I-TASSER results

I-TASSER results for job id Rv0299

[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)
MIAPGDIAPRRDSEHELYVAVLSNALHRAADTGRVITCPFIPGRVPEDLLAMVVAVEQPN
GTLLPELVQWLHVAALGAPLGNAGVAALREAASVVTALLC

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MIAPGDIAPRRDSEHELYVAVLSNALHRAADTGRVITCPFIPGRVPEDLLAMVVAVEQPNGTLLPELVQWLHVAALGAPLGNAGVAALREAASVVTALLC
Prediction	CCCCCCCCCCCCCCCEEEEEEHHHHHHHHHCCCCEEEHCCCCCCCCCHHHHHHHHEHCCCCEHCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
Conf.Score	9998878887788975787654578888747896899667889899577766554556897454778888555457888756789999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MIAPGDIAPRRDSEHELYVAVLSNALHRAADTGRVITCPFIPGRVPEDLLAMVVAVEQPNGTLLPELVQWLHVAALGAPLGNAGVAALREAASVVTALLC
Prediction	7344562344454634000000233134435333103032232513542221122144452321240143132332443234222420452142131237
	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

CCCCCCCCCCCCCCCEEEEEEHHHHHHHHHCCCCEEEHCCCCCCCCCHHHHHHHHEHCCCCEHCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
MIAPGDIAPRRDSEHELYVAVLSNALHRAADTGRVITCPFIPGRVPEDLLAMVVAVEQPNGTLLPELVQWLHVAALGAPLGNAGVAALREAASVVTALLC

1ne8A

0.16

0.98

1.02

MUSTER

IVKRGDVSPVVGSEQVRPVLVIQNDIGNRF-SPTAIVAA-ITAQIQKAKLPTHVEIDAKDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.11

0.99

0.85

dPPAS

IVKRGDVVVGSEQGGVRPVLVIQNDIGNRF-SPTAIVAAITAQKLPTHVEIDAKRYGFERSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.14

0.97

0.99

wdPPAS

IVKRGDVVVGSEQGGVRPVLVIQNDIGNRF-SPTAIVAA-ITAQIQKAKLAKRYGFERD-SVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.18

0.17

0.97

1.03

wMUSTER

IVKRGDVSPVVGSEQVRPVLVIQNDIGNRF-SPTAIVAA-ITAQIQKAKLAKRYGFERD-SVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.15

0.14

0.94

0.97

wPPAS

IVKRGDVYPGSEQGGVRPVLVIQNDIGNRF-SPTAIVAAILPTHID----AKRYGFERD-SVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.13

0.98

1.07

dPPAS2

IVKRGDVVVGSEQGGVRPVLVIQNDIGNRF-SPTAIVAAITAQKLPTHVEAKRYGFERD-SVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ne8A

0.18

0.17

0.97

1.16

PPAS

IVKRGDVSPVVGSEQVRPVLVIQNDIGNRF-SPTAIVAA-ITAQIQKAKLAKRYGFERD-SVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLA

1ub4A

0.22

0.20

0.91

1.31

Env-PPAS

VYVPGDLI-WVDFDGHRPAVVLSPFMYNNK-TGMCLCVPCYPFEVV------LSGQERD-GVALADQVKSIWRARGATKKGTVAPEELQLIKAKINVLIG

2c06A

0.16

0.98

MUSTER

-MERGEIDPTAGHEQTRPVLIVTPAAFNRV-TRLPVVVPVTSGGNFARTAGFAVSLDGVTGVVRCDQPRTIDMKAGGKRLERVPETIMNEVLGRLSTILT

1ub4A

0.16

0.98

0.80

dPPAS

VPDMGDLIWVDFDPGHRPAVVLSPFMYNNK-TGMCLCVP-CTTQSKGYPFEVVLSGQERDGVALADQVKSIWRARGATKKGTVAPEELQLIKAKINVLIG

(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=-0.42

Estimated TM-score = 0.66±0.13

Estimated RMSD = 4.8±3.1Å

Download Model 2

C-score=-3.39

Download Model 3

C-score=-0.40

Download Model 4

C-score=-1.03

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	2c06A	0.814	1.90	0.133	0.980
2	2mf2A	0.810	1.90	0.175	0.970
3	1ne8A	0.808	1.85	0.124	0.970
4	1ub4A	0.776	2.28	0.167	0.950
5	3vubA	0.728	2.50	0.096	0.930
6	4rmoA	0.691	2.56	0.075	0.890
7	2kmtA	0.667	2.91	0.106	0.930
8	4atoA	0.647	2.90	0.066	0.890
9	4glkA	0.611	3.27	0.099	0.900
10	2xd0A	0.594	3.30	0.079	0.880

(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	4	2c06B	RQA	Rep, Mult	30,32,33,34,74
2	0.11	3	3vub0	III	Rep, Mult	4,22,23,24,26,27,32,36,52,66,68,69,70,92,95,96,97,98,99,100
3	0.06	2	4e8lC	MG	Rep, Mult	24,39
4	0.06	2	2c06A	RQA	Rep, Mult	14,15,16,17,41,42,43,50,51,52,61,64,66,67
5	0.03	1	3dl9B	BCD	Rep, Mult	76,79,81
6	0.03	1	3avhA	III	Rep, Mult	47,62,70
7	0.03	1	5cqxA	III	Rep, Mult	10,32,34,39,41,42,53,64,67,69,71,72,74,75
8	0.03	1	2zyqB	TAR	Rep, Mult	4,5
9	0.03	1	2oigD	523	Rep, Mult	66,70

