I-TASSER results

Input Sequence in FASTA format

>protein (83 residues)
MGSDCGCGGYLWSMLKRVEIEVDDDLIQKVIRRYRVKGAREAVNLALRTLLGEADTAEHG
HDDEYDEFSDPNAWVPRRSRDTG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGSDCGCGGYLWSMLKRVEIEVDDDLIQKVIRRYRVKGAREAVNLALRTLLGEADTAEHGHDDEYDEFSDPNAWVPRRSRDTG
Prediction	CCCCCCCCCEEEEEEEEEEEHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98888876545565456766658999999999985688889999999999857888888887655667898777777788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGSDCGCGGYLWSMLKRVEIEVDDDLIQKVIRRYRVKGAREAVNLALRTLLGEADTAEHGHDDEYDEFSDPNAWVPRRSRDTG
Prediction	84652311210141355150514361045004424144445113010320144475464564752561562632444556778
	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

CCCCCCCCCEEEEEEEEEEEHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MGSDCGCGGYLWSMLKRVEIEVDDDLIQKVIRRYRVKGAREAVNLALRTLLGEADTAEHGHDDEYDEFSDPNAWVPRRSRDTG

2m4gA

0.16

0.13

0.82

0.79

MUSTER

PGVFRTRG-------------LTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAI--FGDGFGLKATRRSRKA

2l8tA

0.12

0.10

0.78

0.86

dPPAS

------------------ETKYELNNTKKVANAFGLNELINAVDLDIKNNMQEISSEQQSEQSKQKQYGTTLQNLAKQNRIIK

3jwhA1

0.18

0.14

0.80

0.66

wdPPAS

LG--CGQGNLLKILLQITGVDVSYRSLEIAQERLDRLRLPRNQWERLQ--LIQGALTYQ--DKRFHGY-DAAT----------

2epgB

0.18

1.00

0.75

wMUSTER

VGFDINCGVRLLASHLTLELLPRQKELADALYRLDVRFSKRELKEILKEGAGWLVKRGYGYPEDVRPWANPDKVSERRGAPSG

3jwgA1

0.19

0.16

0.82

0.64

wPPAS

VNADLGCGGLLSLLLQITGVDVSYSVLERAKDRLKIDRLPEMQRKRI-SLF-QSSLVYR--DKRFSGY-DAAT----------

2l8tA

0.12

0.10

0.78

0.73

dPPAS2

------------------ETKYELNNTKKVANAFGLNELINAVDLDIKNNMQEISSEQQSEQSKQKQYGTTLQNLAKQNRIIK

1x59A

0.27

0.23

0.84

0.81

PPAS

-GSS-GSSG----MAERAALEELVKLQGERVRGLKQQKAAELIEEEVAKLLK----AQLGPDESKQKFV-LKT--PKSGPSSG

2c7hA

0.34

0.28

0.82

0.85

Env-PPAS

LGS-MSCVHYKFSKLNYDTVTFDCDLKKQIMGREKLKAADC--DL----QITNAQTKE--------EYTDDNALIPKRIPIGG

5abkA

0.17

0.14

0.83

0.78

MUSTER

AQTDLGV--------------VNEDKLIEMLVRTGQIPADVDKRIALERYLEEKIRSGFKGDAQFGKKALEQRAKILKVIDKQ

2m4gA

0.14

0.12

0.83

0.72

dPPAS

RPGVFRTRG------------LTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAI--FGDGFGLKATRRSRKA

(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=-3.26

Estimated TM-score = 0.35±0.12

Estimated RMSD = 10.8±4.6Å

Download Model 2

C-score=-4.00

Download Model 3

C-score=-4.69

Download Model 4

C-score=-3.99

Download Model 5

C-score=-4.66

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	3ciaA	0.555	2.92	0.060	0.868
2	4kx7A	0.545	3.09	0.024	0.868
3	4p8qA3	0.544	3.32	0.024	0.892
4	2xdtA	0.541	3.27	0.048	0.879
5	2vqxA	0.541	3.47	0.084	0.879
6	3forA	0.536	3.33	0.072	0.868
7	4f5cA	0.532	3.40	0.024	0.892
8	1z5hA3	0.529	3.38	0.036	0.892
9	3ebgA	0.527	3.44	0.036	0.879
10	2dqmA4	0.525	3.46	0.036	0.879

