I-TASSER results

Input Sequence in FASTA format

>protein (140 residues)
MTAKSPPDYPGKTLGLPDTGPGSLAPMGRRLAALLIDWLIAYGLALLGVEFGVWSTPMLS
TVVLVIWLLLGVAAVRLFGFTPGQLMLGLVVVAVGGRRPVGIGRLVVRGLLIGLVVPPLF
TDSDGRGLHDRLTATAVVRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTAKSPPDYPGKTLGLPDTGPGSLAPMGRRLAALLIDWLIAYGLALLGVEFGVWSTPMLSTVVLVIWLLLGVAAVRLFGFTPGQLMLGLVVVAVGGRRPVGIGRLVVRGLLIGLVVPPLFTDSDGRGLHDRLTATAVVRR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCEEHCC
Conf.Score	99888989986446999999988776899999999999999999999986555655478999999999999999998689988888788899788999888999999999999999986445898855777659589859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTAKSPPDYPGKTLGLPDTGPGSLAPMGRRLAALLIDWLIAYGLALLGVEFGVWSTPMLSTVVLVIWLLLGVAAVRLFGFTPGQLMLGLVVVAVGGRRPVGIGRLVVRGLLIGLVVPPLFTDSDGRGLHDRLTATAVVRR
Prediction	85588765131442422673323203333331033123333333333232333333433332323333333333333323231230040101235574312121033133233333210011573200002104131148
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCEEHCC
MTAKSPPDYPGKTLGLPDTGPGSLAPMGRRLAALLIDWLIAYGLALLGVEFGVWSTPMLSTVVLVIWLLLGVAAVRLFGFTPGQLMLGLVVVAVGGRRPVGIGRLVVRGLLIGLVVPPLFTDSDGRGLHDRLTATAVVRR

5a6eB

0.14

0.09

0.61

1.17

wdPPAS

------------------------SAMFNQVLILICTLLCLVFTGTCGIQHLERAGEKLSLFKSFYFCIVTFS----YGKIPSQLLV------------VIMICVALVVLPLQFEELVYLWMERQK--------------

5a6eB

0.14

0.09

0.61

0.96

wPPAS

------------------------SAMFNQVLILICTLLCLVFTGTCGIQHLERAGEKLSLFKSFYFCIVTFS----YGKIPSQLLV---VI---------MICVALVVLPLQFEELVYLWMERQK--------------

1ifpA

0.14

0.04

0.31

1.77

dPPAS2

------------------------------MQSVITDVTGQLTAVQADITTIGGAIIVLAAVVLGIRWIKAQFF------------------------------------------------------------------

4ri2A

0.11

0.98

1.04

PPAS

AKAPKKVEKPKLKVEDGLFGTSGGIGFVGRVAMIGFAASLLGEGITILSQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDR---GRFVDEPTFGFTKSNELFVGRLAQLGFAFSLIGEIITGKGALAQLNIETGVPI

2mawA

0.12

0.09

0.69

1.08

wdPPAS

----------------------------EEELYYGLNLLIPCVLISALALLVSGEKISLGITVLLSLTVFMLLVAEIMPSTIAQYFASTMIIDPDGGEGGGLCLMAFSVFTIICTIGILM-NFVEE--------------

2l35A

0.17

0.08

0.45

1.71

dPPAS2

------------------------------------------------CSTVSPGVLAGIVVGDLVLTVLIALAVYFLGR-------------LGTAEVLGIISIVLVATVLKTIVLIPFLEQN----------------

4ri2A

0.10

0.09

0.87

1.03

wdPPAS

APKKVEKPKLKVEDGLFGT-SGGIG-FVGRVAMIGFAASLLGEGITILSQLNLETGIPIYEAEPLLLFFILFTLLGAIGAL---------RFVDEPTFGFTKSNELFVGRLAQLGFAFSL-------IGEIITGKGALAQ

2mawA

0.11

0.07

0.65

1.61

dPPAS2

LPADSG----------------------EKISLGITVLLSLTVFMLLVAEIMPSTSFASTMIIVGLSVVVTVIVLQYHHHDP-----------DGGEGGGEGIDRLCLMAFSVFTIICTIGVEE----------------

1z8yN

0.11

0.03

0.26

1.58

dPPAS2

---------------------------------------------HPVYTILAVASATVAMMIGVTVAVLCACLARRECLT-----------------------------------------------------------

