I-TASSER results

I-TASSER results for job id Rv1489

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

Input Sequence in FASTA format

>protein (118 residues)
MSGLTSPKTYAVLAALQAGDAVACAIPLPPIARLLDDLDVPVSVRPVLPVVKAASAVGLL
SVTRFPALARLTTAMLTLYFILAVGAHVRVRDRVVNAIPAASFLTLFALMTAKGPERT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSGLTSPKTYAVLAALQAGDAVACAIPLPPIARLLDDLDVPVSVRPVLPVVKAASAVGLLSVTRFPALARLTTAMLTLYFILAVGAHVRVRDRVVNAIPAASFLTLFALMTAKGPERT
Prediction	CCCCCCCCHHHHHHHHHHHHHHHEHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	9987788667799999998655544577889998875599965777899999999998888875458999999999999999999998764445667899999999999998689999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSGLTSPKTYAVLAALQAGDAVACAIPLPPIARLLDDLDVPVSVRPVLPVVKAASAVGLLSVTRFPALARLTTAMLTLYFILAVGAHVRVRDRVVNAIPAASFLTLFALMTAKGPERT
Prediction	7542554421100012332211201432520440164262156221102113222120113133333223212210331122001010314433341231223211211121432768
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHHHHHHEHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC
MSGLTSPKTYAVLAALQAGDAVACAIPLPPIARLLDDLDVPVSVRPVLPVVKAASAVGLLSVTRFPALARLTTAMLTLYFILAVGAHVRVRDRVVNAIPAASFLTLFALMTAKGPERT

