I-TASSER results

I-TASSER results for job id Rv2821c

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

Input Sequence in FASTA format

>protein (236 residues)
MTTSYAKIEITGTLTVLTGLQIGAGDGFSAIGAVDKPVVRDPLSRLPMIPGTSLKGKVRT
LLSRQYGADTETFYRKPNEDHAHIRRLFGDTEEYMTGRLVFRDTKLTNKDDLEARGAKTL
TEVKFENAINRVTAKANLRQMERVIPGSEFAFSLVYEVSFGTPGEEQKASLPSSDEIIED
FNAIARGLKLLELDYLGGSGTRGYGQVKFSNLKARAAVGALDGSLLEKLNHELAAV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTTSYAKIEITGTLTVLTGLQIGAGDGFSAIGAVDKPVVRDPLSRLPMIPGTSLKGKVRTLLSRQYGADTETFYRKPNEDHAHIRRLFGDTEEYMTGRLVFRDTKLTNKDDLEARGAKTLTEVKFENAINRVTAKANLRQMERVIPGSEFAFSLVYEVSFGTPGEEQKASLPSSDEIIEDFNAIARGLKLLELDYLGGSGTRGYGQVKFSNLKARAAVGALDGSLLEKLNHELAAV
Prediction	CCCCCEEEEEEEEEEEHCCCEHCCCCCCCCCCCCCCCEEEHCCCCCCHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCEEEEHCCCCCCCHHHHHCCCCCCEEEHCCCCCCCCCCCCCCEEEEEHCCCEEEEEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCHHHHHHHHHHHHC
Conf.Score	98644589999999996785765789887777666655775679986557756788999999999886666544566776568888768988877656999756667655566546765445654777787778888656677689889999999975677654555666666889999999999999998756667877655579999999999875667756889999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTTSYAKIEITGTLTVLTGLQIGAGDGFSAIGAVDKPVVRDPLSRLPMIPGTSLKGKVRTLLSRQYGADTETFYRKPNEDHAHIRRLFGDTEEYMTGRLVFRDTKLTNKDDLEARGAKTLTEVKFENAINRVTAKANLRQMERVIPGSEFAFSLVYEVSFGTPGEEQKASLPSSDEIIEDFNAIARGLKLLELDYLGGSGTRGYGQVKFSNLKARAAVGALDGSLLEKLNHELAAV
Prediction	55403130203030303010201124454413211210021434620102021002001310141145455533544735423022002336642241020242303635434344343213233412034546454214142035404040301031344444453443253363025005201400410233203133123103010450404333462456315503640576
	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                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCEEEEEEEEEEEHCCCEHCCCCCCCCCCCCCCCEEEHCCCCCCHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCEEEEHCCCCCCCHHHHHCCCCCCEEEHCCCCCCCCCCCCCCEEEEEHCCCEEEEEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCHHHHHHHHHHHHC
MTTSYAKIEITGTLTVLTGLQIGAGDGFSAIGAVDKPVVRDPLSRLPMIPGTSLKGKVRTLLSRQYGADTETFYRKPNEDHAHIRRLFGDTEEYMTGRLVFRDTKLTNKDDLEARGAKTLTEVKFENAINRVTAKANLRQMERVIPGSEFAFSLVYEVSFGTPGEEQKASLPSSDEIIEDFNAIARGLKLLELDYLGGSGTRGYGQVKFSNLKARAAVGALDGSLLEKLNHELAAV

4qtsC

0.37

0.26

0.71

1.64

MUSTER

L-TLKGKVILEGIIELETGMHIN-------------PVIRDAF-GRILIPGSSLKGKIRALLERKDG-------LPHDCGECEICKIFGPHDSKEPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKEYEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

1.78

dPPAS

-LTLKGKVILEGIIELETGMHIN-------------PVIRDA-FGRILIPGSSLKGKIRALLERKDGLPH-------DCGECEICKIFGPHDSKEPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKSDEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

3.67

wdPPAS

L-TLKGKVILEGIIELETGMHIN-------------PVIRDA-FGRILIPGSSLKGKIRALLERKDGLPH-------DCGECEICKIFGPHDSKNIVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKSDEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

2.07

wMUSTER

--TLKGKVILEGIIELETGMHIN-------------PVIRDAF-GRILIPGSSLKGKIRALLERKDG-------LPHDCGECEICKIFGPHDSKEPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKEYEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

