I-TASSER results

Input Sequence in FASTA format

>protein (64 residues)
MDGIVDRGVRARPCQKVVAVLRRSKSHIDKRLDAATGNAFLGKQVLSAAGVVEYRPPRRS
PLST

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MDGIVDRGVRARPCQKVVAVLRRSKSHIDKRLDAATGNAFLGKQVLSAAGVVEYRPPRRSPLST
Prediction	CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCEEHCCCCCCCCCC
Conf.Score	9876555665665568899999767788887776546544455666544656767999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MDGIVDRGVRARPCQKVVAVLRRSKSHIDKRLDAATGNAFLGKQVLSAAGVVEYRPPRRSPLST
Prediction	8633454425443044013104435642454254343432224412422432524346555478
	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

CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCEEHCCCCCCCCCC
MDGIVDRGVRARPCQKVVAVLRRSKSHIDKRLDAATGNAFLGKQVLSAAGVVEYRPPRRSPLST

3h1qB3

0.35

0.27

0.75

0.71

MUSTER

KDGLVD-------YIGAIQIVRELKAKVERLLQAATGNAEACGHVVAGAGLVTLV---------

2khkA

0.33

0.27

0.80

0.75

dPPAS

MAAIEKR-------QKEIADGLASAERAHKDLDLAKASAQLKKAKAEAQVIIEQANKR------

3h1qB3

0.38

0.27

0.70

0.76

wdPPAS

KDGLVD-------YIGAIQIVRELKAKVERLLGAATGNAEACGHVVAGAGLV------------

3h1qB3

0.36

0.27

0.73

0.72

wMUSTER

-DGLVD-------YIGAIQIVRELKAKVERLLQAATGNAEACGHVVAGAGLVTLV---------

3h1qB3

0.38

0.27

0.70

0.68

wPPAS

KDGLVD-------YIGAIQIVRELKAKVERLLQAATGNAEACGHVVAGAGLV------------

2jt1A

0.15

0.12

0.86

0.82

dPPAS2

--------MSESIVTKIISIVQERQNMDTRDIADAAGQVRLYLEQLHDVGVLEKVNAGKG-VPG

2khkA

0.33

0.27

0.80

0.81

PPAS

MAAIEKR-------QKEIADGLASAERAHKDLDLAKASAQLKKAKAEAQVIIE-QANKR-----

1cn2A

0.17

0.16

0.94

0.90

Env-PPAS

KEGLVDKNTG---C-KYECLKLGDNDYCLRECKQQYGKGAGGYCYAFATHLYEQAIVWPLPNKR

2mp8A

0.13

0.12

0.94

0.69

MUSTER

LTANL--GISSYAAKKVIDIINTAVATIIALVTAVVGGGLITAGIVATAKSLKYGAKYAAAW--

2jt1A

0.14

0.12

0.88

0.75

dPPAS

--------MSESIVTKIISIVQERQNMDTRDIADAAGQVRLYLEQLHDVGVLEKVNAGKGVPGL

(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=-1.91

Estimated TM-score = 0.49±0.15

Estimated RMSD = 7.0±4.1Å

Download Model 2

C-score=-4.34

Download Model 3

C-score=-3.61

Download Model 4

C-score=-2.15

Download Model 5

C-score=-4.44

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	1lshA	0.657	2.59	0.078	1.000
2	1lf8B	0.654	2.69	0.094	1.000
3	4kk0A	0.635	2.83	0.048	0.984
4	2qk2A	0.633	2.78	0.047	0.984
5	5ifeC1	0.631	2.78	0.109	1.000
6	4xriA	0.623	2.90	0.079	0.984
7	1szaA	0.622	2.69	0.097	0.969
8	4fgvA	0.620	2.90	0.048	0.969
9	1hx8A	0.620	2.86	0.063	0.984
10	4c9bB1	0.620	2.82	0.063	0.984

(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	2	3g2wB	III	Rep, Mult	12,15,18,19,41,44
2	0.08	2	1o6oA	III	Rep, Mult	3,15,38,41,44,45
3	0.08	2	3pz2A	GRG	Rep, Mult	7,40
4	0.04	1	3c9iE	XE	Rep, Mult	45,62
5	0.04	1	4y18A	III	Rep, Mult	22,23
6	0.04	1	3g31B	GF1	Rep, Mult	54,55
7	0.04	1	1f59A	III	Rep, Mult	29,32,33,36,37,54
8	0.04	1	3eukA	MG	Rep, Mult	63,64
9	0.04	1	4it1D	BCT	Rep, Mult	12,15
10	0.04	1	3gwzD	CA	Rep, Mult	6,12

	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	1vcoA	0.549	2.85	0.145	0.859	6.3.4.2	NA
2	0.060	1vcnA	0.448	3.83	0.068	0.797	6.3.4.2	NA
3	0.060	2uxwA	0.556	3.38	0.016	0.969	1.3.99.-	NA
4	0.060	1ho8A	0.614	3.07	0.111	0.984	3.6.3.14	15
5	0.060	3d9dA	0.574	3.24	0.078	0.969	1.7.3.1	NA
6	0.060	1m7sD	0.565	3.14	0.095	0.891	1.11.1.6	15,41,46
7	0.060	2jifA	0.562	3.21	0.032	0.969	1.3.99.-	42,53
8	0.060	3ihyC	0.551	3.12	0.113	0.969	2.7.1.137	2,6,23
9	0.060	1ye9A	0.352	3.60	0.118	0.594	1.11.1.6	NA
10	0.060	2o5cA	0.567	3.03	0.083	0.938	5.99.1.2	NA
11	0.060	2bneB	0.556	3.06	0.067	0.906	2.7.4.22	NA
12	0.060	1vcmA	0.457	3.37	0.019	0.812	6.3.4.2	NA
13	0.060	1j33A	0.550	3.16	0.103	0.875	2.4.2.21	NA
14	0.060	2va1B	0.568	3.00	0.033	0.906	2.7.4.22	NA
15	0.060	3ej6A	0.551	2.98	0.089	0.859	1.11.1.6	NA
16	0.060	1ye9M	0.497	2.47	0.078	0.734	1.11.1.6	38,46
17	0.060	3ismC	0.549	3.06	0.067	0.938	3.6.1.3	NA
18	0.060	1jqiA	0.560	3.48	0.095	0.969	1.3.99.2	NA
19	0.060	1yn9B	0.557	2.84	0.034	0.859	3.1.3.48	28,37,43

