I-TASSER results

I-TASSER results for job id Rv0918

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

Input Sequence in FASTA format

>protein (158 residues)
MHRAGAAVTANVWCRAGGIRMAPRPVIPVATQQRLRRQADRQSLGSSGLPALNCTPIRHT
IDVMATKPERKTERLAARLTPEQDALIRRAAEAEGTDLTNFTVTAALAHARDVLADRRLF
VLTDAAWTEFLAALDRPVSHKPRLEKLFAARSIFDTEG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MHRAGAAVTANVWCRAGGIRMAPRPVIPVATQQRLRRQADRQSLGSSGLPALNCTPIRHTIDVMATKPERKTERLAARLTPEQDALIRRAAEAEGTDLTNFTVTAALAHARDVLADRRLFVLTDAAWTEFLAALDRPVSHKPRLEKLFAARSIFDTEG
Prediction	CCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHEHCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCC
Conf.Score	98776554444555457765688876666665789999875678877787666777655455678898886545777699999999999999989999999999999999999999744447999999999999869988899999998888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MHRAGAAVTANVWCRAGGIRMAPRPVIPVATQQRLRRQADRQSLGSSGLPALNCTPIRHTIDVMATKPERKTERLAARLTPEQDALIRRAAEAEGTDLTNFTVTAALAHARDVLADRRLFVLTDAAWTEFLAALDRPVSHKPRLEKLFAARSIFDTEG
Prediction	74434331303110423314224431121336543444354642555514425244364344324455654633041304662351043016237441130023202520452146333240347205302510552464264046027545415788
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHEHCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCC
MHRAGAAVTANVWCRAGGIRMAPRPVIPVATQQRLRRQADRQSLGSSGLPALNCTPIRHTIDVMATKPERKTERLAARLTPEQDALIRRAAEAEGTDLTNFTVTAALAHARDVLADRRLFVLTDAAWTEFLAALDRPVSHKPRLEKLFAARSIFDTEG

1y9bA

0.25

0.13

0.50

1.17

MUSTER

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

1.62

dPPAS

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

2.32

wdPPAS

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.26

0.13

0.49

1.42

wMUSTER

----------------------------------------------------------------------TLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

2.11

wPPAS

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

2.97

dPPAS2

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

1.87

PPAS

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

1y9bA

0.25

0.13

0.50

1.66

Env-PPAS

---------------------------------------------------------------------TTLPRITARVDVDTQDLLAKAAALAGSSINSFVLNAAIEKAKQVIEREQALKL-SQADAVLLEALDNPAVVNAKLKLASE---------

5a79A

0.15

0.97

0.69

MUSTER

TQVVEAGVFDDWWVHVEAWNLDNLRGINFSVASSRSQVAEYLAALDRDLPADVDRRFAGARGQIGS-PNYLPAPKFFRLDKRTIAELTRLSRLTDQPHNNRDIELNRAKR--TLRDVQPLKDSALHYQYVLIDLQSPVYTRKTFERELALE--WIIPD

3zifN

0.15

0.09

0.61

0.71

dPPAS

RLPKWSGSVQDK----TGSNMLGGVVLP-PNSQAHRTETVGTEATRDNLHAEGARRPEDQTPYMIL------------VEDSLGGLKRRMDLLEESNQQLLATLNRLRTGLAA---------------------------------------------

(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=-3.22

Estimated TM-score = 0.35±0.12

Estimated RMSD = 12.3±4.4Å

Download Model 2

C-score=-3.49

Download Model 3

C-score=-3.71

Download Model 4

C-score=-3.92

Download Model 5

C-score=-4.41

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	2e1rA	0.476	5.09	0.093	0.842
2	4g32A2	0.472	4.32	0.060	0.715
3	3ivtB	0.470	4.91	0.068	0.785
4	3j38z	0.469	5.06	0.054	0.835
5	2yevA	0.465	4.85	0.058	0.766
6	4byfA1	0.456	4.73	0.070	0.703
7	1dgkN	0.455	5.37	0.069	0.829
8	2j69A	0.454	4.69	0.070	0.709
9	4p7hA	0.454	4.54	0.074	0.696
10	4zg4E	0.451	4.54	0.087	0.703

(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	0.11	5	1qhaA	ANP	Rep, Mult	109,116,120
2	0.09	4	4mbeE	III	Rep, Mult	99,102,103,106,107,109,110,113
3	0.07	3	5bqtB	CA	Rep, Mult	97,100
4	0.04	2	5lsjD	III	Rep, Mult	98,102,103
5	0.04	2	2dkiA	XE	Rep, Mult	49,79,86,87,101
6	0.02	1	1qhaB	ANP	Rep, Mult	4,105,108,112,116
7	0.02	1	2ymkA	ZN	Rep, Mult	116,120
8	0.02	1	3tijA	DMU	Rep, Mult	120,127
9	0.02	1	1xrmA	III	Rep, Mult	131,134
10	0.02	1	3pg9A	AZI	Rep, Mult	89,129
11	0.02	1	3vh7E	MG	Rep, Mult	115,118
12	0.02	1	2uxiA	G50	Rep, Mult	59,111

