I-TASSER results

Input Sequence in FASTA format

>protein (88 residues)
MSGADPPTRRAFGQMARAATGWVSVSGQFAVAADTCRCEGTLFAVDPETHVANHNRCDIV
GRLRDERPNTLRSVRRGDEVRMATWHWI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSGADPPTRRAFGQMARAATGWVSVSGQFAVAADTCRCEGTLFAVDPETHVANHNRCDIVGRLRDERPNTLRSVRRGDEVRMATWHWI
Prediction	CCCCCCCHHHHHHHHHHHHCCEEEEEEEEEEEHCEEEEHCEEEEHCCCCCCCCCCCCEEEEEHCCCCCCHHHHHHHCCEEEEEEEEHC
Conf.Score	9999985678999988775455888656777645566755799867865557788655665434789757776654654677656779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSGADPPTRRAFGQMARAATGWVSVSGQFAVAADTCRCEGTLFAVDPETHVANHNRCDIVGRLRDERPNTLRSVRRGDEVRMATWHWI
Prediction	8766646345223422432332232444222224314053201213363434635304123314764463254245465133332336
	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

CCCCCCCHHHHHHHHHHHHCCEEEEEEEEEEEHCEEEEHCEEEEHCCCCCCCCCCCCEEEEEHCCCCCCHHHHHHHCCEEEEEEEEHC
MSGADPPTRRAFGQMARAATGWVSVSGQFAVAADTCRCEGTLFAVDPETHVANHNRCDIVGRLRDERPNTLRSVRRGDEVRMATWHWI

