I-TASSER results

I-TASSER results for job id Rv3847

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

Input Sequence in FASTA format

>protein (177 residues)
MGTGSGGPIGVSPFHSRGALKGFVISGRWPDSTKEWAQLLMVAVRVASLPGLLSTTTVFG
AREELPDEPEPGTVGLVLAEGTVFGESAIQPGYFADHQPPALLMLHPPSETTPSLPECTG
AASGCVLLPGLPYLGLEHRAAWVEAEADGTITSMVSRVGVDPISHPDTAILAMLLAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTGSGGPIGVSPFHSRGALKGFVISGRWPDSTKEWAQLLMVAVRVASLPGLLSTTTVFGAREELPDEPEPGTVGLVLAEGTVFGESAIQPGYFADHQPPALLMLHPPSETTPSLPECTGAASGCVLLPGLPYLGLEHRAAWVEAEADGTITSMVSRVGVDPISHPDTAILAMLLAA
Prediction	CCCCCCCCEEEEEHCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCHHHHHHHHHHCCCCCEEEEEHHHCCCCCCCCCHHHHHHHHHC
Conf.Score	988888867888874688677999975689878999999999998764778777755777654589999999589999865557876578876678999868997689999999855557767747768997667466666654357886555545447888889658999999879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTGSGGPIGVSPFHSRGALKGFVISGRWPDSTKEWAQLLMVAVRVASLPGLLSTTTVFGAREELPDEPEPGTVGLVLAEGTVFGESAIQPGYFADHQPPALLMLHPPSETTPSLPECTGAASGCVLLPGLPYLGLEHRAAWVEAEADGTITSMVSRVGVDPISHPDTAILAMLLAA
Prediction	765566331311213462403000010312740340031011003112334313332013035633763644200000131413464214214127541100000003664444145146113100201323301252333135244633133214422143364232100111248
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEEEEEHCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCHHHHHHHHHHCCCCCEEEEEHHHCCCCCCCCCHHHHHHHHHC
MGTGSGGPIGVSPFHSRGALKGFVISGRWPDSTKEWAQLLMVAVRVASLPGLLSTTTVFGAREELPDEPEPGTVGLVLAEGTVFGESAIQPGYFADHQPPALLMLHPPSETTPSLPECTGAASGCVLLPGLPYLGLEHRAAWVEAEADGTITSMVSRVGVDPISHPDTAILAMLLAA

5erxA

0.14

0.12

0.90

0.64

MUSTER

TYTPPVTFDQPLDIDLSV--DTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLA-LPLLRPQ--------QVIMLGRPTLHRPVS--VLLADAEVPVFALT-TGPRWPDVSGNSQATGTRAVTTGAPR--PAWLDRCAAMNR--HAIAAVREQLAAHPLTTGLHVAAAVSHA

3vvlA1

0.17

0.15

0.86

0.55

dPPAS

MREFIPPASRFIELPDGFAMRGGALYG----------------ARIAETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPTPGWWEAMVGPGKPVDTDLWHVICVSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAH--------TVRALGISRLAASMGGMSALALLA

3on5A2

0.19

0.15

0.77

0.52

wdPPAS

-------------------KERLIIFGAGPD-----VPPLV---TFASNVGF--YTVVTDWRPNCEKHFFPDADEIIVDFPADFLRKFLIRPDD------FVLITHHFQKDQEILHFLLEKELRYIGI-----LGSKERTRRLL-QNRKPPDHLYSPVGLSIDAQPEESIVAQLIQL

2uvcG

0.17

0.15

0.90

0.58

wMUSTER

QHLPEDRHIGISLVNSARN---FVVTG-----PPISLYGLNLRLRKVKAPTGLDQNRIFVNRF-LP-AGAHAHILGDVDDMKIPASSLVIPGQLRELGDEDIIITYDPVNWETAT-VFPDA-THIVDFPG-GVSGIGVLTNRNK-DGTG-VRVIL--AGAIDGTNTEVGYKPELFDR

1o1yA

0.19

0.15

0.80

0.56

wPPAS

VDLGENWSFDYLDTPKGEKLSLVVLLGG-YEEKYPFLKYEFQLIEEI-IP-------FLGIVYRGKNGEE---IGWYFVE--KVSDNKF----FRE-FPDRLRVFQ--GDT--DLPR------RATRVEKYENVGLQH-KRWIEAYKD------LEKKKIDPTAEREEKVLKGLLRS

3on5A2

0.20

0.15

0.75

0.65

dPPAS2

-------------------KERLIIFGAGPD-----VPPLV---TFASNVGF--YTVVTDWRPNCEKHFFPDADEIIVD----------FPADFLRKFLIFVLITHHFQKDQEILHFLLEKELRYIGI-----LGSKERTRRLL-QNRKPPDHLYSPVGLSIDAQEEIAIVAQLIQL

