I-TASSER results

I-TASSER results for job id Rv0268c

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

Input Sequence in FASTA format

>protein (169 residues)
MGTRSKSRTRQLKQSNGCTATTSGASDRRRRARRRTAPAWLREDEWLRHHLPHPPRQLSR
CLHRRRRSACHHRYSRRTPKGGLPMTSSLVPISEARAHLSRLVRESADDDVVLMNHGRPA
AILISAERYESLMEELEDLRDRLSVHEREHVTMPLDKLGAELGVDIGRV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTRSKSRTRQLKQSNGCTATTSGASDRRRRARRRTAPAWLREDEWLRHHLPHPPRQLSRCLHRRRRSACHHRYSRRTPKGGLPMTSSLVPISEARAHLSRLVRESADDDVVLMNHGRPAAILISAERYESLMEELEDLRDRLSVHEREHVTMPLDKLGAELGVDIGRV
Prediction	CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCEHCHHHHHHHHHHHHHHHCCCCEEEHCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCC
Conf.Score	9865556788888756875556788765444554678865557864457899997566677776654555666546777777655564557999999999999997899799966995689996999999999999999999999997588888999999987865579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTRSKSRTRQLKQSNGCTATTSGASDRRRRARRRTAPAWLREDEWLRHHLPHPPRQLSRCLHRRRRSACHHRYSRRTPKGGLPMTSSLVPISEARAHLSRLVRESADDDVVLMNHGRPAAILISAERYESLMEELEDLRDRLSVHEREHVTMPLDKLGAELGVDIGRV
Prediction	7555566444514765414233544555544555543441345552143414323452054145444423446334414436142143313044036423510560674200004444010000216304401620432412510563673514164025516353467
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCEHCHHHHHHHHHHHHHHHCCCCEEEHCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCC
MGTRSKSRTRQLKQSNGCTATTSGASDRRRRARRRTAPAWLREDEWLRHHLPHPPRQLSRCLHRRRRSACHHRYSRRTPKGGLPMTSSLVPISEARAHLSRLVRESADDDVVLMNHGRPAAILISAERYESLMEELEDLRDRLSVHEREHVTMPLDKLGAELGVDIGRV

3g5oA

0.35

0.17

0.48

1.40

wdPPAS

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEAD-RTYGEDEIRAEFGVP-RR-

3g5oA

0.30

0.15

0.49

0.88

MUSTER

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAERTYGEDEIRAEFGVP-RR-

3g5oA

0.33

0.16

0.49

0.94

dPPAS

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEADARTYGEDEIRAEFGVPRR--

3g5oA

0.31

0.15

0.48

0.97

wMUSTER

--------------------------------------------------------------------------------------MRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAERTYGEDEIRAEFGVP-RR-

3g5oA

0.35

0.17

0.48

1.21

wPPAS

------------------------------------------------------------------------------------L-MRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEAD-RTYGEDEIRAEFGVP-RR-

3g5oA

0.34

0.17

0.49

1.78

dPPAS2

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEADARTYGEDEIRAEFGVP-RR-

3g5oA

0.34

0.17

0.49

1.00

PPAS

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEADARTYGEDEIRAEFGVP-RR-

3g5oA

0.34

0.17

0.49

0.96

Env-PPAS

-------------------------------------------------------------------------------------LMRILPISTIKGKLNEFVDAVSQDQITITKNGAPAAVLVGADEWESLQETLYWLAIRESIAEADARTYGEDEIRAEFGVP-RR-

2a6qA

0.25

0.12

0.49

0.79

MUSTER

---------------------------------------------------------------------------------GPHM--RTISYSEARQNLSATMMKAVHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMD---SIDSLKSGKGTEKDII

2a6qA

0.25

0.12

0.49

0.86

dPPAS

---------------------------------------------------------------------------------GPHM--RTISYSEARQNLSATMMKAVHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMD---SIDSLKSGKGTEKDII

(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=-3.89

Estimated TM-score = 0.30±0.09

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-4.03

Download Model 3

C-score=-4.32

Download Model 4

C-score=-4.82

Download Model 5

C-score=-4.78

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	4a01A	0.470	5.31	0.046	0.840
2	4av3A	0.454	5.24	0.070	0.799
3	5jouA	0.452	5.17	0.060	0.793
4	3kh5A	0.445	4.71	0.043	0.710
5	4v00A	0.445	4.61	0.031	0.704
6	2xvgA	0.442	5.30	0.061	0.787
7	3blvH	0.437	5.01	0.090	0.740
8	1sy7A	0.437	5.84	0.117	0.823
9	4fguA	0.435	5.32	0.055	0.757
10	4an8A	0.434	5.35	0.034	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	0.10	5	4evbA	ZN	Rep, Mult	130,134
2	0.06	3	3lotA	UNL	Rep, Mult	25,71,117
3	0.04	2	2vn9A	GVD	Rep, Mult	89,112,120,122
4	0.04	2	1tkoB	FE	Rep, Mult	134,137
5	0.04	2	1xsnA	MG	Rep, Mult	108,110
6	0.04	2	5i50A	NUC	Rep, Mult	137,140
7	0.04	2	4rkuJ	CLA	Rep, Mult	129,132
8	0.02	1	3dc7B	MG	Rep, Mult	93,94
9	0.02	1	3ecqA	CA	Rep, Mult	148,152,154,157,165
10	0.02	1	3kwoA	ZN	Rep, Mult	127,130
11	0.02	1	2bflA	ZN	Rep, Mult	70,116
12	0.02	1	1a8bA	GPE	Rep, Mult	117,161
13	0.02	1	3hc8A	MG	Rep, Mult	125,127
14	0.02	1	2a0iA	IMD	Rep, Mult	101,104,105,116,117

