I-TASSER results

I-TASSER results for job id Rv1116A

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

Input Sequence in FASTA format

>protein (91 residues)
MGALGTVRGLQDSNTAFVGALHSGNLLGATGAVLQAPGNAVNGFLFGQTSISQSIDVSPE
YGYELVAVSDPVGGTAGSARAGHGYVHADLR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGALGTVRGLQDSNTAFVGALHSGNLLGATGAVLQAPGNAVNGFLFGQTSISQSIDVSPEYGYELVAVSDPVGGTAGSARAGHGYVHADLR
Prediction	CCCHHHHHHHHHHCCEEHCCCCCCCCHHHHCEEEHCCCCHHCHEHCCCCCHCCCCCCCCCCCCCEHCEEHCCCCCCCCCCCCCCEEHCCCC
Conf.Score	9865778887765754445445687435433456558643343334665444456788888985664565678766766667755655579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGALGTVRGLQDSNTAFVGALHSGNLLGATGAVLQAPGNAVNGFLFGQTSISQSIDVSPEYGYELVAVSDPVGGTAGSARAGHGYVHADLR
Prediction	7433442441454333223224544321223231313343231212234214541524653325314242333333343433312233538
	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

CCCHHHHHHHHHHCCEEHCCCCCCCCHHHHCEEEHCCCCHHCHEHCCCCCHCCCCCCCCCCCCCEHCEEHCCCCCCCCCCCCCCEEHCCCC
MGALGTVRGLQDSNTAFVGALHSGNLLGATGAVLQAPGNAVNGFLFGQTSISQSIDVSPEYGYELVAVSDPVGGTAGSARAGHGYVHADLR

4tweA

0.18

1.00

0.64

MUSTER

RGAEEDFKELQTQGIKLEGTTRYGGVGRGAKAVNAAKHGVAGVLVYTDPADINDGLSSPDETFPNSWYLPPSGVERGSYYEYFGDPLTPYL

4ntqA

0.11

0.09

0.78

0.68

dPPAS

LKGKEAQEAASNLGFDRRIPPQKAPFNSHGQPVFYD----------GKNYITPDIDSHNVTNGWKFN----------SKGKRIGTYDSGLN

1b21A

0.21

0.19

0.89

0.76

wdPPAS

NTFDGVADYLQTYHK-YI-AQALG---ASKGNL--APGKSIGGDIFSNR--EGKLPGKSGSTWREADINYT-SGFRNSDRSSNWYKTTDIR

5g2fA

0.17

0.15

0.90

0.73

wMUSTER

----ANLAAGQSYVRNVALALEAQDP--STGALPTHLTDCLSGFGQRPKTVTATITYLNALDY-VIEASLD-GAALKKVKSSDGTLTS-LP

1b21A

0.21

0.19

0.88

0.65

wPPAS

NTFDGVADYLQTYHK-YI-AQALG---ASKGNL--APGKSIGGDIFSNR--EGKLPGKSG-SWREADINYT-SGFRNSDRSSNWYKTTDIR

3iusA1

0.31

0.25

0.82

0.68

dPPAS2

HGARVLSRALAPQGWRIIGTSRNPDAIRASGEPLLWPGEEPS--LDGVTHLLISTA-PDSGGD-------PVLGDQIAARA------AQFR

1p9hA2

0.26

0.23

0.89

0.77

PPAS

YGA-ASTAQ--KDGVAIARASTSDTGV-AVGFNSKADAK--NSVAIGHSSHVAANHGYSAIGDRSKTVSI---GHESLNRAGKDTV-AQLK

3it6B2

0.22

1.00

0.93

Env-PPAS

TGALVAARQIARDSTALFGSDPNGRVLAAVGAPITLDPDRISVSFNGAAVCVHGVGAPVDLSDADIDITVDLGVGDGQARISHAYVESAYS

5bx9A

0.09

0.93

0.64

MUSTER

YLALQRFLKVTGPKLRPADPPVTEDLPGSFSIGWTREDGRNVWLFWSARGGNVRLPKLK-----EATLHDPLSGKVTPLSGSDG-LEVPVK

1b21A

0.16

0.15

0.97

0.67

dPPAS

NTFDGVADYLQTYHKLPDNYITKGWVASKGNLADVAPGKSIGGDIFSNR--EGKLPGKSGSTWREADINYT-SGFRNSDRSSNWYKTTDHY

(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=-2.75

Estimated TM-score = 0.40±0.13

Estimated RMSD = 9.7±4.6Å

Download Model 2

C-score=-3.47

Download Model 3

C-score=-4.75

Download Model 4

C-score=-3.86

Download Model 5

C-score=-4.50

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	3mbrX	0.517	3.83	0.049	0.901
2	4hizA	0.499	4.11	0.059	0.934
3	3nokA	0.498	3.97	0.048	0.901
4	3gvjA	0.494	4.34	0.046	0.945
5	3jb9L	0.493	4.14	0.093	0.901
6	2iwaA	0.492	3.85	0.037	0.879
7	3c7gA1	0.491	4.36	0.047	0.934
8	1nccN	0.489	4.16	0.071	0.890
9	3zwuA	0.489	3.84	0.062	0.857
10	3w15A	0.486	4.23	0.062	0.846

(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	0.10	5	4awuA	4CH	Rep, Mult	8,12
2	0.08	4	4xniA	78M	Rep, Mult	3,10
3	0.06	3	1v0fC	SIA	Rep, Mult	68,69,70,72,74,75,76
4	0.06	3	4eg2G	URI	Rep, Mult	40,46
5	0.06	3	3gvkB	UUU	Rep, Mult	43,44,46,48,49,50,51,52
6	0.04	2	1cb2A	MAN	Rep, Mult	2,6
7	0.02	1	3s6lC	IOD	Rep, Mult	54,66,69
8	0.02	1	2xzqH	ZN	Rep, Mult	53,62
9	0.02	1	5a43A	DMU	Rep, Mult	10,11,13,15
10	0.02	1	3fvyA	MG	Rep, Mult	27,28,31
11	0.02	1	3c9iB	XE	Rep, Mult	61,66

