I-TASSER results

I-TASSER results for job id Rv2562

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

Input Sequence in FASTA format

>seq (129 residues)
MAEQKVKRNVELAGVDVILVHRMLKNEVPVSEYLFMTDVVAQCLDESVRKLATPLTHDFE
GIGETSTHYIDLATSDMPPAVPDHSFFGLLWADVKFEWHALPYLLGFKKACAGFRSLGRG
ATEEPAEMG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAEQKVKRNVELAGVDVILVHRMLKNEVPVSEYLFMTDVVAQCLDESVRKLATPLTHDFEGIGETSTHYIDLATSDMPPAVPDHSFFGLLWADVKFEWHALPYLLGFKKACAGFRSLGRGATEEPAEMG
Prediction	CCEEEHCCCEEHCCCHHHHHHHHHHCCCCCCEEEEHHHHHHHHCCCHHHHHCCCCCEHCCCCCCEEEEEEHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEHCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	957887685665575467888888579998534444388999868657765444444457767689999867755678899998567777766555444476343665554555788888866565579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAEQKVKRNVELAGVDVILVHRMLKNEVPVSEYLFMTDVVAQCLDESVRKLATPLTHDFEGIGETSTHYIDLATSDMPPAVPDHSFFGLLWADVKFEWHALPYLLGFKKACAGFRSLGRGATEEPAEMG
Prediction	634542562450324300300221337153620100034017425551453145235415431514121230552754345463513441343143424213310324521652442643466244748
	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

CCEEEHCCCEEHCCCHHHHHHHHHHCCCCCCEEEEHHHHHHHHCCCHHHHHCCCCCEHCCCCCCEEEEEEHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEHCCCCCCCCCCCCCCCCCCCCCCCC
MAEQKVKRNVELAGVDVILVHRMLKNEVPVSEYLFMTDVVAQCLDESVRKLATPLTHDFEGIGETSTHYIDLATSDMPPAVPDHSFFGLLWADVKFEWHALPYLLGFKKACAGFRSLGRGATEEPAEMG

4yh8B

0.09

0.03

0.36

1.07

dPPAS2

-----------------------------------------------------------------------------------RERSVRSIEQELEQLRDVTPINQWKRKRSLWDIKPPGYELVTADQG

2ndjA

0.13

0.05

0.41

1.03

dPPAS2

----------------------------------------------------------------------------METTNGTETWYESLHAVLKALNATLNLLCRPGPGLGPDNQTEERRASLPGRDD

2ihmB1

0.21

0.18

0.85

0.67

MUSTER

------HHNTLLSEAETLAEAAGFENEGRLLSFS-RAASVLKSLPCPVASLSQ--LHGLPYFGEHSTRVIELLEHGTCEEVKQ--VRCSERYQTMKLFTQVF--VGVKTA-EGLRTLDREQPQR-----

2kk9A

0.09

0.04

0.43

0.82

dPPAS

-------------------------------------------------------------------------KGLRRDLDASREAKKQLEAEQQKLEEQNKISEASRKGLRRDLDASREAKKQVEKA-

5lxlA

0.21

0.13

0.62

0.74

wdPPAS

------------MGIDYSGLRTIFGEKLPES-HIFFATVAAHKYVPSYAFLRREL-------G--------LSSAHT---------NRKVWKKFVEAYKAIP-------PAPPAPPLTLSKLEH-----

2ihmB1

0.20

0.17

0.84

0.63

wMUSTER

-------HNTLLSEAETLAEAAGFENEGRLLSFSRAASVLKSL-PCPVASLSQ--LHGLPYFGEHSTRVIELLEHGTCEEV--KQVRCSERYQTMKLFTQVF--VGVKTA-EGLRTLDREQPQR-----

2mpwA

0.33

0.25

0.74

0.71

wPPAS

---MNGENYFKL-GSD-LLTHNSYQNRL---FYTLKT-------GETVADLSKS-----QDI-NLSTHY---SESEMMKAAPGQQII----KKLPFEYSALP-LLG-SAPVAGHTN-GSGSENLYFQ--

