I-TASSER results

Input Sequence in FASTA format

>protein (53 residues)
MTQPTAWEYATVPLLTHATKQILDQWGADGWELVAVLPGPTGEQHVAYLKRPK

Predicted Secondary Structure

Sequence	20 40 \| \| MTQPTAWEYATVPLLTHATKQILDQWGADGWELVAVLPGPTGEQHVAYLKRPK
Prediction	CCCCCEEEEEEEEEHHHHHHHHHHHHHHHCEEEEEEEHCCCCCCEEEEEHCCC
Conf.Score	99876489987644456789999997655658999975899996899998689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MTQPTAWEYATVPLLTHATKQILDQWGADGWELVAVLPGPTGEQHVAYLKRPK
Prediction	86544534223122334334421553364223113114245473212204458
	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

                   |                   |

Sec.Str
Seq

CCCCCEEEEEEEEEHHHHHHHHHHHHHHHCEEEEEEEHCCCCCCEEEEEHCCC
MTQPTAWEYATVPLLTHATKQILDQWGADGWELVAVLPGPTGEQHVAYLKRPK

3hmjA4

0.20

0.17

0.83

1.02

MUSTER

EEDLEPFEAS-----KETAEQFKHQHGDK----VDIFEIPETGEYSVKLLKPK

2m2jA

0.11

1.00

1.06

dPPAS

AAALKPYDRIVITGAVSAVSRRADEEGAASFYVVDTSEFGNSGNWRVVADVYK

3hmjA4

0.20

0.17

0.83

0.88

wdPPAS

EEDLEPFEAS-----KETAEQFKHQHGDK----VDIFEIPETGEYSVKLLKPK

3hmjA4

0.20

0.17

0.83

1.07

wMUSTER

EEDLEPFEAS-----KETAEQFKHQHGDK----VDIFEIPETGEYSVKLLKPK

3hinA2

0.23

0.19

0.81

0.89

wPPAS

-APLTNF-------VLQALPMIAEANPQTG-ELMTVASDQE-TRIRAFLHKAK

1wplK

0.17

0.15

0.87

1.47

dPPAS2

VLGNNFYEYYVN----DPPRIVLDKLECRGFRVLSMTG--VGQTLVWCLHKE-

2l66A

0.27

0.23

0.85

0.90

PPAS

IVKVSR-NYVTIP------AKVRQKFQKEG-DLVKVTFESEGVVKIQLLKEPK

3i57A1

0.17

1.00

1.06

Env-PPAS

IDGETDQMLRQDDLDPYSTAEGIKKFEGDGYELFKDFPATNDQFYTVIFKHHR

3v8hA1

0.18

0.13

0.74

0.95

MUSTER

-PG-----YKVLDA---HADAQIADATSRGFRIVARFE--GGADKVLLHK---

1wplK

0.17

0.15

0.87

1.01

dPPAS

VLGNNFYEYYVN----DPPRIVLDKLECRGFRVLSMTG--VGQTLVWCLHKE-

(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=-1.38

Estimated TM-score = 0.54±0.15

Estimated RMSD = 5.4±3.5Å

Download Model 2

C-score=-3.04

Download Model 3

C-score=-3.58

Download Model 4

C-score=-2.57

Download Model 5

C-score=-4.24

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	3bh7B	0.676	2.53	0.113	1.000
2	1lwtA	0.650	2.63	0.098	0.924
3	5heiA	0.645	2.50	0.077	0.943
4	3r2cJ	0.645	2.38	0.188	0.906
5	5j6cA	0.643	2.73	0.115	0.962
6	1zchA	0.642	2.53	0.077	0.943
7	3eofA	0.637	2.73	0.059	0.943
8	1yj7D1	0.633	2.13	0.067	0.849
9	1m5sA	0.632	2.46	0.057	1.000
10	1uwkA1	0.632	2.08	0.078	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	0.20	16	4jwsA	CA	Rep, Mult	20,24
2	0.12	10	1e7gA	MYR	Rep, Mult	17,18,20,21
3	0.04	3	3j7yf	NUC	Rep, Mult	20,23,27,36,45
4	0.03	3	2dclB	AMP	Rep, Mult	9,37,47
5	0.03	3	3eofA	FMN	Rep, Mult	31,32,33
6	0.02	2	3zk1R	DMU	Rep, Mult	14,22
7	0.02	2	1f0yB	CAA	Rep, Mult	27,28
8	0.01	1	1hx6B	MPD	Rep, Mult	9,20
9	0.01	1	2fhjC	MFN	Rep, Mult	34,36,37,48
10	0.01	1	3pmzI	MG	Rep, Mult	8,43
11	0.01	1	5l3rC	MG	Rep, Mult	16,43
12	0.01	1	1e9gA	MN	Rep, Mult	9,29

