I-TASSER results

I-TASSER results for job id Rv0396

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

Input Sequence in FASTA format

>protein (130 residues)
MRALGWLREDRKPLLNAKLLVLGHLALNVYDPDNGYGEEVLDFEPRTVWWGSANWTVRAG
SHLEVGFACDDPTLVEEATAFVADVIAFSEPIDTTCAGPEPNLVQVEFDDAAMAEAMEEM
AEPDDDGEDW

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRALGWLREDRKPLLNAKLLVLGHLALNVYDPDNGYGEEVLDFEPRTVWWGSANWTVRAGSHLEVGFACDDPTLVEEATAFVADVIAFSEPIDTTCAGPEPNLVQVEFDDAAMAEAMEEMAEPDDDGEDW
Prediction	CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCEEEEEHCCCCHCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHCCCCCHHHHHHHHHHHCCCCCCCCCC
Conf.Score	9765645689975578899999878876336888984553345677578864544333487689998769867889999999999985688887667888875556678699999999976776777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRALGWLREDRKPLLNAKLLVLGHLALNVYDPDNGYGEEVLDFEPRTVWWGSANWTVRAGSHLEVGFACDDPTLVEEATAFVADVIAFSEPIDTTCAGPEPNLVQVEFDDAAMAEAMEEMAEPDDDGEDW
Prediction	6432414476443113030111030034324566323541241434322223231343344303111106334114403420121023355244614244353041414452045115634744754775
	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

CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCEEEEEHCCCCHCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHCCCCCHHHHHHHHHHHCCCCCCCCCC
MRALGWLREDRKPLLNAKLLVLGHLALNVYDPDNGYGEEVLDFEPRTVWWGSANWTVRAGSHLEVGFACDDPTLVEEATAFVADVIAFSEPIDTTCAGPEPNLVQVEFDDAAMAEAMEEMAEPDDDGEDW

1bysA

0.16

0.12

0.72

MUSTER

VKIVERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAATKNSENAVVINMPKLAESFLEHWQDRWNQGRDYRS------------------------------------

2ltrA

0.12

0.09

0.78

0.56

dPPAS

----------NRTDLEMFLKKTPLMVLEE------AAKAVYQKTPTWGTVELPEMTLILNEITVKGQATSKAARQKAAVEYLRKVVEKGKHEIFFIPG--------TTKEEALSNIDQISDKAEE-----

3ha4A

0.24

0.18

0.73

0.57

wdPPAS

PRRPPW------PLLHQRVVLLRE---------KGAPEDIA-----LMW--PADWTQSSGKYLQ---YVADPDEMRKEVLMQLLNVKYGRVSD-------PNGGRVNKDEEIISMAVDDLENMDLNP---

1bysA

0.16

0.12

0.72

0.78

wMUSTER

VKIVERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVETGSFNFTKAATKNSENAVVINMPKLAESFLEHWQDRWNQGRDYRS------------------------------------

4tl2A2

0.19

0.16

0.85

0.60

wPPAS

APATP--APSARPPLSARTEDLHARAGQLSDGAPVDLPAV------------A-ATLQTREEERVCFVASTGEWLDQLGAFLAD----EVPWSRGRVRATRETLAALAEKDELRALVTRWINRGDKGPDW

4ggjA

0.15

0.10

0.67

0.66

dPPAS2

VRVICDYMGS----QIGLLRKAGIQVR-HDQDLGYMHHKFAIVDKKVLITGSLNWTTQAQNNRENVLIMEDTEYVRLFLEEFERIWEEFDPT--------------------------------------

4tl2A2

0.19

0.17

0.87

0.67

PPAS

TPAPATPAPSARPPLSARTEDLHARAGQLSDGAPVDLPAV------------A-ATLQTGEAERVCFVASTGEWLDQLGAFLAD----EVPWSRGRVRATRETLAALAEKDELRALVTRWINRGDKGPDW

