I-TASSER results

I-TASSER results for job id Rv3259

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

Input Sequence in FASTA format

>protein (139 residues)
MRGPLLPPTVPGWRSRAERFDMAVLEAYEPIERRWQERVSQLDIAVDEIPRIAAKDPESV
QWPPEVIADGPIALARLIPAGVDVRGNATRARIVLFRKPIERRAKDTEELGELLHEILVA
QVAIYLDVDPSVIDPTIDD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRGPLLPPTVPGWRSRAERFDMAVLEAYEPIERRWQERVSQLDIAVDEIPRIAAKDPESVQWPPEVIADGPIALARLIPAGVDVRGNATRARIVLFRKPIERRAKDTEELGELLHEILVAQVAIYLDVDPSVIDPTIDD
Prediction	CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCEHCCEEHCCCCCCCCCCCCCEEEEHCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCC
Conf.Score	9999999888865785899999999999999999999848858999858888777777777876544567755545656766778888887899974578998599889999999999999999989996557899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRGPLLPPTVPGWRSRAERFDMAVLEAYEPIERRWQERVSQLDIAVDEIPRIAAKDPESVQWPPEVIADGPIALARLIPAGVDVRGNATRARIVLFRKPIERRAKDTEELGELLHEILVAQVAIYLDVDPSVIDPTIDD
Prediction	7324234371234333453024003401540374047305603000131154445544526245412553312013223353544655321100000320242064562024102400021014337144551336388
	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                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCEHCCEEHCCCCCCCCCCCCCEEEEHCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCC
MRGPLLPPTVPGWRSRAERFDMAVLEAYEPIERRWQERVSQLDIAVDEIPRIAAKDPESVQWPPEVIADGPIALARLIPAGVDVRGNATRARIVLFRKPIERRAKDTEELGELLHEILVAQVAIYLDVDPSVIDPTIDD

3e11A

0.20

0.16

0.79

2.66

MUSTER

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLH-GY--

3e11A

0.20

0.16

0.80

5.18

dPPAS

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLELGY--

3e11A

0.20

0.16

0.79

5.62

wdPPAS

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLH-GY--

3e11A

0.19

0.15

0.78

3.25

wMUSTER

------------VYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLH-GY--

3e11A

0.20

0.16

0.79

4.07

wPPAS

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLH-GY--

3e11A

0.21

0.16

0.77

13.97

dPPAS2

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERL------

3e11A

0.20

0.16

0.79

3.49

PPAS

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLH-GY--

3e11A

0.20

0.16

0.80

4.19

Env-PPAS

-----------GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDD----------PELLGLYVGIPLTE----RTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELY--

2ejqB

0.16

0.12

0.70

0.97

MUSTER

---------------TYEAFVELVERLWEEVPEDFKRGLQGVHVFPEAKPEPGLE--------------GVWRLGEYLDPGGR--------HIALYYGSFLEVAGEGFDWEAEVWETMLHELRHHL-RDDLVQE----D

2ejqB

0.15

0.10

0.68

1.41

dPPAS

---------------TYEAFVELVERLWEEVPEDFKRGLQGVHVFPEAKPEPG--------------LEGVWRLGEYLDPGGR--------HIALYYGSFLEVAGEGFDWEAEVWETMLHELRHHL---ESLA----GR

(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=0.20

Estimated TM-score = 0.74±0.11

Estimated RMSD = 4.2±2.8Å

Download Model 2

C-score=-1.54

Download Model 3

C-score=-2.63

Download Model 4

C-score=-2.50

Download Model 5

C-score=-0.60

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	3e11A	0.737	1.80	0.196	0.806
2	1xm5A	0.590	3.32	0.102	0.777
3	1oz9A	0.571	3.69	0.114	0.799
4	3cmnA	0.570	2.99	0.040	0.763
5	1jkyA	0.538	3.75	0.078	0.748
6	3o0yA2	0.534	3.67	0.055	0.755
7	3zukA	0.530	4.19	0.092	0.784
8	1r1hA	0.527	4.01	0.058	0.763
9	4iuwA2	0.521	4.20	0.075	0.799
10	2mzeA	0.519	4.18	0.139	0.799

(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	0.09	5	2ovxA	4MR	Rep, Mult	64,65,66,67,117,120,121,123
2	0.05	3	3j47V	III	Rep, Mult	118,122,125
3	0.05	3	1eubA	CA	Rep, Mult	69,70,71,72,74,98,101
4	0.04	2	2hu5A	GLY	Rep, Mult	20,97
5	0.04	2	3wmn2	BCL	Rep, Mult	122,126
6	0.02	1	3wu2h	CLA	Rep, Mult	110,114
7	0.02	1	1ec7A	MG	Rep, Mult	47,48,87
8	0.02	1	1eakA	CA	Rep, Mult	73,74,81,90
9	0.02	1	4g1vA	NO2	Rep, Mult	28,95
10	0.02	1	2xs4A	MG	Rep, Mult	32,40
11	0.02	1	4il6R	HEM	Rep, Mult	27,31
12	0.02	1	1px7B	CA	Rep, Mult	105,109
13	0.02	1	2zyqB	TAR	Rep, Mult	11,12
14	0.02	1	1xmiE	ATP	Rep, Mult	20,21
15	0.02	1	3npyA	ZN	Rep, Mult	18,92
16	0.02	1	1utzB	PF3	Rep, Mult	130,131,135
17	0.02	1	1fjqA	ACN	Rep, Mult	34,39,42,122,126
18	0.02	1	1gkcA	CA	Rep, Mult	43,72,73,79

