I-TASSER results

I-TASSER results for job id Rv2699c

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

Input Sequence in FASTA format

>protein (100 residues)
MPTDYDAPRRTETDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELS
VRVVPKQADEFTCSSCFLVQHRSRLASEKNGVMICTDCAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MPTDYDAPRRTETDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELSVRVVPKQADEFTCSSCFLVQHRSRLASEKNGVMICTDCAA
Prediction	CCCCCCCCCCCCHHHCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEHCCEEEEEHCHHHHHCCCCEEEEHCCCC
Conf.Score	9876678888855555566588887656677777656667766566789987667876799986588885676455677644445545699577633489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MPTDYDAPRRTETDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELSVRVVPKQADEFTCSSCFLVQHRSRLASEKNGVMICTDCAA
Prediction	7544364335556754675326515764666644434444464266251344414646141402254644210230110323331155774431043158
	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

CCCCCCCCCCCCHHHCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEHCCEEEEEHCHHHHHCCCCEEEEHCCCC
MPTDYDAPRRTETDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELSVRVVPKQADEFTCSSCFLVQHRSRLASEKNGVMICTDCAA

4u4cB

0.17

0.08

0.47

1.33

dPPAS

PTTPPDKLVAPSIEEVNSNPNELRALRGQGRYFGVSDDDNDDFISLS-----------------------------------------------------

4u4cB

0.21

0.10

0.47

1.87

dPPAS2

PTTPPDKLVAPSIEEVNSN-PNELRALRGQGRYFGVSDDDNDDFISLS----------------------------------------------------

2kk9A

0.15

0.08

0.52

1.23

dPPAS

LRRDLDASREKKQLEAEQQKLEEQNKISEASRKGLRRDLDASREAKKQVEKA------------------------------------------------

2kk9A

0.15

0.08

0.52

1.63

dPPAS2

LRRDLDASREKKQLEAEQQKLEEQNKISEASRKGLRRDLDASREAKKQVEKA------------------------------------------------

4a54B

0.10

0.05

0.52

1.14

dPPAS

GATTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS------------------------------------------------

1ponB

0.24

0.08

0.33

1.52

dPPAS2

---------------VTEEDIEDLMKDSDKNNDGRIDFDELKMMEGVQ----------------------------------------------------

4cwuT

0.12

0.08

0.66

1.09

dPPAS

QTVDVQETQTSPVASAVADAAVQAVAAAASKTSTEVQTDPWMFRVSAPRRPRGSRKYGAASALLPE----------------------------------

4c2mI

0.18

0.14

0.79

1.45

dPPAS2

YPKSQFSNLKVVTTTADDAFPSSLRAKKSVVK-TSLKKNELKDGATIKEKCPQCGNEEMNYHTLQRSADEYTCTSC---GYKN-----------------

4c2mI

0.17

0.14

0.82

1.04

dPPAS

YPKSQFSNLKVVTTTADDAFPSSLRAKKSVVK-TSLKKNELKDGATIKEKCPQCGNEEMNYHTLQRSADEYTCTSCYKFRTNN-----------------

1jqsB

0.32

0.08

0.25

1.45

dPPAS2

----------------------------------AADFDE-NIMLKY-LEGEEPTEEELTI---------------------------------------

(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=-3.75

Estimated TM-score = 0.31±0.10

Estimated RMSD = 12.5±4.3Å

Download Model 2

C-score=-3.83

Download Model 3

C-score=-4.39

Download Model 4

C-score=-4.41

Download Model 5

C-score=-4.73

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	1jf0A	0.491	4.20	0.053	0.870
2	4nqgA	0.490	4.11	0.022	0.840
3	2jhcA2	0.481	4.70	0.071	0.910
4	4a01A	0.478	4.56	0.061	0.910
5	1uhiA	0.475	4.04	0.043	0.830
6	5e6rA2	0.472	4.41	0.074	0.880
7	4hw6A	0.465	4.20	0.053	0.820
8	2aexA	0.465	4.62	0.063	0.820
9	4n48A	0.464	4.66	0.044	0.880
10	4he8M	0.463	4.71	0.065	0.890

(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	0.20	10	1x4lA	ZN	Rep, Mult	73,76,95,98
2	0.14	7	2uxqA	MG	Rep, Mult	15,19
3	0.10	5	1sl8A	CA	Rep, Mult	37,39,41,44,63
4	0.06	3	3iqeD	CA	Rep, Mult	18,22

