I-TASSER results

I-TASSER results for job id Rv3304

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

Input Sequence in FASTA format

>protein (159 residues)
MPLYAAYGSNMHPEQMLERAPHSPMAGTGWLPGWRLTFGGEDIGWEGALATVVEDPDSKV
FVVLYDMTPADEKNLDRWEGSEFGIHQKIRCRVERISSDTTTDPVLAWLYVLDAWEGGLP
SARYLGVMADAAEIAGAPSDYVHDLRTRPARNIGPGTIA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPLYAAYGSNMHPEQMLERAPHSPMAGTGWLPGWRLTFGGEDIGWEGALATVVEDPDSKVFVVLYDMTPADEKNLDRWEGSEFGIHQKIRCRVERISSDTTTDPVLAWLYVLDAWEGGLPSARYLGVMADAAEIAGAPSDYVHDLRTRPARNIGPGTIA
Prediction	CCEEEEHCCCCCHHHHHHHCCCCCEEEEEEHCCEEEEHCCCCCCCCCCEEEEEHCCCCEEEEEEEEHCHHHHHHHHHHHCCCCCCEEEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCC
Conf.Score	986898656899899999899885568999979799985778888886557887799779999999599999997788698777657999999996688887689999997688888999999999999999998999999999998556788987779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPLYAAYGSNMHPEQMLERAPHSPMAGTGWLPGWRLTFGGEDIGWEGALATVVEDPDSKVFVVLYDMTPADEKNLDRWEGSEFGIHQKIRCRVERISSDTTTDPVLAWLYVLDAWEGGLPSARYLGVMADAAEIAGAPSDYVHDLRTRPARNIGPGTIA
Prediction	343100400002362046324514321203032120202342444522112034367440100013035611530143031443224414040422646556441200011055365340263015101400561603660053046233673455438
	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                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEHCCCCCHHHHHHHCCCCCEEEEEEHCCEEEEHCCCCCCCCCCEEEEEHCCCCEEEEEEEEHCHHHHHHHHHHHCCCCCCEEEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCC
MPLYAAYGSNMHPEQMLERAPHSPMAGTGWLPGWRLTFGGEDIGWEGALATVVEDPDSKVFVVLYDMTPADEKNLDRWEGSEFGIHQKIRCRVERISSDTTTDPVLAWLYVLDAWEGGLPSARYLGVMADAAEIAGAPSDYVHDLRTRPARNIGPGTIA

2rbhA

0.25

0.24

0.97

3.41

MUSTER

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

6.66

dPPAS

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

6.53

wdPPAS

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

4.18

wMUSTER

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

5.60

wPPAS

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

14.00

dPPAS2

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

4.84

PPAS

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2rbhA

0.25

0.24

0.97

5.05

Env-PPAS

SFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQAGVKSGMYVVIEVKVATQEGK----EITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSE

2qikA2

0.19

0.17

0.91

2.59

MUSTER

PIYYFAYGSCDNARFQKAGVDHQDPVGRAVLKGYTTRFT--LKREDGSRADLED--GGTTEGVLYRIPYSALSYLYKREGVESLTYRPAFVDVEA-----GRHYKDCLTFLVQKEAEIAPPQHYQIEIERGAELY-LSPEFTEKLKR--HNSLPKG---

2qikA2

0.18

0.16

0.91

4.68

dPPAS

PIYYFAYGSCDNARFQKAGVDFQDPVGRAVLKGYTTRFTLKR--EDGSRADLED--GGTTEGVLYRIPYSALSYLYKREGVESLTYRPAFVDVEAGGR----HYKDCLTFLVLQEAEIAPPQHYQIEIERGAELYL-SPEFTEKLKRHNSLPKG-----

(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 1 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=1.70

Estimated TM-score = 0.95±0.05

Estimated RMSD = 1.7±1.5Å

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	2rbhA	0.952	0.77	0.245	0.975
2	2qikA	0.802	1.91	0.197	0.893
3	3jucA	0.642	3.18	0.137	0.799
4	2g0qA	0.619	2.71	0.129	0.730
5	2kl2A	0.617	3.57	0.157	0.811
6	2jqvA	0.589	2.77	0.164	0.711
7	4issA	0.588	3.35	0.057	0.748
8	1v30A	0.560	2.90	0.144	0.679
9	5c5zA	0.559	3.12	0.112	0.711
10	1xhsA	0.546	2.60	0.182	0.660

(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	0.13	4	3jucA	PCA	Rep, Mult	6,7,8,9,10,49,79,86
2	0.12	4	3orcA	NUC	Rep, Mult	9,10
3	0.09	3	2zbkF	RDC	Rep, Mult	128,129,131,132,142,148
4	0.04	1	2pn70	III	Rep, Mult	53,54,56,84,86,87,88,89,90,92,108,113,114
5	0.03	1	1z5cA	PO4	Rep, Mult	121,122,124,126,127,128
6	0.03	1	1ux1A	THU	Rep, Mult	5,6,7
7	0.03	1	2buqA	CAQ	Rep, Mult	120,124
8	0.03	1	2z7xB	III	Rep, Mult	136,138,141
9	0.03	1	3ltwA	HLZ	Rep, Mult	10,11,16,19,79

