I-TASSER results

I-TASSER results for job id Rv1156

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

Input Sequence in FASTA format

>protein (195 residues)
MPNLQLVQEPAADALLNANPFALLVGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADY
DPDKFVALCSERPAIHRFPGSMAKRIQALAQIIVDRYDGDAAALWTAGEPDGNELLRRLK
GLPGFGEQKARIFLALLGKQYGVTPKGWQVAAGEFGQPGTYLSVADIVDAGSLGQVRSHK
RQRKAAAKAEGKAPT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MPNLQLVQEPAADALLNANPFALLVGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADYDPDKFVALCSERPAIHRFPGSMAKRIQALAQIIVDRYDGDAAALWTAGEPDGNELLRRLKGLPGFGEQKARIFLALLGKQYGVTPKGWQVAAGEFGQPGTYLSVADIVDAGSLGQVRSHKRQRKAAAKAEGKAPT
Prediction	CCEEHCCCCHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	986765788678888868958999999985888667888999999999889998899859999999999588975688867899999999999999899677876468998999999999799987899999999999985999885456555566777665444579999999999999999999998667899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MPNLQLVQEPAADALLNANPFALLVGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADYDPDKFVALCSERPAIHRFPGSMAKRIQALAQIIVDRYDGDAAALWTAGEPDGNELLRRLKGLPGFGEQKARIFLALLGKQYGVTPKGWQVAAGEFGQPGTYLSVADIVDAGSLGQVRSHKRQRKAAAKAEGKAPT
Prediction	654241364450452047301110001012452425301400430263147130530271426302500574413111454105202400420174261414401456455254015203713421540040001100442704273045213625565223100314457115404513553445356566668
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEHCCCCHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
MPNLQLVQEPAADALLNANPFALLVGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADYDPDKFVALCSERPAIHRFPGSMAKRIQALAQIIVDRYDGDAAALWTAGEPDGNELLRRLKGLPGFGEQKARIFLALLGKQYGVTPKGWQVAAGEFGQPGTYLSVADIVDAGSLGQVRSHKRQRKAAAKAEGKAPT

2abkA1

0.19

0.11

0.58

1.59

MUSTER

-----------TTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVAN--TPAAMLELGVEGVKTYIKTIG----LYNSKAENIIKTCRILLEQHNGEVPE-------D----RAALEALPGVGRKTANVVLNTAFGWPT-----------------------------------------------------

4uobA1

0.14

0.09

0.65

1.53

dPPAS

------------PPRQFPDPLGGLIRTILSQQNTRRVAQRQWEVLTATYP--QWEAALLDGPDGIEATLKSAGG--GLSRMKADYIYGILAHLQEHHGGLSLRFLREFPHTHEQARQALAALPGVGHKTVALVLLFDLR---RPA--------------------------------------------------

2abkA1

0.19

0.11

0.58

2.51

wdPPAS

-----------TTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVAN--TPAAMLELGVEGVKTYIKTIG----LYNSKAENIIKTCRILLEQHNGEV-----------PEDRAALEALPGVGRKTANVVLNTAFGWPT-----------------------------------------------------

4uobA

0.13

0.12

0.92

2.12

wMUSTER

LSRLRDTYAPELPPRQFPDPLGGLIRTILSQQNTRRVAQRQWEVLTATYP--QWEAALLDGPDGIEATLKSAGGG--LSRMKADYIYGILAHLQEHHGGLSLRFLREFPHTHEQARQALAALPGVGHKTVALVLLFDLRRPAMPVDGMERAAKRLE-------LVPAAWN----SHKVERWYAEVMPADWETRFA

2abkA1

0.19

0.11

0.58

2.84

wPPAS

-----------TTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVAN--TPAAMLELGVEGVKTYIKTIG----LYNSKAENIIKTCRILLEQHNGEV-----------PEDRAALEALPGVGRKTANVVLNTAFGWPT-----------------------------------------------------

