I-TASSER results

I-TASSER results for job id Rv0313

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

Input Sequence in FASTA format

>protein (128 residues)
MGDYGPFGFDPDEFDRVIREGSEGLRDAFERIGRFLSSSGAGTGWSAIFEDLSRRSRPAP
ETAGEAGDGVWAIYTVDADGGARVEQVYATELDALRANKDNTDPKRKVRFLPYGIAVSVL
DDPVDEAQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGDYGPFGFDPDEFDRVIREGSEGLRDAFERIGRFLSSSGAGTGWSAIFEDLSRRSRPAPETAGEAGDGVWAIYTVDADGGARVEQVYATELDALRANKDNTDPKRKVRFLPYGIAVSVLDDPVDEAQ
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEEEHHHHHHHHHHCCCCCCCCEEEEHCCCEEEEEHCCCCCCCC
Conf.Score	99999999995899999999989999999999998657888764899999865789999887777788589999995898768988656889999985669998766888757667888578887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGDYGPFGFDPDEFDRVIREGSEGLRDAFERIGRFLSSSGAGTGWSAIFEDLSRRSRPAPETAGEAGDGVWAIYTVDADGGARVEQVYATELDALRANKDNTDPKRKVRFLPYGIAVSVLDDPVDEAQ
Prediction	76774322132730341055226313501540252145545443023215424555546463446423100000113663423144124441531434574454624031123413022125547788
	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

CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEEEHHHHHHHHHHCCCCCCCCEEEEHCCCEEEEEHCCCCCCCC
MGDYGPFGFDPDEFDRVIREGSEGLRDAFERIGRFLSSSGAGTGWSAIFEDLSRRSRPAPETAGEAGDGVWAIYTVDADGGARVEQVYATELDALRANKDNTDPKRKVRFLPYGIAVSVLDDPVDEAQ

4at0A

0.20

0.19

0.93

0.69

MUSTER

MAALGPGA-DEEKITDYCEGSVEHYNWLVDCGVPFKESFWGEPGWEPPFDDLMYSGGENAAPFNEIAAPAPRGHVPQMDGKRTGEKGGYMLMKPLVETAE----KLGVRAE-YDMRVQTL---DDTGR

2e30A1

0.12

0.09

0.80

0.66

dPPAS

MGSRASTLLRDEELEEIKKETGSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDR---------IINAFFPEGEDQVN--FRGFMRTLAHFRPIEDNEKS--------------KDVNGPE

4uicA1

0.16

0.12

0.72

0.62

wdPPAS

----------ATDVATVVSQAKAQMKEAYYTYSHTVTETGQFPDIKDVYAAYNKAKQ--------------AVAVVNKAGGAK-KDAYLADLQAIYET-FKANPKSEARVATY---IDAYN-------

4jxoA

0.18

0.16

0.92

0.67

wMUSTER

HHDFDNVSMTMQGFLNYYDACSEGLRAASPRLG-DSFHTPPRSPLSWGLLRHCHDGTNF--FTGEAGVRL--YISLHRKGARSSISILEQEKVVAQQIRQLFPKFAD---TP--IYNDEADPLVGWSL

2k3mA

0.31

0.26

0.84

0.63

wPPAS

MS-----DFDTERVSRAVAAALVGPGGVALVVKVCAGLPG-------VIHTPARRGRCNPERI-QIGD--W--YEVAHDGAAHVNGI-VIAEDALIAEA--VGPHRALRYIP-NIAIEVLGTGTDYRF

2e30A1

0.12

0.09

0.80

0.67

dPPAS2

MGSRASTLLRDEELEEIKKETGSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDR---------IINAFFPEGEDQVN--FRGFMRTLAHFRPIEDNEKS--------------KDVNGPE

2e30A1

0.16

0.12

0.77

0.67

PPAS

MGSRASTLLRDEELEEIKKETGSQITRLYSRFTSLDKGENGT------REDFQRIPELAINPLGD------IINAFFPEGEDQVN--FRGFMRTLAHPIEDNEKSKDVN--PLN--------------

