I-TASSER results

I-TASSER results for job id Rv3114

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

Input Sequence in FASTA format

>protein (176 residues)
MVAARLPFGWSADSGVTADIIEAAMELAIDTARHATAPFGAALLDVTTLRAFSGGNTYFE
SGDRFAHAETNVLRAAMSTLPELSNHVLISTAEPCPMCAAASVLSGVRAIIFGTSIETLI
QCGWFQIRISASDVVAASTRPTRPSVYSGFLSHKTDLLYRNSENRRAMNPWTDPSH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVAARLPFGWSADSGVTADIIEAAMELAIDTARHATAPFGAALLDVTTLRAFSGGNTYFESGDRFAHAETNVLRAAMSTLPELSNHVLISTAEPCPMCAAASVLSGVRAIIFGTSIETLIQCGWFQIRISASDVVAASTRPTRPSVYSGFLSHKTDLLYRNSENRRAMNPWTDPSH
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCHHHHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	99888888877788699999999999999999989998799999799689999956555779987579999999999996998997899976898899999999799858875799665555777665545676658888886699668769999999999999999756655589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVAARLPFGWSADSGVTADIIEAAMELAIDTARHATAPFGAALLDVTTLRAFSGGNTYFESGDRFAHAETNVLRAAMSTLPELSNHVLISTAEPCPMCAAASVLSGVRAIIFGTSIETLIQCGWFQIRISASDVVAASTRPTRPSVYSGFLSHKTDLLYRNSENRRAMNPWTDPSH
Prediction	74556343534654630450043005104602776710000000367230002022333655201000003002400742660660100002114000100023141420000032540121234434120230254652323030323014500350055016524755466588
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCHHHHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
MVAARLPFGWSADSGVTADIIEAAMELAIDTARHATAPFGAALLDVTTLRAFSGGNTYFESGDRFAHAETNVLRAAMSTLPELSNHVLISTAEPCPMCAAASVLSGVRAIIFGTSIETLIQCGWFQIRISASDVVAASTRPTRPSVYSGFLSHKTDLLYRNSENRRAMNPWTDPSH

1z3aA

0.25

0.22

0.88

4.12

MUSTER

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

7.58

dPPAS

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

6.96

wdPPAS

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.87

4.93

wMUSTER

-----------EVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

5.53

wPPAS

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

8.14

dPPAS2

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

4.86

PPAS

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAG------SLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

1z3aA

0.25

0.22

0.88

5.49

Env-PPAS

----------SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSL------MDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK-----

2b3jC

0.23

0.20

0.85

4.03

MUSTER

-------------MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITK-DDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSG------SLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANK------

2nx8A

0.19

0.18

0.93

7.30

dPPAS

------SFLMPYSLEEQTYFMQEALKESEKSLQKAEIPIGCVIVK-DGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGRLLDTTLFVTIEPCVMCSGAIGLARIPHVIYGASNQKFGGVD------SLYQILTDERLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHL

(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=0.97

Estimated TM-score = 0.85±0.08

Estimated RMSD = 3.2±2.2Å

Download Model 2

C-score=-2.15

Download Model 3

C-score=0.19

Download Model 4

C-score=0.61

Download Model 5

C-score=-4.50

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	2nx8A	0.857	1.72	0.184	0.920
2	1z3aA	0.826	1.38	0.253	0.875
3	2b3jC	0.816	1.09	0.233	0.852
4	1wwrC	0.812	1.39	0.215	0.858
5	3dh1A	0.759	1.63	0.211	0.830
6	2g84A	0.749	2.65	0.211	0.852
7	1ysdB	0.725	2.27	0.172	0.824
8	3zpcA	0.708	2.58	0.186	0.824
9	2hxvA	0.703	2.38	0.224	0.812
10	2d5nD	0.696	2.32	0.179	0.795

(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	0.71	77	2a8nA	ZN	Rep, Mult	67,95,98
2	0.25	25	2fr5B	TYU	Rep, Mult	37,39,56,58,67,68,69,94,95,98
3	0.06	5	2b3jA	NUC	Rep, Mult	35,37,39,56,58,59,67,68,69,92,114,115,116,118,156,159,162,163,166,167
4	0.02	3	1p6oA	HPY	Rep, Mult	39,56,67,68,69,94,95,98,173,174
5	0.02	3	2nx80	III	Rep, Mult	58,59,62,63,64,65,67,70,74,77,82,96,97,100,101,104,105,131,132,134,137,139,140
6	0.02	3	2b3jA	QNA	Rep, Mult	83,85,106,141,143
7	0.01	1	1wkqA	IMD	Rep, Mult	39,56,67,124,128
8	0.00	1	2hvwA	DCP	Rep, Mult	30,54,55,57,58,71
9	0.00	1	1thzA	326	Rep, Mult	19,20,88,112