4uobA1

0.15

0.10

0.65

3.45

dPPAS2

---------P---PRQFPDPLGGLIRTILSQQNTRRVAQRQWEVLTATYP--QWEAALLDGPDGIEATLKSAGG--GLSRMKADYIYGILAHLQEHHGGLSLRFLREFPHTHEQARQALAALPGVGHKTVALVLLFDLR---RPA--------------------------------------------------

4uobA1

0.15

0.10

0.64

1.93

PPAS

---------P---PRQFPDPLGGLIRTILSQQNTRRVAQRQWEVLTATYP--QWEAALLDGPDGIEATLKSAGG---LSRMKADYIYGILAHLQEHHGGLSLRFLREFPHTHEQARQALAALPGVGHKTVALVLLFDLR---RPA--------------------------------------------------

1p59A1

0.21

0.12

0.55

3.38

Env-PPAS

----------------HRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYR--TPHDYIAVPLEELEQDIRSIG----LYRNKARNIQKLCAMLIDKYNGEV-----------PRDRDELMKLPGVGRKTANVVVSTAFG---VP---------------------------------------------------

4uobA1

0.15

0.10

0.64

1.59

MUSTER

---------P---PRQFPDPLGGLIRTILSQQNTRRVAQRQWEVLTATYP--QWEAALLDGPDGIEATLKSAGG---LSRMKADYIYGILAHLQEHHGGLSLRFLREFPHTHEQARQALAALPGVGHKTVALVLLFDLRRPA-----------------------------------------------------

4unfA2

0.21

0.13

0.62

1.47

dPPAS

------------DPTPRRDPMHELISTILSQRTTHADEEAAYQELRTLG---DWDAITLAPTDAVAHAIRRSN----YPESKAPRIQETLRRIKAAPGGYDLDFLRDL--PVKDALKWLTDLPGVGVKTASLVLLFNYA---RPV--------------------------------------------------

(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=-0.40

Estimated TM-score = 0.66±0.13

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-3.27

Download Model 3

C-score=-3.86

Download Model 4

C-score=-1.56

Download Model 5

C-score=-2.39

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	4uobA	0.792	2.69	0.128	0.923
2	1p59A	0.754	2.50	0.159	0.867
3	2abkA	0.743	2.43	0.142	0.856
4	1lwwA	0.737	2.85	0.132	0.892
5	1keaA	0.736	2.51	0.107	0.862
6	4unfA	0.727	3.00	0.149	0.897
7	1pu6A	0.725	2.93	0.149	0.892
8	3f10A	0.723	2.95	0.122	0.867
9	1kqjA	0.720	2.47	0.139	0.846
10	3n5nX	0.713	2.77	0.148	0.867

(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	0.27	33	1lwyA	NUC	Rep, Mult	30,31,32,33,34,35,81,122,123,124,125,126,127,128,129,146,147
2	0.25	26	2i5wA	NUC	Rep, Mult	31,32,81,85,122,123,124,125,126,127,128,129
3	0.04	5	1ornA	QNA	Rep, Mult	32,37,70,71,72,73,78,79,80,81
4	0.01	1	2nobA	QNA	Rep, Mult	37,66,80,81,82,172
5	0.01	1	1ornA	NA	Rep, Mult	120,121,122,123,125
6	0.01	1	2nofA	QNA	Rep, Mult	120,126,127,128