4ambA1

0.21

0.16

0.80

0.69

PPAS

M-------ALFITSPGLSHIL--------P--TVPLAQALRALVRYATGGDIRAVACAVDVSPGVPMHSEGLGEGFFVSAVAV--DGALR---TARSWRPDLVVHTPTQGAGPLTAAALQLP--CVELPGPADSEPGLGALIRRAMSK-----DYERHGVTGEPTGSVRL-------

4wd6A

0.16

0.14

0.91

0.78

Env-PPAS

---DEVPELRIEKV-KENLHTSYSRVNGFTPWSDRDTETLVHWIRKNGYEGSV--STTAGI-KWLNDQSISSTNHLLKENKKEPAKYTLKGNESVDGL---IEVFYPGGHTIDNVPK-SKILGGCFVSEGLGYTGEAHIDQWSRS-----AQNALSRYSEAKIGDIAKHTKSLAETA

2wdwA

0.10

0.98

0.57

MUSTER

PEDVGRNPERLLP-KPPATLLTSTVTFDWEAAFSRLLRNHGEWYERNSGPDSPYTGLWSQLMIGNEVPGMGESGFMMPIQVDATRPDAVIDGVPPAEVPEPIEQRWLASTPGRGGRGPASKTKAGYLRKRLTDRQIQAVYENMTHMDGIDYGAVW--YGVNTVDPAATALLKVNYIT

3bdiA

0.08

0.94

0.54

dPPAS

IDVN-GTRVFQRKVTDSNRRSIALFHGYSFTSDWDKADLFNNYSKAPDYPGFGRSA--------SSEKYGIDRRDYLKANGVARSGGGVITTLQYPDIVDGIIAVAPAWVESLKGDKKIRQKTLLVWGSKDHVVPIALSKEYASI-ISGSRLEIVEGSGHPVYIEKPEEFVRITVDF

(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=-4.08

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.9±3.6Å

Download Model 2

C-score=-4.72

Download Model 3

C-score=-4.65

Download Model 4

C-score=-5.00

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	3bq9A	0.575	4.18	0.140	0.876
2	2we7A	0.567	3.93	0.115	0.819
3	1ydgE	0.566	3.58	0.094	0.785
4	3i39X2	0.565	4.22	0.077	0.825
5	2xtbA	0.565	4.07	0.123	0.853
6	1jqkA3	0.561	4.31	0.064	0.831
7	2zkiE	0.561	3.53	0.073	0.774
8	3i04A2	0.561	4.22	0.051	0.819
9	4e69A	0.559	4.34	0.083	0.864
10	3l3bB	0.559	3.73	0.102	0.774

(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	0.11	7	2ag8A	NAP	Rep, Mult	27,29,37,39,61,62,63,65,68,105,106,107,108,113,129,130,135,166,167
2	0.03	2	3fhxB	SO4	Rep, Mult	38,45,64
3	0.03	2	1ebeA	O	Rep, Mult	139,142
4	0.03	2	1su6A	SF4	Rep, Mult	49,53,54,56,58,59,175
5	0.03	2	3cf4A	SF4	Rep, Mult	89,102,103,104,117
6	0.03	2	3tasA	ZN	Rep, Mult	137,138
7	0.03	2	3taxA	UDP	Rep, Mult	30,61,87,88,91,94,112,114,117
8	0.02	1	1xcbA	NAD	Rep, Mult	42,43,46,166
9	0.02	1	1dxoA	DQN	Rep, Mult	29,81
10	0.02	1	3iukA	MG	Rep, Mult	117,138
11	0.02	1	2a9yA	26A	Rep, Mult	137,140,141,144
12	0.02	1	1bx4A	ADN	Rep, Mult	109,112,138,141,145
13	0.02	1	3mlaA	JJZ	Rep, Mult	25,26,43,127,128,129,130,135,141,142,166
14	0.02	1	1yklG	DHB	Rep, Mult	18,30
15	0.02	1	1yrhG	FMN	Rep, Mult	96,100,122
16	0.02	1	3keuB	MG	Rep, Mult	83,167
17	0.02	1	2o01A	CLA	Rep, Mult	33,47,50
18	0.02	1	2a9zA	NA	Rep, Mult	25,45,47,57,75
19	0.02	1	3cf4A	SF4	Rep, Mult	135,137,161,166

