I-TASSER results

I-TASSER results for job id Rv2108

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

Input Sequence in FASTA format

>protein (243 residues)
MPNFWALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLLESYRGQ
SSQALIQQTLPYVQWLTTTAEHAHKTAIQLTAAANAYEQARAAMVPPAMVRANRVQTTVL
KAINWFGQFSTRIADKEADYEQMWFQDALVMENYWEAVQEAIQSTSHFEDPPEMADDYDE
AWMLNTVFDYHNENAKEEVIHLVPDVNKERGPIELVTKVDKEGTIRLVYDGEPTFSYKEH
PKF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MPNFWALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLLESYRGQSSQALIQQTLPYVQWLTTTAEHAHKTAIQLTAAANAYEQARAAMVPPAMVRANRVQTTVLKAINWFGQFSTRIADKEADYEQMWFQDALVMENYWEAVQEAIQSTSHFEDPPEMADDYDEAWMLNTVFDYHNENAKEEVIHLVPDVNKERGPIELVTKVDKEGTIRLVYDGEPTFSYKEHPKF
Prediction	CCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	997556884666665557999588999999999999999999999999999874766658999999999999999999999999999999999999999999699957888889999999986767765799999999999999999999999999999998757899999877888877655565545567776545666666776467777777888877765666788876556667889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MPNFWALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLLESYRGQSSQALIQQTLPYVQWLTTTAEHAHKTAIQLTAAANAYEQARAAMVPPAMVRANRVQTTVLKAINWFGQFSTRIADKEADYEQMWFQDALVMENYWEAVQEAIQSTSHFEDPPEMADDYDEAWMLNTVFDYHNENAKEEVIHLVPDVNKERGPIELVTKVDKEGTIRLVYDGEPTFSYKEHPKF
Prediction	643321311020001031221111123013103300430230042023101212331132102101310330241024103304421330411010332023222434413412420131122211211111014233424413440030032113102313443452543243345544444444344344444344224224422444444433334434222321342423223562477
	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                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MPNFWALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLLESYRGQSSQALIQQTLPYVQWLTTTAEHAHKTAIQLTAAANAYEQARAAMVPPAMVRANRVQTTVLKAINWFGQFSTRIADKEADYEQMWFQDALVMENYWEAVQEAIQSTSHFEDPPEMADDYDEAWMLNTVFDYHNENAKEEVIHLVPDVNKERGPIELVTKVDKEGTIRLVYDGEPTFSYKEHPKF

2g38B

0.34

0.24

0.71

2.29

MUSTER

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

2.37

dPPAS

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

3.58

wdPPAS

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

2.83

wMUSTER

---FEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

4.96

wPPAS

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

5.05

dPPAS2

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

3.87

PPAS

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

2g38B

0.34

0.24

0.71

5.83

Env-PPAS

--AFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIA--------------------------------------------------------------------

5cwiA

0.09

0.95

0.90

MUSTER

---------DIEKLCKKAESEAREARSKAEELRQRHSQAARDAQKLASQAEEAVKLACELAQEHPNADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKLCIKAASEAAEAASKAAELAQRH-PDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEASKAAEEAQRHPDSQKARDEIKEASQKAEEVK-ERCER-

4ke2A

0.11

0.09

0.81

1.00

dPPAS

-----------------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP------------------------------

(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=-1.26

Estimated TM-score = 0.56±0.15

Estimated RMSD = 8.5±4.5Å

Download Model 2

C-score=-2.11

Download Model 3

C-score=-2.10

Download Model 4

C-score=-2.76

Download Model 5

C-score=-3.21

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	2g38B	0.702	0.72	0.329	0.712
2	4xwpA	0.551	2.44	0.136	0.621
3	4wj1A	0.544	2.57	0.162	0.625
4	4e40A	0.538	3.67	0.064	0.683
5	4k1pA	0.537	4.54	0.076	0.741
6	2nrjA	0.536	4.52	0.054	0.728
7	1y2oA	0.531	3.92	0.091	0.708
8	2d4cB	0.531	3.70	0.059	0.700
9	4wpeA	0.530	4.23	0.084	0.737
10	4nqiA	0.528	4.08	0.096	0.712

(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	0.09	3	2zhzA	MG	Rep, Mult	114,137
2	0.09	3	4d2eC	78M	Rep, Mult	22,90,93,161,162,165
3	0.04	1	2g38B	MN	Rep, Mult	149,152,153
4	0.04	1	2g381	III	Rep, Mult	4,15,16,18,19,20,21,24,25,28,31,32,34,35,38,39,41,42,45,46,49,53,57,65,72,75,83,86,90,97,154,155,158,162,165,166,168,169,171,172,174
5	0.03	1	3c9iC	XE	Rep, Mult	110,113
6	0.03	1	3arcB	CLA	Rep, Mult	25,93,96,97
7	0.03	1	4zzbA	XE	Rep, Mult	110,140,143,144
8	0.03	1	2vs0B	ZN	Rep, Mult	37,84
9	0.03	1	3mk7A	CA	Rep, Mult	30,209
10	0.03	1	3zciA	BU9	Rep, Mult	130,133
11	0.03	1	2yktA	III	Rep, Mult	96,99,150,152,153,154,156,160
12	0.03	1	3rf3A	III	Rep, Mult	54,55,60,63
13	0.03	1	1i4d1	III	Rep, Mult	22,23,26,27,29,30,31,33,34,91,94,98,101,102

