I-TASSER results

I-TASSER results for job id Rv0454

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

Input Sequence in FASTA format

>protein (116 residues)
MKQDFGLDVPQAGNAQNFDGVPEWVQVGVVTFVYRMQMHHVTRPVGAPGSGLAGDSTPVQ
GRQRVWDLVAGRLTHAPRSSVQAMRPTMFTSAPQRHGIPARGRWWLGYQERSRAWP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MKQDFGLDVPQAGNAQNFDGVPEWVQVGVVTFVYRMQMHHVTRPVGAPGSGLAGDSTPVQGRQRVWDLVAGRLTHAPRSSVQAMRPTMFTSAPQRHGIPARGRWWLGYQERSRAWP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCC
Conf.Score	98767888877777667788884578878888877655554677899888888888886555688888876545788654444465444678866688876556655444456789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MKQDFGLDVPQAGNAQNFDGVPEWVQVGVVTFVYRMQMHHVTRPVGAPGSGLAGDSTPVQGRQRVWDLVAGRLTHAPRSSVQAMRPTMFTSAPQRHGIPARGRWWLGYQERSRAWP
Prediction	85662524135345365263124214210121023243441343243434424465343633530141023313424454154243332352465451434331112145456538
	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

CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCC
MKQDFGLDVPQAGNAQNFDGVPEWVQVGVVTFVYRMQMHHVTRPVGAPGSGLAGDSTPVQGRQRVWDLVAGRLTHAPRSSVQAMRPTMFTSAPQRHGIPARGRWWLGYQERSRAWP

4q98A1

0.20

0.19

0.94

0.69

MUSTER

VETNATVSFIIKSGESRAVGDDL--KITKLTAVYAGQVQEGIKTVEEDGGVLKVEGIPCKGANRVLVVVANHLTGKSLNEVEALTTGKSAAFTIKPG-----SNHYGYPGGTASTP

4kk7A2

0.21

0.15

0.70

0.67

dPPAS

----QLPPIPAAGAPNSL-GLPDDLVIGSVFQIHTGPQYYVVLP---------------DGIAQVNATTAAALRATQAHGLVAPPPSLVVRIAERSPLPDE---------------

4kk7A2

0.24

0.16

0.68

0.67

wdPPAS

--Q----PIPAAGAPNSL-GLPDDLVIGSVFQIHTGPQYYVVLP-----DGI----------AQVNATTAAALRATQAVAPPAMVPSLVVRIAERSPLPDE---------------

4cabA

0.19

0.18

0.95

0.67

wMUSTER

PELDFDLDDTKI--PR--EQFP-WRHVGQMTLNRNPENVFFGTGVLVDGLDFSDDKM-LQGRTFSYSDTQRYRVGPNYLQLPINAPKKHVATNQRDGVDTFEDQRVNYEPSLLSGP

4kk7A2

0.27

0.18

0.68

0.57

wPPAS

--Q----PIPAAGAPNSL-GLPDDLVIGSVFQIHTGPQYYV---V------LP-D-----GIAQVNATTAAALRATAHGLVAPMVPSLVVRIAERSPLPDE---------------

4kk7A2

0.23

0.16

0.69

0.77

dPPAS2

-----QLPIPAAGAPNSL-GLPDDLVIGSVFQIHTGPQYYVVLP-----DGI----------AQVNATTAAALRATQAHGLVAPPPSLVVRIAERSPLPDE---------------

4kk7A2

0.27

0.18

0.67

0.66

PPAS

-----QLPIPAAGAPNSL-GLPDDLVIGSVFQIHTGPQYYV---V------LP-D-----GIAQVNATTAAALRATQAHGLVAP-PAM-VRIAERSPLPDE---------------

1l1lA2

0.24

0.19

0.78

0.70

Env-PPAS

---EISLS-AEFIDRVKASVKPHWGKLGWVTY-KRT----YARWL------------PEKGRSENWDETVKRVVDSPSLELKQSLTELYKLIYGLGATPS-GRNWISYQRRT----

3j40N

0.20

0.18

0.91

0.67

MUSTER

MKT-VNMKT-GTDSFVGEDGKPETKD----QYPWGLRINESLQRLGLNAKSLVGDSVSVMAMANVCS-VSTRTTDHGEDNYVELQITDIGLAPQKRDDAKELKDAF-YPDGEDD--

5abkA

0.13

0.08

0.61

0.60

dPPAS

-------------------------------------GAMAQTPIDLGVTGIPADASDVDKRIALERYLEEKIRSGFKGDAQFGKKALEQRAKILKVIDKQK-----GPHKAR---

(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=-3.28

Estimated TM-score = 0.35±0.12

Estimated RMSD = 11.6±4.5Å

Download Model 2

C-score=-4.61

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.51

Download Model 5

C-score=-4.15

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	4kk7A	0.582	2.97	0.131	0.733
2	5cyuA	0.560	3.46	0.167	0.741
3	4r9iA	0.455	4.53	0.043	0.810
4	3mx9A1	0.455	3.63	0.038	0.690
5	2bw3A2	0.452	3.74	0.032	0.741
6	1dq3A	0.447	4.26	0.037	0.741
7	3c68A2	0.447	4.52	0.072	0.784
8	5a72A	0.443	3.42	0.040	0.647
9	2hfzA	0.443	4.74	0.038	0.819
10	1xr5A	0.441	4.41	0.029	0.793

