0.06	0.81	3dpjA	GO:0003677 GO:0006351 GO:0006355
3	0.07	0.538	4.07	0.07	0.92	3f0cA	GO:0003677 GO:0006351 GO:0006355
4	0.07	0.534	3.50	0.09	0.88	3htaA	GO:0003677 GO:0006351 GO:0006355
5	0.07	0.471	4.11	0.03	0.88	1sgmA	GO:0003677 GO:0006351 GO:0006355
6	0.07	0.560	3.00	0.03	0.88	2eh3A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
7	0.07	0.413	3.72	0.03	0.71	2g3bA	GO:0003677 GO:0006351 GO:0006355
8	0.07	0.490	4.05	0.06	0.88	5f1jA	GO:0003677 GO:0006351 GO:0006355
9	0.07	0.487	3.84	0.07	0.84	1rktA	GO:0003677 GO:0006351 GO:0006355
10	0.07	0.547	3.43	0.07	0.93	3g7rB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
11	0.07	0.443	4.24	0.04	0.85	3nnrA	GO:0003677 GO:0006351 GO:0006355
12	0.07	0.492	4.09	0.04	0.93	4hkuA	GO:0003677 GO:0006351 GO:0006355
13	0.07	0.522	3.78	0.04	0.89	3ppbA	GO:0003677 GO:0006351 GO:0006355
14	0.07	0.505	4.12	0.07	0.95	2pbxA
15	0.07	0.449	3.75	0.04	0.85	2g7lA	GO:0003677 GO:0006351 GO:0006355 GO:0045892
16	0.07	0.473	3.90	0.01	0.86	4mk6A	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.486	3.80	0.08	0.89	3kz9B	GO:0003677 GO:0006351 GO:0006355
18	0.07	0.524	3.34	0.09	0.86	3aqtB	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.35
Biological Processes	GO:0006355
GO-Score	0.35
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.