I-TASSER results

I-TASSER results for job id Rv2016

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

Input Sequence in FASTA format

>protein (191 residues)
MTELGDKFLAALVGTIRDTRFDIADMRNWRPGWFPTMHSRCLSNLIHDRIWAHLVTLIAS
NPGTSIKDKGATREIVVGAHLRLRIKRHHAGDEISTYPTRTAIEFWQQGSQPAFPGLEEV
RIAVGYRWDPDTREIGAPLLSLRDGKDHVIWVVELDEPAAGVKITWTPIEPTLPSIDFGD
LGEDSGASGER

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTELGDKFLAALVGTIRDTRFDIADMRNWRPGWFPTMHSRCLSNLIHDRIWAHLVTLIASNPGTSIKDKGATREIVVGAHLRLRIKRHHAGDEISTYPTRTAIEFWQQGSQPAFPGLEEVRIAVGYRWDPDTREIGAPLLSLRDGKDHVIWVVELDEPAAGVKITWTPIEPTLPSIDFGDLGEDSGASGER
Prediction	CCHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHCCCEEEEEHCCEEEEEEEHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCEEEEEEEEEHCCCHHHHCCEEEEEHCCCCCEEEEEEHCCCCCCCCCEEHCCCCCCCHHHHHHHHHHCCCCCCC
Conf.Score	97588999999999746655478999986887655566677789999999999999997599968985875589998558998987656788765678588999987556678998755899998774874665453478765699967999997677788775676589988657899988656778889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTELGDKFLAALVGTIRDTRFDIADMRNWRPGWFPTMHSRCLSNLIHDRIWAHLVTLIASNPGTSIKDKGATREIVVGAHLRLRIKRHHAGDEISTYPTRTAIEFWQQGSQPAFPGLEEVRIAVGYRWDPDTREIGAPLLSLRDGKDHVIWVVELDEPAAGVKITWTPIEPTLPSIDFGDLGEDSGASGER
Prediction	75524440012013215424231440462322111313441114101430044004302654424135664224101342030204434574514523242014104515436134344230221231444365053102313454431101031346245351423314452443414523566665568
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHCCCEEEEEHCCEEEEEEEHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCEEEEEEEEEHCCCHHHHCCEEEEEHCCCCCEEEEEEHCCCCCCCCCEEHCCCCCCCHHHHHHHHHHCCCCCCC
MTELGDKFLAALVGTIRDTRFDIADMRNWRPGWFPTMHSRCLSNLIHDRIWAHLVTLIASNPGTSIKDKGATREIVVGAHLRLRIKRHHAGDEISTYPTRTAIEFWQQGSQPAFPGLEEVRIAVGYRWDPDTREIGAPLLSLRDGKDHVIWVVELDEPAAGVKITWTPIEPTLPSIDFGDLGEDSGASGER

5cwcA

0.13

0.12

0.95

0.62

MUSTER

KEELRERLVKICVENAKRKGDDTEEAREAAREAFELVREAAERAIDSSEVLELAIRLIKECVENAQREGYDISEACRAAAAFKRVAEAAKRAGITSLAIRLIKECVENAQREGYDISEACRAEAFKRVAEAAKRAGI------TSSETLKRAIEEIRKRVEEAQR----EGNDISEACRQAAEEFRKKAEE

4psnA

0.12

0.99

0.60

dPPAS

LPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAAAGNLNRVLFELLVNKLKADKLDVVRIQRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGEDVVYRIYRGSDV--GALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQN

5iy6R

0.12

0.09

0.76

0.73

wdPPAS

LAKIVNYMKTRHQR--DTHPLTLDEILDE----HLDIGLKQKQWLMTE--------ALVNNPKIEVIDGK------------YAFKKYNVRDKKA-------LRLLDQHDQRGLGGILLEDIEEAL-SQKAVKALGDILFVNRPDKKKILFF----DKSCQFSVD---RSVTVDSMDEEKIEEYLKR----

4zniA

0.12

0.99

0.63

wMUSTER

FELLGHHVQLAIHRSACLGRVEAVFELFARPGSQGWIPTYDQAEIIFGRVVEKVERLAEVFPATEVQLQRRRLRLLVHATSEFRGKSADRPDNLRGATLDFVAAMIPFSVWSEAPSVRDGWALIISTPKGLNWFYEFFLMGWRGGLKEGIPNSGINQTHPDFESFHAASW-DVWPERREWYMERRLYIPDL

