I-TASSER results

Input Sequence in FASTA format

>protein (82 residues)
MPCLARQPVDLPPWAGPRCGPYCPRARITLLQRTTIAKSNRKYYENGYPADVKLMPGHAA
VVSNRAAARAGFALPCRKRQPD

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MPCLARQPVDLPPWAGPRCGPYCPRARITLLQRTTIAKSNRKYYENGYPADVKLMPGHAAVVSNRAAARAGFALPCRKRQPD
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHCCCEEEEHCCCCEEEEHCCCCCCCEEHCCCCCCCCC
Conf.Score	9987678889999999988998997568886466778888999985986668875775566546766544565566678999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MPCLARQPVDLPPWAGPRCGPYCPRARITLLQRTTIAKSNRKYYENGYPADVKLMPGHAAVVSNRAAARAGFALPCRKRQPD
Prediction	7543454425134443453434245130311453334534451265624141431443342435534432111121455678
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHCCCEEEEHCCCCEEEEHCCCCCCCEEHCCCCCCCCC
MPCLARQPVDLPPWAGPRCGPYCPRARITLLQRTTIAKSNRKYYENGYPADVKLMPGHAAVVSNRAAARAGFALPCRKRQPD

2budA

0.20

0.18

0.91

0.71

MUSTER

HMDPLMQKIDISENPDKIY--FIRRGQVLQSRTTENAAAPDEYY-VGLRLD-GWVGRH-RISDNADGGITV--LPAPPLAPD

5g2fA

0.09

0.07

0.82

0.70

dPPAS

QRDPSTGALPTHLTDCLSGFGQRPKTVTACTITYLN--------ALDYVIEASLDGAALKKVVYKSSDGTLTSLP-------

1w8xM

0.24

0.22

0.93

0.69

wdPPAS

NPQPYAGPVPIPGPAPTETMPYRVEGRIAGIQQ---ARQFMPFLQGPHRA-VAEQTYHA-IGTGIQMGQT-FNQPLINTQEG

2budA

0.20

0.18

0.91

0.75

wMUSTER

HMDPLMQKIDISENPDKIY--FIRRGQVLQSRTTENAAAPDEYY-VGLRLD-GWVGRH-RISDNADGGITV--LPAPPLAPD

1w8xM

0.23

0.21

0.91

0.75

wPPAS

NPQPYAGPVPIPGPAPTETMP-YREGRIAGIQQ---ARQFMPFLQGPHRA-VAEQTYHA-IGTGIQMGQT-FNQPLINTQEG

4v194

0.24

0.13

0.55

0.86

dPPAS2

---------------------DCNRALLT--------RLHRQTYARLYPVLLVKQDG-STIHIRYREPRRMLTMP-------

1w8xM

0.21

0.20

0.93

0.90

PPAS

NPQPYAGPVPIPGPAPTETMPYRVEGRIAGIQQ---ARQFMPFLQGPHRAVAE--QTYHAIGTGIQMGQT-FNQPLINTQEG

2lp4A2

0.16

0.12

0.77

0.74

Env-PPAS

-------------------SRSQSPRRIILLKAGEVDLLEEELGHLTTLTDVVKGADSLSAILPGDIAEDITAVLCFVIEAD

4jmqA2

0.17

0.98

0.69

MUSTER

LPDPYTNP-EYPGLGFESNDPISAQINISYLEYAFLDSRLLEYKRTGDYLDVRTKLMNFGSTLNNNGTYSGISLSLRESLE-

4bhrA

0.12

0.10

0.79

0.68

dPPAS

ERDPTTGALPQLPQACDQFVANPPASVTQCNVT---------ANNDGVNFTVTAQLTYGSVSFDSSTGQFSFQL--------

(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=-3.65

Estimated TM-score = 0.32±0.10

Estimated RMSD = 11.7±4.5Å

Download Model 2

C-score=-4.30

Download Model 3

C-score=-4.39

Download Model 4

C-score=-4.79

Download Model 5

C-score=-4.57

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	3ngnA	0.526	3.42	0.013	0.866
2	4ruwA1	0.521	3.38	0.077	0.842
3	2fphX	0.521	3.54	0.062	0.854
4	3wcxA	0.519	3.51	0.038	0.866
5	1i9yA	0.518	3.35	0.051	0.854
6	3i41A	0.515	3.46	0.076	0.854
7	4fqdA	0.514	3.49	0.090	0.829
8	4gyzA	0.512	3.11	0.055	0.805
9	1g60A1	0.511	3.61	0.050	0.878
10	3tebA	0.508	3.46	0.068	0.842

