I-TASSER results

Input Sequence in FASTA format

>protein (93 residues)
MCSVIADQRRPDQPCGVGGCKTCQNGFVADIAEGKARKTRYVDHGWPTTDPDDHAVSELV
TDRTGALSPFGELTFPVPSDDLPYIHPVTVINR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MCSVIADQRRPDQPCGVGGCKTCQNGFVADIAEGKARKTRYVDHGWPTTDPDDHAVSELVTDRTGALSPFGELTFPVPSDDLPYIHPVTVINR
Prediction	CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	986555778889876666654344567776655545555788999999999987645443578888898887667888655888898666799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MCSVIADQRRPDQPCGVGGCKTCQNGFVADIAEGKARKTRYVDHGWPTTDPDDHAVSELVTDRTGALSPFGELTFPVPSDDLPYIHPVTVINR
Prediction	714333555446441323204313624345344546655531454127457462201312363643432334351313376241333434458
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MCSVIADQRRPDQPCGVGGCKTCQNGFVADIAEGKARKTRYVDHGWPTTDPDDHAVSELVTDRTGALSPFGELTFPVPSDDLPYIHPVTVINR

4cwuT

0.13

0.10

0.75

1.19

dPPAS

GLGVQTVDVQETQTSPVASAVADAAVQAVAAAASKTSTEVQTDPWMFRVSAPRRPRGSRKYGAASALLPE-----------------------

1dftA

0.23

0.08

0.32

1.25

dPPAS2

--------MDPNCSCSTGGSCTCTSSCACKNCKCTSCK-------------------------------------------------------

2jmvA

0.09

0.98

1.10

dPPAS

PTYCWNEANNPGGPNRCSNNKQCDGARTCSSSGFCQGTSRKPDP--GPKGPTYCWDEAKNPGGPNRCSNSKQCDGARTCSSSGFCQGTAGHAA

1wilA

0.20

0.14

0.70

1.23

dPPAS2

MCDVTAESLFPCRVCTRVFHDGCLRGYIQGDSAAEVTEMAHTETGWHYCDNINLLLTEESGPSSG----------------------------

1m0fB

0.15

0.11

0.73

1.06

dPPAS

MEQLTKNQRKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDK-----NDWRIQPAEFYRFHDAEVNTFGYF--------------------

4cwuT

0.14

0.10

0.70

1.22

dPPAS2

TVDVQETQTSPVASAVAD-----AAVQAVAAAASKTSTEVQTDPWMFRVS---------APRRPRGSRKYGAASALLPE--------------

1w8xM

0.18

0.16

0.88

1.01

dPPAS

--ALINPQFPYAGPVPIPGPAPTETMPLLNYVEGRIAGIQQARQFMPFLQGPHRAVAEQTYHAIGTGIQMG-QTFNQPLINTQEG--------

4yh8B

0.13

0.08

0.59

1.19

dPPAS2

---------------RERSVRSIEQELEQLRDVTPINQWKRKRSLWDIKPPGYELVTADQAKMSG--------VFPLP---------------

2mk0A

0.09

0.94

1.01

dPPAS

--EPSSQPSDCGEVIEECPIDACFLPKSDSARPPDCTAVGRPDCNVLPFPNNIGC----PSCCPFECSPDNPMFTPSPDGSPPNCSPTMLPSP

1m0fB

0.15

0.11

0.73

1.05

dPPAS2

MEQLTKNQRKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDK-----NDWRIQPAEFYRFHDAEVNTFGYF--------------------

(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=-3.55

Estimated TM-score = 0.32±0.11

Estimated RMSD = 11.8±4.5Å

Download Model 2

C-score=-4.12

Download Model 3

C-score=-4.08

Download Model 4

C-score=-3.85

Download Model 5

C-score=-4.24

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	2jmvA	0.651	2.72	0.090	0.935
2	2fozA	0.469	4.13	0.049	0.860
3	3hfwA	0.461	4.73	0.023	0.914
4	2wodA	0.451	4.68	0.048	0.882
5	3g9dA	0.451	4.60	0.036	0.871
6	4kf7A2	0.450	4.54	0.033	0.871
7	1ivhA	0.445	4.52	0.108	0.860
8	3cf4A1	0.441	4.21	0.049	0.828
9	1rx0A	0.441	4.73	0.048	0.871
10	2abmA	0.440	3.98	0.011	0.796

(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	0.14	7	4e4sF	MG	Rep, Mult	58,72
2	0.08	4	2vnuD	MG	Rep, Mult	43,52
3	0.04	2	3o8iA	M1T	Rep, Mult	2,3,91
4	0.04	2	1k9yA	PO4	Rep, Mult	54,75,77,78
5	0.04	2	1ivhC	FAD	Rep, Mult	23,27,41,43,89
6	0.02	1	1f1cA	HEM	Rep, Mult	58,59
7	0.02	1	4asoB	NUC	Rep, Mult	68,93
8	0.02	1	4asoE	NUC	Rep, Mult	72,73,74,76
9	0.02	1	2zkru	NUC	Rep, Mult	55,93
10	0.02	1	2o01L	CLA	Rep, Mult	82,84
11	0.02	1	3fybA	CA	Rep, Mult	44,84
12	0.02	1	3tceB	LYZ	Rep, Mult	54,58
13	0.02	1	3rphA	AMP	Rep, Mult	86,87,91

