I-TASSER results

I-TASSER results for job id Rv1083

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

Input Sequence in FASTA format

>protein (88 residues)
MNQILLSVIAEGGPGNTGPDFGKASPVGLLVIVLLVIATLFLVRSMNQQLKKVPKSFDRD
HPELDQAADEGTDRDGPARPPGPPHESG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MNQILLSVIAEGGPGNTGPDFGKASPVGLLVIVLLVIATLFLVRSMNQQLKKVPKSFDRDHPELDQAADEGTDRDGPARPPGPPHESG
Prediction	CCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC
Conf.Score	9658999999768999998777678556899999999999999999999997656557778764666665567788778899999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MNQILLSVIAEGGPGNTGPDFGKASPVGLLVIVLLVIATLFLVRSMNQQLKKVPKSFDRDHPELDQAADEGTDRDGPARPPGPPHESG
Prediction	6442113112446557434632443233122133333232211221343145237515775455564256445674466655567778
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC
MNQILLSVIAEGGPGNTGPDFGKASPVGLLVIVLLVIATLFLVRSMNQQLKKVPKSFDRDHPELDQAADEGTDRDGPARPPGPPHESG

2jwaA

0.37

0.15

0.40

1.07

wPPAS

-----------------GPAEQRASPVGILLVVVLGVVFGILIKRRQQKIRK------------------------------------

3j2wE

0.26

0.11

0.43

1.07

dPPAS2

ISTTAMSWVQKITGG-----------VGLIVAVAALILIVVLCVSFSRH---------------------------------------

2mv6A

0.31

0.15

0.48

1.03

wPPAS

MSEPVSLL--------TPSDL---DPLSLILVVILVLLTVLALLSHRRALKQ-P----------------------------------

3j2wE

0.32

0.14

0.42

1.01

wPPAS

ISTTAMSWVQK-----TG---G----VGLIVAVAALILIVVLCVSFSRH---------------------------------------

5ijoJ

0.10

1.00

0.78

MUSTER

LLVLTKMFKEQGFGSRQTNRLVDETMDPFVDRIGYFSALILVEGMDIESLHKCALDDRRELHQFAQDGLICQDMDCLMLTFGDIPHHA

2dalA

0.18

0.12

0.70

0.73

dPPAS

--------------GSSGSSGGSAASSALKGLIQQFTTITGASESVGKHMLEA------CNNNLEMAVTMFLDGGGSGPSSG------

3j2wE

0.32

0.14

0.42

0.90

wdPPAS

ISTTAMSWVQK-----TG---G----VGLIVAVAALILIVVLCVSFSRH---------------------------------------

5sy1A

0.12

0.11

0.95

0.82

wMUSTER

WTHFGILVWQKVD--PKTPQIYKY--YALFGSLPQIACLAFLSFQYPLLLFKGLQNTETANASEDSSYYRDLKKKKPTKISSSTSKPK

2mkvA

0.24

0.14

0.58

0.89

wPPAS

----------LDRWYLGGSPKGDVDPGGLIFAGLAFIVGLLILLSRRFR-NKKRRQINEDEP--------------------------

2dalA

0.18

0.12

0.70

0.96

dPPAS2

--------------GSSGSSGGSAASSALKGLIQQFTTITGASESVGKHMLEA------CNNNLEMAVTMFLDGGGSGPSSG------

(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=-2.70

Estimated TM-score = 0.40±0.14

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-3.07

Download Model 3

C-score=-3.98

Download Model 4

C-score=-4.45

Download Model 5

C-score=-4.18

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	1iduA	0.616	3.73	0.081	0.966
2	1yrlA	0.613	2.94	0.023	0.875
3	5t57A	0.610	3.51	0.060	0.875
4	4tskA	0.610	2.95	0.036	0.841
5	4xdzA	0.608	3.00	0.012	0.841
6	1w27A	0.606	3.37	0.058	0.886
7	4kqwA	0.604	2.93	0.047	0.841
8	3tijA	0.604	3.11	0.045	0.852
9	4xdyA	0.603	3.00	0.083	0.841
10	3ba6A	0.601	3.66	0.129	0.955

(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	0.12	17	3e5uC	3C4	Rep, Mult	40,43,44
2	0.07	12	1ji4A	FE	Rep, Mult	45,49
3	0.06	9	4or2A	CLR	Rep, Mult	27,30,31,34,35
4	0.06	10	4xk81	CLA	Rep, Mult	34,35,38,39,42
5	0.05	9	4ufbD	NAG	Rep, Mult	22,25,28
6	0.04	7	1mz9B	VDY	Rep, Mult	50,53,57
7	0.04	6	3vgxC	III	Rep, Mult	26,29,30,33,37,40,43,44,47
8	0.04	6	5l1gC	GYB	Rep, Mult	36,39,40,43
9	0.02	4	2g38B	MN	Rep, Mult	43,46,47
10	0.02	3	5d92A	8K6	Rep, Mult	27,31
11	0.01	1	2e7fA	CA	Rep, Mult	18,20
12	0.01	1	1f8iB	MG	Rep, Mult	20,69
13	0.01	2	2kp8A	XIG	Rep, Mult	43,46,54,57
14	0.01	2	1kb9D	CDL	Rep, Mult	44,51,52
15	0.01	1	1dxrL	BPB	Rep, Mult	38,42,46,73

