I-TASSER results

Input Sequence in FASTA format

>protein (97 residues)
MGIQRAVLLIADIGGYTNYMHWNRKHLAHAQWTVAQLLESVIDAAKGMKLAKLEGDAAFF
WAPGGQHQCPGMRPAPADAPEVPHAARADQKRPSLRL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGIQRAVLLIADIGGYTNYMHWNRKHLAHAQWTVAQLLESVIDAAKGMKLAKLEGDAAFFWAPGGQHQCPGMRPAPADAPEVPHAARADQKRPSLRL
Prediction	CCCCCEEEEEHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCEEEEHCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	9976579998578756788887667478899999999999999789976888758789999758998765789999999999999999987887589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGIQRAVLLIADIGGYTNYMHWNRKHLAHAQWTVAQLLESVIDAAKGMKLAKLEGDAAFFWAPGGQHQCPGMRPAPADAPEVPHAARADQKRPSLRL
Prediction	8743411000013121042145353515204411440042016305715235142210001134565625424522441430242045445554267
	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

CCCCCEEEEEHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCEEEEHCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MGIQRAVLLIADIGGYTNYMHWNRKHLAHAQWTVAQLLESVIDAAKGMKLAKLEGDAAFFWAPGGQHQCPGMRPAPADAPEVPHAARADQKRPSLRL

1y11A

0.22

0.20

0.91

1.00

wMUSTER

PGARQVTVAFADLVGFTQLGEVVSEELGHLAGRLAGLARDLTA--PPVWFIKTIGDAVMLVCPD-------PAPLLDTVLKLVEVVDTDNNFPRLRA

3htuD

0.19

0.06

0.33

1.10

dPPAS2

-----------------------------------------------------------------GSRVTEQDKAILQLKQQRDKLRQYQKRIAQQL

1wc4A

0.21

0.99

1.00

wMUSTER

MRPEPITILFSDIVGFTRMSNALQQGVAELLNEYLGEMTRAVFENQG-TVDKFVGDMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERG

1fx2A

0.11

0.99

1.07

dPPAS2

EPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRY-KCYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNALDDSYREFE

2w01A

0.17

0.16

0.98

1.05

dPPAS2

MGRRPITILTSDLRGFTSTSEG--LNPEEVVKVLNIYFGKMADVITGGTIDEFMGDGILVLFGAPTSQQDDALRAVACGVEMQLALREVNQQVTGLG

2n77B

0.06

0.02

0.34

1.04

dPPAS2

--------------------------------------------------------------FDIDMDAPETERAAVAIQSQFRKFQKKKAGSQS--

1y11A2

0.19

0.18

0.91

0.86

MUSTER

PGARQVTVAFADLVGFTQLGE--VVSAEELGHLAGRLAGLARDLTAPVWFIKTIGDAVMLVCPD-------PAPLLDTVLKLVEVVDTDNNFPRLRA

2zqkM

0.11

0.07

0.64

0.71

dPPAS

---------------------------SATETATRDQLTKEAFQNPDNQKVNIDGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN--------

2ou1K

0.16

0.11

0.71

0.73

wdPPAS

--------------------------EPCVESLVSQYFQTVTDYGKDLKSPELQAEAKSYFEKSKEQLTPLIKKAGTELVNFLSYFVELGTQPAT--

1y11A2

0.22

0.20

0.89

0.95

wMUSTER

PGARQVTVAFADLVGFTQLGE--VVSLGHLAGRLAGLARDLTA--PPVWFIKTIGDAVMLVCPD-------PAPLLDTVLKLVEVVDTDNNFPRLRA

(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=-0.88

Estimated TM-score = 0.60±0.14

Estimated RMSD = 5.7±3.6Å

Download Model 2

C-score=-3.08

Download Model 3

C-score=-4.30

Download Model 4

C-score=-0.83

Download Model 5

C-score=-1.52

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	3r5gA	0.883	1.35	0.104	0.990
2	1wc4A	0.869	1.48	0.177	0.990
3	2w01A	0.838	1.60	0.170	0.969
4	1culA	0.821	1.70	0.117	0.949
5	1culB	0.805	1.96	0.103	0.969
6	2wz1A	0.794	1.89	0.097	0.949
7	3uvjA	0.789	1.87	0.098	0.938
8	5m27A2	0.784	1.91	0.088	0.938
9	4yusA2	0.781	2.03	0.088	0.938
10	3et6A	0.773	1.94	0.151	0.938