3oepA4

0.18

0.16

0.90

0.70

Env-PPAS

I----PVRYDGEDLPEVASRLGLSLEAVKALHQKRVYALGFTPGFPFLAPALPRKPHPRPRVPAHAAGVQTGIYPLPSPGGW---NLLGSLVAVYDPHRETPFLLRRVRFLE--AEGPTPPEPR----

2i7gB

0.18

0.16

0.93

0.66

MUSTER

IESYPLFGYDLEDYDVLFAEKLDLLLALREQEVVTWSGTKHPA-----INGRGVYPRPLPQSVARAGAGLPVALAIIGGEYRRFAPLFDLYHEAARRAGQEKTKLR-TSIN---VHGFIADTTDKAAD

4rbnA1

0.09

0.06

0.72

0.61

dPPAS

-------------IDTLATCTQQNRDAVYTLLRRYFTANRTLLLQSDLREGLLQTEQDCGQSDMLREIAKWEFMRIHQEHLI-PEKLTISEFLKFKETVVKGEATE----------------------

(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=-4.13

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.1±3.8Å

Download Model 2

C-score=-4.72

Download Model 3

C-score=-4.95

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	3tm8A	0.539	4.37	0.085	0.898
2	4hdtA	0.516	4.12	0.061	0.828
3	2e30A1	0.504	3.42	0.096	0.719
4	3ju1A	0.503	4.21	0.028	0.789
5	4cztA	0.503	4.84	0.083	0.922
6	4a35A	0.498	4.75	0.032	0.844
7	3h10A	0.496	4.79	0.034	0.906
8	4o2zA	0.493	4.89	0.067	0.898
9	1lufA	0.493	4.66	0.033	0.891
10	3eqdA	0.493	4.54	0.084	0.883

(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	0.07	3	2y04B	2CV	Rep, Mult	87,90,94,97
2	0.07	3	3q13A	CA	Rep, Mult	68,93,103
3	0.05	2	1iujB	ZN	Rep, Mult	13,16
4	0.05	2	1hwyA	PO4	Rep, Mult	22,112,113
5	0.05	2	3ginA	CA	Rep, Mult	65,100,122,126
6	0.02	1	3py8A	MN	Rep, Mult	20,23
7	0.02	1	4q5jB	III	Rep, Mult	14,17,19,89,92,96
8	0.02	1	3jskM	FE2	Rep, Mult	103,104
9	0.02	1	3athC	AKG	Rep, Mult	8,88
10	0.02	1	4f6xA	MG	Rep, Mult	70,98
11	0.02	1	2ct9A	CA	Rep, Mult	97,101,103,107
12	0.02	1	5apwB	CA	Rep, Mult	27,30
13	0.02	1	1f61A	MG	Rep, Mult	12,65
14	0.02	1	4u10A	ZN	Rep, Mult	99,100
15	0.02	1	1wrlC	TFP	Rep, Mult	35,95,98

	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	1lufA	0.493	4.66	0.033	0.891	2.7.10.1	94,96
2	0.060	2jiiB	0.479	4.67	0.078	0.844	2.7.11.1	65
3	0.060	2f57B	0.478	4.74	0.087	0.875	2.7.11.1,2.7.1.37	NA
4	0.060	2f2uA	0.479	4.78	0.068	0.859	2.7.11.1,2.7.1.37	93
5	0.060	3hx4A	0.478	4.81	0.051	0.867	2.7.11.17	23
6	0.060	3h9fA	0.482	4.61	0.061	0.867	2.7.12.1	93,97,98
7	0.060	2ogvA	0.490	4.88	0.056	0.906	2.7.10.1	89
8	0.060	1rjbA	0.487	5.02	0.063	0.938	2.7.10.1	NA
9	0.060	2h96A	0.477	4.50	0.044	0.836	2.7.11.24	NA
10	0.060	3eqdA	0.493	4.54	0.084	0.883	2.7.12.2	93,98
11	0.060	1csnA	0.468	4.71	0.026	0.859	2.7.11.1	NA
12	0.060	2a1aB	0.477	4.77	0.103	0.852	2.7.11.1	98
13	0.060	3g0eA	0.486	5.10	0.073	0.914	2.7.10.1	NA
14	0.060	2j4zB	0.496	4.79	0.034	0.906	2.7.11.1,	NA
15	0.060	1s9iA	0.480	4.68	0.093	0.867	2.7.12.2,2.7.1.37	98
16	0.060	2fh9A	0.483	4.85	0.085	0.906	2.7.11.1	91
17	0.060	3c4wB	0.477	4.79	0.076	0.875	2.7.11.14	NA
18	0.060	3a62A	0.483	4.78	0.034	0.906	2.7.11.1	93,98
19	0.060	1p4oB	0.493	5.05	0.063	0.922	2.7.10.1,2.7.1.112	94,96