	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	2fknB	0.629	1.99	0.098	0.906	4.2.1.49	23
2	0.060	1ej6A	0.576	2.42	0.020	0.962	2.7.7.50	15
3	0.060	1yzhB	0.593	2.30	0.100	0.849	2.1.1.33	NA
4	0.060	1g60A	0.619	2.44	0.077	0.887	2.1.1.72	NA
5	0.060	3e05D	0.598	2.00	0.039	0.849	2.1.1.132	NA
6	0.060	1jmsA	0.584	2.98	0.094	1.000	2.7.7.31	NA
7	0.060	3ckkA	0.585	2.85	0.132	0.868	2.1.1.33	NA
8	0.060	2fcaA	0.590	2.38	0.113	0.887	2.1.1.33	13
9	0.060	2cw7A	0.619	2.27	0.078	0.868	2.7.7.7	NA
10	0.060	1m5sD	0.629	2.54	0.057	1.000	2.3.1.101	12
11	0.060	3ic1A	0.568	2.05	0.082	0.717	3.5.1.18	NA
12	0.060	1ftrD	0.605	2.62	0.038	1.000	2.3.1.101	12
13	0.060	1jvaB	0.652	2.10	0.096	0.906	3.6.3.14,3.6.1.34	NA
14	0.060	2d3kA	0.585	3.03	0.075	1.000	3.1.1.29	NA
15	0.060	3dnyT	0.523	2.42	0.102	0.811	3.6.5.3	NA
16	0.060	1ef0B	0.605	2.34	0.085	0.830	3.1.-.-	NA
17	0.060	1b9hA	0.570	3.05	0.132	1.000	4.2.1.-	NA
18	0.060	2yxdA	0.596	1.89	0.080	0.830	2.1.1.-	20
19	0.060	2pwyA	0.615	2.15	0.135	0.887	2.1.1.36	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	0.09	0.520	2.95	0.14	0.92	1wkjA	GO:0000166 GO:0004550 GO:0005524 GO:0005737 GO:0006165 GO:0006183 GO:0006228 GO:0006241 GO:0009117 GO:0016301 GO:0016310 GO:0016740 GO:0046872
1	0.09	0.619	2.27	0.08	0.87	2cw7A	GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004519 GO:0006260 GO:0006314 GO:0008408 GO:0016539 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
2	0.08	0.668	2.38	0.12	0.98	3bh6B	GO:0000166 GO:0000902 GO:0003779 GO:0005096 GO:0005525 GO:0005737 GO:0005794 GO:0005814 GO:0005886 GO:0005929 GO:0006457 GO:0006810 GO:0006892 GO:0007010 GO:0007023 GO:0007601 GO:0015031 GO:0016020 GO:0031410 GO:0036064 GO:0042995 GO:0043547 GO:0051082 GO:0070062 GO:0072372 GO:1990075
3	0.08	0.652	2.10	0.10	0.91	1jvaB	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
4	0.08	0.663	2.61	0.10	0.94	1lwtA	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
5	0.07	0.536	2.78	0.18	0.89	3ztoA	GO:0000166 GO:0004550 GO:0005524 GO:0005622 GO:0005737 GO:0006163 GO:0006165 GO:0006183 GO:0006220 GO:0006228 GO:0006241 GO:0009117 GO:0009142 GO:0016301 GO:0016310 GO:0016740 GO:0046872
6	0.07	0.637	2.06	0.10	0.91	1dfaA	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
7	0.07	0.605	2.34	0.09	0.83	1ef0B	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
8	0.07	0.525	2.82	0.12	0.92	2vu5A	GO:0000166 GO:0004550 GO:0005524 GO:0005737 GO:0006165 GO:0006183 GO:0006228 GO:0006241 GO:0009117 GO:0016301 GO:0016310 GO:0016740 GO:0046872