(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	0.09	5	1fj3A	ACN	Rep, Mult	20,22,27,55
2	0.07	4	4iynA	MG	Rep, Mult	40,44
3	0.05	3	2h6bA	3C4	Rep, Mult	47,50
4	0.05	3	1espA	CA	Rep, Mult	23,55,62
5	0.04	2	2xctD	MN	Rep, Mult	23,25
6	0.04	2	1npcA	CA	Rep, Mult	58,59,62
7	0.02	1	1hotB	16G	Rep, Mult	14,17
8	0.02	1	1jb0M	CLA	Rep, Mult	42,46
9	0.02	1	2xkpA	AKG	Rep, Mult	50,53
10	0.02	1	2x98A	MG	Rep, Mult	19,21
11	0.02	1	3bpxA	SAL	Rep, Mult	44,48
12	0.02	1	1uv0A	ZN	Rep, Mult	61,67
13	0.02	1	1espA	CA	Rep, Mult	34,35,39,42,44
14	0.02	1	3v4pA	CA	Rep, Mult	62,64,66,68,69,70
15	0.02	1	1e1cB	DCA	Rep, Mult	30,33

	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	1s4bP	0.504	3.81	0.049	0.904	3.4.24.15	53
2	0.060	2vuxB	0.491	3.54	0.111	0.759	1.17.4.1	NA
3	0.060	3crvA	0.489	3.82	0.055	0.831	3.6.4.12	8,9
4	0.060	3gvdI	0.494	3.59	0.066	0.819	2.3.1.30	NA
5	0.060	3fvyA	0.485	4.32	0.096	0.904	3.4.14.4	25
6	0.060	1w36B	0.512	3.93	0.051	0.928	3.1.11.5	NA
7	0.060	3g4dA	0.507	3.56	0.012	0.819	4.2.3.13	NA
8	0.060	8tlnE	0.536	3.33	0.072	0.868	3.4.24.27	NA
9	0.060	1fj3A	0.535	3.36	0.072	0.868	3.4.24.27	21
10	0.060	3ciaA	0.555	2.92	0.060	0.868	3.4.11.-	NA
11	0.060	2q0cB	0.485	4.17	0.049	0.771	2.7.7.52	NA
12	0.060	1duvG	0.490	4.32	0.062	0.916	2.1.3.3	NA
13	0.060	1syyA	0.505	3.17	0.099	0.759	1.17.4.1	NA
14	0.060	1jk0A	0.491	3.50	0.125	0.759	1.17.4.1	NA
15	0.060	1espA	0.537	3.41	0.060	0.868	3.4.24.28	3,61
16	0.060	1bqbA	0.507	3.53	0.074	0.819	3.4.21.19,3.4.24.29	NA
17	0.060	2nomB	0.488	4.04	0.049	0.771	2.7.7.52	NA
18	0.060	3dwcB	0.487	3.98	0.024	0.879	3.4.17.19	52,69
19	0.060	3hf1B	0.494	3.60	0.107	0.771	1.17.4.1	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	0.07	0.367	4.06	0.04	0.67	4gaaA	GO:0004463 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0019370 GO:0046872
1	0.07	0.545	3.09	0.02	0.87	4kx7A	GO:0001525 GO:0002003 GO:0002005 GO:0003081 GO:0004177 GO:0005765 GO:0005886 GO:0005887 GO:0005903 GO:0006508 GO:0007267 GO:0008233 GO:0008237 GO:0008270 GO:0008283 GO:0009897 GO:0016020 GO:0016021 GO:0016324 GO:0016477 GO:0016787 GO:0031410 GO:0032835 GO:0042277 GO:0043171 GO:0045177 GO:0046872 GO:0070006 GO:0070062
2	0.07	0.527	3.44	0.04	0.88	3ebgA	GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
3	0.07	0.490	3.41	0.02	0.87	5ab0A	GO:0002250 GO:0002376 GO:0002474 GO:0004175 GO:0004177 GO:0005783 GO:0005788 GO:0005789 GO:0005886 GO:0006508 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0019885 GO:0042277 GO:0043171 GO:0046872 GO:0070006
4	0.07	0.527	3.24	0.04	0.88	3q7jA	GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
5	0.07	0.539	3.40	0.02	0.89	4fyrA	GO:0001525 GO:0001618 GO:0004177 GO:0004872 GO:0005615 GO:0005737 GO:0005765 GO:0005793 GO:0005829 GO:0005886 GO:0005887 GO:0006508 GO:0006725 GO:0007275 GO:0008233 GO:0008237 GO:0008270 GO:0009897 GO:0012506 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0030154 GO:0031983 GO:0035814 GO:0042277 GO:0043171 GO:0046718 GO:0046872 GO:0070006 GO:0070062
6	0.07	0.408	4.04	0.08	0.72	2cqzA
7	0.06	0.503	3.65	0.04	0.87	4xo4A	GO:0004177 GO:0005737 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016787 GO:0042277 GO:0042802 GO:0043171 GO:0046872 GO:0070006