2gfnB2

0.21

0.18

0.86

0.66

Env-PPAS

IEKLRNITASILPLDERRLATRVFLFFYAEGAEETARGEIAAFLAR--WRGVVRESVVAAQR-EGTVSTDDADAVTVALVALTDGLALQAILD-------PVVKAISAEDAAARCVDAAVRR--------

4tvxU2

0.08

0.93

0.71

MUSTER

--NQGWQQYGNVEIVTVGLGYKTALRKALYTFAEGFKNKFKGAGVSVHETAERHFYRQSELLIPDVLFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISLALARATLYKHLRELKPQ-------

2ipiA3

0.14

0.13

0.95

0.55

dPPAS

FDTGGFDRTKRKPWTAAQAATLYRHLSADSQVWYSYGGKVNSVPETAT----ATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGVPVPDDRTEGTFIN---YPDVDLVDERWNTSGVPW

(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=-4.21

Estimated TM-score = 0.27±0.08

Estimated RMSD = 14.4±3.7Å

Download Model 2

C-score=-4.31

Download Model 3

C-score=-4.56

Download Model 4

C-score=-4.69

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	2nyfA	0.565	4.02	0.094	0.900
2	1w27A3	0.563	4.32	0.054	0.915
3	2o78A2	0.563	4.24	0.116	0.915
4	4a01A	0.554	3.99	0.071	0.862
5	2rjsB	0.552	4.24	0.056	0.900
6	3nz4A3	0.552	3.87	0.041	0.862
7	3unvA2	0.545	4.05	0.056	0.900
8	2yevA	0.543	4.56	0.072	0.900
9	4av3A	0.524	4.61	0.048	0.892
10	3mk7A	0.518	4.68	0.063	0.885

(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	0.06	3	2r9rB	PGW	Rep, Mult	75,113
2	0.06	3	1jb0I	CLA	Rep, Mult	22,23
3	0.06	3	2a68P	MG	Rep, Mult	77,80
4	0.04	2	3dtuC	DMU	Rep, Mult	81,84,85,88
5	0.04	2	3mk7A	CA	Rep, Mult	116,120,124,129
6	0.04	2	5cwfA	CA	Rep, Mult	29,89
7	0.02	1	2ia5C	MG	Rep, Mult	109,110
8	0.02	1	5irzD	6OE	Rep, Mult	17,21
9	0.02	1	4edgA	MN	Rep, Mult	76,109,110
10	0.02	1	2y4oA	MG	Rep, Mult	59,61,63,86
11	0.02	1	2hj6L	PS2	Rep, Mult	15,68
12	0.02	1	2o01A	CLA	Rep, Mult	22,104
13	0.02	1	4ryoA	MPG	Rep, Mult	40,74,81
14	0.02	1	1bysA	WO4	Rep, Mult	16,18,54
15	0.02	1	2c41G	CL	Rep, Mult	11,15
16	0.02	1	1so2D	MG	Rep, Mult	24,33
17	0.02	1	3dtuA	TRD	Rep, Mult	30,37,81,84,88

