I-TASSER results

Input Sequence in FASTA format

>protein (78 residues)
MLRCRRGAGYGSVVVVGERPGFQSDSAARQTAPPVRPMTSDQLPATKADLYAAVDAMRAD
MRELLEQISTLIREATQK

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLRCRRGAGYGSVVVVGERPGFQSDSAARQTAPPVRPMTSDQLPATKADLYAAVDAMRADMRELLEQISTLIREATQK
Prediction	CCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	986557888757999857888655545556799988888777764689999999999999999999999999998669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLRCRRGAGYGSVVVVGERPGFQSDSAARQTAPPVRPMTSDQLPATKADLYAAVDAMRADMRELLEQISTLIREATQK
Prediction	734045434332110125444365564456434424424676443443412221432444145116403411452578
	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

CCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MLRCRRGAGYGSVVVVGERPGFQSDSAARQTAPPVRPMTSDQLPATKADLYAAVDAMRADMRELLEQISTLIREATQK

2aw7P

0.24

0.22

0.90

0.74

MUSTER

MVTARHGA-FYQVVVADSR--NARNGRFIERVGFFNPIASEKEEGTRLD----LDRIAHWVGQISDRVAALIKEV-NK

2n64A

0.09

0.06

0.73

0.69

dPPAS

---------------------GHMEGKPKMEPAASSQAAVEELRTQVRELRSIIETMKDQQKREIKQLLSELDEEKKI

1no7A2

0.28

0.19

0.69

0.64

wdPPAS

-----------NMVV----PEIAPGEE-----CPSDPVTDPAHPLHPANLVATVNAMFHNGRVVVDGPAMLTLQ----

3zifN

0.18

0.99

0.75

wMUSTER

YVTARVGSNMLGGVVLPPNSETVGTEATRDNAEGARRPE-DQTPYLVEDSLGGLKRRMDLLEESNQQLLATLNRLRTG

2k4fA

0.50

0.28

0.56

0.64

wPPAS

---CRRGTGAGS------RPRGQN----KERPPPV-P-NPDYEPIRKGDLYSGLN-QRA-V-----------------

2n64A

0.15

0.10

0.67

0.63

dPPAS2

--------------------------GHMEGKPKMEPAASSQAATQVRELRSIIETMKDQQKREIKQLLSELDEEKKI

2n73B

0.19

0.18

0.94

0.70

PPAS

MVEARSLAAMGDTVVAPLKPTSEPTSGPPGGGSLLSVITEGVGELSVID----PEVAQKACQEVLEKVKLLHGGVAV-

3hrlA

0.20

0.18

0.91

0.85

Env-PPAS

HLRAGRLNGYK---FRRQQPGYIVDCVTPKLIVEADG-VYDH--ARTVYLNSLNHEILQQTNDVLAEILRVLQELEK-

4b6xA

0.21

0.18

0.85

0.72

MUSTER

------GAGAARQEIEDKQLMVNNLTDELQDA------IDEANPAEIANTSQQLRHARADLADLQRRFAVLRNEDRRI

3zifN

0.10

1.00

0.68

dPPAS

NMLGGVVLPPNSQAHRTETVGTEATRDNLHAEGARRPEDQTPYMILVEDSLGGLKRRMDLLEESNQQLLATLNRLRTG

(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=-3.23

Estimated TM-score = 0.35±0.12

Estimated RMSD = 10.5±4.6Å

Download Model 2

C-score=-3.78

Download Model 3

C-score=-3.79

Download Model 4

C-score=-3.88

Download Model 5

C-score=-4.62

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	1uazA	0.564	2.64	0.068	0.795
2	1h2sA	0.563	2.53	0.094	0.782
3	5b2nA	0.555	3.10	0.071	0.821
4	3am6A	0.553	3.12	0.090	0.808
5	3a7kA	0.553	2.86	0.065	0.795
6	3wt8A	0.549	3.02	0.074	0.795
7	4ryaA2	0.539	3.41	0.097	0.808
8	4fopA	0.538	3.29	0.045	0.833
9	1ukxA	0.534	2.53	0.045	0.756
10	3gvdI	0.533	3.37	0.027	0.859

