I-TASSER results

I-TASSER results for job id Rv2451

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

Input Sequence in FASTA format

>protein (132 residues)
MGRAVSVRHGSGALDLPGAAASRRLRVGQPIQPSPAPLARGSVDSIVEISCCPSAGPRGP
YDNDLDSSSPANRDISSITSRSRRGGTIVVAGQKCGFGSAVSLRPRRYREPNHANIVTPD
TDLSPSWPWSGI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGRAVSVRHGSGALDLPGAAASRRLRVGQPIQPSPAPLARGSVDSIVEISCCPSAGPRGPYDNDLDSSSPANRDISSITSRSRRGGTIVVAGQKCGFGSAVSLRPRRYREPNHANIVTPDTDLSPSWPWSGI
Prediction	CCCCEEEHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCEEEEHCCCCCCCCEEEHCCCCCCCCCCCCHCCCCCCCCCCCCCCCC
Conf.Score	986555655777666885566554445888999888776677664788777688899899888887889887774555544456887999855567775566565544687755455788888988888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGRAVSVRHGSGALDLPGAAASRRLRVGQPIQPSPAPLARGSVDSIVEISCCPSAGPRGPYDNDLDSSSPANRDISSITSRSRRGGTIVVAGQKCGFGSAVSLRPRRYREPNHANIVTPDTDLSPSWPWSGI
Prediction	754424244443114134333444143444254543423434142114032136334624355515665444441540354444411010214413234324243542554641413336462446142757
	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

CCCCEEEHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCEEEEHCCCCCCCCEEEHCCCCCCCCCCCCHCCCCCCCCCCCCCCCC
MGRAVSVRHGSGALDLPGAAASRRLRVGQPIQPSPAPLARGSVDSIVEISCCPSAGPRGPYDNDLDSSSPANRDISSITSRSRRGGTIVVAGQKCGFGSAVSLRPRRYREPNHANIVTPDTDLSPSWPWSGI

3gawA

0.17

1.00

0.71

MUSTER

ATRGNTAKTSTGWIPAPRLKPCDYPDIGLYHENMRRPYFPVAVGKYYSYYCTPSGSYWDHIHCTQDGWSPAVPCLRKCYFPYLENGYNQNHGRKFVQGKSIDVAHPGYALPKAQTTVTMENGWSPTPRCIRV

3qr8A

0.15

0.14

0.95

0.55

dPPAS

TGIIVETDLNAGRCRVQTGGCTDWLQWLTHRAGRSRTWWAPSVGEQVLILA-VGGELDTAFYSGDNPSPSVSADALHIRFPDPETSALTVSGIKTASGSVTATVPVVVKASTRVTLDTPEVVCTNRL-----

1wj5A

0.25

0.20

0.83

0.49

wdPPAS

-GSSGSS-GNKDNLDLAGSLLSEKIKE-KKMQ-YQQELE--TVESLQSLASRPVTHSTGSDQVELKDSG-TSGVAQRVFKN-----ALQL--QEKGL---VFQRDSGSDK----YVTTKDKDLQ-SGPSSG-

1v4nB

0.19

0.16

0.85

0.70

wMUSTER

KEKAIGIIGGSGLYDPQILTNVKEIKVYTPYEPS-DNIILGELE--RKVAFLPRHGRGHRI-------PPHKINYRANIWALKSLGWVIAVS------AVGSLRL-DYK---PGDFVVPNQDMTKGRTYTFF

3glbD2

0.26

0.17

0.64

0.47

wPPAS

--KAIHKHH---HL----NQFAAHLSIDEPLLYPVSQ-KPNFATFI--QSLFTELGPS------------I-REIQLALG--------LVA---AGEG--VCIVPASAMDIGVKNLL-PDDDAS--------

1uf1A

0.26

0.19

0.73

0.51

dPPAS2

---------GS-----SGSSGDRR---------STLHLLQGGDEKKVNLVLGDGRSLRGGAEYGLDPGSEAGRSFLNILHDEKSSRHLILTVKDVG-------RLPHARTTVDE---TKWIASSSG-PSSG-

