I-TASSER results

I-TASSER results for job id Rv2668

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

Input Sequence in FASTA format

>protein (173 residues)
MRHWLIVLATLLVAAAGVAAANDVPRAWAGDAPIGHIGDTLRVDTGTYVADVTVSSVVPV
DPPPGFGYTRSGVPVKSFPDSSVTRADVTVRAVRVPNSFILATNFSFTGVTPFADAYKPR
PCDASDWLDAALGNAPQGSIVRGGVYWDAYRDPVSVVVLLDEKTGQHLAQWNL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRHWLIVLATLLVAAAGVAAANDVPRAWAGDAPIGHIGDTLRVDTGTYVADVTVSSVVPVDPPPGFGYTRSGVPVKSFPDSSVTRADVTVRAVRVPNSFILATNFSFTGVTPFADAYKPRPCDASDWLDAALGNAPQGSIVRGGVYWDAYRDPVSVVVLLDEKTGQHLAQWNL
Prediction	CCEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEHCCCEEEEEEHCCEHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEHCCCCHHHHEEEEEEHCEHCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEHCEEEEEHCCCCCCEEEEHCCCCCCCCCCCCC
Conf.Score	97346789999999875445788887666788887788569998575899999755565899999998889998999999865778999999758866664455788556578876677788997999999875899878985688986578876699976888876555689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRHWLIVLATLLVAAAGVAAANDVPRAWAGDAPIGHIGDTLRVDTGTYVADVTVSSVVPVDPPPGFGYTRSGVPVKSFPDSSVTRADVTVRAVRVPNSFILATNFSFTGVTPFADAYKPRPCDASDWLDAALGNAPQGSIVRGGVYWDAYRDPVSVVVLLDEKTGQHLAQWNL
Prediction	64300101212333333323344334444462221313440304353100202034146363344232367444343335332230402042253333202112131432334244244444632520430144144344041201030244203200112454434145267
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEHCCCEEEEEEHCCEHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEHCCCCHHHHEEEEEEHCEHCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEHCEEEEEHCCCCCCEEEEHCCCCCCCCCCCCC
MRHWLIVLATLLVAAAGVAAANDVPRAWAGDAPIGHIGDTLRVDTGTYVADVTVSSVVPVDPPPGFGYTRSGVPVKSFPDSSVTRADVTVRAVRVPNSFILATNFSFTGVTPFADAYKPRPCDASDWLDAALGNAPQGSIVRGGVYWDAYRDPVSVVVLLDEKTGQHLAQWNL

1lmiA

0.22

0.16

0.73

1.00

MUSTER

---------------------------SAYPIT-GKLGSELTMTDGQVVLGWKVSDLKSS----------TAVIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYR-WQAAGPDTISG--ATIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

1lmiA

0.22

0.16

0.73

1.02

dPPAS

----------------------------SAYPITGKLGSELTMTDGQVVLGWKVSDLKSS----------TAVIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYRLWQAAGPDTISGA--TIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

1lmiA

0.24

0.17

0.71

1.36

wdPPAS

----------------------------SAYPITGKLGSELTMT-GQVVLGWKVSDLKSSTAVPGY-----------PVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYR--QAAGPDTISGA--TIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

1lmiA

0.22

0.16

0.72

1.17

wMUSTER

----------------------------AYPIT-GKLGSELTMTDGQVVLGWKVSDLKSS----------TAVIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYR-WQAAGPDTISG--ATIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

1lmiA

0.26

0.18

0.68

1.37

wPPAS

---------------------------SAY--PTGKLGSELTMT-GQVVLGWKVSDLKSSTAVPG--YP---------VAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYR--QAAGPDTI-----SGPQGEQSTGKIYFDVTGPSPTIVAMNN---MEDLLIWEP

1lmiA

0.22

0.16

0.73

1.64

dPPAS2

----------------------------SAYPITGKLGSELTMTDGQVVLGWKVSDLKSS----------TAVIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYRLWQAAGPDTISGA--TIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