	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	1eakA	0.433	4.98	0.089	0.777	3.4.24.24	NA
2	0.060	2jsdA	0.497	3.74	0.086	0.734	3.4.24.-	NA
3	0.060	1su3B	0.505	4.13	0.130	0.784	3.4.24.7	NA
4	0.060	1khoA	0.486	3.47	0.061	0.676	3.1.4.3	21
5	0.060	1jizA	0.483	3.99	0.123	0.741	3.4.24.65	NA
6	0.060	1ge7A	0.500	2.86	0.085	0.647	3.4.24.20	NA
7	0.060	1ks0A	0.138	4.07	0.035	0.216	3.4.24.24	114
8	0.060	3dwbA	0.484	4.36	0.085	0.791	3.4.24.71	NA
9	0.060	3dslA	0.484	4.40	0.058	0.763	3.4.24.49	NA
10	0.060	1bzsA	0.487	3.90	0.113	0.734	3.4.24.34	NA
11	0.060	3b2zF	0.492	4.45	0.048	0.770	3.4.24.82	19,27
12	0.060	1zkxB	0.479	3.44	0.108	0.655	3.4.24.69	NA
13	0.060	1t3cA	0.479	3.55	0.125	0.662	3.4.24.69	NA
14	0.060	1l6jA	0.512	4.27	0.041	0.813	3.4.24.35	NA
15	0.060	1fblA	0.485	3.97	0.130	0.741	3.4.24.7	NA
16	0.060	1gkcA	0.484	4.10	0.122	0.748	3.4.24.35	NA
17	0.060	3ba0A	0.489	3.77	0.077	0.734	3.4.24.65	NA
18	0.060	1jkyA	0.538	3.75	0.078	0.748	3.4.24.83	101
19	0.060	2hb6A	0.491	4.48	0.059	0.813	3.4.11.1	21

(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	0.09	0.463	4.15	0.08	0.71	1xaxA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
1	0.07	0.571	3.69	0.11	0.80	1oz9A	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
2	0.07	0.590	3.32	0.10	0.78	1xm5A	GO:0000478 GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006412 GO:0006508 GO:0008270 GO:0009408 GO:0016151 GO:0016787 GO:0016892 GO:0030490 GO:0031564 GO:0042254 GO:0042274 GO:0046872
3	0.07	0.510	3.80	0.10	0.74	1tviA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
4	0.07	0.483	3.44	0.08	0.70	4fxqA	GO:0000166 GO:0003824 GO:0005576 GO:0006508 GO:0008237 GO:0009405 GO:0016740 GO:0016779 GO:0046872
5	0.07	0.504	3.76	0.07	0.73	1xfuA	GO:0000166 GO:0003824 GO:0004016 GO:0005516 GO:0005524 GO:0005576 GO:0005829 GO:0005886 GO:0006171 GO:0006508 GO:0008237 GO:0008294 GO:0009405 GO:0010008 GO:0016829 GO:0046872 GO:0052007
6	0.07	0.538	3.75	0.08	0.75	1jkyA	GO:0000122 GO:0001933 GO:0003824 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0010008 GO:0010629 GO:0016787 GO:0035897 GO:0043409 GO:0044533 GO:0046872 GO:0061136 GO:0097300 GO:1903140
7	0.07	0.543	3.80	0.10	0.76	1zxvA	GO:0003824 GO:0005576 GO:0006508 GO:0008237 GO:0009405 GO:0046872
8	0.06	0.399	4.57	0.04	0.63	4be4A	GO:0016787
9	0.06	0.307	5.95	0.07	0.65	1b8pA	GO:0003824 GO:0005975 GO:0006099 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
10	0.06	0.331	4.59	0.09	0.57	1ufyA	GO:0004106 GO:0005737 GO:0008652 GO:0009073 GO:0016853 GO:0046417
11	0.06	0.296	4.37	0.03	0.45	2okfA	GO:0003676 GO:0004518 GO:0090305
12	0.06	0.292	4.63	0.04	0.51	4qnuA	GO:0002098 GO:0006400 GO:0008033 GO:0016300 GO:0016740 GO:0016765 GO:0030488
13	0.06	0.354	5.11	0.06	0.65	4yzrA	GO:0004497 GO:0005506 GO:0005886 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0017000 GO:0020037 GO:0046872 GO:0055114
14	0.06	0.290	5.06	0.03	0.53	5b8iB	GO:0000754 GO:0005509 GO:0005634 GO:0005829 GO:0005955 GO:0006873 GO:0008597 GO:0016311 GO:0031505 GO:0032153 GO:0050790
15	0.06	0.290	4.86	0.05	0.49	2h8kA	GO:0004027 GO:0004062 GO:0005737 GO:0006790 GO:0008146 GO:0016740
16	0.06	0.314	5.00	0.04	0.56	2v1uA	GO:0000166 GO:0003677 GO:0005524 GO:0006260
17	0.06	0.285	4.01	0.06	0.41	2cwjA	GO:0016787
18	0.06	0.291	5.13	0.04	0.52	3hinA	GO:0003824 GO:0003859 GO:0008152 GO:0016829

Consensus prediction of GO terms

Molecular Function	GO:0004519	GO:0046914	GO:0004175	GO:0008237	GO:0004540
GO-Score	0.52	0.52	0.52	0.52	0.52
Biological Processes	GO:0034470	GO:0016072	GO:0042254	GO:0090501	GO:0006508
GO-Score	0.52	0.52	0.52	0.42	0.31
Cellular Component	GO:0044424
GO-Score	0.52

(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.