I-TASSER results

Input Sequence in FASTA format

>protein (84 residues)
MGTADRPLDASALRDWAHAVVSDLILHIDEINRLNVFPVADSDTGVNMLFTMRAAVVEAD
LHANSQADAEDVARVAAALAAGAR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGTADRPLDASALRDWAHAVVSDLILHIDEINRLNVFPVADSDTGVNMLFTMRAAVVEADLHANSQADAEDVARVAAALAAGAR
Prediction	CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
Conf.Score	998877668999999999999999999999877566568999986479999999999999756677757999999999998789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGTADRPLDASALRDWAHAVVSDLILHIDEINRLNVFPVADSDTGVNMLFTMRAAVVEADLHANSQADAEDVARVAAALAAGAR
Prediction	875674514162024003300530463364046132120344433330331142015205635566443630340042226438
	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

CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
MGTADRPLDASALRDWAHAVVSDLILHIDEINRLNVFPVADSDTGVNMLFTMRAAVVEADLHANSQADAEDVARVAAALAAGAR

2btdA

0.14

0.13

0.90

1.45

MUSTER

------SLSRTQIVNWLTRCGDIFSTESEYLTGLDR-EIGDADHGLNMNRGFSKVVEKLPAIADKD-IGFILKNTGMTLLSSVG

2btdA

0.14

0.13

0.90

1.01

wPPAS

------SLSRTQIVNWLTRCGDIFSTESEYLTGLDR-EIGDADHGLNMNRGFSKVVEKLPAIADKDI-GFILKNTGMTLLSSVG

2btdA

0.14

0.13

0.90

1.10

dPPAS2

------SLSRTQIVNWLTRCGDIFSTESEYLTGLDR-EIGDADHGLNMNRGFSKVVEKLPAIADKD-IGFILKNTGMTLLSSVG

2btdA

0.14

0.13

0.90

1.02

Env-PPAS

------SLSRTQIVNWLTRCGDIFSTESEYLTGLDR-EIGDADHGLNMNRGFSKVVEKLPAIADKDI-GFILKNTGMTLLSSVG

1un8A2

0.17

0.99

1.29

MUSTER

ARVEFQPSANALVAGIVELVTATLSDLETHLNALDA-KVGDGDTGSTFAAAAREIASLLHRQQPLNNLATLFALIGERLTVVMG

1un8A2

0.17

0.99

0.95

wPPAS

ARVEFQPSANALVAGIVELVTATLSDLETHLNALDA-KVGDGDTGSTFAAAAREIASLLHRQQPLNNLATLFALIGERLTVVMG

1un8A

0.17

0.99

1.21

MUSTER

ARVEFQPSANALVAGIVELVTATLSDLETHLNALDA-KVGDGDTGSTFAAAAREIASLLHRQQPLNNLATLFALIGERLTVVMG

3cr3A

0.19

0.17

0.87

0.93

wPPAS

L------LTIDTTIEWLGKFNEKIQENKAYLSELDG-PIGDGDHGANARGSETKALEVS----NFGNVSEIFKKVATLSKVGGA

3cr3A

0.19

0.17

0.87

1.12

MUSTER

L------LTIDTTIEWLGKFNEKIQENKAYLSELDG-PIGDGDHGANARGSETKALEVS----NFGNVSEIFKKVATLSKVGGA

2qibA

0.14

0.99

0.64

MUSTER

FVEPRQG-PLGARLLRVGRYFDFVDEHGPGFSALRGGPVGSTTTNALVDSVRQAAYVQILSHLDVTEPPARLELVVRSWISLAE

(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=-0.66

Estimated TM-score = 0.63±0.14

Estimated RMSD = 4.9±3.2Å

Download Model 2

C-score=-1.83

Download Model 3

C-score=-3.51

Download Model 4

C-score=-0.60

Download Model 5

C-score=-5.00

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	2btdA	0.826	1.44	0.145	0.905
2	3cr3A	0.766	1.42	0.169	0.845
3	1un8A2	0.722	2.67	0.157	0.929
4	1yuxB	0.640	3.17	0.049	0.976
5	5ezmA3	0.637	2.43	0.065	0.881
6	3oceA	0.633	3.30	0.083	0.941
7	1tj7A	0.632	3.38	0.107	0.941
8	4djhA1	0.631	2.91	0.036	0.893
9	3vw7A1	0.630	2.45	0.053	0.809
10	4xnvA	0.630	2.91	0.083	0.905

(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	0.76	23	2btdA	MG	Rep, Mult	35,41,43
2	0.05	3	3q2qA	IPE	Rep, Mult	17,18,53,75
3	0.05	3	3pfdA	IOD	Rep, Mult	43,46,47
4	0.03	2	1gzmA	C8E	Rep, Mult	21,24
5	0.02	1	3rj1K	SE	Rep, Mult	51,52

