I-TASSER results

Input Sequence in FASTA format

>protein (68 residues)
MIVVVNEQQVEVDEQTTIAALLDSLGFGDRGIAVALNFSVLPRSDWATKICELRKPVRLE
VVTAVQGG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MIVVVNEQQVEVDEQTTIAALLDSLGFGDRGIAVALNFSVLPRSDWATKICELRKPVRLEVVTAVQGG
Prediction	CEEEHCCEEEEHCCCCCHHHHHHHHCCCCCEEEEEHCCEEHCHHHCCCCCCCCCCCCEEEEEEEHCCC
Conf.Score	98998997787589999999999989999859999979688465554555568999689999985899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MIVVVNEQQVEVDEQTTIAALLDSLGFGDRGIAVALNFSVLPRSDWATKICELRKPVRLEVVTAVQGG
Prediction	75141464636166733044016427266520000134421436516643440455041101213568
	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

CEEEHCCEEEEHCCCCCHHHHHHHHCCCCCEEEEEHCCEEHCHHHCCCCCCCCCCCCEEEEEEEHCCC
MIVVVNEQQVEVDEQTTIAALLDSLGFGDRGIAVALNFSVLPRSDWATKICELRKPVRLEVVTAVQGG

1zud4

0.26

0.25

0.97

4.64

MUSTER

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

11.27

dPPAS

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

6.89

wdPPAS

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.25

0.24

0.96

4.62

wMUSTER

-QILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

4.71

wPPAS

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

13.18

dPPAS2

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

5.16

PPAS

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

1zud4

0.26

0.25

0.97

5.60

Env-PPAS

MQILFNDQAMQCAAGQTVHELLEQLDQRQAGAALAINQQIVPREQWAQ--HIVQDGDQILLFQVIAGG

2kl0A

0.37

0.35

0.96

3.78

MUSTER

MLVTINGEQREVQSA-SVAALMTELDCTGGHFAVALNYDVVPRGKWDE--TPVTAGDEIEILTPRQGG

2kl0A

0.37

0.35

0.96

8.60

dPPAS

MLVTINGEQREVQ-SASVAALMTELDCTGGHFAVALNYDVVPRGKWDE--TPVTAGDEIEILTPRQGG

(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=1.77

Estimated TM-score = 0.96±0.05

Estimated RMSD = 0.5±0.5Å

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	1zud4	0.903	0.86	0.258	0.971
2	2kl0A	0.809	1.49	0.369	0.956
3	1tygB	0.786	1.61	0.250	0.941
4	2m19A	0.753	2.21	0.227	0.971
5	1wgkA	0.748	2.46	0.227	0.971
6	2k5pA	0.727	2.04	0.227	0.941
7	1nviD	0.713	1.79	0.200	0.853
8	4idiA	0.709	1.71	0.111	0.897
9	2ekiA	0.701	1.78	0.081	0.897
10	1ryjA	0.700	1.83	0.194	0.897

(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	0.12	3	1zud5	III	Rep, Mult	7,28,30,31,32,33,38,39,40,42,43,44,60,62,63,64,65,66,67,68
2	0.07	2	2htm4	III	Rep, Mult	6,27,31,32,33,35,38,40,42,60,61,62,63,64
3	0.06	2	1fm00	III	Rep, Mult	5,35,37,38,39,40,58,60,62,63,64
4	0.03	1	1ybaD	AKG	Rep, Mult	43,44
5	0.03	1	2jf5A	MG	Rep, Mult	1,13
6	0.03	1	4k7sB	ZN	Rep, Mult	6,60
7	0.03	1	1qgwA	PEB	Rep, Mult	31,32
8	0.03	1	3qnnA	CA	Rep, Mult	19,23
9	0.03	1	1h9sB	MOO	Rep, Mult	17,21
10	0.03	1	2j8rB	AZI	Rep, Mult	65,68
11	0.03	1	2asqA	III	Rep, Mult	2,5,9,10,11,12,13,16,20,21,24,25
12	0.03	1	1m43A	UUU	Rep, Mult	38,41
13	0.03	1	1tk3A	NAG	Rep, Mult	36,37