	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	3csmA	0.556	3.31	0.059	0.852	5.4.99.5	8
2	0.060	2e5dB	0.546	3.89	0.099	0.909	2.4.2.12	22
3	0.060	3hkzJ	0.538	3.95	0.084	0.875	2.7.7.6	35
4	0.060	1t34A	0.545	3.67	0.057	0.886	4.6.1.2	NA
5	0.060	3ixzA	0.584	3.70	0.047	0.977	3.6.3.10	NA
6	0.060	1y11A	0.581	3.83	0.108	0.920	4.6.1.1	NA
7	0.060	2p0mB	0.545	3.60	0.058	0.818	1.13.11.33	NA
8	0.060	1w27A	0.606	3.37	0.058	0.886	4.3.1.24	NA
9	0.060	1mo7A	0.363	4.37	0.042	0.705	3.6.3.9	44
10	0.060	3fr8B	0.583	2.88	0.024	0.841	1.1.1.86	NA
11	0.060	3tatC	0.543	3.72	0.035	0.795	2.6.1.57	18,24
12	0.060	1yrlC	0.617	2.88	0.023	0.875	1.1.1.86	NA
13	0.060	2hc8A	0.303	4.18	0.063	0.511	3.6.3.-	NA
14	0.060	2rcyA	0.537	3.76	0.024	0.886	1.5.1.2	NA
15	0.060	2jkvA	0.556	3.88	0.069	0.920	1.1.1.44	13
16	0.060	3a1cB	0.341	3.91	0.071	0.625	3.6.3.-	NA
17	0.060	2p0mA	0.554	3.34	0.071	0.807	1.13.11.33	NA
18	0.060	1eulA	0.487	3.14	0.047	0.727	3.6.3.8	NA
19	0.060	3ffzA	0.547	3.80	0.058	0.841	3.4.24.69	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	0.08	0.616	2.92	0.01	0.86	5e4rA	GO:0000166 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0016853 GO:0055114
1	0.08	0.610	2.95	0.04	0.84	4tskA	GO:0000166 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0016853 GO:0046872 GO:0055114
2	0.07	0.554	3.76	0.02	0.91	2rcyA	GO:0000166 GO:0004735 GO:0006561 GO:0016491 GO:0055114
3	0.07	0.603	3.00	0.08	0.84	4xdyA	GO:0000166 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0016853 GO:0055114
4	0.07	0.616	3.73	0.08	0.97	1iduA	GO:0004601 GO:0005576 GO:0016491 GO:0016691 GO:0046872 GO:0055114 GO:0098869
5	0.07	0.604	2.93	0.01	0.86	3ulkA	GO:0000287 GO:0004455 GO:0005829 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0050661 GO:0055114
6	0.07	0.591	2.87	0.02	0.84	1qmgA	GO:0000287 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0009507 GO:0009536 GO:0016491 GO:0042803 GO:0046872 GO:0055114 GO:0070402
7	0.07	0.583	2.88	0.02	0.84	3fr8B	GO:0000287 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0009507 GO:0009536 GO:0016491 GO:0042803 GO:0046872 GO:0055114 GO:0070402
8	0.07	0.586	2.86	0.04	0.81	4xiyA	GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0055114
9	0.07	0.522	3.65	0.05	0.84	4oqyB	GO:0000166 GO:0004616 GO:0016491 GO:0055114
10	0.07	0.483	3.42	0.07	0.73	5je8B	GO:0004616 GO:0008442 GO:0016491 GO:0051287 GO:0055114
11	0.07	0.570	4.10	0.06	0.95	3w36B	GO:0004601 GO:0055114 GO:0098869
12	0.07	0.448	3.04	0.07	0.65	4a6nA	GO:0000166 GO:0016491 GO:0055114 GO:0071949
13	0.07	0.417	4.44	0.10	0.80	3bioB	GO:0008652 GO:0009085 GO:0009089 GO:0016491 GO:0019877 GO:0047850 GO:0055114
14	0.07	0.444	3.79	0.05	0.69	1zlpB	GO:0003824 GO:0008152 GO:0016740 GO:0016787 GO:0016829 GO:0030603 GO:0046872 GO:0047776
15	0.07	0.453	3.63	0.02	0.68	2pv7B	GO:0003824 GO:0004106 GO:0004665 GO:0005737 GO:0006571 GO:0008152 GO:0008652 GO:0008977 GO:0009073 GO:0016491 GO:0016853 GO:0046417 GO:0055114 GO:0070403
16	0.07	0.477	4.00	0.05	0.81	3gvpA	GO:0004013 GO:0005737 GO:0005783 GO:0005829 GO:0006730 GO:0016787 GO:0033353 GO:0043005 GO:0043231
17	0.06	0.384	3.72	0.03	0.60	3pgxA	GO:0016491 GO:0055114
18	0.06	0.415	3.67	0.08	0.67	3wicA	GO:0000166 GO:0005536 GO:0005975 GO:0008270 GO:0016491 GO:0019595 GO:0046872 GO:0047936 GO:0055114 GO:0070401 GO:0070403

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0016616
GO-Score	0.53	0.53	0.42
Biological Processes	GO:0006573	GO:1901607	GO:0009082	GO:0046394	GO:0006549	GO:0055114
GO-Score	0.42	0.42	0.42	0.42	0.42	0.32
Cellular Component	GO:0005576
GO-Score	0.07

(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.