I-TASSER results

Input Sequence in FASTA format

>protein (66 residues)
MQEGGPQETMSARSTQHDAADALFRAIIETLDKHRNERTLTEDVLDTLARAYASISTNVP
EQGRLG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MQEGGPQETMSARSTQHDAADALFRAIIETLDKHRNERTLTEDVLDTLARAYASISTNVPEQGRLG
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	988885777889999999999999999999998764487678999999999988755899888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MQEGGPQETMSARSTQHDAADALFRAIIETLDKHRNERTLTEDVLDTLARAYASISTNVPEQGRLG
Prediction	866644664354554645214311310042045356634134510540253244144514656648
	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

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC
MQEGGPQETMSARSTQHDAADALFRAIIETLDKHRNERTLTEDVLDTLARAYASISTNVPEQGRLG

2wm9A5

0.26

0.24

0.94

0.95

MUSTER

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVT-EVMHSGRR-

4z6yC

0.13

0.11

0.80

0.66

dPPAS

----QLQAAESRYEAQKRITQVFELEILDLYGRLEKDGLLKKLEEEKAEAAEAAEER---------

2wm9A5

0.23

0.21

0.94

0.77

wdPPAS

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVTEVMHSGRR--

2wm9A5

0.27

0.24

0.91

0.93

wMUSTER

--EDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVT-EVMHSGR--

2wm9A5

0.26

0.24

0.92

0.84

wPPAS

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVT-EVMHSGR--

2wm9A5

0.23

0.21

0.94

0.68

dPPAS2

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVTEVMHSGRR--

2wm9A5

0.23

0.21

0.94

0.90

PPAS

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVTEVMHSGRR--

2wm9A5

0.26

0.24

0.94

0.95

Env-PPAS

-NEDVEQCADGLWKAEYELIADIYKLIIPIYEKRRDFERL-AHLYDTLHRAYSKVT-EVMHSGRR-

4egxA1

0.18

0.17

0.91

0.81

MUSTER

---GPGSEFSEEAIERLKETEKIIAELNETWEEKLRR---TEAIRMEREALLAEMGVAMREDGTLG

3e4bC4

0.14

0.12

0.86

0.66

dPPAS

----DICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPD-----

(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=-1.44

Estimated TM-score = 0.54±0.15

Estimated RMSD = 6.0±3.7Å

Download Model 2

C-score=-3.01

Download Model 3

C-score=-3.95

Download Model 4

C-score=-2.06

Download Model 5

C-score=-3.77

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	4gyoA	0.701	1.63	0.086	0.879
2	2yn6A2	0.695	2.48	0.016	0.939
3	2vl0A	0.694	2.20	0.062	0.985
4	2yinA	0.683	2.25	0.123	0.924
5	4ui9O	0.682	2.31	0.185	0.909
6	3i9wA	0.682	2.34	0.091	0.970
7	3fajA	0.681	2.43	0.079	0.955
8	4gpkA	0.680	1.87	0.106	0.864
9	3zciA	0.680	2.29	0.109	0.924
10	2yfaA	0.676	2.23	0.077	0.924

(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	0.18	37	5etzB	22B	Rep, Mult	21,24,28,31,41,44,49,52
2	0.11	24	1u7jA	ZN	Rep, Mult	20,48,51
3	0.08	20	3qbgB	22B	Rep, Mult	24,28,31,41,44
4	0.05	11	3qblD	22B	Rep, Mult	16,20,47,51,54,55,59
5	0.04	11	3gaiA	ATP	Rep, Mult	21,24,25,49
6	0.04	10	5da5C	GOA	Rep, Mult	16,17,20,51
7	0.03	7	3np2X	PLL	Rep, Mult	32,37,41
8	0.02	5	3mt6Y	III	Rep, Mult	10,13,14,47,50
9	0.02	4	2jstB	HLT	Rep, Mult	20,23,47
10	0.01	2	5kp8B	6VG	Rep, Mult	21,22,25
11	0.00	1	4bntD	36E	Rep, Mult	41,45
12	0.00	1	1f4nB	CA	Rep, Mult	17,21