	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	1xmeA	0.447	4.85	0.031	0.715	1.9.3.1	111
2	0.060	3dnyT	0.477	5.08	0.075	0.835	3.6.5.3	NA
3	0.060	2z8yD	0.429	4.78	0.060	0.683	1.2.7.4,1.2.99.2	NA
4	0.060	1no3A	0.441	4.83	0.053	0.722	1.13.11.12	NA
5	0.060	1jcmP	0.345	5.23	0.057	0.614	4.1.1.48,5.3.1.24	NA
6	0.060	1efgA	0.417	5.28	0.090	0.759	3.6.5.3	NA
7	0.060	3eqmA	0.432	4.18	0.045	0.646	1.14.14.1	NA
8	0.060	1ea0A	0.439	5.18	0.075	0.759	1.4.1.13	NA
9	0.060	1n40A	0.395	4.48	0.043	0.589	1.14.-.-	NA
10	0.060	1qlaD	0.409	5.35	0.057	0.715	1.3.99.1	103,106
11	0.060	1darA	0.301	5.76	0.038	0.595	3.6.5.3	59
12	0.060	1ygeA	0.445	4.65	0.038	0.703	1.13.11.12	NA
13	0.060	2vn7A	0.400	5.47	0.073	0.734	3.2.1.3	NA
14	0.060	2iukA	0.442	4.84	0.060	0.715	1.13.11.12	NA
15	0.060	1k1xA	0.345	5.89	0.026	0.683	2.4.1.25	NA
16	0.060	2zbzA	0.432	4.54	0.051	0.677	1.14.14.1	NA
17	0.060	2z3uA	0.433	4.12	0.073	0.646	1.-.-.-	NA
18	0.060	2tmdA	0.357	5.46	0.026	0.646	1.5.8.2	94,104
19	0.060	1qhaA	0.450	5.32	0.069	0.810	2.7.1.1	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	0.452	1.92	0.24	0.51	1y9bA	GO:0006355
1	0.07	0.444	5.17	0.03	0.81	5gamC	GO:0000166 GO:0000244 GO:0000349 GO:0000388 GO:0000398 GO:0003924 GO:0005525 GO:0005634 GO:0005682 GO:0006397 GO:0006412 GO:0008380 GO:0030623 GO:0042256 GO:0046540
2	0.07	0.417	5.01	0.07	0.71	5anbK	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0006412 GO:0042254 GO:0042256 GO:0043022
3	0.06	0.406	5.21	0.06	0.75	4v9hAY	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006414
4	0.06	0.415	5.19	0.03	0.75	3jb9B	GO:0000166 GO:0000244 GO:0000974 GO:0003924 GO:0005525 GO:0005634 GO:0005681 GO:0005682 GO:0005737 GO:0005829 GO:0006397 GO:0006412 GO:0008380 GO:0045292 GO:0046540 GO:1902802
5	0.06	0.375	5.54	0.05	0.73	3vr1A	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0006412 GO:0006415 GO:0006449 GO:0016149
6	0.06	0.371	5.69	0.08	0.72	2bv3A	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006414
7	0.06	0.424	5.32	0.06	0.79	3j0eH	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0006412 GO:0006414
8	0.06	0.379	5.32	0.10	0.69	1b23P	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006414
9	0.06	0.350	5.58	0.05	0.68	3j81k	GO:0000049 GO:0000166 GO:0001731 GO:0003743 GO:0003924 GO:0005525 GO:0005850 GO:0006412 GO:0006413 GO:0016282 GO:0031369 GO:0033290 GO:0043614 GO:0045903
10	0.06	0.477	5.08	0.07	0.84	3dnyT	GO:0000166 GO:0003723 GO:0003746 GO:0003924 GO:0005525 GO:0005737 GO:0005829 GO:0005840 GO:0006412 GO:0006414 GO:0017183 GO:0019843 GO:0045901 GO:1990145
11	0.06	0.343	5.76	0.09	0.68	2dy1A	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0006414
12	0.06	0.408	5.53	0.09	0.77	5hau1z	GO:0000166 GO:0003723 GO:0003735 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0019843 GO:0030529
13	0.06	0.359	5.47	0.06	0.67	2dcuA	GO:0000166 GO:0003743 GO:0003746 GO:0003924 GO:0005525 GO:0006412 GO:0006413 GO:0006414
14	0.06	0.355	5.46	0.07	0.65	4iw3B	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006414
15	0.06	0.337	4.49	0.03	0.48	5j8bz	GO:0000166 GO:0003723 GO:0003735 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005840 GO:0005886 GO:0006412 GO:0006414 GO:0016020 GO:0016787 GO:0019843 GO:0030529 GO:0043022 GO:0045727
16	0.06	0.373	5.62	0.08	0.73	5a9yA	GO:0000166 GO:0003924 GO:0005525 GO:0005829 GO:0009408 GO:0009409
17	0.06	0.341	5.69	0.04	0.65	3japk	GO:0000049 GO:0000166 GO:0001731 GO:0003743 GO:0003924 GO:0005525 GO:0005850 GO:0006412 GO:0006413 GO:0016282 GO:0031369 GO:0033290 GO:0043614 GO:0045903
18	0.06	0.348	5.76	0.05	0.68	3qsyA	GO:0000166 GO:0001731 GO:0003743 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0006412 GO:0006413 GO:0006414
19	0.06	0.295	6.18	0.04	0.59	3izq1	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005737 GO:0006412 GO:0006414 GO:0006417 GO:0032790 GO:0043022 GO:0045727 GO:0070651 GO:0070966 GO:1990533

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0017111	GO:0032561	GO:0032550
GO-Score	0.47	0.47	0.47	0.47
Biological Processes	GO:0034645	GO:0043043	GO:0044267	GO:0010467
GO-Score	0.47	0.47	0.47	0.47
Cellular Component	GO:0005682	GO:0046540	GO:0000974	GO:0005829	GO:0005681
GO-Score	0.13	0.13	0.07	0.07	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.