	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	1zl9B	0.395	3.98	0.060	0.720	2.5.1.18	NA
2	0.060	1kwmA	0.414	4.12	0.024	0.763	3.4.17.2	NA
3	0.060	1n1eA	0.411	4.49	0.033	0.796	1.1.1.8	89
4	0.060	2fp0B	0.465	4.16	0.048	0.871	3.2.1.143	NA
5	0.060	1nxcA	0.419	4.69	0.061	0.828	3.2.1.113	NA
6	0.060	2o3hA	0.415	4.29	0.081	0.785	4.2.99.18	53
7	0.060	2ri9B	0.424	4.29	0.012	0.806	3.2.1.113	42
8	0.060	2pm8A	0.411	4.29	0.038	0.731	3.1.1.8	NA
9	0.060	1gulA	0.421	3.78	0.076	0.699	2.5.1.18	NA
10	0.060	2vdcF	0.415	4.66	0.060	0.828	1.4.1.13	NA
11	0.060	1rx0A	0.441	4.73	0.048	0.871	1.3.99.-	58
12	0.060	2rd5B	0.428	4.56	0.057	0.850	2.7.2.8	NA
13	0.060	1fo2A	0.412	4.69	0.037	0.817	3.2.1.113	NA
14	0.060	1iyhA	0.408	3.76	0.062	0.677	5.3.99.2	NA
15	0.060	2j63A	0.414	4.18	0.054	0.774	4.2.99.18	NA
16	0.060	1bucB	0.440	4.53	0.036	0.839	1.3.99.2	90
17	0.060	1ivhA	0.445	4.52	0.108	0.860	1.3.99.10	NA
18	0.060	1ct9A	0.420	4.50	0.104	0.806	6.3.5.4	NA
19	0.060	2c1cA	0.419	4.45	0.024	0.774	3.4.17.2	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	0.07	0.399	4.15	0.05	0.73	1ukwA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
1	0.07	0.366	4.83	0.06	0.76	3mddA	GO:0000062 GO:0001889 GO:0003995 GO:0005739 GO:0005759 GO:0005777 GO:0005978 GO:0006082 GO:0006111 GO:0006629 GO:0006631 GO:0006635 GO:0007507 GO:0008152 GO:0009055 GO:0009409 GO:0009437 GO:0009791 GO:0016491 GO:0016627 GO:0019254 GO:0033539 GO:0042594 GO:0050660 GO:0051791 GO:0052890 GO:0055007 GO:0055088 GO:0055114 GO:0070991
2	0.07	0.438	4.54	0.04	0.85	1bucA	GO:0003995 GO:0004085 GO:0006629 GO:0006631 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
3	0.06	0.377	4.72	0.03	0.75	3mxlB	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
4	0.06	0.389	4.80	0.09	0.78	5jscA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
5	0.06	0.406	3.83	0.03	0.73	4l1fA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
6	0.06	0.441	4.73	0.05	0.87	1rx0A	GO:0000062 GO:0003995 GO:0005739 GO:0005759 GO:0006351 GO:0006355 GO:0006574 GO:0006629 GO:0008152 GO:0009055 GO:0009083 GO:0016491 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114
7	0.06	0.415	4.02	0.04	0.74	4m9aB	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
8	0.06	0.377	4.38	0.04	0.75	4kf7A	GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
9	0.06	0.344	4.59	0.05	0.69	1r2jA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
10	0.06	0.445	4.52	0.11	0.86	1ivhA	GO:0000062 GO:0003995 GO:0005739 GO:0005759 GO:0006552 GO:0008152 GO:0008470 GO:0009055 GO:0009083 GO:0016491 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114
11	0.06	0.347	4.95	0.05	0.72	3d9dA	GO:0000166 GO:0003995 GO:0006807 GO:0008152 GO:0016491 GO:0016627 GO:0050141 GO:0050660 GO:0052664 GO:0055114 GO:0071949
12	0.06	0.386	4.88	0.05	0.80	3ii9C	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
13	0.06	0.389	4.24	0.03	0.75	2uxwA	GO:0000062 GO:0001659 GO:0003995 GO:0004466 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0015980 GO:0016020 GO:0016491 GO:0016627 GO:0017099 GO:0030855 GO:0033539 GO:0036498 GO:0042645 GO:0042760 GO:0045717 GO:0046322 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0090181
14	0.06	0.398	4.49	0.06	0.77	5iduC	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
15	0.06	0.407	4.15	0.03	0.74	3r7kA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
16	0.06	0.402	4.75	0.07	0.83	4o5mC	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
17	0.06	0.434	4.70	0.00	0.85	3oibA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
18	0.06	0.377	4.23	0.05	0.71	4irnA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016627	GO:0000166	GO:0050662
GO-Score	0.57	0.57	0.57
Biological Processes	GO:0044710
GO-Score	0.57
Cellular Component	GO:0005777	GO:0005759
GO-Score	0.07	0.07

(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 Rv0863

[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]