I-TASSER results

I-TASSER results for job id Rv3745c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (70 residues)
MSDCNVLGGALEQGGTDPLTGFYRDGCCATGPEDLGWHTICAVMTTEFLAHQRSVGNDLS
IARPPRWLRP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSDCNVLGGALEQGGTDPLTGFYRDGCCATGPEDLGWHTICAVMTTEFLAHQRSVGNDLSIARPPRWLRP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	9876888987654589999875568877799556966899998778999999998988899998778999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSDCNVLGGALEQGGTDPLTGFYRDGCCATGPEDLGWHTICAVMTTEFLAHQRSVGNDLSIARPPRWLRP
Prediction	7763444454044125433011312030624771413121003025401520474434132343744738
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCHHHHHHHHHHCCCCCCCCCCCCCCC
MSDCNVLGGALEQGGTDPLTGFYRDGCCATGPEDLGWHTICAVMTTEFLAHQRSVGNDLSIARPPRWLRP

4iohA

0.55

0.51

0.94

3.33

MUSTER

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

8.97

dPPAS

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

5.31

wdPPAS

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.93

3.65

wMUSTER

---TNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

2.95

wPPAS

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

11.00

dPPAS2

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

3.41

PPAS

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

4iohA

0.55

0.51

0.94

3.80

Env-PPAS

--TTNVLGTPLECCCQNPLTGFYRDGFCRTGAGDVGAHVVCAQ-TAEFLTFTRSRGNDLSTPVPAYQ-FP

3ushA

0.54

0.49

0.90

3.07

MUSTER

--SQNVLGGVLRACS-DPETGFYRDGHCRTGPRDTGSHVVCAE-TEAFLEYTKRQGNDL-TPRPE--DFP

2lq3A

0.48

0.47

0.99

8.44

dPPAS

GQGQNVLGQDLEVCCCAPMTGWYRNGFCQTDVQDRGSHTVCAEMTEEFLLFSRDRGNDLMTPRPEFN-FP

(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=-0.16

Estimated TM-score = 0.69±0.12

Estimated RMSD = 3.6±2.5Å

Download Model 2

C-score=-1.21

Download Model 3

C-score=-2.45

Download Model 4

C-score=0.27

Download Model 5

C-score=-1.36

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	4iohA	0.620	2.48	0.484	0.914
2	3ushA	0.605	2.66	0.415	0.857
3	2zwvA	0.482	3.80	0.078	0.886
4	3knzA	0.482	3.32	0.016	0.843
5	3ksyA	0.482	3.79	0.031	0.871
6	1g8sA	0.482	3.63	0.098	0.843
7	4lg1A	0.482	4.12	0.047	0.914
8	3pzdA	0.474	4.22	0.071	0.957
9	3i0zA	0.472	3.20	0.016	0.814
10	5dwbA	0.469	3.56	0.048	0.829

(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	0.11	5	5hhjA	GLY	Rep, Mult	49,52
2	0.11	5	1y9eC	NAD	Rep, Mult	39,40,41
3	0.09	4	4ow9A	IOD	Rep, Mult	53,58,59
4	0.07	3	4ovbA	AUC	Rep, Mult	43,49,52
5	0.02	1	1y9eA	NAD	Rep, Mult	21,36,37,38
6	0.02	1	2v83B	III	Rep, Mult	31,34
7	0.02	1	1u0aA	ZN	Rep, Mult	38,58
8	0.02	1	4rjdA	TFP	Rep, Mult	55,56,57
9	0.02	1	3mbgA	ZN	Rep, Mult	47,51

