I-TASSER results

I-TASSER results for job id Rv1810

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

Input Sequence in FASTA format

>protein (118 residues)
MQLQRTMGQCRPMRMLVALLLSAATMIGLAAPGKADPTGDDAAFLAALDQAGITYADPGH
AITAAKAMCGLCANGVTGLQLVADLRDYNPGLTMDSAAKFAAIASGAYCPEHLEHHPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MQLQRTMGQCRPMRMLVALLLSAATMIGLAAPGKADPTGDDAAFLAALDQAGITYADPGHAITAAKAMCGLCANGVTGLQLVADLRDYNPGLTMDSAAKFAAIASGAYCPEHLEHHPS
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHCCCCC
Conf.Score	9875444555677899999999999997556677888998599999999979999999999999999999998699999999999997899999999999999999959788657899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MQLQRTMGQCRPMRMLVALLLSAATMIGLAAPGKADPTGDDAAFLAALDQAGITYADPGHAITAAKAMCGLCANGVTGLQLVADLRDYNPGLTMDSAAKFAAIASGAYCPEHLEHHPS
Prediction	7625434441432321202313322331112223144664343004204746052633730042033005305655423411330366347144630130002004301253357448
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHCCCCC
MQLQRTMGQCRPMRMLVALLLSAATMIGLAAPGKADPTGDDAAFLAALDQAGITYADPGHAITAAKAMCGLCANGVTGLQLVADLRDYNPGLTMDSAAKFAAIASGAYCPEHLEHHPS

4yy2A

0.07

0.06

0.84

1.02

dPPAS2

--GKSPTEVLLELIAEASGTTREEVKEKFLKELRKGKSPTEVLLELIAEASGTT------KEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL-----------

5cwbA2

0.10

0.08

0.83

1.00

dPPAS2

----SYEVICECVARIVAEIVEALKRSGTSEDEIAEVARVISEVIRTLKESGSSYEVKECVQRIVEEIVEALKRSGTSEDEINEIVRR----VKSEVERTLKESGS------------

4hh0A

0.16

0.15

0.95

0.66

MUSTER

LVADNTNIFSFDRIAAVRRFLSDVCAARTLAP---DTPVEADTFALYALTE--AQAGRSGRAKAVARLSDLLSTDLGRLTEVEELLRAHAP-TAADFARLFEACAERLTRALAEDRIS

5appA

0.06

1.00

0.74

dPPAS

DKIEEILSKIYHIENEIARIKKLIQNVDVRSTENAARSRANEQKIAENKKAIENKADKADVEKNRADIAANSRAIATFRSSSQNIAALTTKMKQIEDKIEEILSKIYHIENEIARIKK

3quqA2

0.17

0.09

0.53

0.76

wdPPAS

-----------------------------SMPYH------SEAWHQVMKTHGLDL-SREEAYMH----------GRTGASTINIVFQRELGATQEEIESIYHEKSILF-P--------

2mqaA

0.10

0.09

0.93

0.77

wMUSTER

-----GNAFAQSLSSNLLSSGDFVQMISSTTSTDQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA---

3quqA2

0.17

0.09

0.53

0.80

wPPAS

-----------------------------SMPYH------SEAWHQVMKTHGLDL-SREEAYMH----------GRTGASTINIVFQRELGATQEEIESIYHEKSILF-P--------

2mqaA

0.10

0.09

0.93

0.99

dPPAS2

-----GNAFAQSLSSNLLSSGDFVQMISSTTSTDQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA---

2mqaA

0.10

0.09

0.93

0.91

PPAS

-----GNAFAQSLSSNLLSSGDFVQMISSTTSTDQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA---

1oftA

0.13

0.11

0.86

0.84

Env-PPAS

LSLSGL--PGHCLTLLAPILRELSELTLIAPPASL--------THEWLRRAGLNREQAKDNAAALALSCEALRLGR-----SHTVVSWLEPLSRAARKQLSRAAQLGQAQSLNIRLG-

(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=-2.71

Estimated TM-score = 0.40±0.14

Estimated RMSD = 10.3±4.6Å

Download Model 2

C-score=-2.91

Download Model 3

C-score=-4.13

Download Model 4

C-score=-4.63

Download Model 5

C-score=-3.92

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	3abbA	0.669	3.27	0.144	0.932
2	1lgfA	0.665	3.00	0.070	0.907
3	2fr7A	0.663	3.38	0.088	0.932
4	1ulwA	0.662	2.92	0.069	0.907
5	2x9pA	0.660	3.24	0.061	0.915
6	4l0eA	0.659	3.45	0.035	0.949
7	4z5qA	0.659	3.10	0.105	0.907
8	1uedA	0.657	3.18	0.088	0.915
9	2c7xA	0.653	3.19	0.096	0.915
10	5l1oA	0.652	3.20	0.070	0.907

