I-TASSER results

I-TASSER results for job id Rv2749

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

Input Sequence in FASTA format

>protein (104 residues)
MPVVVVATLTAKPESVDTVRDILTRAVDDVHREPGCQLYALHETGETFIFVEQWADAEAL
KAHSGAPAVATMFTAAGEHLVGAPDIKLLQPVPAGDPSKGQLRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MPVVVVATLTAKPESVDTVRDILTRAVDDVHREPGCQLYALHETGETFIFVEQWADAEALKAHSGAPAVATMFTAAGEHLVGAPDIKLLQPVPAGDPSKGQLRR
Prediction	CEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEEEHCCHHHHHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCCCC
Conf.Score	95999999997998899999999999999987999579999975998999999889999999996999999999999986478689999875788876554469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MPVVVVATLTAKPESVDTVRDILTRAVDDVHREPGCQLYALHETGETFIFVEQWADAEALKAHSGAPAVATMFTAAGEHLVGAPDIKLLQPVPAGDPSKGQLRR
Prediction	34030203030456225302510451164047363113030343553010002042460154047262044016404721555151431551454475444268
	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                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEEEHCCHHHHHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCCCC
MPVVVVATLTAKPESVDTVRDILTRAVDDVHREPGCQLYALHETGETFIFVEQWADAEALKAHSGAPAVATMFTAAGEHLVGAPDIKLLQPVPAGDPSKGQLRR

1y0hA

0.27

0.25

0.92

3.26

MUSTER

MPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYESGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

3qmqC

0.16

0.14

0.90

5.16

dPPAS

MMHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP----------

1y0hA

0.27

0.25

0.92

4.78

wdPPAS

MPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYEDGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

1y0hA

0.27

0.25

0.92

3.92

wMUSTER

MPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYESGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

1y0hA

0.27

0.25

0.92

4.25

wPPAS

MPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYEDGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

3qmqC

0.16

0.14

0.90

6.66

dPPAS2

MMHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP----------

1y0hA

0.27

0.25

0.92

4.06

PPAS

MPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYEDGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

3qmqC

0.16

0.14

0.90

4.08

Env-PPAS

MMHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP----------

3qmqC

0.16

0.14

0.90

3.16

MUSTER

MMHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP----------

1y0hA

0.26

0.24

0.92

5.14

dPPAS

SPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYEDGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEAS--------

(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=0.91

Estimated TM-score = 0.84±0.08

Estimated RMSD = 2.3±1.8Å

Download Model 2

C-score=-3.59

Download Model 3

C-score=-0.71

Download Model 4

C-score=1.00

Download Model 5

C-score=-4.42

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	1y0hA	0.891	0.77	0.260	0.923
2	3mcsA	0.872	1.73	0.155	0.990
3	4zosA	0.850	1.03	0.255	0.904
4	3qmqC	0.840	1.21	0.149	0.904
5	2omoA	0.831	1.54	0.118	0.894
6	4dpoA	0.820	0.93	0.233	0.865
7	3f44A	0.815	1.89	0.139	0.971
8	3e8oA	0.806	1.87	0.250	0.913
9	2pd1A	0.799	1.72	0.224	0.923
10	2gffB	0.797	1.36	0.160	0.875

(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	29	1n5sB	ADL	Rep, Mult	7,9,39,41,50,52,54,60,63,72,73,76,84
2	0.05	4	3fgvB	UNL	Rep, Mult	26,27,30,63,73
3	0.04	3	3a16D	PXO	Rep, Mult	7,84,85,86
4	0.04	3	1y0h0	III	Rep, Mult	4,6,8,27,31,40,41,42,43,44,49,51,53,88,89,90,91,92,93,94,95
5	0.02	2	3hfkA	4ML	Rep, Mult	5,7,61,70,86
6	0.02	2	3hx9B	HEM	Rep, Mult	7,22,23,30,39,52,61,79,80,81,82
7	0.01	1	1iujB	ZN	Rep, Mult	58,61
8	0.01	1	3hdsC	III	Rep, Mult	27,30,36,37,38,39,40,51
9	0.01	1	3kkfA	CA	Rep, Mult	12,14
10	0.01	1	1r6y0	III	Rep, Mult	3,4,6,8,20,41,42,43,44,47,49,51,57,64,85,86,87,88,89,90,91
11	0.01	1	3hfkB	4ML	Rep, Mult	7,63,64,69,73,84
12	0.01	1	3kkfA	CA	Rep, Mult	1,55