	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	0.152	2jpnA	0.582	2.42	0.127	0.864	3.6.4.12	3,11,23,49
2	0.060	1lf6A	0.620	2.86	0.063	0.970	3.2.1.3	NA
3	0.060	3lomA	0.627	2.84	0.015	0.970	2.5.1.10	NA
4	0.060	3ee4A	0.611	3.05	0.061	0.924	1.17.4.1	NA
5	0.060	2jg0A	0.613	3.12	0.046	0.955	3.2.1.28	NA
6	0.060	2v8tA	0.609	3.10	0.094	0.955	1.11.1.6	NA
7	0.060	1pfuA	0.609	2.48	0.077	0.864	6.1.1.10	NA
8	0.060	2wlaA	0.633	2.71	0.094	0.894	1.16.3.1	NA
9	0.060	1chuA	0.608	2.66	0.111	0.924	1.4.3.16	NA
10	0.060	1ug9A	0.626	2.74	0.063	0.939	3.2.1.70	61
11	0.060	2htnG	0.641	2.77	0.094	0.909	1.16.3.1	NA
12	0.060	1r76A	0.604	3.03	0.094	0.955	4.2.2.2	50
13	0.060	1ksdA	0.603	3.09	0.078	0.955	3.2.1.4	43
14	0.060	1fp3A	0.663	3.04	0.123	0.955	5.1.3.8	44
15	0.060	3i9wA	0.682	2.34	0.091	0.970	2.7.13.3	22,25
16	0.060	1ut9A	0.628	2.77	0.032	0.894	3.2.1.4	NA
17	0.060	1knpA	0.666	2.46	0.092	0.985	1.4.3.16	NA
18	0.060	1nekA	0.529	2.88	0.094	0.955	1.3.99.1,	NA
19	0.060	2o8rA	0.615	2.86	0.032	0.879	2.7.4.1	52
20	0.060	1i8qA	0.622	2.67	0.100	0.849	4.2.2.1	44