	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	2cmlC	0.438	4.47	0.080	0.901	3.2.1.18	NA
2	0.060	2vskC	0.449	4.50	0.024	0.912	3.2.1.18	38
3	0.060	1utwF	0.478	4.02	0.037	0.868	3.2.1.26	75
4	0.060	1c9uB	0.465	4.35	0.057	0.890	1.1.5.2,1.1.99.17	70
5	0.060	1cruB	0.465	4.47	0.047	0.901	1.1.5.2	NA
6	0.060	1oygA	0.477	4.23	0.034	0.945	2.4.1.10	NA
7	0.060	1yiqA	0.454	4.50	0.095	0.901	1.1.99.-	NA
8	0.060	1lrwA	0.463	4.36	0.057	0.890	1.1.99.8	NA
9	0.060	3gvjA	0.494	4.34	0.046	0.945	3.2.1.129	38,42,78
10	0.060	1ncaN	0.437	4.56	0.035	0.890	3.2.1.18	NA
11	0.060	1v0zA	0.449	4.46	0.059	0.890	3.2.1.18	NA
12	0.060	1uv4A	0.461	4.30	0.036	0.835	3.2.1.99	NA
13	0.060	1wn1A	0.471	4.28	0.085	0.813	3.4.-.-	NA
14	0.060	2oknA	0.466	4.06	0.026	0.791	3.4.13.9	NA
15	0.060	1jawA	0.450	4.07	0.065	0.780	3.4.11.9	NA
16	0.060	3dr2A	0.459	4.24	0.074	0.879	3.1.1.17	30
17	0.060	2iwaA	0.492	3.85	0.037	0.879	2.3.2.5	NA
18	0.060	1ri6A	0.452	4.53	0.023	0.868	3.1.1.31	NA
19	0.060	1spiA	0.439	4.20	0.066	0.780	3.1.3.11	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	0.07	0.460	4.20	0.08	0.89	4q6kA	GO:0004308 GO:0009405
1	0.07	0.492	3.85	0.04	0.88	2iwaA	GO:0016603 GO:0016740 GO:0016746 GO:0046872
2	0.06	0.424	4.18	0.04	0.78	4fo8C	GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
3	0.06	0.394	3.92	0.04	0.69	3g7gH	GO:0016021
4	0.06	0.498	3.97	0.05	0.90	3nokA	GO:0016603 GO:0046872
5	0.06	0.450	4.66	0.03	0.88	5f9tA	GO:0004308 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
6	0.06	0.320	5.35	0.09	0.76	2vf8B	GO:0000166 GO:0003677 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009380 GO:0009381 GO:0016887 GO:0046872 GO:0090305
7	0.06	0.340	4.72	0.01	0.65	4bi7A	GO:0003824 GO:0004807 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
8	0.06	0.517	3.83	0.05	0.90	3mbrX	GO:0016740 GO:0046872
9	0.06	0.479	4.03	0.02	0.88	3nolA	GO:0016020 GO:0016021 GO:0016740
10	0.06	0.499	4.11	0.06	0.93	4hizA	GO:0008152 GO:0016787 GO:0016798 GO:0016996 GO:0046872
11	0.06	0.305	4.36	0.05	0.59	2xr7A	GO:0016740 GO:0016747
12	0.06	0.303	4.39	0.06	0.60	4uy4B	GO:0007276
13	0.06	0.325	4.53	0.01	0.62	1jasA	GO:0000166 GO:0000209 GO:0000785 GO:0000790 GO:0001701 GO:0001741 GO:0004842 GO:0005524 GO:0005634 GO:0005654 GO:0005657 GO:0005737 GO:0005886 GO:0006281 GO:0006301 GO:0006344 GO:0006511 GO:0006513 GO:0006974 GO:0007283 GO:0007288 GO:0009411 GO:0010845 GO:0016020 GO:0016567 GO:0016740 GO:0031056 GO:0031625 GO:0033128 GO:0033503 GO:0033522 GO:0042493 GO:0042769 GO:0043066 GO:0043161 GO:0043951 GO:0045141 GO:0050821 GO:0051026 GO:0051865 GO:0060070 GO:0061630 GO:0061631 GO:0070076 GO:0070193 GO:0070534 GO:0070936 GO:0070979
14	0.06	0.370	4.97	0.03	0.79	4kraA	GO:0006810 GO:0006811 GO:0009279 GO:0015288 GO:0016020 GO:0016021 GO:0046930 GO:0055085
15	0.06	0.312	5.01	0.03	0.67	3eqnA	GO:0004338 GO:0008152 GO:0016787 GO:0016798
16	0.06	0.312	4.55	0.04	0.63	4zplA	GO:0005509 GO:0005886 GO:0007155 GO:0007156 GO:0016020 GO:0016021
17	0.06	0.336	4.33	0.09	0.64	4rulA	GO:0000287 GO:0003677 GO:0003916 GO:0003917 GO:0005694 GO:0005829 GO:0006265 GO:0016853 GO:0046872
18	0.06	0.293	4.96	0.07	0.62	2xu2A	GO:0003824 GO:0005975

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.36
Biological Processes	GO:0009405	GO:0006508	GO:0070084
GO-Score	0.07	0.07	0.07
Cellular Component	GO:0016021
GO-Score	0.06

(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.