1lmiA

0.22

0.16

0.71

1.30

PPAS

---------------------------SAYPIT-GKLGSELTMTDTVVVLGWKVSDLKSS----------TAVIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYR-WQAAGPDTI-----SGPQGEQSTGKIYFDVTGPSPTIVAMNN--GMEDLLIWEP

1lmiA

0.22

0.16

0.73

1.14

Env-PPAS

---------------------------SAYPIT-GKLGSELTMTDTVVVLGWKVSDLKSSTA----------VIPGYPVAGQVWEATATVNAIRSVTPAVS----QFNARTADGINYRVWQAAGPDTISGA--TIPQGEQSTGKIYFDVTGPSPTIVAMNNG--MEDLLIWEP

4lesA

0.15

0.12

0.75

0.71

MUSTER

---------------------------SKIKEKEYAVNKDFHTPK----FDVTVKRVVERDKVGK----ESIGFQKPEDGHVFIVVEAEGKNITEPKLAFLPSVDLVDE---NDNAYQS-DVWAASSYDVEKGELKPGEVKRQNKVYVINKDTGKWYVVVNNEYKEQIK----

4lesA

0.13

0.10

0.76

0.59

dPPAS

---------------------------SKIKEKEYAVNKDFHTPK----FDVTVKRVVERDKVGK----ESIGFQKPEDGHVFIVVEAEGKNITSEPKLAFLPSVDLVD--ENDNAYQS-DVWAASSYDVEKGELKPGEVKRQNKVYVINKEKFDTYVVVNNEYKEQIK----

(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=-1.93

Estimated TM-score = 0.48±0.15

Estimated RMSD = 9.3±4.6Å

Download Model 2

C-score=-3.27

Download Model 3

C-score=-3.03

Download Model 4

C-score=-4.28

Download Model 5

C-score=-4.09

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	1lmiA	0.693	1.28	0.205	0.734
2	3cfuA	0.526	3.31	0.134	0.670
3	5a7mA	0.512	4.33	0.037	0.757
4	4lesA	0.511	3.63	0.157	0.682
5	4d0jA	0.511	4.26	0.071	0.746
6	5bxgA	0.510	4.17	0.058	0.746
7	3qfgA	0.509	3.42	0.059	0.682
8	4r4gA	0.506	3.20	0.149	0.647
9	1o75B1	0.498	4.22	0.075	0.757
10	4eaeA	0.495	4.09	0.026	0.728

(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	0.05	3	2vuoA	NAG	Rep, Mult	55,89,142
2	0.05	3	4lm8A	CA	Rep, Mult	53,54,171
3	0.05	3	1swiC	BNZ	Rep, Mult	5,9
4	0.05	3	1p7hM	QNA	Rep, Mult	148,150,151,156
5	0.04	2	3mxgA	XLS	Rep, Mult	171,172
6	0.04	2	2o93M	QNA	Rep, Mult	34,38,39,40,43
7	0.04	2	3ictA	FAD	Rep, Mult	117,119
8	0.02	1	2o93O	QNA	Rep, Mult	33,41,170
9	0.02	1	1smyF	MG	Rep, Mult	7,8,101
10	0.02	1	1o75B	PDX	Rep, Mult	132,140,142
11	0.02	1	2f2hA	XTG	Rep, Mult	41,44
12	0.02	1	2qkiD	III	Rep, Mult	87,88,89,90,99,120,145
13	0.02	1	1uwwA	CA	Rep, Mult	87,144
14	0.02	1	3m9gA	ZN	Rep, Mult	115,165
15	0.02	1	1j9sA	NO2	Rep, Mult	129,167,169
16	0.02	1	3q79A	3CX	Rep, Mult	20,164
17	0.02	1	3pczA	BAM	Rep, Mult	44,80,82,98,99