(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	0.544	1.80	0.08	0.67	1z0jB	GO:0000011 GO:0005768 GO:0005829 GO:0005886 GO:0006810 GO:0006895 GO:0006896 GO:0006897 GO:0007596 GO:0008270 GO:0010008 GO:0010009 GO:0015031 GO:0016020 GO:0016197 GO:0017137 GO:0031901 GO:0034058 GO:0034498 GO:0043231 GO:0046872 GO:0070062 GO:0090160 GO:1903358
1	0.14	0.494	2.39	0.10	0.71	2kc7A
2	0.11	0.511	2.50	0.03	0.71	4ireB	GO:0005230 GO:0005267 GO:0005272 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0035725 GO:0071805
3	0.10	0.674	1.94	0.08	0.91	4i1aB	GO:0004721 GO:0006470 GO:0016787
4	0.10	0.636	2.66	0.15	0.98	4i9eA	GO:0004721 GO:0006470 GO:0016787
5	0.09	0.652	2.44	0.06	0.89	4jhrA	GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005737 GO:0005856 GO:0005938 GO:0007052 GO:0030695 GO:0042802 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0097431
6	0.08	0.569	2.64	0.04	0.76	1z0kB	GO:0000011 GO:0005768 GO:0005829 GO:0005886 GO:0006810 GO:0006895 GO:0006896 GO:0006897 GO:0007596 GO:0008270 GO:0010008 GO:0010009 GO:0015031 GO:0016020 GO:0016197 GO:0017137 GO:0031901 GO:0034058 GO:0034498 GO:0043231 GO:0046872 GO:0070062 GO:0090160 GO:1903358
7	0.08	0.549	2.20	0.10	0.74	4cgwA	GO:0097255
8	0.08	0.572	2.85	0.03	0.95	4tnwA	GO:0005230 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0008068 GO:0016020 GO:0016021 GO:0016595 GO:0030054 GO:0031987 GO:0045202 GO:0045211 GO:0051259 GO:1902476
9	0.08	0.678	2.42	0.02	0.94	4z90A	GO:0005230 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0034220
10	0.08	0.694	1.70	0.09	0.88	4gyoB	GO:0004721 GO:0006470 GO:0016787
11	0.08	0.640	2.33	0.08	0.92	3q15A	GO:0004721 GO:0006470 GO:0016787
12	0.07	0.642	2.50	0.08	0.92	5a6cB	GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005938 GO:0007052 GO:0007155 GO:0007165 GO:0007186 GO:0007267 GO:0008022 GO:0017016 GO:0030054 GO:0030695 GO:0034332 GO:0042802 GO:0043547 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0090557 GO:0097431 GO:0098609 GO:0098641
13	0.07	0.495	2.76	0.03	0.71	4yeuA	GO:0005230 GO:0005267 GO:0005272 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0034220 GO:0035725 GO:0071805
14	0.07	0.570	2.95	0.08	0.94	4cofA	GO:0004890 GO:0005216 GO:0005230 GO:0005254 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0007165 GO:0007605 GO:0016020 GO:0016021 GO:0022851 GO:0030054 GO:0034220 GO:0034707 GO:0043523 GO:0043524 GO:0045202 GO:0045211 GO:0048666 GO:0060021 GO:0060080 GO:0060119 GO:0060384 GO:0071420 GO:0090102 GO:1901215 GO:1902476 GO:1902711
15	0.07	0.630	2.02	0.08	0.85	3uq3A	GO:0003729 GO:0005737 GO:0006457 GO:0008104 GO:0030544 GO:0042030 GO:0043086 GO:0051879
16	0.07	0.688	2.49	0.11	0.98	3jafA	GO:0005230 GO:0005254 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0007218 GO:0007417 GO:0008270 GO:0016020 GO:0016021 GO:0016594 GO:0016934 GO:0022824 GO:0030054 GO:0030425 GO:0034220 GO:0034707 GO:0042995 GO:0043200 GO:0043204 GO:0045202 GO:0045211 GO:0045664 GO:0046872 GO:0051260 GO:0060012 GO:0071230 GO:0071294 GO:0071361 GO:0099565 GO:1902476
17	0.07	0.480	2.68	0.03	0.71	4x5tA	GO:0001508 GO:0001964 GO:0002087 GO:0005230 GO:0005254 GO:0005267 GO:0005272 GO:0005622 GO:0005783 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006820 GO:0006821 GO:0006936 GO:0007218 GO:0007268 GO:0007340 GO:0007601 GO:0007628 GO:0008270 GO:0009897 GO:0016020 GO:0016021 GO:0016594 GO:0016933 GO:0016934 GO:0022824 GO:0030054 GO:0030425 GO:0030977 GO:0034220 GO:0034707 GO:0035725 GO:0042391 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043576 GO:0045202 GO:0045211 GO:0046872 GO:0050884 GO:0050905 GO:0051260 GO:0051291 GO:0051970 GO:0060012 GO:0060013 GO:0060077 GO:0060080 GO:0071230 GO:0071294 GO:0071361 GO:0071805 GO:0097305 GO:1902476 GO:2000344
18	0.07	0.495	2.69	0.05	0.71	2m6bA	GO:0001508 GO:0001964 GO:0002087 GO:0005230 GO:0005254 GO:0005622 GO:0005783 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006820 GO:0006821 GO:0006936 GO:0007218 GO:0007268 GO:0007340 GO:0007601 GO:0007628 GO:0008270 GO:0009897 GO:0016020 GO:0016021 GO:0016594 GO:0016933 GO:0016934 GO:0022824 GO:0030054 GO:0030425 GO:0030977 GO:0034220 GO:0034707 GO:0042391 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043576 GO:0045202 GO:0045211 GO:0046872 GO:0050884 GO:0050905 GO:0051260 GO:0051291 GO:0051970 GO:0060012 GO:0060013 GO:0060077 GO:0060080 GO:0071230 GO:0071294 GO:0071361 GO:0097305 GO:1902476 GO:2000344
19	0.07	0.537	2.39	0.10	0.76	3kd7A
20	0.07	0.524	2.66	0.05	0.76	4cgvB	GO:0097255

Consensus prediction of GO terms

Molecular Function	GO:0016791
GO-Score	0.38
Biological Processes	GO:0051234	GO:0006464	GO:0016311
GO-Score	0.47	0.38	0.38
Cellular Component	GO:0071944	GO:0016020
GO-Score	0.47	0.35

(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 Rv3196A

[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]