5iy6R

0.13

0.09

0.72

0.76

wPPAS

VNYMKTRHQRG-----DTHPLTLDEILDE----HLDIGLKQKQWLMTE--------ALVNNPKIEVIDGK------------YAFKKYNVRDKKA-------LRLLDQHDQRGLGG---ILLDIAL--QKAVKALGDILFVNRPDKKKILFF----DKSCQFSV---E-SVTVDSMDEEKIEEY-----KR

3wmdA

0.18

0.12

0.68

0.73

dPPAS2

MNFARKKRALEHSRRI--NAGDLDAIIDLDPVGLPPVTG-------HDALRAHYEPLLA--AHLREEAAEPVAGQD-ATHALIQISS-----VMDYLPVGPLYAERGWLKAPDAPGTAHRTAMLVIRMDA-----SGLIRHLK-----SYWLTVLG-----------------------------------

5iy6R

0.12

0.09

0.74

0.67

PPAS

VNYMKTRHQRG-----DTHPLTLDEILDE----HLDIGLKQKQWLMTEALVNN--------PKIEVIDGK------------YAFKKYNVRDKKA-------LRLLDQHDQRGLGGILLEDIEEALP-KAVKALGDQILFVNRPDKKKILFF----DKSCQFSV----RSVTVDSMDEEKIEEY-----KR

5iy6R

0.10

0.08

0.81

0.70

Env-PPAS

LAKIVNYMKTRHQRG-DTHPLTLDEILDE--TQHLDIGLKQKQWLMTEALVNN--------PKIEVIDGK----YAFKPKYNVRDKKA-------------LLRLLDQHDQRGLGGILLEDIEEALPQKAVKALGDQILFVNRPDKKKILFFN---DKSCQFSVD--ERSVTVDSMDEEKIEEYLKR----

4psnA

0.12

0.96

0.62

MUSTER

LPTLGLVIAAGYADKVR--RVLFAQLRDAIKSGELSNKDVAAAGNLNRVLFELLVNKLKADKLIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVVYRIYRGSD-VGALIVTPLNGE--ALVRGAVVEP---TPLLLKRTRVQVEADRIDDFVRESAQNVEK

4wsbA2

0.10

0.09

0.94

0.58

dPPAS

-------MENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCFMYSDFHDLEGNTIVKENDDD----NAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFLPYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEESRARIKTRLFVLRQELATA-

(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=-4.17

Estimated TM-score = 0.27±0.08

Estimated RMSD = 15.4±3.4Å

Download Model 2

C-score=-4.68

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	1aq6A	0.475	5.06	0.070	0.780
2	1js4A1	0.463	4.96	0.029	0.749
3	2xfgA	0.458	4.84	0.036	0.733
4	2yikA	0.457	5.11	0.048	0.749
5	1ga2B1	0.457	4.95	0.042	0.738
6	3wc3A	0.456	5.40	0.048	0.775
7	2ymlA	0.454	5.64	0.068	0.806
8	3umgA	0.452	5.37	0.100	0.785
9	1ut9A	0.450	5.38	0.046	0.770
10	2jc5A	0.449	4.86	0.046	0.723

(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	4brbB	78N	Rep, Mult	54,58
2	0.04	2	1o5qA	MG	Rep, Mult	68,127
3	0.04	2	3ae6C	EPH	Rep, Mult	13,50,51,54
4	0.02	1	3ga6A	NA	Rep, Mult	117,121,122,151,152,153
5	0.02	1	1vkxA	NUC	Rep, Mult	82,84
6	0.02	1	1a76A	MN	Rep, Mult	68,134
7	0.02	1	1ia6A	CA	Rep, Mult	65,68,78
8	0.02	1	3e27A	MG	Rep, Mult	129,143
9	0.02	1	3otbA	3PO	Rep, Mult	40,43
10	0.02	1	4c98A	ZN	Rep, Mult	47,80
11	0.02	1	1ga2A	BGC	Rep, Mult	55,63,83
12	0.02	1	1nxd2	AZI	Rep, Mult	97,98
13	0.02	1	3nteA	FE	Rep, Mult	115,118
14	0.02	1	4afyA	MG	Rep, Mult	48,50
15	0.02	1	5absA	ZN	Rep, Mult	44,48
16	0.02	1	2zyqB	TAR	Rep, Mult	31,32
17	0.02	1	2vi7C	AZI	Rep, Mult	84,85
18	0.02	1	2b0qA	MG	Rep, Mult	144,156
19	0.02	1	2muwB	3LW	Rep, Mult	43,46

