I-TASSER results

Input Sequence in FASTA format

>protein (85 residues)
MIGYVAVLGLGYVLGAKAGRRRYEQIASTYRALTGSPVARSMIEGGRRKIANRISPDAGF
VTLAEIDNQTAVVQRGVERQPKTAR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MIGYVAVLGLGYVLGAKAGRRRYEQIASTYRALTGSPVARSMIEGGRRKIANRISPDAGFVTLAEIDNQTAVVQRGVERQPKTAR
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCEEEHCCCCCCCCCCCC
Conf.Score	9468999999998766775899999999999999797899999999999997467776757877746765675578888765689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MIGYVAVLGLGYVLGAKAGRRRYEQIASTYRALTGSPVARSMIEGGRRKIANRISPDAGFVTLAEIDNQTAVVQRGVERQPKTAR
Prediction	6332133333121111423462154036205413744314531640354246414765534514516653534456466456648
	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

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCEEEHCCCCCCCCCCCC
MIGYVAVLGLGYVLGAKAGRRRYEQIASTYRALTGSPVARSMIEGGRRKIANRISPDAGFVTLAEIDNQTAVVQRGVERQPKTAR

2ptfA2

0.14

0.08

0.60

1.19

dPPAS2

GIYAVIESLIAYTRAPLVLRERIAEMNRVARKVG-GPREKEAMRRIIQALES---------------------------------

4ynhA

0.12

0.08

0.68

1.11

dPPAS2

--PLGSKIASAREVIKRDGVIPPEALTIIEQRLRSDPMFRQQIDNVLADAECDANRAAYS-------------------------

4tqlA2

0.11

0.09

0.89

0.91

MUSTER

-------MKKLYDEAKKKIEQMIQQIKQGGDKQKM-EELLKRAKEEMKKVKDKMEKAKQVAE-ELIKKILQLIEKAKEIAEKVLK

4ynhA

0.12

0.08

0.68

0.81

dPPAS

--PLGSKIASAREVIKRDGVIPPEALTIIEQRLRSDPMFRQQIDNVLADAECDANRAAYS-------------------------

2ptfA2

0.14

0.08

0.59

0.88

wdPPAS

GIYAVIESLIAYTRAPLVLRERIAEMNRVARKV--GPREKEAMRRIIQALES---------------------------------

2lseA

0.15

0.99

0.93

wMUSTER

LLEKLEKILDEVTDGA-EARERIEKLAKDVKDELEEGDAKNMIEKFRDEMEQMYKDAPNAVMEQLLEEIEKLLKKAGSLVPRGSY

5m1hA2

0.13

0.12

0.91

0.89

wPPAS

IIVDQEGVATAYTLGMMLSGQNYQLVSGIIRGY---P--QAVVTALQQRLDQEIDDQTRAETIQHLNAVYEILG---NARGQSIR

3zf7T3

0.17

0.08

0.48

1.10

dPPAS2

----------------AAKRLKDEQNRRKARKQELKKREKERERARRDDAAAAAAAK----------------------------

2ptfA2

0.14

0.08

0.59

0.91

PPAS

GIYAVIESLIAYTRAPLVLRERIAEMNRVARKV--GPREKEAMRRIIQALES---------------------------------

1zpwX

0.15

0.13

0.88

0.86

Env-PPAS

RLYAVA-----YIPDDTRRVKLANLLKSYGERVQLSYLDERLLEDLRRRARRLLDLGQDALRIYPVAGQVEVLGVGPLPE-----

(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=-2.02

Estimated TM-score = 0.47±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-3.13

Download Model 3

C-score=-4.14

Download Model 4

C-score=-3.59

Download Model 5

C-score=-2.26

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	3dbyT	0.661	2.85	0.012	1.000
2	1tt9A	0.655	2.80	0.083	0.977
3	1o5hA	0.648	2.89	0.136	0.953
4	1rj1A	0.646	2.74	0.075	0.941
5	2lseA	0.646	2.74	0.099	0.941
6	2jqqA	0.645	2.60	0.062	0.953
7	3ddlA	0.643	2.50	0.061	0.894
8	1tdpA	0.642	2.80	0.120	0.977
9	1e0pA	0.640	2.73	0.036	0.929
10	4hyjA	0.638	2.38	0.099	0.894

(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	0.13	7	1brrC	ARC	Rep, Mult	6,11,23,24,27,28
2	0.07	4	1jv6A	LI1	Rep, Mult	5,7,8,22,23,26,30
3	0.07	4	2bkpA	K	Rep, Mult	13,14,16,17
4	0.04	2	1vd5A	GLY	Rep, Mult	26,43
5	0.04	2	1o0aA	LI1	Rep, Mult	17,18,21,22,24,25
6	0.04	2	2i21A	LI1	Rep, Mult	19,22,25,26,29
7	0.04	2	2i1xA	LI1	Rep, Mult	2,5,6,10
8	0.02	1	1m0mA	LI1	Rep, Mult	47,66,70,73,74,77
9	0.02	1	1o0aA	LI1	Rep, Mult	1,2,9,23,27
10	0.02	1	2h8pC	GOA	Rep, Mult	11,12
11	0.02	1	1jv6A	LI1	Rep, Mult	25,28,29,32,33