3jbrE

0.19

0.97

0.84

MUSTER

MSPTEAPKVRVTLFCILVGIVLAMTSDHEFTTQKEYSISAAAISVFSLGFLIMGTICALMKRDYLPASMFYVFAGLCLFVSLEVMRQSVKR-ACACAAFVLLFLGGISLLLFSLPR--

5cwbA2

0.09

0.08

0.85

0.65

dPPAS

-------------SYEVICECVARI--VAEIVEALKRSGTSEDEIAEIVARVISEVIRTLKESGSSYEVIKECVQRIVEEIVEALKRSGTSEDEINEIVRRVKSEVERTLKESGS---

4tq3A1

0.15

0.14

0.94

0.70

wdPPAS

FGITPNASLQHAVLGLLSFAFWMAF---SFTINALYDRDVP-SVREAWLYCIAFLALSLATAAAIEKFFLAMLGANIIGYVYSAPPRFKAWPVDVICNALAAVLAFYAGLSIGGA---

4tq3A1

0.15

0.14

0.94

0.82

wMUSTER

FGITPNASLQHAVLGLLSFAFWMAF---SFTINALYDRDVP-SVREAWLYCIAFLALSLATAAAINKFFLAMLGANIIGYVYSAPPRFKAWPVDVICNALAAVLAFYAGLSIGGA---

4tq3A1

0.16

0.14

0.92

0.81

wPPAS

FGITPNASLQHAVLGLLSFAFWMAF---SFTINALYDRDVP-SVREAWLYCIAFLALSLATAAAIEKFFLAMLGANIIGYVYSAPPRFKAW--DVICNALAAVLAFYAGLSIGGA---

4tq3A1

0.14

0.95

0.91

dPPAS2

FGITPNASLQHAVLGLLSFAFWMAF---SFTINALYDRDVDGSVREAWLYCIAFLALSLATAAAIEKFFLAMLGANIIGYVYSAPPRFKAWPVDVICNALAAVLAFYAGLSIGGA---

2mqaA

0.12

0.11

0.96

0.86

PPAS

SNLLSSGDFVQMISSTTSTDQAVSV-ATSVAQNVGNQLGLD----ANAMNSLLGAVSGYVSTLGNAISDASAYANAISSAIGNVLANSSISESTASSAASSAASSVTTTLTSYGPAVF

4n5fA1

0.17

0.15

0.89

0.86

Env-PPAS

MDLYTE--DQRMIRDAARAFATEMLAP--NAAQWDHDAHLP------DAIVAQLGELGLL-GMIVPYTD-YVAYALAMEEVAAGDAACATM-MSVHNSVGCGPILGFGTPAQKDADMA

4ryiA

0.10

0.09

0.95

0.84

MUSTER

MK-----KSSIIVFFLTYGLFYVSSVLFPIDRTWYDALEKPSIWAVLFGLIALSVAIIYNNYGFKPKTFWFLFLLNYIFNQAFSYFQFSQKNLFLATVDCLLVAITTLLLIMF-LSKV

5cwiA2

0.14

0.13

0.93

0.65

dPPAS

-------ADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPAKKCIKAASEAAEEASKAAEEAQRHPDSQKARDEIKEASQKAEEVKERCER-

(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=-1.72

Estimated TM-score = 0.51±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-3.35

Download Model 3

C-score=-3.85

Download Model 4

C-score=-4.43

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	4tq3A	0.770	2.47	0.150	0.958
2	4od4A1	0.713	2.95	0.150	0.958
3	4akkA	0.710	2.70	0.078	0.924
4	3rmgA	0.702	3.09	0.125	0.949
5	4wk5A	0.698	2.90	0.097	0.941
6	3oyrA	0.695	2.92	0.089	0.949
7	3lmdA1	0.692	2.73	0.081	0.932
8	1rtrA1	0.691	2.97	0.036	0.932
9	4jyxA	0.690	2.89	0.071	0.932
10	4kkmA	0.686	3.01	0.088	0.941

(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	3angB	DCC	Rep, Mult	34,38,46,47,50,67,70,73,77,79,80
2	0.06	2	1bjyB	CTC	Rep, Mult	103,107,110
3	0.06	2	4ryoA	MPG	Rep, Mult	76,79,108
4	0.06	2	4f6xA	MG	Rep, Mult	32,79
5	0.06	2	3oabA	MG	Rep, Mult	33,34,37,45
6	0.03	1	3anpD	DAO	Rep, Mult	20,31,34,38,50,53,77,79,80
7	0.03	1	3bz1F	PL9	Rep, Mult	69,72
8	0.03	1	3q2qA	IPE	Rep, Mult	32,33,36,39,86,88
9	0.03	1	2o011	CLA	Rep, Mult	82,83,87
10	0.03	1	3oabA	DST	Rep, Mult	23,26,76,80,101
11	0.03	1	1m34A	SF4	Rep, Mult	59,60

	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	0.203	2ksfA	0.575	3.63	0.117	0.856	2.7.13.3	80,83,101,105
2	0.129	3eziA	0.589	3.06	0.082	0.814	2.7.13.3	19
3	0.128	1tqgA	0.539	3.43	0.050	0.797	2.7.13.3	69,71
4	0.060	3gm1B	0.586	2.98	0.093	0.822	2.7.10.2	97
5	0.060	2h8oA	0.664	3.02	0.107	0.924	2.5.1.10	NA
6	0.060	2azkA	0.669	3.08	0.080	0.932	2.5.1.1,2.5.1.29,2.5.1.10	NA
7	0.060	3m9uA	0.666	3.04	0.071	0.932	2.5.1.10	83,100
8	0.060	3cxhN	0.568	3.99	0.045	0.941	1.10.2.2	NA
9	0.060	1qleC	0.585	3.80	0.073	0.898	1.9.3.1	100
10	0.060	2dh4A	0.616	3.33	0.120	0.915	2.5.1.29	NA
11	0.060	3g4xA	0.575	3.30	0.089	0.814	1.15.1.1	NA
12	0.060	2ftzA	0.674	2.98	0.100	0.915	2.5.1.10	NA
13	0.060	1q0mD	0.582	3.26	0.069	0.814	1.15.1.1	10
14	0.060	1occA	0.592	4.06	0.079	0.966	1.9.3.1	NA
15	0.060	2occN	0.590	4.08	0.078	0.966	1.9.3.1	29,35,55,58
16	0.060	1v4eA	0.654	2.99	0.135	0.907	2.5.1.11	NA
17	0.060	3g61A	0.554	4.34	0.070	0.907	3.6.3.44	NA
18	0.060	1k04A	0.429	3.95	0.069	0.669	2.7.10.2	69,71,101,108
19	0.060	2f8zF	0.590	3.32	0.071	0.873	2.5.1.10,2.5.1.1	59
20	0.060	3lmdA	0.691	2.60	0.055	0.915	2.5.1.30	36,104
21	0.060	3ipiA	0.608	3.32	0.083	0.907	2.5.1.-	NA
22	0.060	1kizA	0.553	3.75	0.085	0.856	4.2.3.6	82

