I-TASSER results

I-TASSER results for job id Rv2183c

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

Input Sequence in FASTA format

>protein (131 residues)
MSGAHTDVRPELRKLAQAILDGIDPAVRVAAAMASGGGPGTGKCQQVWCPLCALAALVTG
EQHPLLTVIADHSLALLEVIRAIVDDIDRSAKPPPEGPPGGGQTGASGGENTNGEGSMKS
HYQAIPVTIEE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSGAHTDVRPELRKLAQAILDGIDPAVRVAAAMASGGGPGTGKCQQVWCPLCALAALVTGEQHPLLTVIADHSLALLEVIRAIVDDIDRSAKPPPEGPPGGGQTGASGGENTNGEGSMKSHYQAIPVTIEE
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCC
Conf.Score	98865689999999999999999999999876655788877887755578999999998889689999999999999999999996577899999999999999999999999999999875776555479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSGAHTDVRPELRKLAQAILDGIDPAVRVAAAMASGGGPGTGKCQQVWCPLCALAALVTGEQHPLLTVIADHSLALLEVIRAIVDDIDRSAKPPPEGPPGGGQTGASGGENTNGEGSMKSHYQAIPVTIEE
Prediction	86572560053034005201540341044124445645444351431001000010014454350133025312201310320055247555355554644644544557655566654542341304278
	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

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCC
MSGAHTDVRPELRKLAQAILDGIDPAVRVAAAMASGGGPGTGKCQQVWCPLCALAALVTGEQHPLLTVIADHSLALLEVIRAIVDDIDRSAKPPPEGPPGGGQTGASGGENTNGEGSMKSHYQAIPVTIEE

5bp1A2

0.19

0.16

0.82

0.88

MUSTER

AGNALV-VADALRSTAQHLADWLLRS-----GDGNGRGPAID-------LGDLAYTLARRGFRA-SAVLAGDRGTLVEGLRQIADG----EAMPQQAVDFSVLYPTGRLLDAPLPAWTHSTL-----LDRE

5bp1A2

0.20

0.17

0.82

0.66

dPPAS

VSASS---ADALRSTAQHLADWLLRS----------GDGNGRGPAIDLGDLAYTLARRRGFRAARSAVLAGDRGTLVEGLRQIADGEAMPAVDFSVLYPTGRLLDAPLPAWTHSTLLLDRE----------

5frfA

0.15

0.11

0.69

0.71

wdPPAS

MSAGEPH-CSEILDHLYEFLDKMPDSDAVKFEHHFEE-----------SSPCL-------EKYGLEQAVKKLVKRLRAKVMGRLDLIRSGQSVPEHDVAAAPSSSAPQES---------------------

5bp1A2

0.19

0.15

0.80

0.88

wMUSTER

AGNALV-VADALRSTAQHLADWLLRS-----GDGNGRGPAID-------LGDLAYTLARRGFRA-SAVLAGDRGTLVEGLRQIADG-EAMPQQAVDFSVLYPTGRLLDAPLPA------STL-----LDRE

5frfA

0.15

0.11

0.73

0.96

wPPAS

MSGEPHETCSEILDHLYEFLDKMPDSDAVKFEHHFEE-----------SSPCL-EKY--GLEQAVKKLVKRAAGDLRAKVMGRLDLIRSGQSVPEHDVAAAPSSSAPQES---------------------

5bp1A2

0.17

0.13

0.78

0.83

dPPAS2

SS------ADALRSTAQHLADWLLRS-----GDGNGRGPAID-------LGDLAYTLARRGFRAASAVLAGDRGTLVEGLRQIADGEAMPQQAVDFSVLYPTGRLLDAPLPASTLLLDRE-----------

5bp1A2

0.19

0.15

0.81

0.90

PPAS

-KAGNALVADALRSTAQHLADWLLRS----------GDGNGRGPAIDLGDLAYTLARRR-GFRA-SAVLAGDRGTLVEGLRQIADGE-----AMPQQAVDFSVLYPTGRLLDAPLPA--STL-----LDRE

5bp1A2

0.17

0.15

0.85

0.94

Env-PPAS

-KAGNALVADALRSTAQHLADWLLRS----------GDGNGRGPAIDLGDLAYTLARRRGFRAARSAVLAGDRGTLVEGLRQIADG---------EAMPQQAVDFSVLYPTGRLLDAPLPAWTHSTLLLDR

2lp4A1

0.16

0.15

0.93

0.81

MUSTER

MSMDISDFYQTFFDEADELLADMEQHLLDLVPESPDAEQGAGTFGQETTLMENLLDEARRGEMQLNTDIINLFLETKDIMQEQLDAYKNSEEPDAASLEAKGETPSAVTRLSVVAKSEPQ---------DE

2n7zA

0.10

0.08

0.79

0.62

dPPAS

--GIAQQWIQSKREDIVNQEACLNQSLDALLSRDLIMKEDYELVST--KP--TRTSKVR----QLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-----------------

(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=-3.54

Estimated TM-score = 0.33±0.11

Estimated RMSD = 12.6±4.3Å

Download Model 2

C-score=-4.38

Download Model 3

C-score=-4.40

Download Model 4

C-score=-4.92

Download Model 5

C-score=-4.99

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	4av3A	0.556	3.91	0.024	0.847
2	3dvxA	0.540	3.44	0.063	0.771
3	3a3tA	0.529	3.43	0.088	0.763
4	4kppA	0.527	3.98	0.093	0.832
5	4jrrA	0.526	3.71	0.097	0.771
6	4wisA2	0.521	3.59	0.017	0.733
7	2q6hA	0.516	4.89	0.057	0.893
8	3bciA	0.515	4.08	0.009	0.809
9	2p8uA	0.513	4.60	0.069	0.863
10	5c00A	0.512	3.94	0.053	0.786