	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	1c3cA	0.576	3.37	0.063	0.857	4.3.2.2	NA
2	0.060	1cc1L	0.581	3.23	0.111	0.857	1.12.99.6	NA
3	0.060	2bq1I	0.579	3.53	0.037	0.893	1.17.4.1	NA
4	0.060	2h5gB	0.588	3.46	0.120	0.893	1.2.1.41	NA
5	0.060	2wlaA	0.572	2.89	0.108	0.857	1.16.3.1	22,49,54,78
6	0.060	1jq5A	0.571	3.43	0.087	0.905	1.1.1.6	35
7	0.060	1y5nC	0.576	3.84	0.083	0.988	1.7.99.4	51
8	0.060	2pulA	0.592	3.14	0.054	0.857	2.7.1.100	60
9	0.060	2o6yA	0.614	3.29	0.173	0.893	4.3.1.-	NA
10	0.060	1kizA	0.574	3.38	0.085	0.869	4.2.3.6	24,55,57
11	0.060	1r03A	0.549	3.57	0.039	0.857	1.16.3.1	22,24,27
12	0.060	2vroB	0.584	3.42	0.107	0.893	1.2.1.3	NA
13	0.060	3bhgA	0.598	3.27	0.038	0.917	4.3.2.2	NA
14	0.060	3e04D	0.618	3.24	0.120	0.941	4.2.1.2	NA
15	0.060	3d4sA	0.591	3.35	0.112	0.893	3.2.1.17	58,70,73
16	0.060	1y2mB	0.604	3.41	0.119	0.905	4.3.1.24	NA
17	0.060	1uzrB	0.582	3.25	0.024	0.869	1.17.4.1	NA
18	0.060	1smsA	0.578	3.47	0.036	0.869	1.17.4.1	NA
19	0.060	3lmdA	0.604	2.79	0.095	0.881	2.5.1.30	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	0.45	0.821	1.40	0.18	0.90	3cr3A	GO:0000166 GO:0004371 GO:0005524 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0019563
1	0.42	0.722	2.67	0.16	0.93	1un8A	GO:0000166 GO:0004371 GO:0005524 GO:0006071 GO:0008289 GO:0016301 GO:0016310 GO:0016740 GO:0019588 GO:0046872
2	0.16	0.825	1.44	0.14	0.90	4lrzA	GO:0000166 GO:0000287 GO:0004371 GO:0005524 GO:0005829 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0019563 GO:0043531
3	0.10	0.549	3.99	0.04	0.89	2hr5A	GO:0005506 GO:0016491 GO:0046872 GO:0055114
4	0.10	0.518	2.95	0.04	0.74	4di0B	GO:0016491 GO:0046872 GO:0055114
5	0.09	0.640	3.17	0.05	0.98	1yuxB	GO:0005506 GO:0005737 GO:0016491 GO:0046872 GO:0055114
6	0.08	0.608	3.22	0.04	0.92	3qhbA	GO:0009536 GO:0009842 GO:0016491 GO:0046872 GO:0055114
7	0.07	0.573	3.31	0.13	0.89	1b71A	GO:0005506 GO:0005737 GO:0016491 GO:0046872 GO:0055114
8	0.07	0.527	3.69	0.04	0.86	4k5rB	GO:0000166 GO:0016491 GO:0055114 GO:0071949
9	0.07	0.507	2.56	0.03	0.71	1j30A	GO:0016491 GO:0046872 GO:0055114
10	0.07	0.469	3.49	0.03	0.71	4lrxA	GO:0004371 GO:0005829 GO:0006071 GO:0006974 GO:0016301 GO:0016310 GO:0016740 GO:0019563 GO:0042182 GO:0046365 GO:0047324
11	0.07	0.396	4.06	0.13	0.74	4fc6B	GO:0005102 GO:0005777 GO:0005778 GO:0006629 GO:0006631 GO:0006636 GO:0008670 GO:0016491 GO:0019166 GO:0044255 GO:0055114
12	0.07	0.677	2.62	0.11	0.98	5f15A	GO:0016020 GO:0016021 GO:0016740
13	0.07	0.454	3.42	0.07	0.68	1wfzA	GO:0005506 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006879 GO:0008198 GO:0016226 GO:0032947 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
14	0.06	0.374	3.83	0.07	0.64	5ecjA	GO:0000122 GO:0000902 GO:0001708 GO:0001827 GO:0003676 GO:0003677 GO:0003700 GO:0003714 GO:0003723 GO:0005634 GO:0006351 GO:0006355 GO:0007281 GO:0007566 GO:0008168 GO:0009566 GO:0010468 GO:0010976 GO:0010977 GO:0016740 GO:0019827 GO:0030718 GO:0030855 GO:0031490 GO:0032259 GO:0034972 GO:0040029 GO:0040037 GO:0044030 GO:0045892 GO:0045944 GO:0046872 GO:0048873 GO:0060817
15	0.06	0.463	3.61	0.01	0.71	2iu4B	GO:0004371 GO:0006071 GO:0006351 GO:0006355 GO:0016310
16	0.06	0.395	4.07	0.04	0.70	4oytA	GO:0003824 GO:0008168 GO:0016740 GO:0032259
17	0.06	0.324	4.36	0.03	0.61	1j1iA	GO:0016787
18	0.06	0.378	2.49	0.04	0.52	1whuA	GO:0000175 GO:0000957 GO:0000958 GO:0000962 GO:0000964 GO:0000965 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004654 GO:0005737 GO:0005739 GO:0005758 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006810 GO:0008266 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0034046 GO:0034599 GO:0035198 GO:0035458 GO:0035927 GO:0035928 GO:0043457 GO:0043631 GO:0044822 GO:0045025 GO:0045926 GO:0051260 GO:0061014 GO:0070207 GO:0070584 GO:0071042 GO:0071850 GO:0090503 GO:0097222 GO:2000627 GO:2000772

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0004371	GO:0046872	GO:0008289
GO-Score	0.73	0.73	0.53	0.42
Biological Processes	GO:0016310	GO:0019588
GO-Score	0.73	0.42
Cellular Component	GO:0044444
GO-Score	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 Rv2975c

[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]