(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	0.10	6	3a68A	CA	Rep, Mult	74,77
2	0.07	4	2zfeA	XE	Rep, Mult	53,54,57,64,67,68
3	0.07	4	4zzcA	XE	Rep, Mult	68,71,72
4	0.05	3	1vd5A	GLY	Rep, Mult	50,68
5	0.05	3	2ql2A	NUC	Rep, Mult	62,63,66
6	0.03	2	1ordA	PLP	Rep, Mult	31,39,40
7	0.03	2	4l6vk	CLA	Rep, Mult	65,69
8	0.02	1	2xkpA	AKG	Rep, Mult	71,74
9	0.02	1	1cc1L	SF4	Rep, Mult	18,23
10	0.02	1	4ijxA	MG	Rep, Mult	60,63
11	0.02	1	3qbiD	22B	Rep, Mult	53,63,67,70,74
12	0.02	1	1u10A	ZN	Rep, Mult	55,58
13	0.02	1	4h3yB	SAH	Rep, Mult	25,26
14	0.02	1	3tqxB	PLP	Rep, Mult	40,41
15	0.02	1	2h9dD	CA	Rep, Mult	52,55

	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	1mc0A	0.342	4.42	0.041	0.641	3.1.4.17	NA
2	0.060	3fslA	0.499	3.14	0.054	0.744	2.6.1.57	NA
3	0.060	1yaaA	0.516	3.28	0.079	0.782	2.6.1.1	NA
4	0.060	1ajsA	0.510	3.39	0.105	0.795	2.6.1.1	NA
5	0.060	1l1lA	0.500	3.09	0.091	0.731	1.17.4.2	NA
6	0.060	1fohC	0.488	3.47	0.052	0.821	1.14.13.7	NA
7	0.060	1i29A	0.491	3.66	0.066	0.795	4.4.1.16	NA
8	0.060	1aatA	0.496	3.36	0.092	0.795	2.6.1.1	NA
9	0.060	1u7uA	0.386	3.67	0.043	0.667	6.3.2.5	NA
10	0.060	3c4qA	0.518	3.81	0.123	0.846	2.4.1.14	15,26
11	0.060	7aatA	0.510	3.37	0.053	0.782	2.6.1.1	NA
12	0.060	2gsaA	0.493	3.63	0.095	0.769	5.4.3.8	NA
13	0.060	3tatC	0.476	3.26	0.054	0.744	2.6.1.57	51
14	0.060	1txoB	0.502	3.50	0.098	0.756	3.1.3.16	17
15	0.060	2fknB	0.494	4.12	0.118	0.846	4.2.1.49	41,43
16	0.060	1iduA	0.501	3.36	0.039	0.821	1.11.1.10	NA
17	0.060	1t3iA	0.493	3.77	0.078	0.808	2.8.1.7	NA
18	0.060	1ay4A	0.506	3.24	0.107	0.756	2.6.1.57	NA
19	0.060	1dodA	0.499	4.10	0.110	0.897	1.14.13.2	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	0.15	0.420	3.53	0.12	0.65	3qbgA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
1	0.11	0.400	2.60	0.03	0.53	1cwqA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
2	0.10	0.387	4.63	0.01	0.77	2o1oA	GO:0008299 GO:0016740
3	0.07	0.428	3.15	0.05	0.67	4qi1A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
4	0.07	0.369	3.54	0.02	0.62	4yziA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220 GO:0046872
5	0.07	0.432	3.78	0.01	0.77	2l6xA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
6	0.07	0.553	3.12	0.09	0.81	3am6A	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
7	0.07	0.475	3.29	0.07	0.79	1brdA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
8	0.07	0.455	3.19	0.07	0.76	4klyB	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
9	0.07	0.549	3.02	0.07	0.79	5awzA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
10	0.07	0.404	2.51	0.04	0.53	4fbzA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
11	0.06	0.394	2.64	0.01	0.53	1c8sA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
12	0.06	0.465	3.64	0.01	0.77	4l35A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
13	0.06	0.425	3.47	0.07	0.69	5azdA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
14	0.06	0.347	3.39	0.10	0.60	5ahzA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
15	0.06	0.515	2.85	0.09	0.76	3ddlA	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
16	0.06	0.564	2.48	0.08	0.78	2ksyA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
17	0.06	0.390	3.92	0.02	0.69	4jq6B	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
18	0.06	0.564	2.64	0.07	0.79	1uazA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896

Consensus prediction of GO terms

Molecular Function	GO:0038023	GO:0005216
GO-Score	0.59	0.34
Biological Processes	GO:0006464	GO:0007165	GO:0009583	GO:0015672	GO:0006818	GO:0034220
GO-Score	0.59	0.59	0.59	0.35	0.35	0.34
Cellular Component	GO:0071944	GO:0016021
GO-Score	0.59	0.34

(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 Rv2237A

[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]