I-TASSER results

I-TASSER results for job id Rv0122

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

Input Sequence in FASTA format

>protein (122 residues)
MAGSVSAAAGIGWVGLNVTETNRDQCYRVERTTVDALTHPEYRVHTRGVQRVRVTRNARK
HRVSKHRIVAAMRHCGVPVIQEDGSLYYQGRDTSGRLTEVVAVEADDGDLIITHAMPKEW
KR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAGSVSAAAGIGWVGLNVTETNRDQCYRVERTTVDALTHPEYRVHTRGVQRVRVTRNARKHRVSKHRIVAAMRHCGVPVIQEDGSLYYQGRDTSGRLTEVVAVEADDGDLIITHAMPKEWKR
Prediction	CCCCCCCCCCCEEEEEEEHCCCCCCEEEEEEEHCCCCCCCCEEEEHCCCEEEEEEEHHHHHHCHHHHHHHHHHHHCCCEEHCCCEEEEEHCCCCCCEEEEEEEHCCCCCEEEEEHCCCCCCC
Conf.Score	98754444455566655544665445676664445557875577745656888753456665457899998887588667658857998657888657899988589968987646655479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAGSVSAAAGIGWVGLNVTETNRDQCYRVERTTVDALTHPEYRVHTRGVQRVRVTRNARKHRVSKHRIVAAMRHCGVPVIQEDGSLYYQGRDTSGRLTEVVAVEADDGDLIITHAMPKEWKR
Prediction	75442433221121213235454630241543314314346142345215424234514644145430121144141210365241214245353413411214175331102213366268
	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

CCCCCCCCCCCEEEEEEEHCCCCCCEEEEEEEHCCCCCCCCEEEEHCCCEEEEEEEHHHHHHCHHHHHHHHHHHHCCCEEHCCCEEEEEHCCCCCCEEEEEEEHCCCCCEEEEEHCCCCCCC
MAGSVSAAAGIGWVGLNVTETNRDQCYRVERTTVDALTHPEYRVHTRGVQRVRVTRNARKHRVSKHRIVAAMRHCGVPVIQEDGSLYYQGRDTSGRLTEVVAVEADDGDLIITHAMPKEWKR

5fzpA3

0.19

0.17

0.89

0.69

MUSTER

-TG-LSATAGGKSNLFAAS-ADRNVVYALGIDLVEAAPNSGYRSTDGGRTYTRIVDDTPDTELTNSTLLAP--SPVDP----NVLYFEYGTYFQAYGTDLYRYDARTGKVGKTHN-AHD---

5fzpA3

0.17

0.16

0.92

0.63

dPPAS

TGLSATAGGKSNLFAASVSPADRNVVYALGIDLVEAAPNSGYRSTDGGRTYTRIVDDTPDTELTNSTLLAP--SPVDP----NVLYFEYGTYFQAYGTDLYRYDARTGKVGKTHNAHD----

2qc5A2

0.15

0.10

0.66

0.60

wdPPAS

LSIPDSGPYGIG--KVWFTQHKANKISSLDQS--GRIK--EFEVPTPD---------AKVMCL---------------IVSSLGDIWFTENGAN----KIGKLSKK-GG-FTEYPLP-----

3el6A1

0.24

0.20

0.87

0.67

wMUSTER

ALG--VRGAEHPLLLAAVDVPGHGG--AVFTGRLSTDEQPEHVVG--G--RTLV------GSVLVDLALAAGEDVGLPVLEEQRPLVL--AGAGALLRMSVGAPDESGRTIDVHAAEDQWSQ

4dixA2

0.33

0.26

0.80

0.56

wPPAS

-------AAGLGYV-----EAKHDVDFNVVVTQMSGEDHTSESIHL-GKMRIKLCKG--KTVIAKEYYSSAMQLCGV---RGGGALYWQAK--KG-VSFVIAFESEDCNVTL--AGPED--R