	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	2c0yA	0.435	3.56	0.015	0.757	3.4.22.27	NA
2	0.060	1sk6C	0.300	4.88	0.000	0.714	4.6.1.1	19,46
3	0.060	2o2rC	0.430	3.99	0.000	0.886	1.5.1.6	NA
4	0.060	1g8aA	0.426	4.03	0.103	0.857	2.1.1.-	NA
5	0.060	1jvbA	0.370	4.36	0.076	0.786	1.1.1.1	NA
6	0.060	1dusA	0.445	4.08	0.045	0.929	2.1.1.-	NA
7	0.060	2qmxB	0.343	4.05	0.045	0.714	4.2.1.51	61
8	0.060	1nb3A	0.447	3.81	0.061	0.800	3.4.22.16	NA
9	0.060	2eerB	0.449	4.19	0.077	0.857	1.1.1.1	NA
10	0.060	1onxA	0.357	3.75	0.078	0.686	3.4.19.-	NA
11	0.060	1ybqA	0.450	4.06	0.087	0.857	3.4.19.1	57
12	0.060	2bgjA	0.441	4.67	0.086	0.929	1.18.1.2	NA
13	0.060	3nivA	0.437	3.94	0.117	0.829	5.2.1.2	23
14	0.060	2v45A	0.438	4.25	0.130	0.900	1.7.99.4	NA
15	0.060	1kpiA	0.272	4.30	0.049	0.571	2.1.1.79	44
16	0.060	1v9lA	0.444	4.12	0.076	0.857	1.4.1.2	34
17	0.060	2wodA	0.441	3.04	0.078	0.771	3.2.2.24	11,25
18	0.060	3id5B	0.450	3.78	0.072	0.886	2.1.1.-	NA
19	0.060	8pchA	0.450	3.65	0.061	0.786	3.4.22.16	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	0.07	0.482	4.12	0.05	0.91	4lg1A	GO:0005737 GO:0008168 GO:0016279 GO:0016740 GO:0018023 GO:0032259
1	0.07	0.395	4.01	0.09	0.80	3cjtA	GO:0005737 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0032259
2	0.07	0.482	3.80	0.08	0.89	2zwvA	GO:0000154 GO:0000179 GO:0003676 GO:0008168 GO:0008649 GO:0016740 GO:0031167 GO:0032259 GO:0046872 GO:0051536 GO:0051539
3	0.07	0.456	4.18	0.06	0.96	1dusA	GO:0008168 GO:0016740 GO:0032259
4	0.07	0.410	4.27	0.07	0.86	4qdkA	GO:0005737 GO:0008168 GO:0008757 GO:0015979 GO:0015995 GO:0016740 GO:0032259 GO:0036068 GO:0046406
5	0.07	0.305	4.21	0.06	0.66	3bkwA	GO:0008152 GO:0008168 GO:0032259
6	0.07	0.381	4.35	0.07	0.87	3fuxC	GO:0000154 GO:0000179 GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0016433 GO:0016740 GO:0031167 GO:0032259 GO:0052908
7	0.07	0.332	4.69	0.03	0.83	4dcmA	GO:0003676 GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052916 GO:0070475
8	0.06	0.368	4.35	0.07	0.81	1wy7D	GO:0003676 GO:0008168 GO:0032259
9	0.06	0.395	4.25	0.10	0.80	5bp7A	GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259
10	0.06	0.388	4.29	0.16	0.86	1ws6A	GO:0008168 GO:0016740 GO:0031167 GO:0032259
11	0.06	0.386	3.95	0.05	0.76	5bp9A	GO:0008168 GO:0016740 GO:0032259
12	0.06	0.447	4.03	0.09	0.86	3evzA	GO:0008168 GO:0032259
13	0.06	0.432	4.37	0.10	0.96	4lecA	GO:0005737 GO:0006479 GO:0008168 GO:0016279 GO:0016740 GO:0018022 GO:0030544 GO:0032259 GO:0043462 GO:0051117
14	0.06	0.413	3.91	0.10	0.77	3cggA	GO:0008168 GO:0016740 GO:0032259
15	0.06	0.393	4.14	0.13	0.83	4ax8A	GO:0000166 GO:0004672 GO:0005524 GO:0005886 GO:0006468 GO:0008168 GO:0009103 GO:0009243 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0032259
16	0.06	0.407	4.26	0.04	0.77	1kywC	GO:0008168 GO:0008171 GO:0009699 GO:0009809 GO:0016740 GO:0032259 GO:0046983 GO:0047763
17	0.06	0.395	3.95	0.12	0.80	4uw0A	GO:0004672 GO:0005524 GO:0006468
18	0.06	0.309	4.39	0.05	0.64	2gluA	GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259

Consensus prediction of GO terms

Molecular Function	GO:0016741
GO-Score	0.58
Biological Processes	GO:0008152
GO-Score	0.38
Cellular Component	GO:0044424
GO-Score	0.37

(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.