(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	0.516	4.12	0.06	0.83	4hdtA	GO:0003860 GO:0016787 GO:0046872
1	0.07	0.509	3.92	0.07	0.80	3ju1A	GO:0003860 GO:0005829 GO:0006635 GO:0016787
2	0.07	0.502	4.55	0.03	0.85	3bptA	GO:0003860 GO:0005739 GO:0005759 GO:0006574 GO:0006635 GO:0009083 GO:0016787 GO:0070062
3	0.07	0.505	4.48	0.10	0.84	4j2uA	GO:0003860 GO:0004300 GO:0016829
4	0.07	0.378	4.67	0.03	0.65	1wdlA	GO:0003824 GO:0003857 GO:0004165 GO:0004300 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0008692 GO:0009062 GO:0016042 GO:0016491 GO:0016829 GO:0016853 GO:0036125 GO:0055114
5	0.07	0.360	4.92	0.07	0.65	3peaC	GO:0003824 GO:0008152 GO:0016853
6	0.06	0.433	4.40	0.06	0.70	3fduA
7	0.06	0.380	5.19	0.02	0.72	2ogiB	GO:0046872
8	0.06	0.406	4.69	0.06	0.70	3gkbB	GO:0003824 GO:0008152
9	0.06	0.372	4.56	0.07	0.62	3g64A	GO:0003824 GO:0008152
10	0.06	0.385	4.41	0.06	0.66	4jcsA	GO:0003824 GO:0004300 GO:0008152 GO:0016829 GO:0016853
11	0.06	0.376	5.05	0.07	0.70	4i42A	GO:0003824 GO:0005829 GO:0008152 GO:0008935 GO:0009234 GO:0016829 GO:0071890
12	0.06	0.367	4.53	0.02	0.62	4og1A	GO:0003824 GO:0008152 GO:0016853
13	0.06	0.362	4.97	0.10	0.65	2wtbA	GO:0003824 GO:0003857 GO:0004165 GO:0004300 GO:0005618 GO:0005730 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0008692 GO:0009506 GO:0009514 GO:0016491 GO:0016508 GO:0016829 GO:0016853 GO:0055114
14	0.06	0.345	5.39	0.03	0.66	5e0nX	GO:0003824 GO:0008152 GO:0016853
15	0.06	0.362	4.80	0.05	0.66	4i4zA	GO:0003824 GO:0005829 GO:0008152 GO:0008935 GO:0009234 GO:0016829 GO:0042372
16	0.06	0.376	5.02	0.08	0.69	4jsbA	GO:0003824 GO:0004300 GO:0008152 GO:0016829
17	0.06	0.423	4.53	0.07	0.70	3p5mB	GO:0003824 GO:0008152 GO:0016853
18	0.06	0.379	4.82	0.07	0.66	3r9tB	GO:0003824 GO:0008152

Consensus prediction of GO terms

Molecular Function	GO:0016289
GO-Score	0.48
Biological Processes	GO:0009062	GO:0019395
GO-Score	0.37	0.37
Cellular Component	GO:0005759	GO:0005829	GO:0070062	GO:0036125
GO-Score	0.07	0.07	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.