8	0.06	0.387	4.01	0.07	0.69	4wz9B	GO:0005737 GO:0005886 GO:0006508 GO:0008237 GO:0008270 GO:0042277 GO:0043171 GO:0070006
9	0.06	0.357	4.98	0.05	0.82	5ch9A	GO:0008270 GO:0009056 GO:0016787 GO:0046872
10	0.06	0.413	4.31	0.12	0.78	2g0tB
11	0.06	0.555	2.92	0.06	0.87	3ciaA	GO:0004177 GO:0006508 GO:0008237 GO:0008270 GO:0016787 GO:0046872
12	0.06	0.487	3.50	0.04	0.87	5ab0C	GO:0002250 GO:0002376 GO:0002474 GO:0004175 GO:0004177 GO:0005783 GO:0005788 GO:0005789 GO:0005886 GO:0006508 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0019885 GO:0042277 GO:0043171 GO:0046872 GO:0070006
13	0.06	0.360	3.56	0.05	0.59	3v33A	GO:0000294 GO:0000932 GO:0001525 GO:0001933 GO:0002230 GO:0002376 GO:0003677 GO:0003682 GO:0003723 GO:0003729 GO:0003730 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004532 GO:0004540 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005791 GO:0005856 GO:0005886 GO:0006351 GO:0006355 GO:0006508 GO:0006915 GO:0006954 GO:0007275 GO:0007399 GO:0008152 GO:0008233 GO:0008234 GO:0010468 GO:0010508 GO:0010595 GO:0010628 GO:0010629 GO:0010656 GO:0010884 GO:0010942 GO:0016020 GO:0016579 GO:0016787 GO:0030154 GO:0030867 GO:0032088 GO:0032715 GO:0032720 GO:0034599 GO:0035198 GO:0035613 GO:0035925 GO:0036459 GO:0042149 GO:0042307 GO:0042347 GO:0042406 GO:0043022 GO:0043031 GO:0043124 GO:0044828 GO:0045019 GO:0045600 GO:0045766 GO:0045944 GO:0046872 GO:0050713 GO:0051259 GO:0051607 GO:0055118 GO:0061014 GO:0061158 GO:0071222 GO:0071347 GO:0071356 GO:0090501 GO:0090502 GO:0090503 GO:0098586 GO:1900016 GO:1900119 GO:1900165 GO:1900745 GO:1902714 GO:1903799 GO:1903936 GO:1904468 GO:1904628 GO:1904637 GO:1990869 GO:2000379 GO:2000627
14	0.06	0.382	2.64	0.08	0.54	4bxoA	GO:0000166 GO:0000712 GO:0003677 GO:0003682 GO:0004386 GO:0004518 GO:0005524 GO:0005634 GO:0005654 GO:0006259 GO:0006281 GO:0006974 GO:0016787 GO:0031297 GO:0036297 GO:0043240 GO:0071821 GO:0090305
15	0.06	0.354	4.37	0.07	0.73	3qvgB	GO:0000012 GO:0003684 GO:0005634 GO:0006281 GO:0006284 GO:0006974 GO:0019899 GO:0021766
16	0.06	0.534	3.24	0.04	0.88	5c97A	GO:0000209 GO:0002480 GO:0004177 GO:0005576 GO:0005622 GO:0005765 GO:0005829 GO:0005886 GO:0005887 GO:0006508 GO:0007165 GO:0007267 GO:0007565 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0030163 GO:0030659 GO:0031905 GO:0042277 GO:0043171 GO:0046872 GO:0048471 GO:0060395 GO:0061024 GO:0070006
17	0.06	0.330	4.85	0.07	0.75	3b7rL	GO:0004177 GO:0004301 GO:0004463 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0006691 GO:0008233 GO:0008237 GO:0008270 GO:0010043 GO:0016787 GO:0019370 GO:0042277 GO:0043171 GO:0043434 GO:0044822 GO:0046872 GO:0060509 GO:0070006 GO:0070062
18	0.06	0.365	4.27	0.01	0.61	5dllA	GO:0004177 GO:0006508 GO:0008237 GO:0008270 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0008238
GO-Score	0.58	0.48
Biological Processes	GO:0019538
GO-Score	0.58
Cellular Component	GO:0044424
GO-Score	0.37

(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 Rv0634A

[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]