2j5tD2

0.21

0.19

0.92

0.64

MUSTER

PAGEDEGATAAILERGSSPKGIKSVTGNFS-RGEVIRICGRDIAH----GVSRYNSDAIAGH-HSQEIDAILGYEYGPVA-VHRDDMI

4z04A

0.13

0.12

0.99

0.73

dPPAS

FNIADMKKSRAFYDAALSPLGI-GHAMEFGDWVGYGRNGKPEFWIGAQKGAKLEGVLHVAFSAGTRSEVYEAAIAAGGRDNGKPGLRP

4jbjA2

0.15

0.11

0.77

0.67

wdPPAS

----TLKISKIKEL----DSG-TLIYGVFAVEKKKVNDKSITFKIKDNE-----DNIKVVW----KEQHNIN--EKGDKLQLFSFHLR

2j5tD2

0.21

0.19

0.91

0.63

wMUSTER

-AGEDEGATAAILERGSSPKGIKSVTGNFS-RGEVIRICGRDIAH----GVSRYNSDAIAGH-HSQEIDAILGYEYGPVA-VHRDDMI

4hl6A1

0.27

0.17

0.62

0.57

wPPAS

L-GRHPP--DVF----NTQDKPITICKLFS------A----L--------------CQALELLNDPR-NILRVQNQ-AILKLKTQVWL

5kowA1

0.17

0.12

0.74

0.68

dPPAS2

ID-VPVETLTAVVAEVRKTQL------RFGAVPAG---DGFFRLIVPAQGLSA----------DRAAP-TLDELKRC--LHVHSPRWL

2j5tD2

0.21

0.19

0.92

0.66

PPAS

PAGEDEGATAAILERGSSPKGIKSVTGNFS-RGEVIRICGRDIAH----GVSRYNSDAIAGH-HSQEIDAILGYEYGPVA-VHRDDMI

2zm5A1

0.31

0.22

0.69

0.91

Env-PPAS

LPSADPEVRARIEQQAAEQ-GW-----------ESLHRQ--LQEVDPVA--AA--------RI---HPNDPQRLSRALEVFFISLTQT

3jb9H

0.24

0.19

0.80

0.64

MUSTER

MI---PPINFIFKLLQQHT--PVSIWLF----QTDIRLQGQIRGFDE--FM---N--DAVQVDAKNNKRELRILLKGDNI--TLIQAI

5gkeA1

0.13

0.12

0.98

0.63

dPPAS

ITSPSTEELVSLVNSALLEEAMLTIFARCKVHYDIVKPDGSFLIHQSKKREPQPPGSRVRLELRENP--VLVSIRRPRETLEVELEEV

(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=-2.48

Estimated TM-score = 0.43±0.14

Estimated RMSD = 9.0±4.6Å

Download Model 2

C-score=-3.92

Download Model 3

C-score=-4.62

Download Model 4

C-score=-4.87

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	1qzgA	0.473	4.10	0.063	0.886
2	4ka7A	0.471	4.02	0.057	0.830
3	2o36A	0.469	4.45	0.023	0.852
4	1wm5A	0.468	3.86	0.027	0.807
5	4h02A	0.467	4.27	0.063	0.875
6	3rfoA	0.466	3.80	0.068	0.818
7	2m9vA	0.466	3.85	0.066	0.841
8	1z7eD4	0.465	3.45	0.097	0.773
9	3rmhA	0.464	4.12	0.065	0.864
10	3bjuA	0.460	4.30	0.086	0.898

(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	3r8xA	MET	Rep, Mult	11,12,13,24,26,44
2	0.07	3	5ej1B	XP5	Rep, Mult	5,9
3	0.07	3	1vf5B	TDS	Rep, Mult	12,15
4	0.07	3	1iw7F	MG	Rep, Mult	10,14
5	0.05	2	3jzvA	MN	Rep, Mult	48,50,54,86
6	0.05	2	1hloA	NUC	Rep, Mult	14,17
7	0.03	1	1g8kA	CA	Rep, Mult	78,79
8	0.02	1	2b3g0	III	Rep, Mult	4,5,8,25,26,27,28
9	0.02	1	3r8xA	MOE	Rep, Mult	8,81,82
10	0.02	1	3fjwA	UUU	Rep, Mult	2,51,52,78,79,81

	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	2f4eA	0.298	4.56	0.078	0.557	5.2.1.8	NA
2	0.060	3fjwA	0.453	4.00	0.057	0.818	1.11.1.16	NA
3	0.060	1i1iP	0.450	4.52	0.081	0.830	3.4.24.16	NA
4	0.060	1c3cA	0.449	3.46	0.069	0.739	4.3.2.2	NA
5	0.060	1bbuA	0.420	4.83	0.062	0.886	6.1.1.6	NA
6	0.060	1kc7A	0.425	4.20	0.023	0.773	2.7.9.1	34
7	0.060	3fq3A	0.417	4.26	0.052	0.818	3.6.1.1	NA
8	0.060	1ayxA	0.416	3.96	0.048	0.750	3.2.1.3	NA
9	0.060	3hdlA	0.434	4.05	0.095	0.727	1.11.1.-	NA
10	0.060	2f6dA	0.428	3.90	0.047	0.750	3.2.1.3	NA
11	0.060	3e9iA	0.431	4.39	0.101	0.864	6.1.1.6	NA
12	0.060	1qgjA	0.425	3.99	0.027	0.716	1.11.1.7	44
13	0.060	1s4bP	0.473	4.07	0.011	0.841	3.4.24.15	NA
14	0.060	1asyA	0.441	4.05	0.053	0.784	6.1.1.12	NA
15	0.060	2if4A	0.426	3.92	0.026	0.682	5.2.1.8	NA
16	0.060	3e9hA	0.418	4.42	0.100	0.875	6.1.1.6	NA
17	0.060	1schA	0.431	3.93	0.068	0.716	1.11.1.7	NA
18	0.060	1y791	0.442	4.10	0.035	0.807	3.4.15.5	NA
19	0.060	2o36A	0.469	4.45	0.023	0.852	3.4.24.15	61

