I-TASSER results

Input Sequence in FASTA format

>protein (88 residues)
MRIPGNRQCLLVQVLRQVDGSAHRLILTSLHRDARADAHRYSNGTDHAGRAADEPAETAH
EPCWVAARGLASQASRAMSATYRPSSFI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MRIPGNRQCLLVQVLRQVDGSAHRLILTSLHRDARADAHRYSNGTDHAGRAADEPAETAHEPCWVAARGLASQASRAMSATYRPSSFI
Prediction	CCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	9999985456888999847756678888877777777775467776555556774665678556788877899998877546787789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MRIPGNRQCLLVQVLRQVDGSAHRLILTSLHRDARADAHRYSNGTDHAGRAADEPAETAHEPCWVAARGLASQASRAMSATYRPSSFI
Prediction	7735664311013004425442331102313552445344255345433533654373344302110432354244324243446537
	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

CCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
MRIPGNRQCLLVQVLRQVDGSAHRLILTSLHRDARADAHRYSNGTDHAGRAADEPAETAHEPCWVAARGLASQASRAMSATYRPSSFI

5jqzA

0.21

0.17

0.83

0.59

MUSTER

TAIEANSLKALIEIAKAI---WKALWANSLLLEAT------SRGDTERMR---QWAEEARK-IYKEAEKIIDRADEIVEEAKKRHD--

4lunU2

0.14

0.95

0.59

dPPAS

----DSKLKGALQSLFKNFIDATFARATELHKKVNKLQREHQKCQIRTGKLRDEYVEEYDKLLPIFIRFKTSAITLGEFFKLEIPELH

2vh3A

0.23

0.22

0.93

0.66

wdPPAS

SEIPGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYKEGVDHEGNP--ELIEEGFE-KFLASLKIDRKALGSLCTLFQPH---

2vh3A

0.25

0.23

0.92

0.63

wMUSTER

SEIPGSKECLAEALQKH-QGKKKSYALICAYLNYKEDAENYKEGVDHEGNP--ELIEEGFE-KFLASLKIDRKALGSLCTLFQPH---

2v6jA2

0.34

0.30

0.86

0.57

wPPAS

RELPGTR-RVLPQLVREAVKKRLRVILA---RVVASETYEALRGEPYMGNEIDE----AHDPASVAARGYIETRVSMMTAT--PGT--

2jlbA2

0.32

0.25

0.78

0.58

dPPAS2

--EPYITAQLLNWRRRLCDWRA----LDVLSAQVRAAVAQ--------GVGAVEPFAFLSEDA-SAAEQLACARTRAQAIA---ASV-

2n11A

0.23

0.18

0.78

0.63

PPAS

-----QQQAVLEQERRDRE--ALRIAQSEAEDEAQADLALRRSLDSYPVSKNDG---TRPKMT---PEQMAKEMSEFLS---RPA---

3zey43

0.27

0.16

0.58

0.71

Env-PPAS

-DVVGRR----WRY--RTDGS--KLM--KVFLD-ARDRKR----VES---------------------RLPLLAHVYKLLTHRTVTFM

4b4oA1

0.14

0.94

0.59

MUSTER

-RV-GTGTALTQLLNARVKPGPGRITWDELAASGLPSCDAGENILNPLRRWNETFQKEVLGSRLETTQLLAKAITKA---PQPPKAWV

2kfdA

0.14

0.10

0.74

0.57

dPPAS

--------------------NERRILEQKKHYFWLLLQRTYTKTGKPKPSTWDLASKELGESLEYKALGDEDNIRRQIFEDFKPE---

(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=-3.48

Estimated TM-score = 0.33±0.11

Estimated RMSD = 11.5±4.5Å

Download Model 2

C-score=-3.57

Download Model 3

C-score=-3.79

Download Model 4

C-score=-4.90

Download Model 5

C-score=-5.00

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	2kfoA	0.599	3.23	0.038	0.864
2	4q2eA	0.598	2.57	0.039	0.852
3	3dl8G	0.588	3.34	0.084	0.943
4	1b10A	0.578	3.38	0.040	0.818
5	3ayfA1	0.578	3.41	0.064	0.864
6	3p5nA	0.575	3.14	0.000	0.864
7	3tekA	0.575	3.47	0.063	0.875
8	4cruA	0.571	2.73	0.047	0.807
9	2zqpY1	0.569	3.41	0.073	0.920
10	4cadC	0.568	3.41	0.061	0.920

(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	0.08	4	1a4fB	OXY	Rep, Mult	30,66,70
2	0.06	3	2vwaF	PTY	Rep, Mult	8,12,62,66,69,73,74,77
3	0.05	3	1leiB	QNA	Rep, Mult	35,42,43,44
4	0.04	2	2vunA	FE	Rep, Mult	13,39,60
5	0.04	2	2jfaB	III	Rep, Mult	27,31,35,57,60,61,64
6	0.04	2	2zseA	PAU	Rep, Mult	26,29,30,33,70
7	0.04	2	3ce2A	ZN	Rep, Mult	31,35,57
8	0.04	2	3svlB	CA	Rep, Mult	15,16
9	0.02	1	3opqA	PO4	Rep, Mult	21,23,24
10	0.02	1	1t3tA	SO4	Rep, Mult	43,83,84,85,86
11	0.02	1	3e27A	MG	Rep, Mult	33,50
12	0.02	1	2w6dA	GDP	Rep, Mult	25,26,28,29,67
13	0.02	1	3jcuX	CLA	Rep, Mult	65,69
14	0.02	1	4i7zD	OZ2	Rep, Mult	80,82
15	0.02	1	3zt6A	ACX	Rep, Mult	4,5
16	0.02	1	2h88C	UNL	Rep, Mult	75,79