(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	0.09	4	3pmdA	11A	Rep, Mult	40,44,61,64,65,68,88,91,101
2	0.07	3	3eerA	ZN	Rep, Mult	69,109,110
3	0.04	2	3a44A	ZN	Rep, Mult	69,72
4	0.04	2	3fyeD	HEA	Rep, Mult	12,16
5	0.04	2	3sjqC	PHU	Rep, Mult	24,27
6	0.02	1	1un9A	MG	Rep, Mult	36,40
7	0.02	1	3b9mA	SAL	Rep, Mult	48,102
8	0.02	1	2cg5B	COA	Rep, Mult	41,42
9	0.02	1	3wmoP	BCL	Rep, Mult	29,30
10	0.02	1	1jb0L	CLA	Rep, Mult	44,68,69
11	0.02	1	2wssX	III	Rep, Mult	13,17
12	0.02	1	1trrB	NUC	Rep, Mult	54,57
13	0.02	1	2rh1A	CLR	Rep, Mult	27,44
14	0.02	1	1mz9A	VDY	Rep, Mult	3,6,17
15	0.02	1	2wi9A	1D2	Rep, Mult	65,101,104,105

	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	2q9fA	0.631	3.50	0.078	0.924	1.14.13.98	NA
2	0.060	1hbmA	0.607	3.45	0.061	0.898	2.8.4.1	NA
3	0.060	1lgfA	0.665	3.00	0.070	0.907	1.14.-.-	41
4	0.060	2zbzA	0.643	2.86	0.079	0.890	1.14.14.1	63
5	0.060	3l4dB	0.608	3.57	0.018	0.907	1.14.13.70	NA
6	0.060	1w0eA	0.637	3.43	0.071	0.949	1.14.13.67,1.14.14.1	NA
7	0.060	1uedA	0.657	3.18	0.088	0.915	1.14.-.-	109
8	0.060	1n40A	0.616	3.13	0.063	0.873	1.14.-.-	109
9	0.060	1egyA	0.605	3.36	0.086	0.907	1.14.-.-	NA
10	0.060	2w0aA	0.608	3.34	0.064	0.898	1.14.13.70	NA
11	0.060	3ejbH	0.633	3.28	0.026	0.890	1.14.-.-	111
12	0.060	2wm4A	0.646	2.88	0.078	0.898	1.14.-.-	63
13	0.060	2z36B	0.628	3.45	0.009	0.915	1.-.-.-	111
14	0.060	2d09A	0.615	3.39	0.070	0.907	1.14.-.-	NA
15	0.060	3k9vA	0.612	3.59	0.045	0.949	1.14.13.-	NA
16	0.060	3e6iA	0.617	3.46	0.036	0.915	1.14.13.-	NA
17	0.060	3juvA	0.638	3.47	0.063	0.915	1.14.13.70	100
18	0.060	1oxaA	0.604	3.21	0.009	0.873	3.4.23.23	79
19	0.060	3gw9A	0.507	4.32	0.061	0.831	1.14.13.70	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	0.10	0.607	3.47	0.05	0.93	2xbkA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
1	0.10	0.626	3.23	0.04	0.91	4mm0B	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
2	0.09	0.659	3.45	0.04	0.95	4l0eA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
3	0.09	0.652	3.55	0.08	0.97	3hf2A	GO:0003824 GO:0003958 GO:0004497 GO:0005506 GO:0005737 GO:0008152 GO:0010181 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0042802 GO:0046872 GO:0055114 GO:0070330
4	0.09	0.621	3.28	0.04	0.89	5e58C	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0046872 GO:0055114
5	0.09	0.638	3.47	0.06	0.92	3juvA	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005886 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008398 GO:0016020 GO:0016021 GO:0016125 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033488 GO:0043231 GO:0046872 GO:0055114 GO:0070988
6	0.08	0.574	3.79	0.04	0.92	3zbyB	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
7	0.08	0.520	4.55	0.09	0.90	3r9cA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0070330
8	0.08	0.639	3.13	0.03	0.91	3oftA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
9	0.08	0.642	3.33	0.09	0.93	4j6cA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
10	0.08	0.637	3.19	0.11	0.92	4z5pA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
11	0.08	0.638	3.09	0.08	0.90	4oqrA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
12	0.08	0.613	3.20	0.06	0.87	4i91A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006805 GO:0008202 GO:0008392 GO:0008395 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019373 GO:0019825 GO:0020037 GO:0031090 GO:0042180 GO:0042738 GO:0043231 GO:0046872 GO:0055114
13	0.08	0.632	3.17	0.10	0.91	1gwiA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
14	0.08	0.635	3.24	0.10	0.92	5hh3C	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
15	0.08	0.545	3.57	0.09	0.85	2dkkA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0042440 GO:0046872 GO:0055114
16	0.08	0.639	2.90	0.07	0.88	3bujA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
17	0.08	0.627	3.58	0.08	0.93	3tbgA	GO:0004497 GO:0005506 GO:0005739 GO:0005783 GO:0005789 GO:0006629 GO:0006805 GO:0008144 GO:0008202 GO:0008392 GO:0008395 GO:0009804 GO:0009820 GO:0009822 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019369 GO:0019825 GO:0020037 GO:0031090 GO:0033076 GO:0042737 GO:0043231 GO:0046483 GO:0046872 GO:0051100 GO:0055114 GO:0070330 GO:0070989 GO:0090350
18	0.08	0.647	3.18	0.11	0.93	3tywD	GO:0004497 GO:0005506 GO:0005886 GO:0006707 GO:0008395 GO:0016491 GO:0016705 GO:0020037 GO:0036199 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0005506	GO:0004497	GO:0016705	GO:0020037
GO-Score	0.39	0.39	0.39	0.39
Biological Processes	GO:0055114
GO-Score	0.39
Cellular Component	GO:0005737
GO-Score	0.09

(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.