	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	3no9A	0.462	3.60	0.066	0.692	4.2.1.2	16,80
2	0.060	1qleA	0.482	4.60	0.031	0.808	1.9.3.1	NA
3	0.060	1syyA	0.457	4.72	0.053	0.823	1.17.4.1	NA
4	0.060	1q5nA	0.483	4.32	0.066	0.785	5.5.1.2	NA
5	0.060	1m56A	0.501	5.14	0.048	0.915	1.9.3.1	NA
6	0.060	1z7hA	0.456	4.92	0.074	0.854	3.4.24.68	NA
7	0.060	1j3uA	0.480	3.38	0.024	0.692	4.3.1.1	NA
8	0.060	2ohyB	0.551	4.24	0.056	0.900	5.4.3.6	NA
9	0.060	3czoB	0.456	4.38	0.041	0.746	4.3.1.3	NA
10	0.060	2o6yA	0.563	4.13	0.116	0.908	4.3.1.-	NA
11	0.060	2r0nA	0.455	4.50	0.026	0.769	1.3.99.7	NA
12	0.060	2z8yD	0.504	4.55	0.049	0.877	1.2.7.4,1.2.99.2	80
13	0.060	2fpqA	0.471	5.35	0.056	0.915	3.4.24.69	NA
14	0.060	1u8vA	0.461	4.52	0.072	0.769	5.3.3.3	NA
15	0.060	1b8fA	0.464	4.25	0.082	0.739	4.3.1.3	NA
16	0.060	1w27A	0.460	4.58	0.039	0.769	4.3.1.24	NA
17	0.060	1occA	0.491	4.51	0.023	0.808	1.9.3.1	NA
18	0.060	2nyfA	0.565	4.02	0.094	0.900	4.3.1.5	NA
19	0.060	3fieA	0.475	4.65	0.079	0.808	3.4.24.69	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	0.06	0.463	5.00	0.11	0.80	4c6gB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
1	0.06	0.467	4.52	0.08	0.76	1gk2A	GO:0003824 GO:0004397 GO:0005737 GO:0006547 GO:0006548 GO:0016829 GO:0016841 GO:0019556 GO:0019557
2	0.06	0.528	4.42	0.07	0.89	1y2mB	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0052883
3	0.06	0.557	4.23	0.03	0.92	4v2rB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
4	0.06	0.565	4.02	0.09	0.90	2nyfA	GO:0003824 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
5	0.06	0.460	4.58	0.04	0.77	1w27A	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548
6	0.06	0.468	4.47	0.10	0.77	3kdyA	GO:0003824 GO:0009403 GO:0016829 GO:0016841 GO:0016853 GO:0017000 GO:0050368 GO:0052883
7	0.06	0.552	3.98	0.04	0.87	3nz4B	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
8	0.06	0.329	4.63	0.04	0.58	1h6dA	GO:0006061 GO:0008152 GO:0016491 GO:0042597 GO:0047061 GO:0055114
9	0.06	0.456	4.38	0.04	0.75	3czoB	GO:0003824 GO:0004397 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
10	0.06	0.298	5.21	0.04	0.56	1e3wD	GO:0001540 GO:0003857 GO:0004303 GO:0005496 GO:0005739 GO:0007569 GO:0008033 GO:0016491 GO:0018454 GO:0030283 GO:0030331 GO:0033327 GO:0042802 GO:0047015 GO:0051287 GO:0051289 GO:0055114
11	0.06	0.321	4.89	0.07	0.58	3nojA	GO:0008948 GO:0016829 GO:0046872 GO:0047443
12	0.06	0.337	4.67	0.09	0.61	4bhhF	GO:0003723 GO:0016032 GO:0019012 GO:0019013 GO:0019028 GO:0019029 GO:0039657
13	0.06	0.563	4.13	0.12	0.91	2o6yA	GO:0003824 GO:0006572 GO:0009698 GO:0009699 GO:0016829 GO:0016841 GO:0042802 GO:0051289 GO:0052883
14	0.06	0.315	5.25	0.03	0.59	1ef9A	GO:0003824 GO:0004300 GO:0004492 GO:0005829 GO:0006635 GO:0008152 GO:0016829 GO:0016831
15	0.06	0.505	4.26	0.05	0.83	3unvA	GO:0003824
16	0.06	0.340	4.87	0.06	0.60	3zizA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985

Consensus prediction of GO terms

Molecular Function	GO:0016840
GO-Score	0.57
Biological Processes	GO:0009803	GO:0072330	GO:0009699	GO:0051260	GO:0009063	GO:0051262	GO:0006558
GO-Score	0.47	0.47	0.47	0.36	0.36	0.36	0.36
Cellular Component	GO:0044424
GO-Score	0.57

(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.