	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	1o5fH	0.409	4.29	0.079	0.750	3.4.21.106	NA
2	0.060	2qxfA	0.458	3.52	0.085	0.710	3.1.11.1	NA
3	0.060	2puxB	0.369	4.99	0.055	0.760	3.4.21.5	NA
4	0.060	1fxxA	0.478	4.12	0.066	0.810	3.1.11.1	NA
5	0.060	1p57A	0.363	4.25	0.052	0.660	3.4.21.106	12,62
6	0.060	1z8gA	0.437	4.09	0.045	0.770	3.4.21.106	NA
7	0.060	1qqwB	0.375	4.27	0.081	0.690	1.11.1.6	NA
8	0.060	1mkwK	0.405	4.40	0.034	0.780	3.4.21.5	NA
9	0.060	1a4eA	0.433	4.06	0.127	0.770	1.11.1.6	NA
10	0.060	1myrA	0.420	3.85	0.044	0.670	3.2.1.147	NA
11	0.060	1sy7B	0.463	3.78	0.092	0.730	1.11.1.6	84
12	0.060	1ksiA	0.431	4.21	0.047	0.760	1.4.3.21	NA
13	0.060	1bdaA	0.302	4.52	0.076	0.550	3.4.21.68	NA
14	0.060	1sy7A	0.464	3.62	0.105	0.720	1.11.1.6	NA
15	0.060	2rnzA	0.403	2.68	0.090	0.530	2.3.1.48	17,22
16	0.060	3h09B	0.432	4.08	0.047	0.730	3.4.21.72	NA
17	0.060	2j2mA	0.458	3.93	0.091	0.740	1.11.1.6	NA
18	0.060	1ucyE	0.305	4.13	0.014	0.530	3.4.21.5	19
19	0.060	2h47H	0.433	3.57	0.065	0.680	1.4.99.4	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	0.36	0.810	1.90	0.17	0.97	2mf2A	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0090305
1	0.33	0.768	2.09	0.16	0.92	3nfcA	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006402 GO:0006417 GO:0009372 GO:0016075 GO:0016787 GO:0030308 GO:0051607 GO:0090305 GO:0090502
2	0.30	0.823	1.73	0.13	0.97	4hkeA	GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0090305
3	0.29	0.814	1.90	0.13	0.98	2c06A	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0090305
4	0.27	0.792	2.12	0.16	0.96	5cqxB	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006402 GO:0006417 GO:0009372 GO:0016075 GO:0016787 GO:0030308 GO:0051607 GO:0090305 GO:0090502
5	0.22	0.732	2.51	0.08	0.94	3g7zA	GO:0006276 GO:0006351 GO:0006355 GO:0008657 GO:2000372
6	0.18	0.667	2.91	0.11	0.93	2kmtA	GO:0006276 GO:0008657 GO:2000372
7	0.07	0.611	3.27	0.10	0.90	4glkA	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0016787 GO:0051607 GO:0090305 GO:0090502
8	0.07	0.594	3.30	0.08	0.88	2xd0A	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006276 GO:0006351 GO:0006355 GO:0016787 GO:0045892 GO:0051607 GO:0090305 GO:0090502
9	0.06	0.394	4.44	0.07	0.71	1xxpA	GO:0004721 GO:0004725 GO:0005576 GO:0006470 GO:0009405 GO:0016311 GO:0016787 GO:0016791 GO:0035335
10	0.06	0.330	4.99	0.04	0.70	3w8wB	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
11	0.06	0.357	5.26	0.05	0.78	4ln5A	GO:0006810 GO:0008643 GO:0030288 GO:0042597
12	0.06	0.336	4.76	0.04	0.64	1sdjA	GO:0003824 GO:0009058 GO:0016853
13	0.06	0.364	3.76	0.04	0.60	5amoB	GO:0001540 GO:0003190 GO:0005576 GO:0005615 GO:0005783 GO:0007275 GO:0007399 GO:0010628 GO:0010629 GO:0010718 GO:0023041 GO:0030054 GO:0030424 GO:0030516 GO:0032281 GO:0042995 GO:0043025 GO:0043204 GO:0044295 GO:0045202 GO:0051259 GO:0060317 GO:0097060 GO:1902003 GO:1902430 GO:2001223
14	0.06	0.307	4.30	0.08	0.58	3thwB	GO:0000166 GO:0000228 GO:0000710 GO:0003677 GO:0003684 GO:0003697 GO:0005524 GO:0005654 GO:0006281 GO:0006298 GO:0006974 GO:0007131 GO:0016020 GO:0019899 GO:0030983 GO:0032137 GO:0032139 GO:0032142 GO:0032181 GO:0032302 GO:0032357 GO:0042803 GO:0043570 GO:0045910 GO:0051096
15	0.06	0.313	5.53	0.04	0.70	5i6hB	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0006633 GO:0016874 GO:0046872
16	0.06	0.326	4.73	0.04	0.65	4pdeA	GO:0003824 GO:0005737 GO:0005829 GO:0006777 GO:0006810 GO:0016783 GO:0043546 GO:0097163
17	0.06	0.321	5.05	0.08	0.63	3p0bA	GO:0003824 GO:0003844 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757
18	0.06	0.329	4.56	0.07	0.64	2gjlA	GO:0003824 GO:0004497 GO:0016491 GO:0018580 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003723	GO:0004521
GO-Score	0.85	0.78	0.51
Biological Processes	GO:0006402	GO:0016075	GO:0009372	GO:0006355	GO:0030308	GO:0051607	GO:0006417	GO:0090502
GO-Score	0.51	0.51	0.51	0.51	0.51	0.51	0.51	0.51
Cellular Component
GO-Score

(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.