	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	2fugU	0.642	2.46	0.156	0.941	1.6.99.5	24,36
2	0.060	2ckjA	0.655	2.39	0.206	0.926	1.17.1.4,1.17.3.2	NA
3	0.060	2jrhA	0.603	2.75	0.078	0.926	2.7.11.25	39,45,49,50,58
4	0.060	2o2vA	0.541	2.94	0.150	0.868	2.7.12.2	44,49,56
5	0.060	1zxiA	0.675	2.36	0.095	0.926	1.2.99.2	18
6	0.060	1c4aA	0.653	2.48	0.127	0.926	1.12.7.2	NA
7	0.060	1ogpA	0.617	2.73	0.119	0.926	1.8.3.1	NA
8	0.060	1sb3C	0.669	2.41	0.111	0.926	1.3.99.20	21
9	0.060	1qlaE	0.598	2.73	0.156	0.941	1.3.99.1	NA
10	0.060	1zoyB	0.634	2.60	0.127	0.926	1.3.5.1	55
11	0.060	3it6B	0.541	3.71	0.147	0.956	2.3.1.1,2.3.1.35	26
12	0.060	1ffvD	0.588	2.86	0.161	0.897	1.2.99.2	NA
13	0.060	1fo4A	0.672	2.31	0.206	0.926	1.17.1.4	NA
14	0.060	1nyqB	0.621	2.32	0.145	0.912	6.1.1.3	54
15	0.060	2nptD	0.596	2.35	0.052	0.853	2.7.11.25	49
16	0.060	2e1qA	0.673	2.38	0.206	0.926	1.17.3.2,1.17.1.4	NA
17	0.060	1ogpE	0.618	2.73	0.119	0.926	1.8.3.1	NA
18	0.060	2wqtT	0.532	3.34	0.077	0.838	4.2.1.80	26
19	0.060	1v8cA	0.647	2.34	0.177	0.882	4.2.3.1	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	0.42	0.767	1.75	0.23	0.94	1f0zA	GO:0000166 GO:0009228 GO:0009229
1	0.31	0.753	2.21	0.23	0.97	2m19A	GO:0000166
2	0.25	0.647	2.34	0.18	0.88	1v8cA	GO:0004795
3	0.24	0.699	1.88	0.24	0.87	1vjkA	GO:0006777
4	0.21	0.748	2.46	0.23	0.97	1wgkA	GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0016783 GO:0032447 GO:0034227 GO:0070062
5	0.20	0.637	2.02	0.12	0.87	3hvzA	GO:0008152 GO:0015969 GO:0016597
6	0.19	0.786	1.61	0.25	0.94	1tygB	GO:0000166 GO:0009228 GO:0009229
7	0.19	0.642	2.50	0.14	0.90	3dwgC	GO:0005829 GO:0006535 GO:0008652 GO:0019344 GO:0043234
8	0.18	0.637	2.31	0.18	0.90	2kmmA	GO:0008152 GO:0015969 GO:0016597 GO:0016787
9	0.14	0.631	2.66	0.15	0.96	1v2yA	GO:0005634 GO:0005654 GO:0005681 GO:0005689 GO:0005737 GO:0006397 GO:0008380 GO:0045171
10	0.14	0.702	2.06	0.15	0.87	1fm0D	GO:0000166 GO:0005829 GO:0006777
11	0.13	0.696	1.84	0.23	0.91	3po0A	GO:0000166 GO:0031386 GO:0032446
12	0.11	0.709	1.71	0.11	0.90	4idiA	GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0032447 GO:0034227
13	0.11	0.693	2.61	0.21	0.97	2ax5A	GO:0001403 GO:0002098 GO:0002143 GO:0005634 GO:0005737 GO:0005829 GO:0007114 GO:0008033 GO:0016783 GO:0031386 GO:0032447 GO:0034227 GO:0034599 GO:0042803
14	0.10	0.660	2.67	0.18	0.96	2k9xA	GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0032447 GO:0034227
15	0.10	0.584	2.59	0.09	0.85	3rd2A	GO:0001816 GO:0005634 GO:0005737 GO:0016925 GO:0031386 GO:0045944
16	0.09	0.643	2.18	0.12	0.84	4wwmA	GO:0005737 GO:0034227
17	0.06	0.417	3.95	0.05	0.81	4a62A	GO:0030541
18	0.06	0.313	4.27	0.04	0.71	2oqzA	GO:0016020 GO:0016021 GO:0016787
19	0.06	0.328	4.22	0.05	0.74	1l0lF	GO:0005739 GO:0005743 GO:0005750 GO:0006122 GO:0008121 GO:0009060 GO:0016020 GO:0034551 GO:0055114 GO:0070469 GO:1902600
20	0.06	0.325	3.88	0.07	0.63	2a00A	GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0008556 GO:0016020 GO:0016021 GO:0016787 GO:0043231 GO:0046872 GO:0071805
21	0.06	0.323	4.13	0.02	0.68	1o4sB	GO:0003824 GO:0004069 GO:0005737 GO:0008483 GO:0009058 GO:0016740 GO:0030170 GO:0080130

Consensus prediction of GO terms

Molecular Function	GO:0000166	GO:0016838	GO:0016782
GO-Score	0.60	0.50	0.42
Biological Processes	GO:0019720	GO:0002097	GO:0032446	GO:0009229	GO:0009228
GO-Score	0.48	0.42	0.42	0.42	0.42
Cellular Component	GO:0044444	GO:1903561	GO:0031988
GO-Score	0.42	0.42	0.42

(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.

I-TASSER results for job id Rv0416

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

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