	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	2wpnB	0.560	3.56	0.071	0.918	1.12.7.2	11
2	0.060	2q8gA	0.575	3.47	0.071	0.953	2.7.11.2	NA
3	0.060	3e6sF	0.575	3.43	0.085	0.871	1.16.3.1	13,14
4	0.060	1jswB	0.553	3.67	0.096	0.918	4.3.1.1	NA
5	0.060	1r03A	0.593	3.33	0.037	0.871	1.16.3.1	NA
6	0.060	2pfdB	0.654	2.82	0.083	0.977	2.1.2.5,4.3.1.4	NA
7	0.060	1yqwR	0.556	3.69	0.071	0.929	1.12.2.1	NA
8	0.060	2pnrF	0.579	3.46	0.012	0.929	2.7.11.2	54,67
9	0.060	2e9fB	0.573	3.76	0.060	0.894	4.3.2.1	NA
10	0.060	1jkuA	0.582	3.72	0.060	0.906	1.11.1.6	NA
11	0.060	1frvB	0.551	3.14	0.062	0.894	1.12.2.1	NA
12	0.060	3gtdA	0.559	3.68	0.094	0.906	4.2.1.2	NA
13	0.060	3es3A	0.581	3.43	0.037	0.871	1.16.3.1	NA
14	0.060	1knpA	0.558	2.98	0.036	0.835	1.4.3.16	NA
15	0.060	3iam4	0.562	3.42	0.143	0.918	1.6.99.5	61
16	0.060	2v8tA	0.564	3.27	0.049	0.906	1.11.1.6	76
17	0.060	1chuA	0.541	3.29	0.086	0.835	1.4.3.16	NA
18	0.060	1krqA	0.556	3.51	0.024	0.847	1.16.3.1	28
19	0.060	1sk6C	0.588	3.65	0.085	0.929	4.6.1.1	30

(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	0.10	0.646	2.74	0.07	0.94	1rj1A	GO:0004857 GO:0043086
1	0.09	0.630	2.97	0.14	0.95	3d19A	GO:0046872
2	0.07	0.670	2.65	0.11	0.99	2pfdA	GO:0000139 GO:0003824 GO:0005542 GO:0005737 GO:0005783 GO:0005793 GO:0005794 GO:0005814 GO:0005829 GO:0005856 GO:0006547 GO:0007010 GO:0008017 GO:0008152 GO:0016740 GO:0016829 GO:0019215 GO:0019556 GO:0019557 GO:0030407 GO:0030409 GO:0030412 GO:0030868 GO:0035999 GO:0044237 GO:0070062
3	0.07	0.645	2.60	0.06	0.95	2jqqA	GO:0000139 GO:0000301 GO:0005794 GO:0006810 GO:0006888 GO:0006891 GO:0015031 GO:0016020 GO:0016236 GO:0017119 GO:0019898 GO:0030242 GO:0032258
4	0.07	0.603	2.95	0.04	0.93	5azdA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
5	0.07	0.585	3.23	0.02	0.92	4yziA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220 GO:0046872
6	0.07	0.635	2.84	0.03	0.93	1xg2B	GO:0004857 GO:0005737 GO:0043086
7	0.07	0.646	2.99	0.04	0.93	1o5hA	GO:0003824 GO:0016829 GO:0030412 GO:0044237
8	0.07	0.660	2.86	0.01	1.00	3dbyC	GO:0046872
9	0.07	0.634	3.05	0.06	0.94	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
10	0.07	0.527	2.96	0.01	0.78	4xdnA	GO:0000790 GO:0005634 GO:0006302 GO:0007049 GO:0007059 GO:0007064 GO:0007067 GO:0007076 GO:0032116 GO:0051301 GO:0070550 GO:0071169
11	0.07	0.469	4.25	0.06	0.81	1colA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
12	0.07	0.595	2.97	0.05	0.92	4jq6B	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
13	0.07	0.503	4.24	0.05	0.89	4ojzA	GO:0000272 GO:0005975 GO:0016829 GO:0042597 GO:0046872
14	0.07	0.463	4.14	0.05	0.80	4ln1B	GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
15	0.07	0.489	3.73	0.10	0.82	4xtnA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
16	0.07	0.638	2.38	0.10	0.89	4hyjA	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
17	0.07	0.562	2.92	0.09	0.87	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
18	0.07	0.554	3.01	0.06	0.91	2m3gA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220

Consensus prediction of GO terms

Molecular Function	GO:0004857	GO:0046872	GO:0005542	GO:0030409	GO:0019215	GO:0030412	GO:0008017	GO:0005216
GO-Score	0.10	0.09	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0043086	GO:0019557	GO:0000301	GO:0032258	GO:0035999	GO:0006888	GO:0016236	GO:0019556	GO:0007010	GO:0030242	GO:0034220
GO-Score	0.10	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0000139	GO:0030868	GO:0017119	GO:0005793	GO:0005829	GO:0019898	GO:0005814	GO:0070062	GO:0016021
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07

(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 Rv2342

[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]