I-TASSER results

I-TASSER results for job id Rv0061c

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

Input Sequence in FASTA format

>protein (112 residues)
MKLKFARLSTAILGCAAALVFPASVASADPPDPHQPDMTKGYCPGGRWGFGDLAVCDGEK
YPDGSFWHQWMQTWFTGPQFYFDCVSGGEPLPGPPPPGGCGGAIPSEQPNAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MKLKFARLSTAILGCAAALVFPASVASADPPDPHQPDMTKGYCPGGRWGFGDLAVCDGEKYPDGSFWHQWMQTWFTGPQFYFDCVSGGEPLPGPPPPGGCGGAIPSEQPNAP
Prediction	CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCEHCCCCCCCEEEEHCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9876567899999999987645555668999999988776668998865688887676658998634445554567877999966899999999999999888999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MKLKFARLSTAILGCAAALVFPASVASADPPDPHQPDMTKGYCPGGRWGFGDLAVCDGEKYPDGSFWHQWMQTWFTGPQFYFDCVSGGEPLPGPPPPGGCGGAIPSEQPNAP
Prediction	6434444112112212113332333364635544436334330343432313122034451462520243143323334031302456453553444442644235755758
	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

CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCEHCCCCCCCEEEEHCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MKLKFARLSTAILGCAAALVFPASVASADPPDPHQPDMTKGYCPGGRWGFGDLAVCDGEKYPDGSFWHQWMQTWFTGPQFYFDCVSGGEPLPGPPPPGGCGGAIPSEQPNAP

4nl6A

0.13

0.12

0.99

0.84

MUSTER

LLSPICEVANNIEQNAQENENESQVSTDESENSRSPGNKSDNIKPKSAPWNSFLP-PPPPMPGPRLGPGKPGLKFNGPPPPPPPPPPHLLSCWLPPFPSGPPIIPPPPPICP

2h7tA

0.15

0.12

0.84

0.96

dPPAS

PPPARTPCQQELDQVLERISTMRLPDERGPLE----HLYSLHIPN----------CD----KHGLYNLKQCKMSLNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEARG

2h7tA

0.15

0.12

0.83

0.97

wdPPAS

PPPARTPCQQELDQVLERISTMRLPDERGPLE----HLYSLHIP-----------CD----KHGLYNLKQCKMSLNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEARG

2h7tA

0.17

0.13

0.80

0.92

wMUSTER

PARTQQELDQVLERISTMRLPDERGPLEHLYSLHIPN------------------CD----KHGLYNLKQCKMSLNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEAVH

2h7tA

0.18

0.14

0.78

0.79

wPPAS

PAR-QQELDQVLERISTMRLPDERGPLEHLYSLHIPN------------------CD----KHGLY-KQCKMS-LNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEAVH

2h7tA

0.17

0.13

0.80

1.05

dPPAS2

PARTQQELDQVLERISTMRLPDERGPLEHLYSLHIPN------------------CD----KHGLYNLKQCKMSLNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEAVH

2h7tA

0.17

0.13

0.79

0.91

PPAS

PAR-QQELDQVLERISTMRLPDERGPLEHLYSLHIPN------------------CD----KHGLYNLKQCKMSLNGQRGECWCVNTGKLIQGAPTIRGCHLFYNEQQEAVH

1ignA2

0.18

0.15

0.84

0.71

Env-PPAS

SADEDYTLAIAVKKQFYRDLFQIDPDTGRSLIRT--QSRRG--PIAREFFKHFA----EEHAAHTEWRDRFRKFLLGIDDYISYYEAEEPMKNLTPPGNYNS----------

4ut1A

0.14

1.00

0.79

MUSTER

TRGALDGFSLATANGSAIAAASPVLAAGVATNSGTGVISQGSVSAGYQLGTTTLAYNAASKTLSGFPVGTTVTIAGTPPTSINITSATTPVPYDPSKGASMTISSTTQPAPS

5g2fA

0.12

0.09

0.77

0.90

dPPAS

-------ANLAAGQSYVRNVALALEAQRDPSTGALPTHLTDCLSGFGQRPKTVTACTITYLNALDYVIEASLDGAALKKVVYKSSDGTLTSLP-------------------

(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=-3.38

Estimated TM-score = 0.34±0.11

Estimated RMSD = 11.8±4.5Å

Download Model 2

C-score=-3.85

Download Model 3

C-score=-4.65

Download Model 4

C-score=-4.27

Download Model 5

C-score=-4.67

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	4f4hA	0.515	4.24	0.056	0.884
2	3n05A	0.513	4.18	0.056	0.857
3	5khaA	0.504	4.46	0.046	0.893
4	4cyfA	0.484	4.58	0.049	0.857
5	2h7tA	0.483	3.08	0.102	0.661
6	1jdnA	0.476	4.67	0.050	0.875
7	4nfuA	0.475	4.91	0.055	0.920
8	3kg2A	0.472	4.76	0.040	0.893
9	1llwA2	0.472	5.09	0.055	0.911
10	4xqkA3	0.470	4.46	0.075	0.839