(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	2z0aA	GLY	Rep, Mult	24,77,78,81
2	0.06	3	2bx2L	ZN	Rep, Mult	49,52
3	0.06	3	2elmA	ZN	Rep, Mult	49,52,63,72
4	0.04	2	3fggB	ZN	Rep, Mult	7,11
5	0.04	2	1ppjC	CDL	Rep, Mult	11,12,13,16,79,83
6	0.04	2	2a06C	CDL	Rep, Mult	12,16,19,76
7	0.02	1	2rh1A	CLR	Rep, Mult	27,77
8	0.02	1	3mjlB	2AI	Rep, Mult	63,72
9	0.02	1	3h1jC	CDL	Rep, Mult	17,22,25,26
10	0.02	1	1vykA	ZN	Rep, Mult	17,21,81
11	0.02	1	1q05A	CU1	Rep, Mult	44,49
12	0.02	1	5ebzK	GLC	Rep, Mult	11,15
13	0.02	1	2vn4A	MAN	Rep, Mult	107,108
14	0.02	1	1pp9P	CDL	Rep, Mult	12,15,19,76,124
15	0.02	1	2xz1A	CA	Rep, Mult	17,81,85
16	0.02	1	2gyiB	MG	Rep, Mult	61,63

	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	1lbzA	0.466	4.30	0.066	0.763	3.1.3.25	18,21
2	0.060	2ifcC	0.467	4.81	0.042	0.801	2.3.3.1	NA
3	0.060	1d9qB	0.467	4.66	0.051	0.748	3.1.3.11	61
4	0.060	1cmkE	0.484	4.51	0.036	0.832	2.7.11.11,2.7.1.37	NA
5	0.060	2de0X	0.488	4.50	0.116	0.832	2.4.1.68	NA
6	0.060	3crlB	0.479	4.12	0.051	0.733	2.7.11.2	77,81
7	0.060	1lbvA	0.470	4.26	0.067	0.756	3.1.3.25,	NA
8	0.060	2a06C	0.482	3.97	0.016	0.725	1.10.2.2	12,53,55,83
9	0.060	3d0eA	0.470	4.48	0.045	0.794	2.7.11.1	NA
10	0.060	1k9yA	0.482	4.41	0.066	0.779	3.1.3.7	NA
11	0.060	3c51B	0.428	4.71	0.065	0.771	2.7.11.14	NA
12	0.060	1gzkA	0.357	5.23	0.064	0.672	2.7.11.1,2.7.1.-	NA
13	0.060	1fotA	0.467	4.38	0.036	0.779	2.7.11.11	NA
14	0.060	3cquA	0.450	4.82	0.061	0.809	2.7.11.26,2.7.11.1	NA
15	0.060	3ff1A	0.481	4.19	0.024	0.779	5.3.1.9	NA
16	0.060	1b0zA	0.475	4.38	0.032	0.786	5.3.1.9	NA
17	0.060	1qgxA	0.484	4.49	0.066	0.786	3.1.3.7	20,22
18	0.060	2o36A	0.479	4.55	0.104	0.771	3.4.24.15	NA
19	0.060	2bjiA	0.468	4.47	0.050	0.748	3.1.3.25	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	0.526	3.71	0.10	0.77	4jrrA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
1	0.07	0.545	3.43	0.06	0.78	3dvxA	GO:0042597 GO:0045454
2	0.07	0.509	3.85	0.10	0.77	3h93A	GO:0015035 GO:0042597 GO:0045454 GO:0055114
3	0.07	0.529	3.43	0.09	0.76	3a3tA	GO:0005623 GO:0045454
4	0.07	0.502	3.79	0.05	0.77	4k2dA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
5	0.07	0.495	4.07	0.04	0.77	4dvcA	GO:0003756 GO:0006457 GO:0009405 GO:0015035 GO:0042597 GO:0055114
6	0.07	0.496	3.97	0.03	0.78	4p3yB	GO:0015035 GO:0016853 GO:0042597 GO:0055114
7	0.07	0.503	4.09	0.10	0.80	3l9uA	GO:0015035 GO:0016853 GO:0042597 GO:0055114
8	0.07	0.490	4.26	0.10	0.81	3l9vA	GO:0015035 GO:0016853 GO:0042597 GO:0045454 GO:0055114
9	0.07	0.492	4.11	0.05	0.79	4oceA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
10	0.07	0.484	4.15	0.04	0.77	2mbsA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
11	0.07	0.506	4.22	0.10	0.80	2remC	GO:0042597 GO:0045454
12	0.07	0.493	4.17	0.07	0.79	3eu3A	GO:0016491 GO:0030420 GO:0055114
13	0.07	0.485	4.31	0.10	0.79	3hd5A	GO:0015035 GO:0042597 GO:0045454 GO:0055114
14	0.07	0.487	3.88	0.05	0.73	4gxzA	GO:0005623 GO:0015035 GO:0045454 GO:0055114
15	0.07	0.470	4.45	0.07	0.75	4xvwL	GO:0005623 GO:0045454
16	0.07	0.478	4.27	0.05	0.79	1a23A	GO:0003756 GO:0015035 GO:0030288 GO:0042597 GO:0045454 GO:0055114 GO:0071236
17	0.07	0.476	4.17	0.06	0.77	3feuA	GO:0046872
18	0.07	0.458	4.65	0.02	0.80	3gmfA	GO:0016020 GO:0016021 GO:0016853

Consensus prediction of GO terms

Molecular Function	GO:0015036
GO-Score	0.37
Biological Processes	GO:0019725	GO:0050794	GO:0044710
GO-Score	0.58	0.58	0.37
Cellular Component	GO:0044464
GO-Score	0.40

(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.