	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	0.424	1r5tA	0.531	3.42	0.131	0.670	3.5.4.5	69
2	0.419	1jtkA	0.508	3.22	0.149	0.625	3.5.4.5	69
3	0.416	2d30A	0.500	2.89	0.177	0.602	3.5.4.5	69
4	0.411	1mq0A	0.505	3.25	0.150	0.625	3.5.4.5	69
5	0.376	1ox7B	0.724	2.27	0.159	0.824	3.5.4.1	69,95
6	0.256	1wkqA	0.569	2.29	0.189	0.631	3.5.4.3	28,38,56,63,67,93,95,97,101
7	0.168	1vq2A	0.632	2.94	0.157	0.761	3.5.4.12	95,101
8	0.135	2w4lE	0.610	2.98	0.135	0.727	3.5.4.12	NA
9	0.124	3ijfX	0.492	3.39	0.193	0.631	3.5.4.5	95
10	0.115	2z3iA	0.503	3.23	0.167	0.625	3.5.4.23	NA
11	0.114	1zabA	0.522	3.05	0.157	0.636	3.5.4.5	69
12	0.109	1af2A	0.503	3.58	0.104	0.653	3.5.4.5	69
13	0.095	3dmoA	0.515	3.35	0.164	0.642	3.5.4.5	69
14	0.060	3bg3A	0.508	5.11	0.057	0.847	6.4.1.1	19
15	0.060	3f93A	0.536	4.99	0.060	0.886	3.2.1.-	NA
16	0.060	2z1aA	0.509	4.91	0.092	0.830	3.1.3.5	NA
17	0.060	2gq3A	0.500	4.53	0.078	0.778	2.3.3.9	NA
18	0.060	1vffA	0.494	5.07	0.058	0.824	3.2.1.21	26
19	0.060	1zczB	0.550	3.26	0.098	0.693	3.5.4.10,2.1.2.3	NA
20	0.060	1cttA	0.503	3.60	0.104	0.653	3.5.4.5	56,67,95
21	0.060	3cuzA	0.516	4.75	0.045	0.807	2.3.3.9	NA
22	0.060	2x42A	0.498	5.20	0.066	0.852	3.2.1.21	NA
23	0.060	2obcB	0.658	2.52	0.184	0.773	1.1.1.193,3.5.4.26	33,38,54,69,94
24	0.060	1iayA	0.511	4.83	0.039	0.801	4.4.1.14	154
25	0.060	3dmoD	0.515	3.33	0.164	0.642	3.5.4.5	95
26	0.060	2d5nD	0.696	2.32	0.179	0.795	1.1.1.193,3.5.4.26	27,54,66,95,158
27	0.060	2z1sA	0.499	4.91	0.035	0.807	3.2.1.21	NA
28	0.060	1rhcA	0.502	4.67	0.058	0.795	1.1.99.5	NA
29	0.060	3cuxA	0.519	4.71	0.038	0.812	2.3.3.9	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	0.58	0.826	1.38	0.25	0.88	1z3aA	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
1	0.54	0.812	1.39	0.21	0.86	1wwrC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0019239 GO:0046872 GO:0052717
2	0.53	0.816	1.09	0.23	0.85	2b3jC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
3	0.53	0.749	2.65	0.21	0.85	2g84A	GO:0003824 GO:0008270 GO:0016787 GO:0046872
4	0.53	0.857	1.72	0.18	0.92	2nx8A	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
5	0.53	0.727	1.38	0.29	0.77	2a8nB	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
6	0.52	0.759	1.63	0.21	0.83	3dh1A	GO:0002100 GO:0003824 GO:0005654 GO:0006400 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717 GO:0052718
7	0.48	0.569	2.29	0.19	0.63	1wkqA	GO:0003824 GO:0006144 GO:0006147 GO:0008270 GO:0008892 GO:0009451 GO:0016787 GO:0019239 GO:0046872
8	0.45	0.599	2.79	0.19	0.71	2hvwA	GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
9	0.44	0.632	2.94	0.16	0.76	1vq2A	GO:0003824 GO:0004132 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046872
10	0.43	0.610	2.98	0.14	0.73	2w4lE	GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
11	0.42	0.592	2.84	0.14	0.69	2w4lC	GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
12	0.39	0.718	2.38	0.22	0.83	2hxvA	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0019239 GO:0046872 GO:0055114
13	0.26	0.724	2.27	0.16	0.82	1ox7B	GO:0003824 GO:0004131 GO:0008270 GO:0008655 GO:0009451 GO:0016787 GO:0019858 GO:0044206 GO:0046087 GO:0046872
14	0.23	0.602	2.43	0.17	0.69	4p9cA	GO:0000166 GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
15	0.23	0.696	2.57	0.18	0.81	4g3mA	GO:0003824 GO:0005829 GO:0008152 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
16	0.10	0.708	2.58	0.19	0.82	3zpcA	GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
17	0.10	0.689	2.82	0.17	0.82	2g6vB	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
18	0.06	0.348	5.46	0.05	0.62	3q1yA	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:2001059

Consensus prediction of GO terms

Molecular Function	GO:0008270	GO:0052717
GO-Score	0.98	0.96
Biological Processes	GO:0002100
GO-Score	0.96
Cellular Component
GO-Score

(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.