	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	3bllA	0.400	4.46	0.063	0.716	2.4.2.29	NA
2	0.060	2f9qA	0.552	3.57	0.011	0.864	1.14.14.1	NA
3	0.060	3dsiA	0.532	3.57	0.012	0.841	4.2.1.92	15,66
4	0.060	2ibpA	0.525	3.40	0.051	0.830	2.3.3.1	23
5	0.060	2p2wA	0.562	3.21	0.036	0.886	2.3.3.-	31
6	0.060	3b98A	0.527	3.15	0.080	0.830	5.3.99.4	6,34,36
7	0.060	2ckpB	0.465	3.55	0.053	0.795	2.7.1.32	NA
8	0.060	3dpgA	0.536	3.64	0.077	0.875	3.1.21.4	NA
9	0.060	3hwkE	0.553	3.65	0.071	0.898	2.3.3.1	31
10	0.060	2hi4A	0.547	3.21	0.023	0.830	1.14.14.1	NA
11	0.060	2ashD	0.542	3.30	0.047	0.830	2.4.2.29	NA
12	0.060	2fp0B	0.546	3.92	0.085	0.898	3.2.1.143	NA
13	0.060	2ashA	0.547	3.28	0.047	0.830	2.4.2.29	NA
14	0.060	3fegA	0.466	3.88	0.047	0.818	2.7.1.82	NA
15	0.060	2ve3A	0.532	3.52	0.071	0.886	1.14.-.-	NA
16	0.060	3dlaD	0.549	2.76	0.069	0.773	6.3.5.1	NA
17	0.060	2geuA	0.547	2.95	0.074	0.773	2.7.1.33	73
18	0.060	1q5eA	0.531	3.35	0.128	0.841	1.14.-.-	NA
19	0.060	1jawA	0.527	3.76	0.049	0.875	3.4.11.9	54

(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	0.08	0.509	3.44	0.09	0.77	1xu0A	GO:0005886 GO:0016020 GO:0046872 GO:0051260
1	0.08	0.521	4.20	0.04	0.89	5awwY	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
2	0.07	0.551	3.68	0.05	0.93	5eulY	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
3	0.07	0.599	3.23	0.04	0.86	2kfoA	GO:0001933 GO:0005507 GO:0005521 GO:0005737 GO:0005741 GO:0005783 GO:0005794 GO:0005886 GO:0006139 GO:0006878 GO:0006979 GO:0007611 GO:0008017 GO:0009986 GO:0015631 GO:0016020 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043008 GO:0043066 GO:0043433 GO:0044325 GO:0045121 GO:0046007 GO:0046686 GO:0046688 GO:0046872 GO:0050860 GO:0051087 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
4	0.07	0.601	2.90	0.04	0.83	2kflA	GO:0001933 GO:0005507 GO:0005783 GO:0005794 GO:0005886 GO:0006979 GO:0008017 GO:0009986 GO:0015631 GO:0016020 GO:0016021 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043066 GO:0043433 GO:0045121 GO:0046007 GO:0046872 GO:0050860 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
5	0.07	0.474	3.93	0.08	0.85	2wwbA	GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
6	0.07	0.526	3.86	0.10	0.85	3mp7A	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
7	0.07	0.520	3.41	0.08	0.88	4q2gB	GO:0004605 GO:0005886 GO:0006629 GO:0006655 GO:0008654 GO:0016020 GO:0016021 GO:0016024 GO:0016740 GO:0016772 GO:0016779
8	0.07	0.456	4.46	0.01	0.78	3ayfA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
9	0.07	0.588	3.34	0.08	0.94	3dl8G	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
10	0.07	0.487	3.35	0.00	0.74	3bo0A	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
11	0.07	0.445	3.53	0.06	0.73	1u5lA	GO:0005886 GO:0016020 GO:0016021 GO:0046872 GO:0051260
12	0.07	0.530	3.77	0.03	0.93	2yxrA	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
13	0.07	0.544	3.62	0.07	0.93	5abbA	GO:0005622 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
14	0.06	0.443	3.65	0.06	0.73	1i17A	GO:0005507 GO:0005886 GO:0006878 GO:0016020 GO:0031225 GO:0051260
15	0.06	0.451	3.45	0.09	0.68	1u3mA	GO:0001933 GO:0001948 GO:0005507 GO:0005605 GO:0005623 GO:0005783 GO:0005794 GO:0005886 GO:0006979 GO:0008017 GO:0009986 GO:0010628 GO:0010870 GO:0015631 GO:0016020 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043066 GO:0043083 GO:0043433 GO:0045121 GO:0046007 GO:0046872 GO:0050731 GO:0050860 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:0098737 GO:1901379
16	0.06	0.547	3.76	0.07	0.90	3dinC	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
17	0.06	0.427	3.48	0.00	0.69	2kunA	GO:0001933 GO:0005507 GO:0005521 GO:0005634 GO:0005737 GO:0005783 GO:0005794 GO:0005886 GO:0006878 GO:0006979 GO:0007049 GO:0007050 GO:0007611 GO:0008017 GO:0008152 GO:0009986 GO:0015631 GO:0016020 GO:0019898 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043008 GO:0043066 GO:0043433 GO:0044325 GO:0045121 GO:0046007 GO:0046686 GO:0046688 GO:0046872 GO:0050860 GO:0051087 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
18	0.06	0.409	3.98	0.04	0.70	2vcvA	GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.40
Biological Processes	GO:0051259
GO-Score	0.40
Cellular Component	GO:0031224	GO:0005886
GO-Score	0.32	0.32

(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 Rv0616c

[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]