	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	3czkA	0.410	5.08	0.077	0.698	3.2.1.48	NA
2	0.060	1s46A	0.406	4.90	0.058	0.698	2.4.1.4	NA
3	0.060	1is2A	0.417	5.05	0.062	0.704	1.3.3.6	NA
4	0.060	2zc0A	0.411	5.06	0.044	0.704	2.6.1.44	NA
5	0.060	3l4uA	0.405	5.50	0.034	0.734	3.2.1.20,3.2.1.3	NA
6	0.060	1j36A	0.416	4.82	0.056	0.686	3.4.15.1	129
7	0.060	2akaB	0.413	5.24	0.072	0.734	3.6.5.5	NA
8	0.060	1darA	0.389	5.67	0.067	0.751	3.6.5.3	NA
9	0.060	1oqzB	0.405	5.14	0.039	0.686	3.5.1.93	111
10	0.060	1jqmB	0.413	5.49	0.054	0.757	3.6.5.3	NA
11	0.060	1br2A	0.313	5.84	0.061	0.604	3.6.1.32	NA
12	0.060	1j38A	0.413	4.78	0.056	0.680	3.4.15.1	NA
13	0.060	1iomA	0.407	5.85	0.068	0.746	4.1.3.7	NA
14	0.060	1eloA	0.443	4.91	0.082	0.734	3.6.5.3	NA
15	0.060	1sy7B	0.435	5.85	0.104	0.840	1.11.1.6	NA
16	0.060	3ecqB	0.425	5.65	0.042	0.793	3.2.1.97	NA
17	0.060	2ifcC	0.406	5.30	0.071	0.722	2.3.3.1	NA
18	0.060	1t3tA	0.408	5.36	0.055	0.704	6.3.5.3	NA
19	0.060	2dkiA	0.411	5.61	0.054	0.746	1.14.13.23	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	0.426	4.37	0.07	0.66	3tdhC	GO:0000166 GO:0001302 GO:0003824 GO:0004679 GO:0005524 GO:0005634 GO:0005641 GO:0005737 GO:0005886 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0006468 GO:0007031 GO:0031588 GO:0043539 GO:0045722 GO:0071902
1	0.07	0.445	4.64	0.04	0.70	3lfzA
2	0.06	0.423	4.87	0.04	0.70	2ooxE	GO:0000166 GO:0003824 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0007165 GO:0016208 GO:0030295 GO:0031588 GO:0032147
3	0.06	0.418	5.07	0.04	0.70	3ddjA	GO:0000166 GO:0003824
4	0.06	0.310	4.77	0.04	0.49	2v8qE	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
5	0.06	0.408	5.00	0.01	0.69	4qfsC	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
6	0.06	0.358	5.65	0.04	0.66	2qh1B	GO:0046872
7	0.06	0.457	5.47	0.09	0.85	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
8	0.06	0.360	5.43	0.02	0.62	3l0iC	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
9	0.06	0.344	5.77	0.04	0.65	1b3oB	GO:0000166 GO:0003677 GO:0003723 GO:0003824 GO:0003938 GO:0005634 GO:0005737 GO:0005778 GO:0005829 GO:0006164 GO:0006177 GO:0009168 GO:0016020 GO:0016491 GO:0046651 GO:0046872 GO:0051289 GO:0055114 GO:0060041 GO:0070062 GO:0071353
10	0.06	0.326	5.01	0.03	0.53	4z87A	GO:0000166 GO:0003824 GO:0003938 GO:0005737 GO:0005829 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
11	0.06	0.341	5.12	0.04	0.58	3k5pA	GO:0004617 GO:0006564 GO:0008152 GO:0016491 GO:0016597 GO:0016616 GO:0051287 GO:0055114
12	0.06	0.306	5.94	0.04	0.59	5bv7A	GO:0004607 GO:0004623 GO:0005576 GO:0005615 GO:0006629 GO:0006644 GO:0006656 GO:0008202 GO:0008203 GO:0008374 GO:0016740 GO:0016746 GO:0030301 GO:0034186 GO:0034364 GO:0034372 GO:0034375 GO:0034435 GO:0042157 GO:0042158 GO:0042632 GO:0043691 GO:0046470 GO:0046688 GO:0051384 GO:0070062 GO:0090107
13	0.06	0.320	4.92	0.04	0.53	1nf7A	GO:0000166 GO:0003677 GO:0003723 GO:0003824 GO:0003938 GO:0005634 GO:0005737 GO:0005778 GO:0005829 GO:0006164 GO:0006177 GO:0009168 GO:0016020 GO:0016491 GO:0046651 GO:0046872 GO:0051289 GO:0055114 GO:0060041 GO:0070062 GO:0071353
14	0.06	0.294	5.72	0.04	0.56	2yvxA	GO:0000287 GO:0005886 GO:0006810 GO:0006812 GO:0008324 GO:0015095 GO:0015693 GO:0016020 GO:0016021 GO:0042803 GO:0046872 GO:0098655 GO:1903830
15	0.06	0.322	4.42	0.07	0.50	4esyA	GO:0006950
16	0.06	0.304	4.91	0.05	0.50	5aweA	GO:0003824
17	0.06	0.316	4.32	0.07	0.47	2rifA	GO:0000166
18	0.06	0.319	5.71	0.04	0.60	4dqwA	GO:0000166 GO:0003824 GO:0003938 GO:0005524 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032550	GO:0032559
GO-Score	0.36	0.36	0.36
Biological Processes	GO:0006357	GO:0007031	GO:0032147	GO:0071902	GO:0045722	GO:0007165	GO:0051291	GO:0001302	GO:0042304
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:1902911	GO:0044424
GO-Score	0.36	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.