2cp5A

0.22

0.20

0.89

0.63

PPAS

-GSGSSGMSMLKPSGLK--APTKILKPGSTALKTPTAVVAPVEKTISSEK--SSTPSSETQEEFVDDFRVGER---WVNG-NKPGGETQWAGEPIGKNDG-SVAGVRY-EPLKGIFTRPSKVSGPS---SG-

1wj5A

0.24

0.20

0.86

0.71

Env-PPAS

-GSSGSS-GNKDNLDLAGSLLSEKIKEEKKMQSYQQELE--TVESLQSLASRPVTHSTGSDQVELKDSG-TSGVAQRVFKN-----ALQLL-QEKGL---VFQRDSGSDKLYY--VTTKDKDLQ-SGPSSG-

3gavA

0.17

1.00

0.71

MUSTER

ATRGNTAKTSTGWIPAPRCTLKPDIKHGGLYHENRRPYFPVAVGKYYSYYCTPSGSYWDHIHCTQDGWSPAVPCLRKCYFPYLENGYNQNHGRKFVQGKSIDVAHPGYALPKAQTTVTMENGWSPTPRCIRV

4d0kA3

0.14

0.13

0.91

0.55

dPPAS

DWDEVTRIAYPAPGTFPRPATAVAF------DPIAELLWAGFDRGRVCSFYGRDLTRYTAFKIQPASEGPVSSYVKLFEI-APSGEALVIGDADC----NIHLWGSP-TKIHFTDMAIPIELPEPVLDWSET

(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=-4.28

Estimated TM-score = 0.26±0.08

Estimated RMSD = 14.6±3.7Å

Download Model 2

C-score=-4.99

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	3j8gX	0.489	4.37	0.041	0.826
2	3w5fA	0.479	4.30	0.042	0.803
3	2w0yA1	0.477	4.34	0.074	0.803
4	3w5iA	0.475	4.83	0.077	0.818
5	1qpkA	0.475	4.89	0.060	0.871
6	4zqmA	0.474	5.01	0.073	0.856
7	3cp8A	0.474	4.79	0.110	0.864
8	1zfjA1	0.474	5.13	0.089	0.864
9	3hyxA	0.473	4.46	0.088	0.841
10	1llwA	0.472	4.91	0.043	0.841

(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	0.14	7	1f2nA	CA	Rep, Mult	62,64
2	0.12	6	3i8hE	MG	Rep, Mult	23,26
3	0.08	4	1ofdA	F3S	Rep, Mult	15,21,22,23,24,26,27,28,40,43,47,48
4	0.02	1	1noyB	MN	Rep, Mult	6,115
5	0.02	1	3lmtA	IOD	Rep, Mult	26,63
6	0.02	1	2doiX	III	Rep, Mult	108,119,120,121,122,127,129
7	0.02	1	4wzsA	NUC	Rep, Mult	18,19
8	0.02	1	4o6mA	MPG	Rep, Mult	65,77
9	0.02	1	1c8iA	HOA	Rep, Mult	8,9
10	0.02	1	2i89B	MG	Rep, Mult	27,28
11	0.02	1	4a5tS	UUU	Rep, Mult	68,70

	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	2w5vA	0.468	4.66	0.098	0.811	3.1.3.1	NA
2	0.060	1zefA	0.470	4.58	0.069	0.818	3.1.3.1	NA
3	0.060	3khjH	0.465	4.98	0.081	0.833	1.1.1.205	NA
4	0.060	2gq3A	0.472	5.32	0.079	0.871	2.3.3.9	15
5	0.060	1xdiA	0.468	4.55	0.113	0.826	1.6.5.2	21
6	0.060	2cu0A	0.464	5.22	0.056	0.864	1.1.1.205	NA
7	0.060	1hvxA	0.462	4.80	0.052	0.841	3.2.1.1	8
8	0.060	1sy7A	0.465	4.66	0.071	0.818	1.11.1.6	NA
9	0.060	1amyA	0.462	4.60	0.035	0.788	3.2.1.1	48
10	0.060	1llwA	0.472	4.91	0.043	0.841	1.4.7.1	NA
11	0.060	3dk9A	0.333	5.03	0.102	0.636	1.8.1.7	10,58,60,92
12	0.060	3bcfA	0.462	4.81	0.043	0.833	3.2.1.98	NA
13	0.060	2dieA	0.456	4.88	0.033	0.833	3.2.1.1	36,77
14	0.060	3bsgA	0.469	4.64	0.060	0.803	3.2.1.1	18
15	0.060	1ht6A	0.466	4.72	0.060	0.811	3.2.1.1	48
16	0.060	1jdaA	0.475	4.80	0.060	0.856	3.2.1.60	66
17	0.060	3bc9A	0.464	4.78	0.052	0.833	3.2.1.1	66
18	0.060	1eg7A	0.464	4.31	0.055	0.773	6.3.4.3	NA
19	0.060	1wp6A	0.465	4.84	0.043	0.856	3.2.1.98	122