4.25

wPPAS

L-TLKGKVILEGIIELETGMHIN-------------PVIRDAF-GRILIPGSSLKGKIRALLERKDGL-------PHDCGECEICKIFGPHDSKNPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKEDEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

6.06

dPPAS2

-LTLKGKVILEGIIELETGMHIN-------------PVIRDA-FGRILIPGSSLKGKIRALLERKDGLPH-------DCGECEICKIFGPHDSKEPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKSDEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

3.16

PPAS

L-TLKGKVILEGIIELETGMHIN-------------PVIRDAF-GRILIPGSSLKGKIRALLERKDGL-------PHDCGECEICKIFGPHDSKNPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKSDEVESLNELESELDKI

4qtsC

0.37

0.26

0.71

3.42

Env-PPAS

L-TLKGKVILEGIIELETGMHIN-------------PVIRDAF-GRILIPGSSLKGKIRALLERKDG-------LPHDCGECEICKIFGPHDSKEPVRVIVRDAYLQPE--------------------------------ERVVAGSKFKFEVVFNIYKES--------------DKELIKKFIEGMKLLEDDYLGGSGSRGYGKIKFRDIKLICKPKSDEVESLNELESELDKI

4n0lA2

0.30

0.23

0.77

1.45

MUSTER

--GIGGTITLVGEIRLRTGTRIGTSEEEIEIGGLDNPVIRDPVSGYPYVPGSSLKGRARALFELAWMKSRER--------------------------VAFRDAHPTTYTVNDVFERA-------------GEPTEVKHSMERVPKGSRFGLEVVYRVED-------------GEELESDLKYLMSSLKLVEDQGIGHSTSRGYGRVEFRIAALCARSTGPEEEDKDEAADEVTYL

4n0lA2

0.31

0.24

0.77

1.71

dPPAS

--GIGGTITLVGEIRLRTGTRIGTSEEEIEIGGLDNPVIRDPVSGYPYVPGSSLKGRARALFELAWMKSRER--------------------------VAFRDAHPTTYTVNDVFERA-------------GEPTEVKHSMERVPKGSRFGLEVVYRVED-------------GEELESDLKYLMSSLKLVEDQGIGHSTSRGYGRVEFRIAALCARSDPGAGEGFPEEEDKDEAA

(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=0.11

Estimated TM-score = 0.73±0.11

Estimated RMSD = 5.5±3.5Å

Download Model 2

C-score=-1.68

Download Model 3

C-score=-1.65

Download Model 4

C-score=-2.95

Download Model 5

C-score=-2.16

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	4n0lA	0.794	2.11	0.298	0.881
2	4qtsC	0.682	1.33	0.375	0.712
3	4txdA	0.606	3.70	0.171	0.750
4	4tvxF	0.591	3.95	0.132	0.771
5	3ps0A	0.578	4.17	0.115	0.775
6	4regA	0.554	3.81	0.114	0.729
7	3x1lC	0.547	4.18	0.154	0.720
8	3x1lH	0.540	3.59	0.185	0.665
9	4w8vA	0.526	3.37	0.164	0.648
10	4w8wA	0.515	3.67	0.190	0.648

(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	0.10	5	1wplA	3PO	Rep, Mult	55,59
2	0.10	5	4zjbG	PNS	Rep, Mult	53,54
3	0.04	2	4bcxA	PDO	Rep, Mult	9,215
4	0.04	2	3bpdC	MG	Rep, Mult	13,211
5	0.04	2	2rbfB	NUC	Rep, Mult	201,203,208
6	0.04	2	3bx1C	CA	Rep, Mult	38,40,47
7	0.02	1	3hm6X	III	Rep, Mult	57,60,195
8	0.02	1	1nh0B	III	Rep, Mult	21,22,23
9	0.02	1	2v9jE	MG	Rep, Mult	10,86
10	0.02	1	2ri8B	MAN	Rep, Mult	54,208
11	0.02	1	3ke6B	MN	Rep, Mult	41,49,51
12	0.02	1	5sv1F	III	Rep, Mult	181,184,191