2qc5A2

0.14

0.09

0.65

0.67

dPPAS2

IPDSTSSEDG----KVWFTQHKANKISSLDQS--GRIK--EFEVPTPD---------AKVMCL---------------IVSSLGDIWFTENGAN----KIGKLSKKGG--FTEYPLP-----

3el6A1

0.24

0.20

0.84

0.59

PPAS

ALGV--RGAEHPLLLAAVDVPGHGG--AVFTGRLSTDEQPEHVVG--G--RTLV------GSVLVDLALAAGEDVGLPVLE---ELVLQ--GAGALLRMSVGAPDESGRTIDVHAAEAQWSQ

1go0A

0.26

0.21

0.81

0.79

Env-PPAS

--GSVDFAFEL---RK-AQDTGK--IVMGARKSIQYA-----K---MGAKLIIVARNARPDIKEDIEYYARLSG--IPVYEFEGTSVELGTLL-GRPVSALAVV-DPGESRILALGGKE---

4bifA

0.18

0.17

0.95

0.66

MUSTER

MVGSQASGTGTVRIDPLFQAPDPAL-VAGASVTFEPGARTAWHTHPLG-QTLIVTAGCGWAQREGGAVEEI--HPGDVVWFSPGEKHWHGAAPTTAMTHLAIQERLDGKA--VDWMEHQYRR

1mpyA1

0.18

0.98

0.59

dPPAS

MNKGV---MRPGHVQLRVIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDFMGFKVVDEDALRQLERDLMAYGCAVEQLPAGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPR

(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=-3.35

Estimated TM-score = 0.34±0.12

Estimated RMSD = 12.0±4.4Å

Download Model 2

C-score=-3.61

Download Model 3

C-score=-4.25

Download Model 4

C-score=-4.29

Download Model 5

C-score=-5.00

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	3el6A	0.606	3.35	0.131	0.861
2	2cf2C1	0.605	3.39	0.063	0.853
3	4b8uA	0.604	3.54	0.072	0.861
4	4ln9A	0.600	3.25	0.103	0.853
5	3hrqB1	0.584	3.62	0.046	0.853
6	3esiA	0.582	3.19	0.069	0.795
7	3f5oA	0.576	3.46	0.049	0.828
8	5buyA	0.574	3.44	0.046	0.836
9	5buxA	0.571	3.69	0.047	0.844
10	4i83A	0.570	3.48	0.065	0.828

(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	2glpB	BDE	Rep, Mult	17,100,102
2	0.06	3	4atkB	NUC	Rep, Mult	63,64,67
3	0.06	3	2ql2C	NUC	Rep, Mult	43,62
4	0.04	2	4q9lA	PHE	Rep, Mult	68,72
5	0.04	2	1wn3B	HXC	Rep, Mult	69,78,79,80,81
6	0.02	1	3gf0A	MG	Rep, Mult	89,90
7	0.02	1	1lajA	NUC	Rep, Mult	9,10
8	0.02	1	3n6rA	BTI	Rep, Mult	116,121
9	0.02	1	2w35A	MG	Rep, Mult	24,83
10	0.02	1	1xtmB	CU	Rep, Mult	43,45,61,114
11	0.02	1	4rb62	MG	Rep, Mult	65,68
12	0.02	1	2vuoA	MAN	Rep, Mult	17,96
13	0.02	1	1j88A	UUU	Rep, Mult	17,77
14	0.02	1	2pk0C	MG	Rep, Mult	24,92
15	0.02	1	3r2aB	III	Rep, Mult	69,73,79