(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	0.16	8	3hl2D	NUC	Rep, Mult	38,42
2	0.06	3	3pt6A	ZN	Rep, Mult	3,7,10,76
3	0.04	2	3nm9A	NUC	Rep, Mult	34,37,38
4	0.04	2	2iceA	CA	Rep, Mult	21,51,52,54
5	0.04	2	1c8fA	CA	Rep, Mult	77,80
6	0.04	2	2rfmA	BU2	Rep, Mult	42,45,46
7	0.04	2	1mj2B	NUC	Rep, Mult	28,29,34
8	0.02	1	1pegB	ZN	Rep, Mult	19,23
9	0.02	1	2r45A	PO4	Rep, Mult	22,25,27
10	0.02	1	1i95K	WO2	Rep, Mult	21,22
11	0.02	1	2ei0A	BP7	Rep, Mult	47,49,65,66,67,68

	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	1zwxA	0.507	3.54	0.063	0.866	3.1.4.12	NA
2	0.060	1g60A	0.509	3.54	0.075	0.866	2.1.1.72	33
3	0.060	1db3A	0.472	3.42	0.025	0.805	4.2.1.47	38
4	0.060	1epsA	0.500	3.65	0.091	0.842	2.5.1.19,2.5.1.9	NA
5	0.060	2iirA	0.469	3.84	0.064	0.866	2.7.2.1	NA
6	0.060	3kx2B	0.466	4.25	0.085	0.866	3.6.4.13	36
7	0.060	1dctA	0.471	3.72	0.063	0.829	2.1.1.37	NA
8	0.060	1dctB	0.472	3.65	0.050	0.829	2.1.1.37	NA
9	0.060	1p33B	0.472	4.15	0.041	0.854	1.5.1.33,1.1.1.253	NA
10	0.060	2a3zB	0.513	3.68	0.052	0.878	3.1.21.1	NA
11	0.060	2bfpD	0.472	4.00	0.053	0.842	1.5.1.33	48
12	0.060	1nw7A	0.499	3.86	0.051	0.915	2.1.1.72	37
13	0.060	3ek6A	0.488	3.73	0.027	0.805	2.7.4.22	NA
14	0.060	1dusA	0.472	3.33	0.062	0.756	2.1.1.-	NA
15	0.060	1p89A	0.426	3.58	0.032	0.695	2.5.1.19	34
16	0.060	3l76A	0.469	3.90	0.053	0.780	2.7.2.4	38
17	0.060	2va1B	0.467	4.05	0.025	0.829	2.7.4.22	35
18	0.060	2o3hA	0.485	3.70	0.013	0.829	4.2.99.18	NA
19	0.060	1akoA	0.491	3.70	0.013	0.854	3.1.11.2	10