	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	0.194	1mudA	0.718	2.47	0.139	0.846	3.2.2.-	32,136
2	0.188	2abkA	0.743	2.43	0.142	0.856	4.2.99.18	NA
3	0.158	3fhgA	0.708	3.27	0.145	0.882	4.2.99.18	NA
4	0.092	1keaA	0.736	2.51	0.107	0.862	3.2.2.-	NA
5	0.079	3fhfA	0.687	3.29	0.119	0.856	4.2.99.18	NA
6	0.067	3f0zA	0.724	2.80	0.118	0.862	4.2.99.18	NA
7	0.060	3cf4A	0.442	5.21	0.079	0.744	1.2.99.2	125,128
8	0.060	1xqoA	0.611	3.80	0.114	0.841	4.2.99.18	NA
9	0.060	1occA	0.430	5.35	0.063	0.749	1.9.3.1	125
10	0.060	1w07B	0.435	5.48	0.051	0.744	1.3.3.6	NA
11	0.060	1y9mA	0.453	5.33	0.033	0.769	3.2.1.80	64,67
12	0.060	1n6bA	0.441	4.57	0.058	0.661	1.14.14.1	65
13	0.060	1kg5A	0.720	2.47	0.145	0.846	3.2.2.-	NA
14	0.060	1szqA	0.435	4.66	0.041	0.682	4.2.1.79	23,51,129
15	0.060	1xg7A	0.618	3.95	0.072	0.846	4.2.99.18	85
16	0.060	2jhnA	0.676	3.45	0.161	0.856	3.2.2.21	NA
17	0.060	1fn7A	0.737	2.88	0.132	0.892	4.2.99.18,3.2.2.-	NA
18	0.060	2z1qB	0.441	5.56	0.059	0.754	1.3.99.3	NA
19	0.060	2ac1A	0.451	5.55	0.040	0.785	3.2.1.26	NA
20	0.060	2aeyA	0.446	5.47	0.072	0.769	3.2.1.80	NA
21	0.060	3i39X	0.440	5.22	0.074	0.739	1.2.99.2	NA
22	0.060	1p7mA	0.531	4.15	0.107	0.754	3.2.2.20	138
23	0.060	1y4wA	0.452	5.33	0.044	0.769	3.2.1.80	NA
24	0.060	1dizA	0.663	3.08	0.167	0.826	3.2.2.21	NA
25	0.060	1utwF	0.434	5.54	0.052	0.764	3.2.1.26	17