	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	3hhsA	0.452	4.61	0.043	0.699	1.14.18.1	NA
2	0.060	2qhfA	0.430	4.92	0.105	0.699	4.2.3.5	154
3	0.060	1lnsA	0.430	4.87	0.063	0.676	3.4.14.11	NA
4	0.060	1g0dA	0.427	4.23	0.080	0.630	2.3.2.13	NA
5	0.060	1umfC	0.429	4.91	0.059	0.688	4.2.3.5	71
6	0.060	1qbaA	0.443	4.25	0.113	0.659	3.2.1.52	108,110
7	0.060	3im1A	0.450	4.73	0.056	0.694	3.6.4.13	NA
8	0.060	1rm6A	0.434	5.35	0.064	0.775	1.3.99.20	NA
9	0.060	2x42A	0.486	4.18	0.095	0.705	3.2.1.21	46
10	0.060	1gc5A	0.448	5.15	0.037	0.751	2.7.1.147	154
11	0.060	1qaxA	0.432	5.03	0.076	0.723	1.1.1.88	NA
12	0.060	3hhsB	0.449	4.46	0.057	0.682	1.14.18.1	NA
13	0.060	1yq2A	0.451	4.43	0.091	0.682	3.2.1.23	NA
14	0.060	2e1qA	0.344	5.52	0.061	0.613	1.17.3.2,1.17.1.4	NA
15	0.060	1dgjA	0.435	5.68	0.055	0.803	1.2.-.-	NA
16	0.060	1gp6A	0.437	4.75	0.039	0.682	1.14.11.19	NA
17	0.060	1jrpB	0.436	4.98	0.056	0.740	1.17.1.4	132,138
18	0.060	1ua4A	0.454	4.99	0.057	0.757	2.7.1.147	NA
19	0.060	1q1lA	0.430	4.68	0.062	0.676	4.2.3.5	145

(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	0.36	0.693	1.28	0.20	0.73	1lmiA	GO:0005576 GO:0005615 GO:0005618
1	0.21	0.542	3.17	0.14	0.68	3cfuA	GO:0005886 GO:0016020
2	0.07	0.511	4.26	0.07	0.75	4d0jA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
3	0.07	0.514	3.23	0.15	0.66	4r4gA	GO:0005886 GO:0016020
4	0.07	0.486	4.02	0.10	0.69	2x41A	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
5	0.06	0.382	5.94	0.07	0.71	4i8dB	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
6	0.06	0.366	5.42	0.07	0.66	4iibA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
7	0.06	0.358	5.11	0.03	0.58	3ut0A	GO:0004553 GO:0005975 GO:0008152 GO:0016798 GO:0046872
8	0.06	0.505	4.26	0.09	0.74	5fjiA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
9	0.06	0.353	5.88	0.04	0.67	3wlqA	GO:0004553 GO:0005975 GO:0016787
10	0.06	0.473	4.20	0.08	0.69	4zo6A	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
11	0.06	0.342	5.96	0.03	0.65	4gnvB	GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0016787 GO:0016798 GO:0051301 GO:0071555
12	0.06	0.354	5.39	0.05	0.63	3abzB	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
13	0.06	0.353	5.34	0.06	0.62	3abzA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
14	0.06	0.508	4.27	0.09	0.75	5fjjA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016052 GO:0016787 GO:0016798 GO:0030245 GO:0102483
15	0.06	0.342	5.34	0.04	0.60	3sqlA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
16	0.06	0.330	5.20	0.04	0.57	4gyjA	GO:0004553 GO:0004563 GO:0005576 GO:0005618 GO:0005886 GO:0005975 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0016020 GO:0016787 GO:0016798 GO:0071555
17	0.06	0.496	4.05	0.11	0.71	4i3gB	GO:0004553 GO:0005975
18	0.06	0.322	5.43	0.05	0.59	2oxnA	GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0009273 GO:0016787 GO:0016798 GO:0046677 GO:0051301 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0102483	GO:0008422
GO-Score	0.13	0.13
Biological Processes	GO:0030245
GO-Score	0.07
Cellular Component	GO:0016020	GO:0005618	GO:0005615
GO-Score	0.39	0.36	0.36

(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.