	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	2q80A	0.448	4.14	0.031	0.750	2.5.1.29,2.5.1.10,2.5.1.1	20
2	0.060	1wndA	0.456	4.35	0.112	0.800	1.2.1.19	77
3	0.060	3eqoA	0.447	4.48	0.065	0.840	3.2.1.58	NA
4	0.060	1hm7A	0.450	4.41	0.042	0.770	4.2.3.7,4.6.1.5	NA
5	0.060	1dmuA	0.442	4.42	0.054	0.780	3.1.21.4	NA
6	0.060	2f89F	0.446	4.19	0.031	0.770	2.5.1.1,2.5.1.10	47
7	0.060	1m21A	0.457	4.67	0.053	0.780	3.5.1.-	NA
8	0.060	1xjjA	0.455	4.24	0.056	0.790	1.17.4.1	NA
9	0.060	1zumI	0.444	4.41	0.082	0.790	1.2.1.3	NA
10	0.060	1uxvA	0.438	4.42	0.071	0.790	1.2.1.9	57
11	0.060	1wnbA	0.455	4.43	0.111	0.810	1.2.1.19,1.2.1.8	95
12	0.060	1o01C	0.400	4.92	0.011	0.740	1.2.1.3	58
13	0.060	2j6lB	0.431	4.51	0.030	0.770	1.2.1.31,1.2.1.3	NA
14	0.060	2wj2A	0.441	4.62	0.064	0.770	3.5.1.99	60
15	0.060	2gl9C	0.292	4.16	0.022	0.500	3.5.1.26	NA
16	0.060	1bxsA	0.436	4.62	0.071	0.810	1.2.1.36	NA
17	0.060	2z4yB	0.400	4.17	0.021	0.700	2.5.1.29	NA
18	0.060	2azjA	0.446	4.18	0.031	0.760	2.5.1.1	9
19	0.060	2ftzA	0.447	4.17	0.021	0.730	2.5.1.10	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	0.20	0.484	4.33	0.06	0.87	1el4A	GO:0005509 GO:0008218 GO:0046872
1	0.13	0.308	5.04	0.08	0.57	2aaoA	GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005509 GO:0005516 GO:0005524 GO:0005634 GO:0005777 GO:0005778 GO:0005886 GO:0006468 GO:0009738 GO:0009931 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035556 GO:0046777 GO:0046872
2	0.12	0.298	4.99	0.09	0.61	3kf9A	GO:0005509 GO:0007049 GO:0007067 GO:0046872 GO:0051301
3	0.11	0.331	4.10	0.10	0.56	5palA	GO:0005509 GO:0046872
4	0.09	0.348	3.94	0.09	0.56	2kn2A	GO:0005509 GO:0046872
5	0.07	0.490	4.11	0.02	0.84	4nqgA	GO:0005509 GO:0008218 GO:0046872
6	0.07	0.491	4.20	0.05	0.87	1jf0A	GO:0005509 GO:0008218 GO:0046872
7	0.07	0.493	4.12	0.07	0.86	3kpxA
8	0.07	0.458	4.63	0.04	0.83	2hpsA	GO:0005509 GO:0046872
9	0.07	0.404	4.42	0.07	0.78	1nyaA	GO:0005509 GO:0046872
10	0.06	0.363	4.39	0.05	0.63	1v1fA	GO:0004723 GO:0005509 GO:0005513 GO:0005634 GO:0005737 GO:0005886 GO:0005955 GO:0006470 GO:0016020 GO:0030007 GO:0042539 GO:0046872
11	0.06	0.342	4.86	0.02	0.71	3qfhD	GO:0004252 GO:0006508 GO:0008233 GO:0016787
12	0.06	0.296	4.65	0.04	0.55	4n5xA	GO:0003735 GO:0005347 GO:0005509 GO:0005739 GO:0005743 GO:0006412 GO:0006810 GO:0006839 GO:0010941 GO:0015867 GO:0016020 GO:0016021 GO:0034599 GO:0046872 GO:0055085 GO:0071277
13	0.06	0.404	4.19	0.04	0.75	2l2eA	GO:0005509 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0010515 GO:0016020 GO:0030435 GO:0042327 GO:0043950 GO:0046872 GO:0071277 GO:0090281 GO:0098744
14	0.06	0.360	4.43	0.07	0.65	1uhnA	GO:0005509 GO:0005773 GO:0005774 GO:0009705 GO:0016020 GO:0019722 GO:0022626 GO:0046872 GO:0055075
15	0.06	0.397	4.07	0.08	0.68	2r2iA	GO:0001750 GO:0005509 GO:0005886 GO:0007601 GO:0007602 GO:0008048 GO:0030249 GO:0031282 GO:0031284 GO:0046872 GO:0050896 GO:0071277
16	0.06	0.380	4.22	0.07	0.68	2lhiA	GO:0000131 GO:0000742 GO:0000754 GO:0004721 GO:0004723 GO:0005509 GO:0005516 GO:0005737 GO:0005816 GO:0005823 GO:0005856 GO:0005934 GO:0005935 GO:0005955 GO:0006470 GO:0006607 GO:0006661 GO:0006873 GO:0006897 GO:0006898 GO:0007010 GO:0007114 GO:0016237 GO:0016787 GO:0031505 GO:0042144 GO:0042991 GO:0043332 GO:0046872 GO:0048306 GO:0051300 GO:1903525
17	0.06	0.385	4.60	0.06	0.73	3cs1A	GO:0005509 GO:0005929 GO:0031514 GO:0042995 GO:0046872
18	0.06	0.356	4.58	0.04	0.65	2ggzA	GO:0005509 GO:0007165 GO:0007601 GO:0008048 GO:0022400 GO:0031282 GO:0031284 GO:0046872 GO:0097381

Consensus prediction of GO terms

Molecular Function	GO:0005509
GO-Score	0.51
Biological Processes	GO:0044237
GO-Score	0.34
Cellular Component	GO:0005886	GO:0005634	GO:0005778
GO-Score	0.13	0.13	0.13

(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.