(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	0.08	4	1ykpC	DHB	Rep, Mult	39,41,44
2	0.06	3	2aiyB	IPH	Rep, Mult	8,11
3	0.06	3	2d2cA	CLA	Rep, Mult	19,55
4	0.04	2	1wemA	ZN	Rep, Mult	43,56,68,84
5	0.04	2	3cezA	ZN	Rep, Mult	43,56,84,100
6	0.04	2	2qfwE	ICT	Rep, Mult	3,69
7	0.02	1	4n1aA	MG	Rep, Mult	9,64
8	0.02	1	3n3qB	NIZ	Rep, Mult	4,7
9	0.02	1	3pmvA	557	Rep, Mult	16,36,37,38,40,52,53
10	0.02	1	3pe7A	CA	Rep, Mult	57,59
11	0.02	1	3wmgA	DMU	Rep, Mult	14,18
12	0.02	1	3lsfE	PZI	Rep, Mult	9,13,14,17
13	0.02	1	4lh4A	MG	Rep, Mult	83,84
14	0.02	1	3tdjA	3TJ	Rep, Mult	19,20,21,22
15	0.02	1	3il1B	B5D	Rep, Mult	72,96,99,106
16	0.02	1	4brbA	78N	Rep, Mult	7,15,70,73

	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	2nn3D	0.448	4.60	0.060	0.830	3.4.22.36	NA
2	0.060	3mddA	0.448	4.22	0.045	0.750	1.3.99.3	52
3	0.060	2uxyA	0.452	4.51	0.046	0.812	3.5.1.4	NA
4	0.060	1udyA	0.448	4.18	0.054	0.750	1.3.99.3	NA
5	0.060	1emsA	0.450	4.46	0.061	0.812	3.6.1.29	NA
6	0.060	1llwA	0.471	5.08	0.055	0.911	1.4.7.1	NA
7	0.060	2prmA	0.459	4.46	0.010	0.848	1.3.5.2	10,64
8	0.060	1ng4B	0.351	4.84	0.029	0.688	1.4.3.19	58
9	0.060	3dlaD	0.459	4.66	0.064	0.848	6.3.5.1	NA
10	0.060	3cmmC	0.449	5.09	0.067	0.920	6.3.2.19	12,44
11	0.060	1u7zC	0.468	4.11	0.082	0.786	4.1.1.36,6.3.2.5	NA
12	0.060	1jqiA	0.456	4.18	0.054	0.741	1.3.99.2	NA
13	0.060	1peuA	0.466	4.62	0.037	0.830	1.17.4.1	NA
14	0.060	2a06C	0.405	4.56	0.028	0.714	1.10.2.2	NA
15	0.060	2masA	0.456	4.94	0.045	0.866	3.2.2.1	NA
16	0.060	1u7uA	0.425	4.17	0.080	0.714	6.3.2.5	37
17	0.060	1ofdA	0.393	4.56	0.036	0.723	1.4.7.1	NA
18	0.060	1bucB	0.454	4.50	0.058	0.812	1.3.99.2	NA
19	0.060	1t34A	0.414	4.72	0.061	0.759	4.6.1.2	52,76

(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	0.443	4.45	0.08	0.78	5h8jH	GO:0006596 GO:0006807 GO:0016787 GO:0016810 GO:0050126
1	0.06	0.418	4.55	0.06	0.79	3hkxA	GO:0004040 GO:0006807 GO:0016810
2	0.06	0.513	4.18	0.06	0.86	3n05A	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0009435 GO:0016810 GO:0016874
3	0.06	0.518	4.22	0.06	0.88	4f4hB	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874
4	0.06	0.430	4.57	0.03	0.80	5h8iC	GO:0006596 GO:0006807 GO:0016787 GO:0016810 GO:0050126
5	0.06	0.458	4.49	0.07	0.81	1erzA	GO:0006807 GO:0016787 GO:0016810 GO:0047417
6	0.06	0.388	5.16	0.05	0.80	5ahmA	GO:0000166 GO:0003824 GO:0003938 GO:0005524 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
7	0.06	0.366	5.09	0.01	0.73	2ohhA	GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
8	0.06	0.470	4.52	0.04	0.84	3seqA	GO:0000166 GO:0003952 GO:0005524 GO:0005618 GO:0005737 GO:0005886 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874 GO:0040007
9	0.06	0.444	4.50	0.05	0.80	2vhhC	GO:0003837 GO:0006207 GO:0006208 GO:0006807 GO:0016787 GO:0016810
10	0.06	0.341	4.93	0.09	0.62	5f23A	GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874
11	0.06	0.316	5.61	0.04	0.70	2pzbA	GO:0000166 GO:0003952 GO:0005524 GO:0006734 GO:0008795 GO:0009435 GO:0016874 GO:0030436
12	0.06	0.435	4.30	0.04	0.77	3ilvA	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0009435 GO:0016810 GO:0016874
13	0.06	0.311	5.15	0.04	0.60	3dpiA	GO:0000166 GO:0003952 GO:0005524 GO:0008795 GO:0009435 GO:0016874
14	0.06	0.301	4.50	0.05	0.52	3dpiB	GO:0000166 GO:0003952 GO:0005524 GO:0008795 GO:0009435 GO:0016874
15	0.06	0.449	4.40	0.03	0.79	1j31A	GO:0006807 GO:0016810
16	0.06	0.345	5.12	0.05	0.67	2dplA	GO:0000166 GO:0003922 GO:0005524 GO:0006164 GO:0006177 GO:0016462 GO:0016874
17	0.06	0.337	5.01	0.04	0.62	1ih8B	GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874 GO:0030435
18	0.06	0.333	4.95	0.02	0.62	4q16D	GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0016787
GO-Score	0.57
Biological Processes	GO:0008152
GO-Score	0.38
Cellular Component
GO-Score

(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.