I-TASSER results

I-TASSER results for job id Rv3363c

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

Input Sequence in FASTA format

>protein (122 residues)
MFNPAGDRPKAGLVRPYTLTAGRTGTDVDLPLQAPVQTLPAGPAGRWPAYDMRRRILQLC
IGSPSVAEISARLDLPVGVARVLVGDLVTSGYLRVHATLTDRSTRDERHELIGRTLRGLK
AL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFNPAGDRPKAGLVRPYTLTAGRTGTDVDLPLQAPVQTLPAGPAGRWPAYDMRRRILQLCIGSPSVAEISARLDLPVGVARVLVGDLVTSGYLRVHATLTDRSTRDERHELIGRTLRGLKAL
Prediction	CCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEHCCCCCCCCCCCCHHHHHHHHHHHHHC
Conf.Score	99988888888887865554888888888766899997689888888899899999999858875899999869994799999999999899899679988778898999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFNPAGDRPKAGLVRPYTLTAGRTGTDVDLPLQAPVQTLPAGPAGRWPAYDMRRRILQLCIGSPSVAEISARLDLPVGVARVLVGDLVTSGYLRVHATLTDRSTRDERHELIGRTLRGLKAL
Prediction	86554476764320211020122343536040201020334445554434411320141055331001002317230200200011025333031343446564454325004301531476
	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

CCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEHCCCCCCCCCCCCHHHHHHHHHHHHHC
MFNPAGDRPKAGLVRPYTLTAGRTGTDVDLPLQAPVQTLPAGPAGRWPAYDMRRRILQLCIGSPSVAEISARLDLPVGVARVLVGDLVTSGYLRVHATLTDRSTRDERHELIGRTLRGLKAL

3i71B

0.19

0.09

0.48

1.68

dPPAS

----------------------------------------------AESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKRSSRYRLKP------------------

3i71B

0.19

0.09

0.48

1.14

wdPPAS

----------------------------------------------AESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKRSSRYRLKP------------------

3i71B

0.19

0.09

0.48

3.46

dPPAS2

----------------------------------------------AESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKRSSRYRLKP------------------

3majA2

0.20

0.10

0.48

1.37

dPPAS

--------------------------------------------EGEPDTGDRTRILALLGSPVGIDDLIRLSGISPAVVRTILLELELAGRLERHGGSLVSL-------------------

1z05A1

0.11

0.06

0.52

1.07

wdPPAS

---------------------------------------------DHIKQINAGRVYKLIDQPISRIDLSKESELAPASITKITRELIDAHLIHETTVQEAISRGRPN--------------

1z05A1

0.11

0.06

0.52

2.83

dPPAS2

---------------------------------------------DHIKQINAGRVYKLIDQPISRIDLSKESELAPASITKITRELIDAHLIHETTVQEAISRGRPN--------------

2krfA

0.12

0.07

0.57

1.34

dPPAS

----------------------------------------SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNK-----------LNVGSRTEAVLIAKSDGVL--

1jhhA1

0.18

0.09

0.50

1.07

wdPPAS

----------------------------------------------KALTARQQEVFDLIRDPPTRAEIAQRLGF--NAAEEHLKALARKGVIEIVSGASRG-LQEEEEG------------

1jhhA1

0.18

0.09

0.51

2.81

dPPAS2

----------------------------------------------KALTARQQEVFDLIRDPPTRAEIAQRLGFRPNAAEEHLKALARKGVIEIVSGASRGQEEEEG--------------

2p8tA1

0.19

0.11

0.55

1.33

dPPAS

----------------------------------------------EYTVEDVLAVIFLLKEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKGHFLTLKGKEIRDKLLS---------

(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=-3.49

Estimated TM-score = 0.33±0.11

Estimated RMSD = 12.3±4.4Å

Download Model 2

C-score=-3.74

Download Model 3

C-score=-3.83

Download Model 4

C-score=-4.17

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	1a04A	0.490	3.37	0.127	0.647
2	1z6tB	0.481	4.16	0.063	0.721
3	2kkoA	0.476	2.78	0.163	0.590
4	5dlqB	0.476	4.58	0.073	0.844
5	1r1uC	0.475	2.65	0.134	0.582
6	3lfkA	0.470	3.37	0.071	0.680
7	1fokA	0.469	3.89	0.092	0.664
8	1r23A	0.468	3.23	0.098	0.607
9	3f72B	0.468	2.81	0.096	0.582
10	5ehkA	0.466	4.26	0.107	0.730

(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	6	1je8A	NUC	Rep, Mult	49,51,52,75,76,78,79,82,83
2	0.08	4	2hozA	PMP	Rep, Mult	22,24
3	0.04	2	3gw20	III	Rep, Mult	41,45,46,49,51,54,58,118,121,122
4	0.04	2	4a12A	NUC	Rep, Mult	52,75,76,78,79,82
5	0.04	2	1u2w0	III	Rep, Mult	44,45,46,49,54,58,65,67,68,71,72,90,116,118,119,122
6	0.04	2	4kt0J	CLA	Rep, Mult	111,115,119
7	0.02	1	1zb8B	PE4	Rep, Mult	23,36,91,92
8	0.02	1	2vunA	FE	Rep, Mult	68,96
9	0.02	1	3a8mB	TAN	Rep, Mult	17,23
10	0.02	1	2rb1X	261	Rep, Mult	15,17
11	0.02	1	2h27A	NUC	Rep, Mult	60,65,66,81,85,86,88
12	0.02	1	2id3B	CA	Rep, Mult	68,72
13	0.02	1	5ktqA	DCP	Rep, Mult	66,77,81,85