	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	0.066	1u1zB	0.574	3.48	0.046	0.836	4.2.1.-	NA
2	0.060	2ejwA	0.459	4.64	0.076	0.803	1.1.1.3	NA
3	0.060	2vz8A	0.492	4.01	0.045	0.779	2.3.1.85	39
4	0.060	1qaxA	0.484	4.06	0.063	0.770	1.1.1.88	NA
5	0.060	2vkzG	0.481	3.78	0.061	0.705	2.3.1.38,3.1.2.14	68
6	0.060	2qvrA	0.465	4.77	0.067	0.836	3.1.3.11	14
7	0.060	1lo8A	0.462	3.55	0.073	0.664	3.1.2.23	70,98
8	0.060	2vz8B	0.490	4.03	0.087	0.746	2.3.1.85	39
9	0.060	2zt5A	0.462	4.80	0.042	0.811	6.1.1.14	NA
10	0.060	3el6A	0.606	3.35	0.131	0.861	4.2.1.61	NA
11	0.060	3d6xB	0.559	3.57	0.048	0.811	4.2.1.-	NA
12	0.060	3khpC	0.483	4.15	0.071	0.730	1.-.-.-	NA
13	0.060	3khpA	0.475	3.88	0.079	0.697	1.-.-.-	NA
14	0.060	1mskA	0.470	4.37	0.048	0.770	2.1.1.13	61
15	0.060	1jx1A	0.457	4.04	0.062	0.746	5.5.1.6	NA
16	0.060	3cmqA	0.438	4.75	0.052	0.787	6.1.1.20	NA
17	0.060	1pn4D	0.470	4.00	0.113	0.721	4.2.1.-	90
18	0.060	2gllA	0.570	3.63	0.056	0.836	4.2.1.-	NA
19	0.060	2gq1A	0.344	4.57	0.052	0.574	3.1.3.11	35
20	0.060	1iq6B	0.476	3.86	0.079	0.713	4.2.1.17	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	0.600	3.25	0.10	0.85	4ln9A	GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0048037
1	0.07	0.607	3.47	0.04	0.86	5hd6A	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0008693 GO:0016829 GO:0016853 GO:0019171 GO:0034017 GO:0047451
2	0.07	0.563	3.94	0.07	0.84	5bp4R	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0031177 GO:0050111 GO:0055114
3	0.07	0.564	3.94	0.07	0.84	5bp4L	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0031177 GO:0050111 GO:0055114
4	0.07	0.574	3.48	0.05	0.84	1u1zB	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
5	0.07	0.574	3.44	0.05	0.84	5buyA	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
6	0.07	0.606	3.35	0.13	0.86	3el6A	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0033068 GO:0047879 GO:0048037 GO:0055114
7	0.07	0.604	3.40	0.06	0.85	2cf2C
8	0.07	0.563	3.90	0.08	0.84	5bp4A	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0031177 GO:0050111 GO:0055114
9	0.07	0.605	3.52	0.07	0.86	4b0cA	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006636 GO:0008693 GO:0016829 GO:0016853 GO:0019171 GO:0034017 GO:0047451
10	0.07	0.604	3.37	0.04	0.85	5hd6F	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0008693 GO:0016829 GO:0016853 GO:0019171 GO:0034017 GO:0047451
11	0.07	0.568	3.68	0.05	0.84	5buwA	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
12	0.07	0.564	3.55	0.05	0.82	5buyE	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
13	0.07	0.602	3.50	0.07	0.86	4cl6C	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006636 GO:0008693 GO:0016829 GO:0016853 GO:0019171 GO:0034017 GO:0047451
14	0.07	0.564	3.87	0.04	0.84	3az9G	GO:0005737 GO:0006633 GO:0016836
15	0.07	0.572	3.38	0.06	0.83	3d6xB	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
16	0.07	0.570	3.48	0.07	0.83	4i83A	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
17	0.07	0.569	3.82	0.05	0.84	3b7jA	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
18	0.07	0.551	3.62	0.06	0.82	4zw0C	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451

Consensus prediction of GO terms

Molecular Function	GO:0019842	GO:0033218	GO:0072341
GO-Score	0.38	0.38	0.38
Biological Processes	GO:0006633	GO:0055114	GO:0009245
GO-Score	0.13	0.13	0.07
Cellular Component	GO:0005737
GO-Score	0.13

(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.