(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	0.07	3	2z7eA	FES	Rep, Mult	66,73
2	0.05	2	1af50	III	Rep, Mult	45,46,49,78
3	0.05	2	3kziX	CLA	Rep, Mult	68,71
4	0.05	2	2y6zA	POP	Rep, Mult	7,112
5	0.02	1	103mA	NBN	Rep, Mult	32,70,74
6	0.02	1	1ki0A	BCN	Rep, Mult	4,19,24,35,36
7	0.02	1	3ipoB	PG0	Rep, Mult	115,116
8	0.02	1	3quiD	ANP	Rep, Mult	7,63
9	0.02	1	1agsA	GTX	Rep, Mult	3,11
10	0.02	1	3lj7A	OHO	Rep, Mult	12,77,78,79,80
11	0.02	1	3o72C	OXY	Rep, Mult	4,85
12	0.02	1	2wse1	CLA	Rep, Mult	81,85
13	0.02	1	2od0A	MG	Rep, Mult	64,67
14	0.02	1	2wpnB	SF4	Rep, Mult	72,82
15	0.02	1	4ujkD	MG	Rep, Mult	34,37
16	0.02	1	3hx6A	CA	Rep, Mult	8,17,19,21,23
17	0.02	1	2olnA	NA	Rep, Mult	44,47,48,49

	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	1khvB	0.415	4.49	0.051	0.733	2.7.7.48	NA
2	0.060	1fziA	0.364	4.88	0.071	0.664	1.14.13.25	NA
3	0.060	1ahpA	0.413	4.04	0.057	0.681	2.4.1.1	NA
4	0.060	1dq3A	0.447	4.26	0.037	0.741	1.17.4.1	NA
5	0.060	2r72A	0.430	4.54	0.040	0.767	2.7.7.48	21,97
6	0.060	2ijd1	0.434	4.62	0.058	0.810	3.6.1.15	70
7	0.060	1l2aE	0.417	4.34	0.020	0.741	3.2.1.4	28
8	0.060	3hq2B	0.425	4.83	0.069	0.810	3.4.24.-	NA
9	0.060	1xr5A	0.441	4.41	0.029	0.793	3.4.22.28	74
10	0.060	1h54B	0.427	4.36	0.061	0.750	2.4.1.8	NA
11	0.060	1mhyD	0.422	4.74	0.043	0.759	1.14.13.25	NA
12	0.060	1adeA	0.408	4.38	0.032	0.733	6.3.4.4	NA
13	0.060	1rs0A	0.394	4.10	0.029	0.655	3.4.21.47	NA
14	0.060	2wj2A	0.439	4.62	0.080	0.776	3.5.1.99	49,50
15	0.060	1ia7A	0.417	4.69	0.130	0.784	3.2.1.4	NA
16	0.060	2jg0A	0.428	5.25	0.054	0.845	3.2.1.28	NA
17	0.060	1p9bA	0.412	4.89	0.058	0.793	6.3.4.4	101
18	0.060	1n1hA	0.422	4.92	0.051	0.802	2.7.7.48	14,17
19	0.060	1iw1A	0.417	4.75	0.027	0.750	1.14.99.3	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	0.12	0.409	3.80	0.03	0.66	3fd2A	GO:0004519 GO:0009507 GO:0009536 GO:0090305
1	0.07	0.579	2.98	0.13	0.73	3x3mA	GO:0005576 GO:0005618 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0052553
2	0.07	0.444	3.42	0.04	0.65	5a72B	GO:0004518 GO:0004519 GO:0006314 GO:0009507 GO:0009536 GO:0016787 GO:0090305
3	0.06	0.457	3.59	0.04	0.69	3mxaA
4	0.06	0.427	3.61	0.03	0.65	3e54A	GO:0004519 GO:0046872 GO:0090305
5	0.06	0.333	5.13	0.04	0.65	4yhxA	GO:0004519 GO:0005739 GO:0005840 GO:0090305
6	0.06	0.435	3.44	0.02	0.64	2fldA	GO:0004519 GO:0009507 GO:0009536 GO:0090305
7	0.06	0.383	3.65	0.02	0.61	4lq0A	GO:0004519 GO:0005739 GO:0090305
8	0.06	0.418	4.09	0.04	0.67	2ex5A	GO:0003677 GO:0004518 GO:0004519 GO:0006314 GO:0009507 GO:0009536 GO:0016787 GO:0046872 GO:0090305
9	0.06	0.421	3.44	0.02	0.62	3qqyA	GO:0004519 GO:0005739 GO:0005840 GO:0090305
10	0.06	0.333	5.08	0.03	0.65	5espA	GO:0004519 GO:0005739 GO:0090305
11	0.06	0.404	3.68	0.04	0.63	4efjA	GO:0004519 GO:0005739 GO:0090305
12	0.06	0.336	4.84	0.02	0.62	3pybB	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0009686 GO:0009740 GO:0009905 GO:0010333 GO:0016829 GO:0016853
13	0.06	0.316	5.05	0.04	0.62	1l9uC	GO:0003677 GO:0003899 GO:0006351 GO:0016740 GO:0016779 GO:0032549
14	0.06	0.379	4.92	0.04	0.73	3stoA	GO:0005615 GO:0006508 GO:0008233
15	0.06	0.329	4.90	0.08	0.62	2of7A	GO:0003677 GO:0006351 GO:0006355
16	0.06	0.385	4.32	0.07	0.68	3f5nE	GO:0004867 GO:0005576 GO:0005615 GO:0007417 GO:0007422 GO:0010466 GO:0010951 GO:0030155 GO:0030414 GO:0070062
17	0.06	0.328	4.84	0.05	0.62	2odlA
18	0.06	0.410	3.87	0.04	0.64	3r7pA	GO:0004519 GO:0005739 GO:0005840 GO:0046872 GO:0090305

Consensus prediction of GO terms

Molecular Function	GO:0004518
GO-Score	0.47
Biological Processes	GO:0090304
GO-Score	0.47
Cellular Component	GO:0009536
GO-Score	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.