	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	1ofdA	0.424	5.67	0.056	0.764	1.4.7.1	NA
2	0.060	3m1gA	0.426	5.49	0.053	0.723	2.5.1.18	67
3	0.060	2vdcF	0.416	6.24	0.079	0.833	1.4.1.13	NA
4	0.060	1gq2A	0.411	5.41	0.055	0.717	1.1.1.40	NA
5	0.060	1ea0A	0.359	5.93	0.030	0.670	1.4.1.13	NA
6	0.060	3a5vA	0.430	5.43	0.032	0.738	3.2.1.22	NA
7	0.060	3i39X	0.433	5.87	0.044	0.817	1.2.99.2	124
8	0.060	2z8yD	0.435	5.90	0.061	0.822	1.2.7.4,1.2.99.2	124
9	0.060	1llwA	0.436	6.15	0.062	0.833	1.4.7.1	NA
10	0.060	2w11A	0.434	5.50	0.078	0.770	3.8.1.2	NA
11	0.060	2jc5A	0.449	4.86	0.046	0.723	3.1.11.2	NA
12	0.060	1ia7A	0.448	5.04	0.044	0.728	3.2.1.4	NA
13	0.060	2aw5B	0.429	5.43	0.025	0.749	1.1.1.40	NA
14	0.060	2no4B	0.439	5.57	0.044	0.791	3.8.1.2	NA
15	0.060	1qq5A	0.474	5.01	0.076	0.775	3.8.1.2	NA
16	0.060	2vdcA	0.428	6.34	0.051	0.833	1.4.1.13	NA
17	0.060	2b3oA	0.433	5.37	0.018	0.733	3.1.3.48	NA
18	0.060	2o1xC	0.394	5.49	0.099	0.696	2.2.1.7	NA
19	0.060	2o1xB	0.442	5.51	0.076	0.764	2.2.1.7	148

(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	0.448	5.35	0.11	0.77	3um9A	GO:0008152 GO:0016787 GO:0018784 GO:0019120
1	0.07	0.454	5.64	0.07	0.81	2ymlA	GO:0008152 GO:0016787 GO:0019120
2	0.07	0.475	5.06	0.07	0.78	1aq6A	GO:0008152 GO:0016787 GO:0018784 GO:0019120
3	0.07	0.458	4.92	0.08	0.72	3umgD	GO:0008152 GO:0016787 GO:0018784 GO:0019120
4	0.07	0.439	5.20	0.09	0.74	1judA	GO:0008152 GO:0016787 GO:0018784 GO:0019120
5	0.07	0.439	5.57	0.04	0.79	2no4B	GO:0008152 GO:0016787 GO:0018784 GO:0019120
6	0.07	0.435	5.51	0.08	0.79	3umbA	GO:0008152 GO:0016787 GO:0019120
7	0.07	0.415	5.96	0.05	0.76	2hszA	GO:0005975 GO:0008152 GO:0008967 GO:0016311 GO:0016787 GO:0046295 GO:0046872
8	0.07	0.434	5.50	0.08	0.77	2w11A	GO:0008152 GO:0016787 GO:0018784 GO:0019120
9	0.07	0.420	5.78	0.02	0.77	3smvA	GO:0008152 GO:0016787 GO:0019120
10	0.07	0.429	5.60	0.04	0.77	3umcA	GO:0008152 GO:0016787 GO:0019120
11	0.07	0.397	5.89	0.05	0.73	4gibA	GO:0000287 GO:0005975 GO:0008152 GO:0008801 GO:0016787 GO:0016853
12	0.06	0.402	5.85	0.07	0.74	1te2A	GO:0000287 GO:0003850 GO:0004346 GO:0005829 GO:0008152 GO:0016311 GO:0016787 GO:0016791 GO:0046872 GO:0050308
13	0.06	0.428	5.76	0.06	0.79	4ffdA	GO:0008152 GO:0016787
14	0.06	0.403	6.03	0.04	0.78	1o03A	GO:0000287 GO:0005737 GO:0005975 GO:0008152 GO:0008801 GO:0016787 GO:0016853 GO:0046872
15	0.06	0.412	5.74	0.06	0.76	2nyvA	GO:0005975 GO:0008152 GO:0008967 GO:0016311 GO:0016787 GO:0046295 GO:0046872
16	0.06	0.410	5.72	0.05	0.75	2fdrA	GO:0008152 GO:0016787 GO:0046872
17	0.06	0.416	5.86	0.07	0.77	4uauA	GO:0008152 GO:0016787
18	0.06	0.391	5.65	0.04	0.68	2i6xA	GO:0008152 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0016824
GO-Score	0.57
Biological Processes	GO:0008152
GO-Score	0.29
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.