(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	0.462	4.15	0.05	0.90	2ddsA	GO:0004767 GO:0005576 GO:0008081 GO:0016787 GO:0019835 GO:0044179
1	0.07	0.520	3.41	0.06	0.85	3i48A	GO:0005576 GO:0008081 GO:0046872
2	0.07	0.532	3.30	0.06	0.84	4ruwA	GO:0004519 GO:0004527 GO:0046872 GO:0090305
3	0.07	0.519	3.51	0.04	0.87	3wcxA	GO:0004767 GO:0005576 GO:0008081 GO:0016787
4	0.07	0.507	3.54	0.06	0.87	1zwxA	GO:0004767 GO:0005576 GO:0008081 GO:0009405 GO:0016787 GO:0019835 GO:0044179
5	0.07	0.521	3.54	0.06	0.85	2fphX	GO:0003723
6	0.07	0.505	3.70	0.05	0.89	4zkfA	GO:0004518 GO:0004527 GO:0004535 GO:0005739 GO:0005759 GO:0006397 GO:0016787 GO:0046872 GO:0090305 GO:0090503
7	0.07	0.521	3.65	0.01	0.88	3ngoA	GO:0000288 GO:0000289 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006397 GO:0006417 GO:0006977 GO:0008284 GO:0010606 GO:0016787 GO:0030014 GO:0031047 GO:0046872 GO:0061157 GO:0090503
8	0.07	0.490	3.51	0.09	0.88	2imqX	GO:0016787 GO:0046856 GO:0046872
9	0.07	0.518	3.35	0.05	0.85	1i9yA	GO:0004439 GO:0005509 GO:0005737 GO:0005829 GO:0006629 GO:0006810 GO:0006897 GO:0015031 GO:0016787 GO:0030487 GO:0032153 GO:0034485 GO:0036092 GO:0042578 GO:0043813 GO:0046856 GO:0048017 GO:0051286 GO:0052658 GO:0052659 GO:1990640 GO:1990648 GO:1990649 GO:1990650 GO:1990651
10	0.07	0.520	3.22	0.08	0.83	3mprA	GO:0004519 GO:0004527 GO:0090305
11	0.07	0.518	3.19	0.03	0.82	3g6sA	GO:0004519 GO:0004527 GO:0090305
12	0.07	0.484	3.84	0.09	0.87	5a7iA	GO:0001701 GO:0004439 GO:0005096 GO:0005737 GO:0005768 GO:0005793 GO:0005794 GO:0005829 GO:0005886 GO:0007165 GO:0007283 GO:0016020 GO:0016021 GO:0016787 GO:0030317 GO:0030670 GO:0031410 GO:0031901 GO:0043547 GO:0043647 GO:0046856 GO:0046872 GO:0051056 GO:0052658 GO:0052659 GO:0070613
13	0.07	0.487	3.95	0.05	0.89	4cmnA	GO:0001701 GO:0001750 GO:0004439 GO:0005096 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005795 GO:0005798 GO:0005802 GO:0005829 GO:0005886 GO:0005905 GO:0005929 GO:0006629 GO:0006661 GO:0007165 GO:0016020 GO:0016023 GO:0016787 GO:0030030 GO:0030136 GO:0030670 GO:0031410 GO:0031901 GO:0042384 GO:0042995 GO:0043087 GO:0043547 GO:0043647 GO:0046856 GO:0048365 GO:0051056 GO:0052658 GO:0052659 GO:0052745 GO:0070062
14	0.07	0.496	3.77	0.06	0.91	3nr8B	GO:0001958 GO:0002376 GO:0003779 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0006006 GO:0006661 GO:0006897 GO:0007015 GO:0007155 GO:0008285 GO:0009791 GO:0010629 GO:0016020 GO:0016787 GO:0017124 GO:0030027 GO:0030175 GO:0032868 GO:0034485 GO:0042169 GO:0042995 GO:0043647 GO:0044255 GO:0046856 GO:0052659 GO:0097178
15	0.07	0.500	3.70	0.06	0.87	2xswA	GO:0000139 GO:0001726 GO:0004439 GO:0004445 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005929 GO:0005930 GO:0006629 GO:0006661 GO:0010976 GO:0016020 GO:0016787 GO:0032580 GO:0042995 GO:0046488 GO:0046855 GO:0046856 GO:0072372
16	0.07	0.408	4.69	0.03	0.87	4xxhA	GO:0003677 GO:0003700 GO:0005991 GO:0006351 GO:0006355 GO:0045892
17	0.06	0.414	4.33	0.03	0.82	4gfvB	GO:0004721 GO:0004725 GO:0004726 GO:0005634 GO:0005737 GO:0006470 GO:0016311 GO:0016787 GO:0016791 GO:0035335
18	0.06	0.351	4.48	0.05	0.71	3nwuB	GO:0001558 GO:0001890 GO:0004252 GO:0005520 GO:0005576 GO:0005615 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787 GO:0019838 GO:0022617 GO:0030512 GO:0030514 GO:0031012 GO:0050679 GO:0050687 GO:0060718 GO:0070062 GO:0097187

Consensus prediction of GO terms

Molecular Function	GO:0042578	GO:0004620
GO-Score	0.49	0.38
Biological Processes	GO:0044179	GO:0090305	GO:0009405
GO-Score	0.14	0.07	0.07
Cellular Component	GO:0005576
GO-Score	0.25

(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.

I-TASSER results for job id Rv2722

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

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