5fbmA1

0.11

0.03

0.26

1.57

dPPAS2

-------------------------------------ANKQDLIAKVAEATELTKKDSAAAVDAVFSAVSSYLA------------------------------------------------------------------

(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=-3.87

Estimated TM-score = 0.30±0.10

Estimated RMSD = 13.7±4.0Å

Download Model 2

C-score=-4.11

Download Model 3

C-score=-4.45

Download Model 4

C-score=-4.67

Download Model 5

C-score=-4.79

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	2jlnA	0.577	3.56	0.087	0.793
2	3l1lA	0.575	3.07	0.066	0.771
3	5i6xA	0.574	3.47	0.036	0.793
4	3gi9C	0.573	3.73	0.086	0.779
5	3i9yA	0.556	3.63	0.073	0.764
6	4q2eA	0.550	4.43	0.078	0.914
7	4wd9A2	0.548	3.56	0.031	0.736
8	2l7bA	0.547	4.32	0.079	0.829
9	4kppA	0.547	3.26	0.065	0.729
10	1l2jA	0.546	3.78	0.101	0.764

(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	0.18	14	1x7bB	III	Rep, Mult	86,96,99,100,103,104
2	0.04	3	4xdkB	405	Rep, Mult	39,42,69,72,73,110,114
3	0.03	2	3phxA	ZN	Rep, Mult	127,130
4	0.03	2	3pyrY	MG	Rep, Mult	34,110,111
5	0.03	2	1fbmD	RTL	Rep, Mult	39,46
6	0.03	2	3olsB	III	Rep, Mult	39,44,65,68,69,73,136,137
7	0.03	2	4xk8l	CLA	Rep, Mult	85,110,114
8	0.03	2	4tnwQ	POV	Rep, Mult	45,49,102,103,106,107,114
9	0.01	1	3ob6A	ARG	Rep, Mult	36,40,44,105
10	0.01	1	1j95A	TBA	Rep, Mult	81,116
11	0.01	1	3um7B	K	Rep, Mult	13,14,81
12	0.01	1	2bsqH	NUC	Rep, Mult	137,139
13	0.01	1	4r7cA	GLY	Rep, Mult	35,39,113
14	0.01	1	3mioA	PO4	Rep, Mult	122,123,126
15	0.01	1	3mi1B	FE	Rep, Mult	81,83
16	0.01	1	2hvjC	L2C	Rep, Mult	105,108,112
17	0.01	1	2wse1	CLA	Rep, Mult	72,76
18	0.01	1	4amiA	2CV	Rep, Mult	36,40