	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	0.066	1qzuC	0.516	4.09	0.119	0.763	4.1.1.36	37,102,115
2	0.066	2q4oA	0.531	4.23	0.106	0.785	3.2.2.-	NA
3	0.060	3fz0B	0.543	3.96	0.069	0.785	3.2.2.1	NA
4	0.060	1t90A	0.534	3.95	0.070	0.785	1.2.1.18,1.2.1.27	128
5	0.060	2a9yA	0.544	4.22	0.100	0.842	2.7.1.20	NA
6	0.060	1lj8A	0.545	4.36	0.079	0.831	1.1.1.67	33,40
7	0.060	1p9oB	0.553	4.39	0.105	0.842	6.3.2.5	NA
8	0.060	2ff2B	0.539	4.09	0.102	0.802	3.2.2.1	NA
9	0.060	1wyeA	0.543	4.16	0.062	0.825	2.7.1.45	NA
10	0.060	2w8nA	0.539	3.97	0.106	0.791	1.2.1.24	NA
11	0.060	2rg1B	0.534	3.57	0.078	0.729	1.6.5.2	NA
12	0.060	2v78A	0.539	4.41	0.054	0.831	2.7.1.4	81
13	0.060	2jg1A	0.543	4.09	0.081	0.814	2.7.1.144	NA
14	0.060	2gasA	0.533	4.24	0.085	0.797	1.3.1.45	27,37,169
15	0.060	1ua4A	0.546	4.57	0.036	0.859	2.7.1.147	NA
16	0.060	2w8oA	0.536	4.01	0.107	0.785	1.2.1.24	112
17	0.060	2i6aA	0.558	4.27	0.046	0.859	2.7.1.20	NA
18	0.060	7mdhB	0.553	4.48	0.094	0.876	1.1.1.82	NA
19	0.060	1fa9A	0.540	4.08	0.059	0.791	2.4.1.1	NA
20	0.060	1gqtB	0.539	4.06	0.121	0.797	2.7.1.15	NA
21	0.060	1cf9A	0.538	4.16	0.076	0.797	1.11.1.6	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	0.20	0.541	4.15	0.10	0.79	2a33A	GO:0005634 GO:0005737 GO:0009691 GO:0016787 GO:0016799
1	0.09	0.566	3.58	0.09	0.79	1ydgE	GO:0000166 GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0055114
2	0.07	0.561	3.60	0.10	0.77	4lafA	GO:0003955 GO:0010181 GO:0016491 GO:0019439 GO:0045892 GO:0046196 GO:0050660 GO:0050661 GO:0051287 GO:0055114
3	0.07	0.555	3.50	0.07	0.76	2zkiA	GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0055114
4	0.07	0.574	4.24	0.09	0.89	3gh1A	GO:0005829 GO:0009691 GO:0016799
5	0.07	0.474	3.33	0.03	0.64	3eqzB	GO:0000156 GO:0000160 GO:0005622
6	0.07	0.534	3.57	0.09	0.73	5f51A	GO:0000166 GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
7	0.07	0.547	3.51	0.10	0.75	3b6iA	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
8	0.07	0.518	4.39	0.11	0.79	1j2rA	GO:0003824 GO:0005829 GO:0006769 GO:0008152 GO:0008936 GO:0016787 GO:0019674
9	0.07	0.467	3.29	0.13	0.62	1dc7A	GO:0000156 GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005622 GO:0006351 GO:0006355 GO:0006808 GO:0008134 GO:0009399 GO:0043565
10	0.07	0.543	3.48	0.10	0.74	2rg1A	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
11	0.07	0.522	4.12	0.05	0.77	2fzvB	GO:0000166 GO:0010181 GO:0016491 GO:0050446 GO:0051289 GO:0052873 GO:0055114
12	0.07	0.523	4.24	0.08	0.79	1t35E	GO:0005829 GO:0009691 GO:0016799
13	0.07	0.532	4.34	0.10	0.82	1wekA	GO:0009691 GO:0016787 GO:0016799
14	0.07	0.541	3.55	0.08	0.74	5f4bA	GO:0000166 GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
15	0.07	0.520	3.65	0.08	0.72	2a5lB	GO:0000166 GO:0003955 GO:0009055 GO:0010181 GO:0016491 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
16	0.07	0.517	4.15	0.12	0.77	3quaA	GO:0009691 GO:0016787 GO:0016799
17	0.07	0.522	3.48	0.05	0.72	2arkA	GO:0009055 GO:0010181 GO:0055114
18	0.07	0.504	4.66	0.10	0.80	4ureA	GO:0016491 GO:0055114
19	0.07	0.501	4.34	0.10	0.75	1wehA	GO:0016020 GO:0016021
20	0.07	0.493	3.77	0.09	0.70	3d7nA	GO:0009055 GO:0010181 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016798	GO:0032553	GO:0048037	GO:0016655
GO-Score	0.52	0.41	0.41	0.41
Biological Processes	GO:0042446	GO:0009690	GO:1903507	GO:0044710	GO:0006355	GO:2000113	GO:0010629
GO-Score	0.52	0.52	0.41	0.41	0.41	0.41	0.41
Cellular Component	GO:0043231
GO-Score	0.41

(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.