(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	0.42	0.667	3.11	0.16	0.83	3ogdA	GO:0003824 GO:0003905 GO:0005737 GO:0006281 GO:0006284 GO:0006307 GO:0006974 GO:0008725 GO:0016787 GO:0043916 GO:0052821 GO:0052822
1	0.32	0.749	2.54	0.17	0.87	1ornA
2	0.30	0.741	2.85	0.13	0.89	2xhiA	GO:0002526 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0004519 GO:0005634 GO:0005654 GO:0005739 GO:0006281 GO:0006284 GO:0006289 GO:0006355 GO:0006974 GO:0006979 GO:0007568 GO:0008017 GO:0008152 GO:0008534 GO:0009314 GO:0009416 GO:0016363 GO:0016607 GO:0016787 GO:0016798 GO:0016829 GO:0019104 GO:0032355 GO:0032357 GO:0033158 GO:0033683 GO:0034039 GO:0042493 GO:0043066 GO:0043234 GO:0045007 GO:0045008 GO:0045471 GO:0051593 GO:0071276 GO:1901291
3	0.20	0.652	3.59	0.16	0.84	2yg8A	GO:0003824 GO:0006281 GO:0006284 GO:0008152 GO:0016798 GO:0019104
4	0.20	0.723	2.95	0.12	0.87	3f10A	GO:0003684 GO:0003824 GO:0006281 GO:0006284 GO:0006289 GO:0008534
5	0.19	0.792	2.69	0.13	0.92	4uobA	GO:0003824 GO:0004519 GO:0006281 GO:0006284 GO:0046872 GO:0051536 GO:0051539 GO:0090305
6	0.18	0.678	3.49	0.14	0.88	3s6iD	GO:0003684 GO:0003824 GO:0003905 GO:0005634 GO:0006281 GO:0006284 GO:0006285 GO:0006307 GO:0006974 GO:0008725 GO:0016787 GO:0032131 GO:0032993 GO:0043916 GO:0045007 GO:0052820 GO:0052821 GO:0052822
7	0.18	0.727	3.00	0.15	0.90	4unfA	GO:0003824 GO:0003906 GO:0004519 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0051536 GO:0051539 GO:0090305
8	0.17	0.676	3.45	0.16	0.86	2jhnA	GO:0003824 GO:0006281 GO:0006284
9	0.15	0.547	3.41	0.10	0.67	4evvA	GO:0000785 GO:0003677 GO:0003824 GO:0005634 GO:0005654 GO:0005737 GO:0006281 GO:0006306 GO:0006974 GO:0007095 GO:0008263 GO:0008630 GO:0009314 GO:0016787
10	0.13	0.725	2.93	0.15	0.89	1pu6A	GO:0003677 GO:0003824 GO:0004519 GO:0006281 GO:0006284 GO:0090305
11	0.13	0.743	2.43	0.14	0.86	2abkA	GO:0000703 GO:0003677 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006285 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0016829 GO:0019104 GO:0034644 GO:0046872 GO:0051536 GO:0051539
12	0.12	0.716	2.60	0.17	0.85	4yprA	GO:0003677 GO:0003824 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0019104 GO:0046872 GO:0051536 GO:0051539
13	0.12	0.720	2.47	0.14	0.85	1kg5A	GO:0003677 GO:0003824 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0019104 GO:0046872 GO:0051536 GO:0051539
14	0.11	0.736	2.51	0.11	0.86	1keaA	GO:0003677 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0051536 GO:0051539
15	0.11	0.708	2.83	0.15	0.87	3n5nY	GO:0003677 GO:0003824 GO:0005634 GO:0005654 GO:0005739 GO:0006281 GO:0006284 GO:0006298 GO:0006974 GO:0006979 GO:0008152 GO:0016787 GO:0016798 GO:0019104 GO:0032405 GO:0032406 GO:0032407 GO:0032408 GO:0045007 GO:0046872 GO:0051536 GO:0051539
16	0.07	0.657	3.48	0.13	0.85	2h56A	GO:0003824 GO:0006281 GO:0006284 GO:0008152 GO:0016798
17	0.07	0.712	2.75	0.11	0.86	4ejyA	GO:0003684 GO:0003824 GO:0006281 GO:0006284 GO:0006289 GO:0008534
18	0.06	0.348	4.99	0.05	0.57	4o26A	GO:0000333 GO:0000781 GO:0003677 GO:0003721 GO:0003723 GO:0003964 GO:0005634 GO:0005694 GO:0006278 GO:0016740 GO:0016779 GO:0022616 GO:0030529 GO:0046872
19	0.06	0.351	5.40	0.05	0.60	4lmoA	GO:0000333 GO:0000781 GO:0003677 GO:0003721 GO:0003723 GO:0003964 GO:0005634 GO:0005694 GO:0006278 GO:0016740 GO:0016779 GO:0022616 GO:0030529 GO:0046872
20	0.06	0.304	5.91	0.02	0.55	2gcaA	GO:0000166 GO:0004326 GO:0005524 GO:0006730 GO:0009058 GO:0009396 GO:0016874 GO:0046901
21	0.06	0.276	6.02	0.06	0.51	3zc0B	GO:0043565

Consensus prediction of GO terms

Molecular Function	GO:0043916	GO:0052822	GO:0008725	GO:0052821	GO:0032357	GO:0034039	GO:0008017
GO-Score	0.42	0.42	0.42	0.42	0.30	0.30	0.30
Biological Processes	GO:0006307	GO:0051593	GO:0043066	GO:0045471	GO:0033158	GO:0007568	GO:1901291	GO:0045008	GO:0009416	GO:0071276	GO:0002526	GO:0032355	GO:0006355	GO:0045007	GO:0006979	GO:0033683	GO:0042493
GO-Score	0.42	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30	0.30
Cellular Component	GO:0016363	GO:0043234	GO:0005739	GO:0016607
GO-Score	0.30	0.30	0.30	0.30

(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.