5awwG

0.17

0.06

0.36

1.00

dPPAS2

-----------------------------------------------------------------------------------MDLLYTLVILFYLGVAGLVYLVLVQEPKQGAGDLMGGSADLFSARG

2muxA

0.15

0.96

0.81

PPAS

VLQQSLNQLREITGNDTQILQQALKDSNGN-----LELAVAFLTAKNAKTPQQEETTYYQTALPGNDRYISVGSQADTLTGDDKDDLQRAIALSLAESNRAFRETGITDEEQAIRVLEASIAENKACLK

1fx7A2

0.21

0.12

0.59

0.69

Env-PPAS

--------------IAVMRKHRLAE--------RLLVDVI--GLP---WEEVHAEACRWEHV---------MSE----------DVERRLVKVLNNPTTS-PF--G--NPIPGLDELGVG-PEPGADD-

(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=-4.09

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.1±3.9Å

Download Model 2

C-score=-3.82

Download Model 3

C-score=-4.67

Download Model 4

C-score=-4.92

Download Model 5

C-score=-4.77

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	3rimA1	0.512	4.41	0.059	0.853
2	1r9jB1	0.504	4.79	0.049	0.891
3	2r8oB	0.500	4.52	0.085	0.845
4	1ay0A	0.500	4.79	0.057	0.884
5	4lhgX	0.494	4.33	0.045	0.798
6	5hgxA	0.494	4.57	0.092	0.845
7	3l84A	0.493	4.75	0.050	0.868
8	2q3dA	0.491	4.57	0.054	0.814
9	3dwgA	0.490	4.38	0.036	0.806
10	1wkvB	0.488	4.36	0.056	0.806

(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	5	3l9xA	ESG	Rep, Mult	11,17,18,21,37
2	0.06	3	5sv1F	III	Rep, Mult	86,89,96
3	0.06	3	3ta8A	FE	Rep, Mult	68,87
4	0.06	3	2q3bA	MPD	Rep, Mult	20,21,32
5	0.06	3	1fcjB	SO4	Rep, Mult	11,12,14,15,16,17
6	0.04	2	3i8hE	MG	Rep, Mult	22,25
7	0.02	1	3sxqA	CO	Rep, Mult	5,21
8	0.02	1	1p8nA	MN	Rep, Mult	57,71,76
9	0.02	1	2anuA	ZN	Rep, Mult	60,68
10	0.02	1	1u4jA	MAN	Rep, Mult	18,105
11	0.02	1	4ag5C	MG	Rep, Mult	93,97
12	0.02	1	3egmA	FE	Rep, Mult	84,89
13	0.02	1	2buqA	CAQ	Rep, Mult	29,33
14	0.02	1	2v8vD	URP	Rep, Mult	14,26

	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	3n2oA	0.466	4.94	0.076	0.837	4.1.1.19	35
2	0.060	3dkiB	0.426	4.77	0.008	0.736	2.5.1.65	31
3	0.060	2zr8A	0.468	5.03	0.042	0.868	5.1.1.18	NA
4	0.060	1trkA	0.486	4.86	0.025	0.868	2.2.1.1	NA
5	0.060	1ay0A	0.500	4.79	0.057	0.884	2.2.1.1	41
6	0.060	1vb3A	0.473	4.59	0.027	0.806	4.2.3.1	NA
7	0.060	1uwkA	0.473	4.49	0.043	0.814	4.2.1.49	NA
8	0.060	2o1xC	0.419	4.53	0.043	0.721	2.2.1.7	57
9	0.060	1o58A	0.475	4.85	0.033	0.837	2.5.1.47	7,116
10	0.060	1p5jA	0.450	4.96	0.049	0.845	4.3.1.17	NA
11	0.060	2gn0C	0.458	4.99	0.059	0.830	4.3.1.19	NA
12	0.060	2rhgB	0.466	4.50	0.089	0.760	4.2.1.20	NA
13	0.060	3dwgA	0.490	4.38	0.036	0.806	2.5.1.47	7
14	0.060	1pwhA	0.457	4.95	0.049	0.853	4.3.1.17,4.3.1.19	NA
15	0.060	1r8lB	0.459	4.91	0.063	0.837	3.2.1.89	NA
16	0.060	1hkvA	0.447	4.68	0.094	0.814	4.1.1.20	NA
17	0.060	1wkvB	0.488	4.36	0.056	0.806	2.5.1.47	116
18	0.060	1v8zB	0.470	4.85	0.034	0.853	4.2.1.20	NA
19	0.060	2r8oB	0.500	4.52	0.085	0.845	2.2.1.1	68