	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	0.195	2acyA	0.582	3.42	0.078	0.865	3.6.1.7	32
2	0.195	2zdpA	0.681	2.58	0.063	0.913	1.14.99.3	25,37
3	0.181	2zdoD	0.680	2.72	0.095	0.913	1.14.99.3	7,25,59
4	0.109	1ulrA	0.556	3.23	0.140	0.827	3.6.1.7	NA
5	0.107	1y9oA	0.620	2.55	0.151	0.827	3.6.1.7	NA
6	0.106	2ko1A	0.526	2.88	0.049	0.760	2.7.6.5	24,41
7	0.103	1v3zA	0.555	3.30	0.105	0.827	3.6.1.7	NA
8	0.102	1urrA	0.587	3.20	0.055	0.856	3.6.1.7	NA
9	0.073	1w2iA	0.550	3.34	0.103	0.837	3.6.1.7	20,104
10	0.072	2fhmA	0.547	3.41	0.069	0.837	3.6.1.7	NA
11	0.067	1apsA	0.604	2.96	0.101	0.846	3.6.1.7	20
12	0.067	1x8dA	0.614	3.33	0.128	0.904	5.1.3.-	30,39
13	0.067	1s6oA	0.495	3.27	0.080	0.712	3.6.3.4	24
14	0.066	2k7jA	0.577	3.37	0.101	0.856	3.6.1.7	NA
15	0.066	1fvqA	0.491	2.90	0.070	0.673	3.6.3.4	24
16	0.066	1gxtA	0.536	3.29	0.060	0.798	2.1.3.-	NA
17	0.066	1y3jA	0.483	2.99	0.081	0.673	3.6.3.4	40,52,77
18	0.066	1aw0A	0.472	3.04	0.085	0.683	3.6.3.4	66
19	0.066	1fwpA	0.452	3.15	0.044	0.654	2.7.13.3	38
20	0.060	1cjkB	0.635	2.94	0.084	0.894	4.6.1.1	25
21	0.060	3nn1A	0.596	3.75	0.096	0.885	1.13.11.49	42,44
22	0.060	2gv1A	0.606	2.97	0.080	0.846	3.6.1.7	25
23	0.060	3ic1A	0.620	3.32	0.091	0.865	3.5.1.18	21,79
24	0.060	1azsA	0.627	3.08	0.072	0.913	4.6.1.1	NA
25	0.060	1m5sD	0.646	2.86	0.095	0.913	2.3.1.101	45,51
26	0.060	1fx2A	0.631	3.24	0.051	0.923	4.6.1.1	25
27	0.060	1fnoA	0.597	3.11	0.092	0.846	3.4.11.4	71
28	0.060	2fgeA	0.584	3.40	0.098	0.913	3.4.24.-	NA
29	0.060	2w01A	0.614	3.29	0.135	0.904	4.6.1.2	NA
30	0.060	3l76A	0.580	3.43	0.085	0.904	2.7.2.4	NA
31	0.060	3eoqB	0.602	3.06	0.087	0.865	3.4.24.56	NA
32	0.060	3cxhL	0.587	3.27	0.039	0.885	1.10.2.2	NA
33	0.060	1yk9A	0.623	3.18	0.094	0.875	4.6.1.1	NA
34	0.060	1ftrD	0.646	3.09	0.103	0.933	2.3.1.101	27
35	0.060	2pfdB	0.629	2.73	0.103	0.875	2.1.2.5,4.3.1.4	NA
36	0.060	1z2lA	0.645	3.24	0.127	0.913	3.5.3.-	NA
37	0.060	2fyuA	0.576	3.40	0.087	0.885	1.10.2.2	NA
38	0.060	1be3A	0.584	3.35	0.087	0.885	1.10.2.2	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	0.40	0.834	1.27	0.25	0.89	2bbeA	GO:0004497 GO:0055114
1	0.40	0.790	1.27	0.27	0.87	4hl9A	GO:0004497 GO:0055114
2	0.37	0.757	1.52	0.23	0.87	1r6yA	GO:0005829 GO:0010447 GO:0016491 GO:0055114
3	0.36	0.891	0.77	0.26	0.92	1y0hA	GO:0004497 GO:0016491 GO:0055114
4	0.34	0.758	1.89	0.19	0.90	4dn9A	GO:0004497 GO:0055114
5	0.31	0.792	1.35	0.28	0.88	1x7vC
6	0.31	0.831	1.54	0.12	0.89	2omoA
7	0.30	0.751	2.13	0.17	0.92	1iujB
8	0.30	0.790	1.32	0.31	0.87	3bm7A
9	0.28	0.824	1.45	0.14	0.90	2gffB	GO:0005737 GO:0016853
10	0.23	0.840	1.21	0.15	0.90	3qmqC
11	0.22	0.780	1.11	0.17	0.84	2fb0A
12	0.20	0.873	1.72	0.15	0.99	3mcsB
13	0.19	0.686	2.03	0.14	0.82	1q8bA
14	0.18	0.821	1.68	0.18	0.94	3kkfA	GO:0046872
15	0.16	0.815	1.89	0.14	0.97	3f44A
16	0.07	0.494	3.47	0.08	0.80	2pffB	GO:0003824 GO:0004312 GO:0004313 GO:0004314 GO:0004318 GO:0004319 GO:0004320 GO:0004321 GO:0005811 GO:0005829 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016295 GO:0016296 GO:0016297 GO:0016409 GO:0016491 GO:0016740 GO:0016787 GO:0016829 GO:0019171 GO:0042759 GO:0047451 GO:0055114
17	0.07	0.434	4.23	0.07	0.73	5k8bA	GO:0000271 GO:0003824 GO:0008483 GO:0009103 GO:0016740
18	0.06	0.456	3.63	0.08	0.69	2vneA	GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
19	0.06	0.407	3.94	0.02	0.66	3zyjB	GO:0005886 GO:0007275 GO:0007399 GO:0007409 GO:0016020 GO:0030154 GO:0031225 GO:0046658

Consensus prediction of GO terms

Molecular Function	GO:0004497
GO-Score	0.85
Biological Processes	GO:0055114	GO:0010447
GO-Score	0.91	0.37
Cellular Component	GO:0005829
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.