	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	1bgxT	0.459	4.76	0.110	0.803	2.7.7.7	NA
2	0.060	2x58A	0.443	4.34	0.061	0.738	5.3.3.8,4.2.1.17,1.1.1.35	NA
3	0.060	1z11A	0.439	4.58	0.042	0.730	1.14.14.1	NA
4	0.060	1ffyA	0.440	4.74	0.046	0.803	6.1.1.5	NA
5	0.060	2zbzA	0.440	4.80	0.082	0.779	1.14.14.1	NA
6	0.060	1bgpA	0.424	4.44	0.055	0.705	1.11.1.7	55
7	0.060	3kalA	0.424	4.74	0.043	0.770	6.3.2.3	NA
8	0.060	1zcjA	0.444	4.40	0.061	0.746	1.1.1.35	NA
9	0.060	2wm4A	0.430	4.58	0.102	0.746	1.14.-.-	NA
10	0.060	2cfoB	0.437	4.15	0.087	0.689	6.1.1.17	NA
11	0.060	1umbA	0.418	4.85	0.082	0.762	1.2.4.4	96
12	0.060	1ixsB	0.429	3.91	0.103	0.623	3.6.4.12	94
13	0.060	1oyyA	0.437	4.18	0.045	0.705	3.6.4.12	114,117,118
14	0.060	1um9C	0.333	4.67	0.038	0.574	1.2.4.4	109
15	0.060	1c8bA	0.439	4.35	0.055	0.713	3.4.24.78	29,85
16	0.060	3igxA	0.427	4.48	0.105	0.713	2.2.1.2	25
17	0.060	1tazA	0.429	4.63	0.064	0.730	3.1.4.17	111
18	0.060	1mgtA	0.425	4.33	0.036	0.680	2.1.1.63	96
19	0.060	3c6gB	0.460	4.55	0.050	0.746	1.14.13.15	99,109

(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	0.14	0.490	3.37	0.13	0.65	1a04A	GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005829 GO:0006351 GO:0006355 GO:0010468 GO:0042128 GO:0090352
1	0.07	0.389	2.95	0.11	0.50	1fseB	GO:0003677 GO:0006351 GO:0006355
2	0.07	0.449	3.55	0.09	0.61	3p7nA	GO:0000155 GO:0000160 GO:0000166 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0018298 GO:0023014
3	0.07	0.444	2.66	0.07	0.55	1yioA	GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872
4	0.07	0.428	3.79	0.06	0.60	3klnA	GO:0000166 GO:0003677 GO:0003700 GO:0006351 GO:0006355
5	0.07	0.442	2.80	0.07	0.56	4gvpA	GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0046677
6	0.06	0.436	3.01	0.13	0.57	1x3uA	GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0009399 GO:0046872
7	0.06	0.417	2.50	0.08	0.51	4y13A	GO:0003677 GO:0006351 GO:0006355
8	0.06	0.396	3.91	0.11	0.55	3c3wA	GO:0000160 GO:0001666 GO:0003677 GO:0003700 GO:0005615 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006351 GO:0006355 GO:0009405 GO:0019217 GO:0022611 GO:0044161 GO:0045893 GO:0072493 GO:0080134
9	0.06	0.418	3.72	0.10	0.59	3cloA	GO:0003677 GO:0006351 GO:0006355
10	0.06	0.434	2.59	0.14	0.53	4wu4A	GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355
11	0.06	0.387	3.19	0.07	0.52	3qp5A	GO:0003677 GO:0006351 GO:0006355
12	0.06	0.429	3.06	0.10	0.56	1p4wA	GO:0000160 GO:0003677 GO:0004871 GO:0005622 GO:0006351 GO:0006355
13	0.06	0.408	5.04	0.07	0.75	3qp6A	GO:0003677 GO:0006351 GO:0006355
14	0.06	0.375	4.05	0.10	0.51	4ldzA	GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355
15	0.06	0.363	4.35	0.04	0.60	1a2oA	GO:0000156 GO:0000160 GO:0004871 GO:0005737 GO:0006935 GO:0007165 GO:0008984 GO:0016787
16	0.06	0.323	4.66	0.02	0.57	5ic5A	GO:0000160 GO:0005622
17	0.06	0.305	4.65	0.07	0.54	1i3cA	GO:0000160 GO:0005622
18	0.06	0.338	4.16	0.06	0.55	1s8nA	GO:0000160 GO:0003723 GO:0005618 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0031564 GO:0040007

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0003677
GO-Score	0.50	0.50	0.35
Biological Processes	GO:0035556	GO:0006355
GO-Score	0.50	0.35
Cellular Component	GO:0005829
GO-Score	0.14

(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.