	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	3hf1B	0.534	4.71	0.066	0.814	1.17.4.1	NA
2	0.060	1aj8A	0.496	4.77	0.046	0.821	2.3.3.1	NA
3	0.060	1ctsA	0.510	4.08	0.047	0.793	2.3.3.1,4.1.3.7	NA
4	0.060	1h0nA	0.529	4.43	0.058	0.793	1.17.4.1	NA
5	0.060	2uw1B	0.511	4.75	0.045	0.829	1.14.99.6	NA
6	0.060	1o9iA	0.491	4.27	0.029	0.771	1.11.1.6	NA
7	0.060	3do6A	0.508	4.37	0.102	0.793	6.3.4.3	NA
8	0.060	3m9uA	0.490	3.42	0.120	0.657	2.5.1.10	NA
9	0.060	1jkuA	0.492	4.13	0.061	0.764	1.11.1.6	NA
10	0.060	3i9wA	0.495	4.04	0.051	0.736	2.7.13.3	NA
11	0.060	1otwA	0.494	4.74	0.055	0.807	1.3.3.11	NA
12	0.060	1rqiA	0.515	3.42	0.044	0.721	2.5.1.10	NA
13	0.060	1zvuA	0.503	4.07	0.083	0.771	5.99.1.-	NA
14	0.060	1xvgC	0.533	4.90	0.095	0.864	1.14.13.25	47,112
15	0.060	1xmeA	0.504	3.15	0.092	0.657	1.9.3.1	NA
16	0.060	1biqB	0.490	4.06	0.030	0.764	1.17.4.1	NA
17	0.060	3ipiA	0.494	3.21	0.086	0.679	2.5.1.-	NA
18	0.060	3ilwA	0.531	3.94	0.072	0.807	5.99.1.3	NA
19	0.060	2j2fA	0.513	4.85	0.060	0.850	1.14.19.2,1.14.99.6	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	0.10	0.495	4.04	0.05	0.74	3i9wA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006470 GO:0007165 GO:0009061 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016868 GO:0018106 GO:0023014 GO:0046777 GO:0071310
1	0.09	0.503	4.43	0.04	0.78	2q6hA	GO:0005215 GO:0005328 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
2	0.07	0.566	3.46	0.07	0.79	2x79A	GO:0005215 GO:0016020 GO:0016021 GO:0055085
3	0.07	0.554	4.30	0.08	0.87	4q2gB	GO:0004605 GO:0005886 GO:0006629 GO:0006655 GO:0008654 GO:0016020 GO:0016021 GO:0016024 GO:0016740 GO:0016772 GO:0016779
4	0.07	0.590	3.11	0.07	0.78	3ob6B	GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015181 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475 GO:1903826
5	0.07	0.548	3.56	0.03	0.74	4wd9A	GO:0005886 GO:0006810 GO:0016020 GO:0016021
6	0.07	0.463	4.80	0.06	0.77	4us3A	GO:0005328 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
7	0.07	0.573	3.73	0.09	0.78	3gi9C	GO:0003333 GO:0005886 GO:0005887 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:1902475
8	0.07	0.574	3.47	0.04	0.79	5i6xA	GO:0001666 GO:0005328 GO:0005335 GO:0005768 GO:0005829 GO:0005886 GO:0005887 GO:0006810 GO:0006836 GO:0006837 GO:0007268 GO:0007420 GO:0007584 GO:0007613 GO:0007623 GO:0008504 GO:0009636 GO:0010008 GO:0010033 GO:0010628 GO:0012505 GO:0015222 GO:0015293 GO:0015844 GO:0016020 GO:0016021 GO:0017022 GO:0017075 GO:0017137 GO:0019811 GO:0021794 GO:0021941 GO:0032227 GO:0032355 GO:0035176 GO:0042310 GO:0042493 GO:0042713 GO:0042803 GO:0043005 GO:0045121 GO:0045665 GO:0045787 GO:0046621 GO:0046872 GO:0048854 GO:0050998 GO:0051015 GO:0051259 GO:0051260 GO:0051610 GO:0055085 GO:0071300 GO:0071310 GO:0071321 GO:0098793
9	0.07	0.505	4.01	0.07	0.74	3o1jA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
10	0.06	0.523	3.73	0.07	0.79	4djiA	GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475
11	0.06	0.556	3.63	0.07	0.76	3i9yA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
12	0.06	0.575	3.22	0.07	0.78	3lrbA	GO:0003333 GO:0005886 GO:0006810 GO:0006865 GO:0015171 GO:0015297 GO:0016020 GO:0016021
13	0.06	0.441	4.94	0.05	0.80	4z3nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
14	0.06	0.338	5.53	0.05	0.64	4f2pB	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
15	0.06	0.505	4.45	0.08	0.82	4iojA	GO:0000166 GO:0004329 GO:0005524 GO:0006730 GO:0009396 GO:0016874 GO:0035999
16	0.06	0.368	4.72	0.02	0.61	3jysA	GO:0046872
17	0.06	0.483	4.32	0.03	0.74	4xp9C	GO:0005328 GO:0005329 GO:0005330 GO:0005886 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0015872 GO:0016020 GO:0016021 GO:0019811 GO:0030431 GO:0042745 GO:0043005 GO:0046872 GO:0051583 GO:0055085 GO:0072488 GO:0098793 GO:0099509 GO:1990834
18	0.06	0.329	4.95	0.05	0.56	3we7A	GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0004721	GO:0000155	GO:0005524	GO:0016868	GO:0005328	GO:0004605	GO:0015181	GO:0015179	GO:0015297
GO-Score	0.10	0.10	0.10	0.10	0.09	0.07	0.07	0.07	0.07
Biological Processes	GO:0018106	GO:0046777	GO:0006470	GO:0023014	GO:0071310	GO:0000160	GO:0009061	GO:0006836	GO:0006655	GO:0016024	GO:1903826	GO:1902475	GO:0015807	GO:0051454
GO-Score	0.10	0.10	0.10	0.10	0.10	0.10	0.10	0.09	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0071944	GO:0016021
GO-Score	0.44	0.34

(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 Rv2219A

[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]