	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	0.238	3jucA	0.642	3.18	0.137	0.799	2.3.2.4	3,7,76,87
2	0.060	2kl2A	0.617	3.57	0.157	0.811	2.3.2.4	7,65,75,110
3	0.060	1q1dB	0.417	4.99	0.052	0.711	5.99.1.3	NA
4	0.060	1fw8A	0.412	4.89	0.040	0.679	2.7.2.3	8,12,125
5	0.060	1bgaA	0.411	5.01	0.052	0.711	3.2.1.21	130
6	0.060	1qqwB	0.409	5.22	0.061	0.736	1.11.1.6	74
7	0.060	1vcmA	0.406	4.90	0.057	0.692	6.3.4.2	125
8	0.060	3c39A	0.364	5.48	0.031	0.673	2.7.2.3	NA
9	0.060	13pkA	0.402	5.14	0.031	0.717	2.7.2.3	NA
10	0.060	1vcoA	0.405	4.56	0.075	0.667	6.3.4.2	NA
11	0.060	2nvrA	0.367	4.89	0.048	0.610	3.5.1.98	130,133
12	0.060	2j2mA	0.408	5.41	0.027	0.748	1.11.1.6	NA
13	0.060	1a4eA	0.406	5.34	0.034	0.755	1.11.1.6	NA
14	0.060	1m7sD	0.403	5.55	0.034	0.755	1.11.1.6	NA
15	0.060	1gweA	0.410	5.31	0.047	0.748	1.11.1.6	NA
16	0.060	1kf0A	0.411	4.90	0.056	0.679	2.7.2.3	NA
17	0.060	1ajbA	0.406	5.06	0.066	0.692	3.1.3.1	151
18	0.060	2rbhA	0.952	0.77	0.245	0.975	2.3.2.4	4,8,10,31,76,89,110
19	0.060	2vfbA	0.415	4.27	0.071	0.654	2.3.1.5	NA
20	0.060	1u60C	0.396	5.38	0.021	0.717	3.5.1.2	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	0.44	0.950	0.79	0.24	0.97	3cryA	GO:0001836 GO:0003839 GO:0005829 GO:0006750 GO:0016740 GO:0016746 GO:0042803 GO:0070062
1	0.29	0.814	1.89	0.20	0.91	2qikA	GO:0016740 GO:0016746
2	0.24	0.619	2.71	0.13	0.73	2g0qA	GO:0016740 GO:0016746
3	0.24	0.642	3.18	0.14	0.80	3jucA	GO:0003839 GO:0016740 GO:0016746 GO:0042219 GO:0070062
4	0.20	0.589	2.77	0.16	0.71	2jqvA
5	0.19	0.617	3.57	0.16	0.81	2kl2A	GO:0003839 GO:0016740 GO:0016746 GO:0042219 GO:0070062
6	0.17	0.576	2.90	0.11	0.72	5c5zA	GO:0016740
7	0.16	0.560	2.90	0.14	0.68	1v30A	GO:0016740 GO:0016746
8	0.14	0.546	2.60	0.18	0.66	1xhsA	GO:0005829
9	0.06	0.330	4.75	0.03	0.53	4ax3D	GO:0005507 GO:0006807 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0050421 GO:0055114
10	0.06	0.322	5.22	0.05	0.58	4hecB	GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004532 GO:0008408 GO:0016787 GO:0040007 GO:0046872 GO:0090305 GO:0090503
11	0.06	0.294	5.52	0.03	0.54	4c2dD	GO:0006508 GO:0006518 GO:0007165 GO:0008233 GO:0008236 GO:0016787 GO:0030435 GO:0042277 GO:0042802 GO:0042803
12	0.06	0.299	4.95	0.04	0.48	5a6cB	GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005938 GO:0007052 GO:0007155 GO:0007165 GO:0007186 GO:0007267 GO:0008022 GO:0017016 GO:0030054 GO:0030695 GO:0034332 GO:0042802 GO:0043547 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0090557 GO:0097431 GO:0098609 GO:0098641
13	0.06	0.313	5.62	0.07	0.58	4jhrA	GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005737 GO:0005856 GO:0005938 GO:0007052 GO:0030695 GO:0042802 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0097431
14	0.06	0.335	5.22	0.03	0.58	3l84A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
15	0.06	0.284	5.19	0.04	0.49	1jzuA	GO:0002376 GO:0005215 GO:0005576 GO:0006629 GO:0006810 GO:0036094 GO:0042742 GO:0045087 GO:0050544 GO:0070538 GO:1903981
16	0.06	0.282	5.00	0.02	0.45	1spgB	GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
17	0.06	0.324	5.62	0.06	0.60	4aoeA	GO:0005230 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0034220
18	0.06	0.264	4.77	0.08	0.43	3lasA	GO:0004089 GO:0008270 GO:0016829 GO:0046872
19	0.06	0.231	4.94	0.04	0.40	3gnjA	GO:0005623 GO:0006662 GO:0015035 GO:0045454 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003839	GO:0042803
GO-Score	0.57	0.43
Biological Processes	GO:1901565	GO:0006750	GO:0001836
GO-Score	0.47	0.43	0.43
Cellular Component	GO:0070062	GO:0005829
GO-Score	0.57	0.43

(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.