I-TASSER results

Input Sequence in FASTA format

>protein (100 residues)
MCSGPKQGLTLPASVDLEKETVITGRVVDGDGQAVGGAFVRLLDSSDEFTAEVVASATGD
FRFFAAPGSWTLRALSAAGNGDAVVQPSGAGIHEVDVKIT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MCSGPKQGLTLPASVDLEKETVITGRVVDGDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFFAAPGSWTLRALSAAGNGDAVVQPSGAGIHEVDVKIT
Prediction	CCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCEEEEEHCCCCCEEEEEHCCCCCCEEEEHCCCEEEEEEEHCCCCCEEEEEHCCCCCEEEEEEHC
Conf.Score	9988788877666666776689999998699975699589997799987899875899768998589869999997688765899975787579999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MCSGPKQGLTLPASVDLEKETVITGRVVDGDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFFAAPGSWTLRALSAAGNGDAVVQPSGAGIHEVDVKIT
Prediction	7243466446244525364412031304447343233020300256452334234476240302134441202101563546351447454336151538
	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                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCEEEEEHCCCCCEEEEEHCCCCCCEEEEHCCCEEEEEEEHCCCCCEEEEEHCCCCCEEEEEEHC
MCSGPKQGLTLPASVDLEKETVITGRVVDGDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFFAAPGSWTLRALSAAGNGDAVVQPSGAGIHEVDVKIT

2nsmA2

0.20

0.15

0.75

1.38

MUSTER

---------------------GIKGMVLDQNYNNLANAVISVS----GINHDVTSGDHGDYFRLLLPGIYTVSATAGYDPETVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

1.24

dPPAS

---------------------GIKGMVLDQNYNNLANAVISVSG----INHDVTSGDHGDYFRLLLPGIYTVSATAPGDPETVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.74

1.62

wdPPAS

---------------------GIKGMVLDQNYNNLANAVISV-----GINHDVTSGDHGDYFRLLLPGIYTVSATAPGYDPTVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

1.60

wMUSTER

---------------------GIKGMVLDQNYNNLANAVISVS----GINHDVTSGDHGDYFRLLLPGIYTVSATAPGDPETVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

1.76

wPPAS

---------------------GIKGMVLDQNYNNLANAVISVSG----INHDVTSGDHGDYFRLLLPGIYTVSATAPGYDPTVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

2.17

dPPAS2

---------------------GIKGMVLDQNYNNLANAVISVSG----INHDVTSGDHGDYFRLLLPGIYTVSATAPGDPETVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

1.53

PPAS

---------------------GIKGMVLDQNYNNLANAVISVSG----INHDVTSGDHGDYFRLLLPGIYTVSATAPGDPETVTVTVGPAEPTLVNFHLK

2nsmA2

0.20

0.15

0.75

1.86

Env-PPAS

---------------------GIKGMVLDQNYNNLANAVISVSG----INHDVTSGDHGDYFRLLLPGIYTVSATAPGDPETVTVTVGPAEPTLVNFHLK

1h8lA2

0.20

0.15

0.75

1.34

MUSTER

---------------------GIWGFVLDADGRGILNATISVA----DINHPVTTYKDGDYWRLLVQGTYKVTASAGYDPVTKTVEVDSKGGVQVNFTLS

1h8lA2

0.21

0.16

0.75

1.16

dPPAS

---------------------GIWGFVLDADGRGILNATISVAD----INHPVTTYKDGDYWRLLVQGTYKVTASARGDPVTKTVEVDSKGGVQVNFTLS

(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=-1.07

Estimated TM-score = 0.58±0.14

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-2.68

Download Model 3

C-score=-3.25

Download Model 4

C-score=-1.33

Download Model 5

C-score=-4.31

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	2nsmA	0.793	2.18	0.177	0.920
2	1h8lA	0.755	1.82	0.177	0.860
3	3mn8A	0.741	1.94	0.165	0.870
4	1dlqA2	0.718	2.73	0.104	0.960
5	3th1A	0.718	2.71	0.140	0.930
6	2azqA2	0.714	2.72	0.147	0.950
7	3n9tA	0.710	2.72	0.104	0.950
8	1tmxA	0.710	2.68	0.146	0.950
9	2boyA	0.707	2.76	0.074	0.940
10	1s9aA	0.706	2.83	0.156	0.960

(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	0.40	14	1dvyA	BPD	Rep, Mult	24,26,28,60,94,96,98
2	0.05	2	2boyB	LPP	Rep, Mult	48,50,51,53
3	0.03	1	3hgiA	CO3	Rep, Mult	23,63,72,86,93
4	0.03	1	2g2pA	BR	Rep, Mult	24,25,26,60,94
5	0.03	1	3lxvN	CO3	Rep, Mult	73,79