(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	0.403	4.88	0.07	0.73	1itzA	GO:0003824 GO:0004802 GO:0008152 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0016740 GO:0019253 GO:0046872
1	0.07	0.389	5.09	0.03	0.74	4c7vA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
2	0.07	0.371	5.12	0.07	0.71	4kxwA	GO:0003824 GO:0004802 GO:0005634 GO:0005654 GO:0005777 GO:0005829 GO:0005999 GO:0006098 GO:0008152 GO:0009052 GO:0016740 GO:0031982 GO:0040008 GO:0042803 GO:0043209 GO:0046166 GO:0046872 GO:0048037 GO:0070062
3	0.07	0.487	4.73	0.08	0.84	4xeuA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
4	0.07	0.500	4.79	0.06	0.88	1ay0A	GO:0003824 GO:0004802 GO:0005737 GO:0006098 GO:0008152 GO:0016740 GO:0046872
5	0.07	0.472	4.69	0.05	0.84	3l84A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
6	0.07	0.403	4.72	0.04	0.72	3uptA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
7	0.07	0.489	4.89	0.07	0.85	2e6kA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
8	0.07	0.501	4.46	0.08	0.84	3komA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
9	0.07	0.418	5.24	0.04	0.78	3uk1A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
10	0.06	0.419	4.53	0.04	0.72	2o1xC	GO:0000287 GO:0003824 GO:0008152 GO:0008299 GO:0008661 GO:0009228 GO:0016114 GO:0016740 GO:0030976 GO:0046872 GO:0052865
11	0.06	0.393	5.00	0.05	0.72	1r9jB	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
12	0.06	0.500	4.52	0.09	0.84	2r8oB	GO:0003824 GO:0004802 GO:0005829 GO:0008152 GO:0009052 GO:0016740 GO:0030145 GO:0030976 GO:0046872
13	0.06	0.397	4.75	0.03	0.71	3m49A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
14	0.06	0.340	4.84	0.06	0.58	2ej0B	GO:0003824 GO:0004084 GO:0008152 GO:0008483 GO:0009081 GO:0016740
15	0.06	0.321	4.96	0.04	0.57	2pl2A
16	0.06	0.376	5.39	0.07	0.75	4ni3B	GO:0004560 GO:0005975 GO:0006004
17	0.06	0.404	4.95	0.03	0.73	3rimA	GO:0003824 GO:0004802 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0008152 GO:0016740 GO:0040007 GO:0046872
18	0.06	0.279	5.02	0.03	0.53	2a2gA	GO:0005009 GO:0005215 GO:0005550 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0005829 GO:0006112 GO:0006810 GO:0007610 GO:0008286 GO:0009060 GO:0010628 GO:0010888 GO:0010907 GO:0031649 GO:0036094 GO:0042593 GO:0045475 GO:0045721 GO:0045834 GO:0045892 GO:0051055 GO:0051897 GO:0061179 GO:0070584 GO:0071396

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0016744
GO-Score	0.58	0.58
Biological Processes	GO:0040008	GO:0046166	GO:0019253	GO:0009052	GO:0005999
GO-Score	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0043209	GO:0005777	GO:0009535	GO:0070062	GO:0005829	GO:0005654
GO-Score	0.07	0.07	0.07	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.