(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	0.22	0.681	3.07	0.07	0.94	1rqiA	GO:0004161 GO:0004337 GO:0005737 GO:0005829 GO:0008299 GO:0016740 GO:0033384 GO:0045337 GO:0046872
1	0.20	0.713	2.95	0.15	0.96	4od4A	GO:0004659 GO:0016020 GO:0016021 GO:0016740
2	0.19	0.668	3.16	0.07	0.93	3wjkA	GO:0008299 GO:0016740
3	0.18	0.691	2.60	0.06	0.92	3lmdA	GO:0008299 GO:0016740 GO:0036422 GO:0046872
4	0.17	0.603	3.28	0.06	0.90	4lobA	GO:0008299 GO:0016740
5	0.16	0.636	3.14	0.07	0.90	4f62A	GO:0008299 GO:0016740
6	0.16	0.770	2.49	0.14	0.96	4tq4D	GO:0004659 GO:0016020 GO:0016021
7	0.15	0.750	2.68	0.14	0.95	4tq6A	GO:0004659 GO:0016020 GO:0016021
8	0.13	0.693	2.92	0.09	0.94	3mzvB	GO:0008299 GO:0016740
9	0.12	0.702	3.09	0.12	0.95	3rmgA	GO:0008299 GO:0016020 GO:0016021 GO:0016740
10	0.12	0.695	2.92	0.09	0.95	3oyrA	GO:0008299 GO:0016740
11	0.12	0.690	2.89	0.07	0.93	4jyxA	GO:0008299 GO:0016740 GO:0036422
12	0.11	0.682	3.08	0.10	0.94	3nf2A	GO:0008299 GO:0016740
13	0.11	0.671	3.16	0.10	0.94	2q80A	GO:0004161 GO:0004311 GO:0004337 GO:0005737 GO:0005829 GO:0006695 GO:0006720 GO:0008299 GO:0016740 GO:0033384 GO:0033386 GO:0045337 GO:0046872
14	0.11	0.655	3.18	0.09	0.92	2azjA	GO:0008299 GO:0016740 GO:0046872 GO:0052922
15	0.11	0.683	3.05	0.07	0.92	3aqbD	GO:0000287 GO:0008299 GO:0009234 GO:0016740 GO:0016765 GO:0036423 GO:0046872
16	0.11	0.685	3.11	0.05	0.92	4fp4A	GO:0008299 GO:0016740
17	0.10	0.633	3.10	0.08	0.90	4lfgA	GO:0004337 GO:0008299 GO:0016740
18	0.10	0.677	3.13	0.09	0.94	1wy0A	GO:0008299 GO:0016740

Consensus prediction of GO terms

Molecular Function	GO:0004659	GO:0046872
GO-Score	0.44	0.36
Biological Processes	GO:0016114	GO:0033383	GO:0045338	GO:0008654
GO-Score	0.44	0.44	0.44	0.44
Cellular Component	GO:0044444	GO:0031224
GO-Score	0.44	0.31

(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.