	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	0.122	2h6uC	0.619	2.50	0.099	0.810	3.5.2.17	73,84
2	0.066	2iglA	0.632	2.33	0.071	0.800	3.5.2.17	NA
3	0.066	1kumA	0.575	3.10	0.075	0.790	3.2.1.3	24
4	0.060	2boyA	0.707	2.76	0.074	0.940	1.13.11.1	NA
5	0.060	1dlmA	0.715	2.74	0.113	0.960	1.13.11.1	NA
6	0.060	2a7oA	0.274	4.81	0.047	0.570	2.1.1.43	49
7	0.060	2q0zX	0.525	3.79	0.098	0.810	3.6.4.13	NA
8	0.060	1ug9A	0.529	3.21	0.078	0.720	3.2.1.70	NA
9	0.060	1b90A	0.603	2.82	0.045	0.840	3.2.1.2	NA
10	0.060	1cygA	0.588	3.36	0.040	0.840	2.4.1.19	48
11	0.060	1veoA	0.605	2.82	0.045	0.840	3.2.1.2	NA
12	0.060	1bglA	0.546	3.13	0.091	0.730	3.2.1.23	NA
13	0.060	2buzB	0.682	3.42	0.131	0.950	1.13.11.3	96
14	0.060	1a47A	0.602	3.14	0.041	0.830	2.4.1.19	NA
15	0.060	1h8lA	0.755	1.82	0.177	0.860	3.4.17.22	38,42
16	0.060	1dlmB	0.719	2.72	0.113	0.960	1.13.11.1	85
17	0.060	1pcdA	0.665	3.32	0.143	0.960	1.13.11.3	NA
18	0.060	4kbpA	0.530	3.21	0.052	0.740	3.1.3.2	NA
19	0.060	1eo2B	0.683	3.40	0.131	0.950	1.13.11.3	NA
20	0.060	2j73A	0.578	2.88	0.138	0.800	3.2.1.41	59
21	0.060	3hgiA	0.706	2.78	0.146	0.960	1.13.11.1	38,55
22	0.060	2h0jB	0.607	2.19	0.117	0.770	3.5.2.17	24,53

(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	0.24	0.739	1.95	0.17	0.87	3mn8B	GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0016787 GO:0046872
1	0.19	0.500	2.39	0.11	0.63	3fcgA	GO:0005215 GO:0006810 GO:0009279 GO:0009297 GO:0015473 GO:0016020 GO:0016021 GO:0055085
2	0.15	0.793	2.18	0.18	0.92	2nsmA	GO:0004180 GO:0004181 GO:0004185 GO:0005576 GO:0005615 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0010815 GO:0016485 GO:0016787 GO:0046872 GO:0051384
3	0.14	0.755	1.82	0.18	0.86	1h8lA	GO:0004180 GO:0004181 GO:0004185 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016021 GO:0016787 GO:0046872
4	0.12	0.695	2.35	0.12	0.86	1uwyA	GO:0004180 GO:0004181 GO:0004185 GO:0005615 GO:0005886 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0009653 GO:0009986 GO:0016020 GO:0016485 GO:0016787 GO:0031225 GO:0046872 GO:0070062
5	0.06	0.381	4.26	0.02	0.65	4b6zB	GO:0004181 GO:0006508 GO:0008270 GO:0046872
6	0.06	0.385	3.99	0.02	0.63	3l2nA	GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0046872
7	0.06	0.374	4.38	0.04	0.71	2yw5A	GO:0003682 GO:0005634 GO:0006351 GO:0006355 GO:0006357 GO:0016568 GO:0070577
8	0.06	0.380	4.25	0.02	0.65	3k2kA	GO:0004181 GO:0006508 GO:0008270
9	0.06	0.367	5.70	0.05	0.86	2c1cA	GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0016787 GO:0046872
10	0.06	0.382	4.34	0.03	0.70	4k7iA	GO:0000302 GO:0001016 GO:0004601 GO:0005102 GO:0005615 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005777 GO:0005782 GO:0005829 GO:0006915 GO:0006954 GO:0006979 GO:0008379 GO:0016209 GO:0016480 GO:0016491 GO:0031410 GO:0032967 GO:0034614 GO:0042744 GO:0043027 GO:0043066 GO:0043154 GO:0043231 GO:0046983 GO:0048471 GO:0051354 GO:0051920 GO:0055114 GO:0060785 GO:0070062 GO:0070995 GO:0072541 GO:0098869 GO:2001057
11	0.06	0.380	4.94	0.05	0.75	4djlA	GO:0004180 GO:0004181 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
12	0.06	0.342	5.29	0.06	0.73	1xkvB	GO:0000166 GO:0004611 GO:0004612 GO:0005524 GO:0005737 GO:0006094 GO:0016829 GO:0016831 GO:0017076 GO:0046872
13	0.06	0.384	5.03	0.06	0.73	1lq9A
14	0.06	0.345	4.62	0.06	0.62	4axvA	GO:0008152 GO:0016787 GO:0016788 GO:0046872
15	0.06	0.365	4.61	0.07	0.66	2qvpC	GO:0008152 GO:0016787 GO:0016788 GO:0046872
16	0.06	0.345	4.49	0.01	0.67	3dgvA	GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0006508 GO:0007596 GO:0007599 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0042730 GO:0046872 GO:0070062
17	0.06	0.345	5.22	0.03	0.64	5hvfA	GO:0003331 GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0005623 GO:0006508 GO:0007596 GO:0007599 GO:0008233 GO:0008237 GO:0008270 GO:0009408 GO:0010757 GO:0016787 GO:0042493 GO:0042730 GO:0046872 GO:0051918 GO:0070062 GO:0071333 GO:0097421 GO:2000346
18	0.06	0.373	4.23	0.04	0.64	3iehA	GO:0008152 GO:0016787 GO:0016788 GO:0046872
19	0.06	0.331	5.25	0.06	0.76	2pizA	GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0004181	GO:0008270	GO:0015288	GO:0004185
GO-Score	0.51	0.51	0.37	0.36
Biological Processes	GO:0006508	GO:0051604	GO:0043603	GO:1901564	GO:0030031	GO:0043711	GO:0044765
GO-Score	0.51	0.50	0.50	0.50	0.37	0.37	0.37
Cellular Component	GO:0044421	GO:0044462	GO:0019867	GO:0030313	GO:0016021
GO-Score	0.50	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 Rv0814c

[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]