	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	2e9fB	0.441	4.43	0.088	0.609	4.3.2.1	91
2	0.060	1w27A	0.460	4.90	0.040	0.675	4.3.1.24	NA
3	0.060	2np0A	0.435	5.36	0.042	0.683	3.4.24.69	NA
4	0.060	2ohyB	0.456	5.50	0.051	0.716	5.4.3.6	NA
5	0.060	2zr3B	0.415	5.02	0.045	0.609	6.1.1.11	91
6	0.060	1k62B	0.434	4.86	0.027	0.621	4.3.2.1	NA
7	0.060	1q5nA	0.424	4.66	0.033	0.597	5.5.1.2	NA
8	0.060	1dcnB	0.426	4.62	0.043	0.597	4.3.2.1	81
9	0.060	2pfmA	0.427	4.80	0.042	0.597	4.3.2.2	NA
10	0.060	1occA	0.422	5.11	0.050	0.625	1.9.3.1	NA
11	0.060	3ffzA	0.468	5.37	0.043	0.720	3.4.24.69	NA
12	0.060	1f1oA	0.418	4.65	0.038	0.580	4.3.2.2	NA
13	0.060	3i9wA	0.480	3.70	0.090	0.617	2.7.13.3	27,34
14	0.060	2nyfA	0.430	5.08	0.031	0.650	4.3.1.5	NA
15	0.060	1vdkA	0.455	4.89	0.045	0.646	4.2.1.2	NA
16	0.060	3g61A	0.424	5.22	0.039	0.654	3.6.3.44	25,91
17	0.060	1b8fA	0.453	5.32	0.083	0.704	4.3.1.3	NA
18	0.060	1i0aA	0.436	4.92	0.040	0.625	4.3.2.1	NA
19	0.060	1c3cA	0.430	4.81	0.043	0.605	4.3.2.2	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	0.39	0.681	1.41	0.34	0.72	4kxrB	GO:0005576 GO:0009405 GO:0009986
1	0.12	0.572	2.39	0.14	0.65	3j83A	GO:0005576 GO:0009405 GO:0044315
2	0.07	0.547	4.24	0.05	0.73	2nrjA	GO:0005576 GO:0009405 GO:0016020 GO:0016021 GO:0019835 GO:0020002 GO:0033644 GO:0044179
3	0.07	0.516	4.55	0.06	0.72	4k1pB	GO:0009405 GO:0016020
4	0.07	0.538	3.48	0.06	0.67	5jdoA	GO:0016020 GO:0016021
5	0.07	0.558	2.38	0.14	0.63	4xxxA	GO:0005576 GO:0009405 GO:0044315
6	0.06	0.263	6.12	0.04	0.45	2j5bA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0006412 GO:0006418 GO:0016874 GO:0042802
7	0.06	0.266	6.37	0.03	0.49	3nvaA	GO:0000166 GO:0003883 GO:0005524 GO:0006221 GO:0006541 GO:0016874 GO:0044210
8	0.06	0.256	6.26	0.04	0.45	4dq6A	GO:0003824 GO:0009058 GO:0016740 GO:0030170
9	0.06	0.245	5.65	0.03	0.40	3bghA	GO:0009279
10	0.06	0.240	4.91	0.03	0.36	3lesA	GO:0001123 GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006352 GO:0006355 GO:0010468 GO:0016987
11	0.06	0.235	5.82	0.04	0.40	3cddD	GO:0016032 GO:0019038
12	0.06	0.231	5.27	0.05	0.36	3q1tD	GO:0003824 GO:0008152
13	0.06	0.244	6.02	0.03	0.42	2cf5A	GO:0005829 GO:0008270 GO:0009699 GO:0009809 GO:0016491 GO:0045551 GO:0046872 GO:0052747 GO:0055114
14	0.06	0.195	5.78	0.06	0.34	1lckA	GO:0000166 GO:0000242 GO:0001772 GO:0001948 GO:0004672 GO:0004713 GO:0004715 GO:0004722 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006882 GO:0006919 GO:0007169 GO:0008022 GO:0014066 GO:0016020 GO:0016032 GO:0016301 GO:0016310 GO:0016740 GO:0019901 GO:0019903 GO:0030097 GO:0030168 GO:0030217 GO:0031234 GO:0031295 GO:0038083 GO:0042127 GO:0042169 GO:0042493 GO:0042609 GO:0042610 GO:0042802 GO:0043548 GO:0045087 GO:0045121 GO:0046854 GO:0046934 GO:0048015 GO:0050690 GO:0050852 GO:0050853 GO:0050862 GO:0050870 GO:0050900 GO:0051117 GO:0051209 GO:0051249 GO:0070062 GO:2001244
15	0.06	0.241	4.60	0.05	0.35	1fx3B	GO:0005737 GO:0006457 GO:0006810 GO:0015031 GO:0051082 GO:0051262
16	0.06	0.219	5.78	0.03	0.36	2wsuB	GO:0007155 GO:0019028 GO:0019058 GO:0019062 GO:0030246
17	0.06	0.228	5.71	0.05	0.38	4zpkB	GO:0001077 GO:0001525 GO:0001666 GO:0001892 GO:0001974 GO:0002027 GO:0003677 GO:0003700 GO:0005634 GO:0005667 GO:0005737 GO:0006351 GO:0006355 GO:0006366 GO:0006979 GO:0007005 GO:0007275 GO:0007601 GO:0008134 GO:0016607 GO:0030097 GO:0030154 GO:0030218 GO:0030324 GO:0035035 GO:0042415 GO:0043129 GO:0043565 GO:0043619 GO:0045944 GO:0046982 GO:0046983 GO:0048469 GO:0048625 GO:0055072 GO:0071456
18	0.06	0.192	5.27	0.01	0.30	2vyiA	GO:0005737 GO:0005829 GO:0016020 GO:0016032 GO:1903071 GO:1904288

Consensus prediction of GO terms

Molecular Function
GO-Score
Biological Processes	GO:0009405
GO-Score	0.53
Cellular Component	GO:0005576	GO:0009986
GO-Score	0.49	0.39

(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.