(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	0.19	0.554	2.94	0.03	0.97	3g2sA	GO:0005622 GO:0005654 GO:0005768 GO:0005794 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0043231 GO:0044267 GO:0045732 GO:1901998
1	0.18	0.588	3.03	0.02	0.98	1qgkA	GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
2	0.08	0.595	2.98	0.06	0.98	1dvpA	GO:0001933 GO:0005737 GO:0005768 GO:0005769 GO:0005770 GO:0005829 GO:0005938 GO:0006886 GO:0006887 GO:0006897 GO:0007269 GO:0007275 GO:0007298 GO:0008021 GO:0008293 GO:0008333 GO:0008593 GO:0016050 GO:0016079 GO:0016082 GO:0016197 GO:0016322 GO:0031398 GO:0032509 GO:0033565 GO:0033619 GO:0042059 GO:0043130 GO:0045743 GO:0045752 GO:0046872 GO:0048471 GO:0051726 GO:1990182 GO:2000274
3	0.07	0.588	3.12	0.06	0.98	3nd2A	GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
4	0.07	0.551	3.57	0.05	0.92	2l0tB	GO:0005654 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:0043231
5	0.07	0.555	3.41	0.12	0.94	2qk1A	GO:0000776 GO:0000778 GO:0005200 GO:0005737 GO:0005816 GO:0005819 GO:0005856 GO:0005874 GO:0005876 GO:0005938 GO:0007020 GO:0008017 GO:0030472
6	0.07	0.585	2.84	0.02	0.97	1jplA	GO:0005622 GO:0005768 GO:0005794 GO:0005802 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0030306 GO:0044267 GO:0045732
7	0.07	0.593	3.10	0.03	1.00	3rruA	GO:0005622 GO:0005737 GO:0005764 GO:0005768 GO:0005794 GO:0005795 GO:0005829 GO:0006810 GO:0006886 GO:0007165 GO:0010008 GO:0015031 GO:0016020 GO:0017124 GO:0019901 GO:0030276 GO:0030295 GO:0031954 GO:0032147 GO:0043130 GO:0043162 GO:0045839 GO:0070062 GO:2000278
8	0.07	0.579	3.08	0.05	0.98	1elkA	GO:0005622 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006810 GO:0006886 GO:0006897 GO:0015031 GO:0016020 GO:0016197 GO:0030276 GO:0070062
9	0.07	0.544	3.33	0.08	0.97	1ialA	GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0042826 GO:0044822
10	0.07	0.596	3.17	0.02	1.00	2q5dB	GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
11	0.07	0.591	3.08	0.16	0.97	1qbkB	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
12	0.07	0.623	2.90	0.08	0.98	4xriA	GO:0005622 GO:0006886 GO:0008536
13	0.07	0.572	2.91	0.06	0.97	3ldzA	GO:0005070 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0007165 GO:0009967 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:1903543 GO:1903551
14	0.07	0.575	2.81	0.03	0.95	1mhqB	GO:0005622 GO:0005768 GO:0005794 GO:0005802 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0030136 GO:0030306 GO:0044267
15	0.07	0.592	3.12	0.03	1.00	4avxA	GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006622 GO:0006810 GO:0006886 GO:0006914 GO:0007165 GO:0008285 GO:0010324 GO:0010628 GO:0015031 GO:0016020 GO:0016197 GO:0019904 GO:0031901 GO:0032585 GO:0033565 GO:0036258 GO:0042059 GO:0042176 GO:0043231 GO:0043405 GO:0046426 GO:0046872 GO:0070062 GO:0072657 GO:1903543
16	0.07	0.555	3.38	0.12	0.95	3w3zA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
17	0.07	0.554	3.26	0.07	0.95	3w3uA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
18	0.07	0.586	3.02	0.12	0.95	4jlqA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372

Consensus prediction of GO terms

Molecular Function	GO:0017016	GO:0005048	GO:0022892	GO:0003723	GO:0031072	GO:0046914
GO-Score	0.48	0.48	0.48	0.37	0.37	0.37
Biological Processes	GO:0043623	GO:0006606	GO:0042176	GO:0051247	GO:0009896	GO:0000070	GO:0030262	GO:0000737	GO:0019048	GO:0046794	GO:1902850	GO:0051293	GO:0051225	GO:0007265	GO:1902583	GO:0051310	GO:0031122	GO:0051305	GO:0019058	GO:0044068
GO-Score	0.48	0.48	0.38	0.38	0.38	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37	0.37
Cellular Component	GO:0005635	GO:0005654	GO:0030119	GO:0044440	GO:0005774	GO:0030118	GO:0031988	GO:0098827	GO:1903561	GO:0005829
GO-Score	0.48	0.38	0.38	0.38	0.38	0.38	0.37	0.37	0.37	0.30

(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 Rv2255c

[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]