(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	0.65	105	1wc0B	APC	Rep, Mult	12,13,14,15,16,17,54,55,56
2	0.08	13	1culA	103	Rep, Mult	17,54,55,56
3	0.01	2	2gvdA	128	Rep, Mult	13,15,16,24,27,28,31,55,56
4	0.00	1	3qzcB	ZN	Rep, Mult	39,43

	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	0.119	1mwyA	0.490	2.45	0.099	0.639	3.6.3.3,3.6.3.5	35,53
2	0.073	1kviA	0.496	2.63	0.093	0.691	3.6.3.4	52
3	0.069	1ulrA	0.500	2.84	0.071	0.660	3.6.1.7	NA
4	0.066	2ebbA	0.546	2.76	0.026	0.763	4.2.1.96	NA
5	0.060	1yk9A	0.697	2.53	0.176	0.938	4.6.1.1	NA
6	0.060	2i4nB	0.628	2.85	0.032	0.835	6.1.1.15	NA
7	0.060	3eoqB	0.610	3.14	0.115	0.866	3.4.24.56	NA
8	0.060	1t3nA	0.609	2.88	0.138	0.835	2.7.7.7	20
9	0.060	2wz1A	0.794	1.89	0.097	0.949	4.6.1.2	NA
10	0.060	1yuyA	0.619	2.81	0.085	0.856	2.7.7.48	NA
11	0.060	1azsA	0.816	1.73	0.117	0.949	4.6.1.1	NA
12	0.060	3ikmD	0.672	2.70	0.065	0.938	2.7.7.7	NA
13	0.060	1mu2A	0.626	2.95	0.132	0.856	3.4.23.47	NA
14	0.060	1sq1A	0.615	3.09	0.093	0.866	4.2.3.5	40
15	0.060	2j3lB	0.622	3.18	0.010	0.845	6.1.1.15	NA
16	0.060	2hvtB	0.529	3.18	0.065	0.783	2.7.7.49	NA
17	0.060	1htoA	0.612	3.21	0.042	0.887	6.3.1.2	NA
18	0.060	1fx2A	0.734	2.14	0.161	0.887	4.6.1.1	NA
19	0.060	1umfC	0.567	3.33	0.056	0.866	4.2.3.5	78
20	0.060	1l3sA	0.618	2.92	0.102	0.887	2.7.7.7	NA
21	0.060	1y11A	0.730	1.81	0.172	0.866	4.6.1.1	NA
22	0.060	1wnlA	0.600	3.12	0.075	0.887	6.3.4.15	NA
23	0.060	1d8yA	0.622	3.05	0.101	0.887	2.7.7.7	17