9	0.07	0.532	2.81	0.12	0.92	4c6aA	GO:0000166 GO:0004550 GO:0005524 GO:0005737 GO:0005840 GO:0005856 GO:0005886 GO:0006165 GO:0006183 GO:0006186 GO:0006187 GO:0006220 GO:0006228 GO:0006241 GO:0006414 GO:0007186 GO:0009117 GO:0009142 GO:0009617 GO:0015629 GO:0016049 GO:0016301 GO:0016310 GO:0016740 GO:0030036 GO:0030141 GO:0045335 GO:0045920 GO:0046872 GO:0048550 GO:0050765
10	0.07	0.530	2.85	0.12	0.94	4uofA	GO:0000166 GO:0004550 GO:0005524 GO:0006165 GO:0006183 GO:0006228 GO:0006241 GO:0016301 GO:0016310 GO:0016740
11	0.07	0.514	2.98	0.16	0.92	3pj9D	GO:0000166 GO:0004550 GO:0005524 GO:0005737 GO:0006165 GO:0006183 GO:0006228 GO:0006241 GO:0009117 GO:0016301 GO:0016310 GO:0016740 GO:0046872
12	0.07	0.465	2.98	0.13	0.75	3iclA
13	0.06	0.379	2.71	0.08	0.70	4ldbC	GO:0003723 GO:0016020 GO:0016032 GO:0019012 GO:0019076 GO:0020002 GO:0033644 GO:0033645 GO:0039660 GO:0039702 GO:0044174 GO:0044185 GO:0044385 GO:0044414 GO:0045121 GO:0046755 GO:0046761 GO:0055036 GO:0075733
14	0.06	0.379	3.07	0.08	0.64	3u5mE	GO:0000122 GO:0003677 GO:0004842 GO:0005622 GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0008270 GO:0016567 GO:0016874 GO:0017015 GO:0030514 GO:0043231 GO:0045892 GO:0046872 GO:0070410 GO:0070412
15	0.06	0.377	2.98	0.08	0.70	3bepA	GO:0003677 GO:0003887 GO:0005737 GO:0005829 GO:0006260 GO:0006271 GO:0006974 GO:0008408 GO:0009360 GO:0016740 GO:0016779 GO:0042802 GO:0071897 GO:0090305
16	0.06	0.520	2.84	0.10	0.92	1w7wA	GO:0000166 GO:0004550 GO:0005524 GO:0006165 GO:0006183 GO:0006228 GO:0006241 GO:0016301 GO:0016310 GO:0016740
17	0.06	0.487	3.90	0.04	0.91	1f89A	GO:0006807 GO:0016787 GO:0016810
18	0.06	0.518	2.79	0.12	0.91	3bbbA	GO:0000166 GO:0001726 GO:0003677 GO:0003700 GO:0004550 GO:0004673 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005925 GO:0006163 GO:0006165 GO:0006183 GO:0006220 GO:0006228 GO:0006241 GO:0006351 GO:0006355 GO:0007155 GO:0007229 GO:0009117 GO:0009142 GO:0015949 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0030027 GO:0042995 GO:0043066 GO:0045618 GO:0045682 GO:0045944 GO:0046872 GO:0050679 GO:0070062 GO:0071944 GO:0098779

Consensus prediction of GO terms

Molecular Function	GO:0032559	GO:0032550	GO:0035639	GO:0004518	GO:0003676
GO-Score	0.46	0.46	0.46	0.44	0.44
Biological Processes	GO:0030908	GO:0006310	GO:0051234
GO-Score	0.44	0.44	0.44
Cellular Component	GO:0044424
GO-Score	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 Rv3678A

[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]