(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	0.450	4.52	0.08	0.83	1i1iP	GO:0004222 GO:0005737 GO:0005739 GO:0005758 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0070012
1	0.07	0.449	4.24	0.08	0.88	2i0qA	GO:0000723 GO:0000781 GO:0000784 GO:0003677 GO:0005634 GO:0005694 GO:0016233 GO:0043047
2	0.07	0.471	4.02	0.06	0.83	4ka7A	GO:0004222 GO:0005739 GO:0005759 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0009507 GO:0009536 GO:0009570 GO:0016787 GO:0046872
3	0.07	0.441	3.95	0.04	0.75	3sksA	GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
4	0.07	0.473	4.10	0.06	0.89	1qzgA	GO:0000723 GO:0000781 GO:0000783 GO:0000784 GO:0003677 GO:0005634 GO:0005694 GO:0005724 GO:0005829 GO:0010521 GO:0016233 GO:0032211 GO:0043047 GO:0051974 GO:0070187 GO:0098505
5	0.07	0.468	3.86	0.03	0.81	1wm5A	GO:0001669 GO:0002479 GO:0005730 GO:0005737 GO:0005829 GO:0006801 GO:0006968 GO:0008022 GO:0009055 GO:0016175 GO:0032010 GO:0042554 GO:0043020 GO:0045087 GO:0045454 GO:0045730 GO:0048010 GO:0048365 GO:0055114
6	0.07	0.368	4.37	0.05	0.70	3ahmA	GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
7	0.06	0.423	4.02	0.06	0.76	3kjpA	GO:0000723 GO:0000781 GO:0000783 GO:0000784 GO:0003677 GO:0005634 GO:0005654 GO:0005694 GO:0007004 GO:0010521 GO:0016233 GO:0017151 GO:0032202 GO:0032212 GO:0032508 GO:0042162 GO:0043047 GO:0051096 GO:0051973 GO:0051974 GO:0060383 GO:0070187 GO:0070200 GO:0098505
8	0.06	0.373	3.50	0.06	0.62	4cgwA	GO:0097255
9	0.06	0.371	4.11	0.08	0.68	3oc3A	GO:0004386 GO:0005524
10	0.06	0.392	4.21	0.07	0.74	1cz7D	GO:0000022 GO:0000166 GO:0000212 GO:0001578 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005872 GO:0005874 GO:0007018 GO:0007049 GO:0007051 GO:0007052 GO:0007056 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008569 GO:0016887 GO:0030981 GO:0031534 GO:0032837 GO:0032888 GO:0042803 GO:0048471 GO:0051028 GO:0051297 GO:0051298 GO:0051301 GO:0051321 GO:0072687 GO:0090306 GO:0090307 GO:1901673 GO:1990498
11	0.06	0.364	4.01	0.05	0.62	1w3bA	GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
12	0.06	0.379	3.33	0.06	0.57	1w3bB	GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
13	0.06	0.371	4.21	0.03	0.73	2gw1A	GO:0005739 GO:0005741 GO:0005742 GO:0006626 GO:0006886 GO:0015266 GO:0015450 GO:0016020 GO:0016021 GO:0030150 GO:0030943 GO:0031307 GO:0045039
14	0.06	0.442	4.10	0.04	0.81	1y791	GO:0004180 GO:0004222 GO:0005737 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0030288 GO:0046872
15	0.06	0.380	3.86	0.03	0.67	5a31F	GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005876 GO:0007091 GO:0008283 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051436 GO:0051437 GO:0051439 GO:0070979
16	0.06	0.469	4.45	0.02	0.85	2o36A	GO:0004222 GO:0005737 GO:0005758 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0042277 GO:0046872
17	0.06	0.364	3.68	0.04	0.60	2fo7A
18	0.06	0.347	4.27	0.01	0.67	3kd7A

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0070011
GO-Score	0.37	0.37
Biological Processes	GO:0019538
GO-Score	0.37
Cellular Component	GO:0044444
GO-Score	0.37

(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 Rv3566A

[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]