	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	1qh4A	0.384	4.33	0.085	0.525	2.7.3.2	98
2	0.060	2ogsA	0.387	5.32	0.068	0.610	3.1.1.1	NA
3	0.060	1aknA	0.389	4.92	0.099	0.589	3.1.1.13,3.1.1.3	NA
4	0.060	1gz7C	0.395	4.67	0.088	0.572	3.1.1.3	NA
5	0.060	3ixzA	0.401	5.45	0.045	0.652	3.6.3.10	NA
6	0.060	3bkkA	0.412	5.56	0.040	0.665	3.4.15.1	NA
7	0.060	1up8A	0.394	6.09	0.078	0.716	1.11.1.18	57
8	0.060	1j38A	0.404	5.60	0.044	0.648	3.4.15.1	NA
9	0.060	1eveA	0.387	4.83	0.088	0.576	3.1.1.7	NA
10	0.060	1q2vA	0.386	5.58	0.051	0.644	3.6.4.9	NA
11	0.060	1jqoA	0.401	5.68	0.091	0.682	4.1.1.31	NA
12	0.060	1mx9D	0.387	5.05	0.100	0.598	3.1.1.1	NA
13	0.060	1maaD	0.388	5.07	0.087	0.598	3.1.1.7	NA
14	0.060	1thgA	0.396	4.80	0.068	0.576	3.1.1.3	NA
15	0.060	1jqnA	0.405	5.79	0.063	0.682	4.1.1.31	NA
16	0.060	1n16B	0.379	4.36	0.069	0.530	2.7.3.2	98
17	0.060	3ihyC	0.387	5.74	0.086	0.640	2.7.1.137	62,184
18	0.060	1f6wA	0.392	4.97	0.099	0.589	3.1.1.13,3.1.1.3	41
19	0.060	1crlA	0.403	4.92	0.067	0.610	3.1.1.3	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	0.41	0.794	2.11	0.30	0.88	4n0lA	GO:0046872
1	0.40	0.682	1.33	0.38	0.71	4qtsC	GO:0051607
2	0.21	0.578	4.17	0.12	0.78	3ps0A	GO:0003723 GO:0051607
3	0.19	0.510	3.94	0.19	0.66	4w8wD	GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0016787 GO:0051607 GO:0090305
4	0.18	0.606	3.70	0.17	0.75	4txdA	GO:0046872
5	0.13	0.526	3.37	0.16	0.65	4w8vA	GO:0003723 GO:0005737 GO:0051607
6	0.13	0.566	3.89	0.14	0.72	4qyzI	GO:0003723 GO:0043234 GO:0051607 GO:0071667
7	0.11	0.537	3.78	0.12	0.70	3ps0B	GO:0003723 GO:0051607
8	0.07	0.591	4.06	0.13	0.78	5cd4F	GO:0003723 GO:0043234 GO:0051607 GO:0071667
9	0.07	0.551	3.74	0.14	0.71	5h9eD	GO:0003723 GO:0043234 GO:0051607 GO:0071667
10	0.06	0.438	3.91	0.12	0.56	4qtsA	GO:0051607
11	0.06	0.358	6.04	0.05	0.63	4fgmA	GO:0004177 GO:0006508 GO:0046872
12	0.06	0.289	5.73	0.05	0.47	3m5uA	GO:0003824 GO:0004648 GO:0005737 GO:0006564 GO:0008483 GO:0008615 GO:0008652 GO:0016740 GO:0030170
13	0.06	0.282	5.92	0.02	0.50	5ebeA	GO:0004767 GO:0005576 GO:0005615 GO:0006685 GO:0008081 GO:0008270 GO:0009143 GO:0016787 GO:0046872 GO:0070062
14	0.06	0.290	6.39	0.06	0.51	5eowA	GO:0004497 GO:0016491 GO:0019439 GO:0055114 GO:0071949
15	0.06	0.230	6.47	0.02	0.42	3ch0A	GO:0006629 GO:0008081 GO:0008889 GO:0016787
16	0.06	0.278	3.61	0.06	0.36	2dnzA	GO:0000166 GO:0003676 GO:0003723 GO:0005634 GO:0006397 GO:0016020
17	0.06	0.336	5.39	0.06	0.53	4f62A	GO:0008299 GO:0016740
18	0.06	0.256	6.21	0.03	0.46	4wj3M	GO:0000166 GO:0003676 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874 GO:0050560

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0016788	GO:0003723
GO-Score	0.52	0.38	0.36
Biological Processes	GO:0051607	GO:0090304
GO-Score	0.61	0.38
Cellular Component	GO:0044424
GO-Score	0.38

(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.