(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	0.47	0.869	1.48	0.18	0.99	1wc4A	GO:0000155 GO:0000160 GO:0004016 GO:0005622 GO:0006171 GO:0007165 GO:0009190 GO:0016310 GO:0016772 GO:0016829 GO:0016849 GO:0018298 GO:0023014 GO:0035556 GO:0046872
1	0.47	0.816	1.73	0.12	0.95	1azsA	GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0005929 GO:0006171 GO:0007189 GO:0007193 GO:0007204 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0019933 GO:0035556 GO:0042995 GO:0046872 GO:0061178 GO:0072372 GO:1904322
2	0.38	0.884	1.34	0.10	0.99	3r5gB	GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0009405 GO:0016020 GO:0016021 GO:0016849 GO:0035556
3	0.35	0.743	1.66	0.12	0.85	1ybtB	GO:0004016 GO:0004383 GO:0004601 GO:0005622 GO:0006171 GO:0006182 GO:0009190 GO:0016787 GO:0016849 GO:0030145 GO:0035556 GO:0042803 GO:0046872 GO:0098869
4	0.33	0.798	1.93	0.09	0.96	1cjkB	GO:0000166 GO:0000287 GO:0004016 GO:0005524 GO:0005622 GO:0005737 GO:0005886 GO:0005887 GO:0006171 GO:0007188 GO:0007189 GO:0007193 GO:0008179 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0019933 GO:0030145 GO:0030425 GO:0031683 GO:0035556 GO:0043234 GO:0045121 GO:0046872 GO:0046982 GO:1904322
5	0.29	0.740	2.18	0.17	0.90	1fx4A	GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0006171 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0035556 GO:0046872
6	0.22	0.734	2.14	0.16	0.89	1fx2A	GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0006171 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0035556 GO:0046872
7	0.20	0.838	1.60	0.17	0.97	2w01A	GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016849 GO:0035556
8	0.15	0.767	1.89	0.17	0.93	4p2fA	GO:0000166 GO:0000287 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0030145 GO:0035556 GO:0046872
9	0.14	0.773	1.94	0.15	0.94	3et6A	GO:0000166 GO:0004016 GO:0004383 GO:0005886 GO:0006182 GO:0007165 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556
10	0.14	0.788	2.15	0.10	0.96	4ni2B	GO:0000166 GO:0004016 GO:0004383 GO:0004872 GO:0005525 GO:0005737 GO:0005886 GO:0006182 GO:0007263 GO:0008015 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556 GO:0038060 GO:0043231 GO:0046872 GO:0071732
11	0.14	0.730	2.05	0.17	0.88	4wp3C	GO:0004016 GO:0005622 GO:0006171 GO:0009190 GO:0016829 GO:0016849 GO:0035556
12	0.13	0.777	1.88	0.10	0.93	4ni2A	GO:0000166 GO:0004016 GO:0004383 GO:0004872 GO:0005525 GO:0005737 GO:0005886 GO:0006182 GO:0007263 GO:0008015 GO:0008074 GO:0008217 GO:0009190 GO:0009635 GO:0014070 GO:0016829 GO:0016849 GO:0020037 GO:0030828 GO:0035556 GO:0043167 GO:0043234 GO:0046982 GO:0052565 GO:0060087
13	0.13	0.770	2.08	0.09	0.94	4yutA	GO:0005622 GO:0009190 GO:0009785 GO:0009882 GO:0016849 GO:0035556 GO:0071949
14	0.12	0.742	2.32	0.14	0.93	4oyzA	GO:0000166 GO:0000287 GO:0003351 GO:0004016 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005856 GO:0005886 GO:0005929 GO:0006171 GO:0007283 GO:0009190 GO:0015630 GO:0016020 GO:0016829 GO:0016849 GO:0030145 GO:0030424 GO:0030425 GO:0030426 GO:0031514 GO:0035556 GO:0042995 GO:0043025 GO:0043065 GO:0045177 GO:0045178 GO:0046872 GO:0048471 GO:0051117 GO:0071241 GO:0071890
15	0.09	0.656	2.88	0.21	0.90	3mr7A	GO:0005622 GO:0009190 GO:0016787 GO:0016849 GO:0035556
16	0.06	0.365	4.24	0.06	0.64	2chhA	GO:0030246 GO:0046872
17	0.06	0.353	4.46	0.07	0.66	4jejA	GO:0000287 GO:0005737 GO:0006650 GO:0016765 GO:0047294
18	0.06	0.343	4.61	0.04	0.63	4b4dA	GO:0000166 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0004016	GO:0005524	GO:0030145	GO:0000155	GO:0042803	GO:0004601	GO:0004383	GO:0016787	GO:0046982	GO:0031683	GO:0000287	GO:0008179
GO-Score	0.92	0.64	0.57	0.47	0.35	0.35	0.35	0.35	0.33	0.33	0.33	0.33
Biological Processes	GO:0006171	GO:0007189	GO:0019933	GO:0007193	GO:1904322	GO:0018298	GO:0023014	GO:0000160	GO:0007204	GO:0061178	GO:0009405	GO:0006182	GO:0098869
GO-Score	0.92	0.64	0.64	0.64	0.64	0.47	0.47	0.47	0.47	0.47	0.38	0.35	0.35
Cellular Component	GO:0072372	GO:0043234	GO:0005887	GO:0005737	GO:0030425	GO:0045121
GO-Score	0.47	0.33	0.33	0.33	0.33	0.33

(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 Rv2561

[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]