(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	0.456	4.90	0.11	0.79	3zjcE	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005811 GO:0042803
1	0.07	0.454	5.23	0.06	0.84	3ibyD	GO:0000166 GO:0005525 GO:0005886 GO:0006810 GO:0006811 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
2	0.07	0.386	4.64	0.03	0.68	3zjcF	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005811 GO:0042803
3	0.07	0.421	4.90	0.08	0.78	1h65A	GO:0000166 GO:0005525 GO:0006810 GO:0006886 GO:0009507 GO:0009527 GO:0009536 GO:0009707 GO:0015031 GO:0015450 GO:0016020 GO:0016021 GO:0016787 GO:0071806
4	0.07	0.444	4.47	0.07	0.75	2cxxA	GO:0000166 GO:0000287 GO:0003924 GO:0005525 GO:0007049 GO:0046872 GO:0051301
5	0.07	0.467	5.25	0.03	0.86	3w5iB	GO:0005525 GO:0005886 GO:0006810 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
6	0.07	0.439	5.33	0.10	0.86	3v70A	GO:0000139 GO:0000166 GO:0005525 GO:0005783 GO:0005789 GO:0005794 GO:0016020 GO:0016021
7	0.07	0.445	5.04	0.08	0.81	2wibA	GO:0005525 GO:0005886 GO:0006810 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
8	0.07	0.424	4.70	0.06	0.76	3tk1A	GO:0003924 GO:0005525 GO:0016301 GO:0016310
9	0.07	0.432	4.90	0.09	0.79	3k53D	GO:0005525 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:1903874
10	0.07	0.439	4.98	0.06	0.80	4q5iB	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006810 GO:0006811 GO:0006974 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0042802 GO:0055072 GO:1903874
11	0.06	0.443	5.46	0.05	0.86	3a1sA	GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006810 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
12	0.06	0.429	4.32	0.10	0.71	1sulB	GO:0000166 GO:0000287 GO:0003924 GO:0005525 GO:0005829 GO:0007049 GO:0046872 GO:0051301
13	0.06	0.432	5.11	0.07	0.81	3b1vA	GO:0005525 GO:0005886 GO:0006810 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
14	0.06	0.419	4.66	0.12	0.72	3pqcB	GO:0000166 GO:0000287 GO:0003924 GO:0005525 GO:0005829 GO:0007049 GO:0046872 GO:0051301
15	0.06	0.381	5.17	0.14	0.72	1wxqA	GO:0005525
16	0.06	0.414	4.79	0.10	0.72	2wjgA	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006810 GO:0006811 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
17	0.06	0.387	4.78	0.05	0.69	3ievA	GO:0000028 GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0019843 GO:0042254 GO:0042274 GO:0043024 GO:0070181
18	0.06	0.391	5.17	0.06	0.78	1ni3A	GO:0000166 GO:0005524 GO:0005525 GO:0005634 GO:0005737 GO:0005829 GO:0016787 GO:0016887 GO:0043022 GO:0043023 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0032550	GO:0032561	GO:0035639	GO:0017111
GO-Score	0.57	0.57	0.57	0.37
Biological Processes	GO:0055072	GO:1903874	GO:0006886	GO:0071806	GO:0007049	GO:0051301
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0016021	GO:0005811	GO:0005886	GO:0009707
GO-Score	0.13	0.13	0.07	0.07

(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.