I-TASSER results

I-TASSER results for job id Rv1975

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

Input Sequence in FASTA format

>protein (221 residues)
MSRRASATCALSATTAVAIMAAPAARADDKRLNDGVVANVYTVQRQAGCTNDVTINPQLQ
LAAQWHTLDLLNNRHLNDDTGSDGSTPQDRAHAAGFRGKVAETVAINPAVAISGIELINQ
WYYNPAFFAIMSDCANTQIGVWSENSPDRTVVVAVYGQPDRPSAMPPRGAVTGPPSPVAA
QENVPIDPSPDYDASDEIEYGINWLPWILRGVYPPPAMPPQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSRRASATCALSATTAVAIMAAPAARADDKRLNDGVVANVYTVQRQAGCTNDVTINPQLQLAAQWHTLDLLNNRHLNDDTGSDGSTPQDRAHAAGFRGKVAETVAINPAVAISGIELINQWYYNPAFFAIMSDCANTQIGVWSENSPDRTVVVAVYGQPDRPSAMPPRGAVTGPPSPVAAQENVPIDPSPDYDASDEIEYGINWLPWILRGVYPPPAMPPQ
Prediction	CCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHEHCCCCCCCCHHHHHHHHHCCHHHHHHHCCCCCCEEEEEEEHCCCEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98776445566555455667888888885799999999999999999599987569999999999999999979988999999999999999989976455444436777789999999987597888886799998889999876997999999578888888888888888888887777888888888788887666666677766667788999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSRRASATCALSATTAVAIMAAPAARADDKRLNDGVVANVYTVQRQAGCTNDVTINPQLQLAAQWHTLDLLNNRHLNDDTGSDGSTPQDRAHAAGFRGKVAETVAINPAVAISGIELINQWYYNPAFFAIMSDCANTQIGVWSENSPDRTVVVAVYGQPDRPSAMPPRGAVTGPPSPVAAQENVPIDPSPDYDASDEIEYGINWLPWILRGVYPPPAMPPQ
Prediction	85332322220222333334333345354642144004300330156451520421740250034105320664301223344132013004424142120002021343343024004201725301200123604200001144642100000002255444444454454444424454624454446354665342224224333443325656468
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHEHCCCCCCCCHHHHHHHHHCCHHHHHHHCCCCCCEEEEEEEHCCCEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSRRASATCALSATTAVAIMAAPAARADDKRLNDGVVANVYTVQRQAGCTNDVTINPQLQLAAQWHTLDLLNNRHLNDDTGSDGSTPQDRAHAAGFRGKVAETVAINPAVAISGIELINQWYYNPAFFAIMSDCANTQIGVWSENSPDRTVVVAVYGQPDRPSAMPPRGAVTGPPSPVAAQENVPIDPSPDYDASDEIEYGINWLPWILRGVYPPPAMPPQ

4d53A

0.18

0.10

0.59

2.02

MUSTER

----------------------MGHKIDTKEDMKILYSEIAELRKKL-NLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFLTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTTNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

2.80

dPPAS

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTDNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

4.50

wdPPAS

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGI----ELNRVVNAWLNSPSHKEALINTDTDKIGGYRLKTTNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

2.85

wMUSTER

-----------------------GHKIDTKEDMKILYSEIAELRKKL-NLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFLTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTDNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

4.73

wPPAS

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGI----ELNRVVNAWLNSPSHKEALINTDTDKIGGYRLKTTNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

7.08

dPPAS2

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTDNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

3.27

PPAS

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTTNIDIFVVLFGKRK-------------------------------------------------------------

4d53A

0.18

0.10

0.59

3.67

Env-PPAS

-----------------------MGHKIDTKEDMKILYSEIAELRKKLNLNHLEIDDTLEKVAKEYAIKLGENRTITHT--LFGTTPMQRIHKYDQSFNTREILASGIELN----RVVNAWLNSPSHKEALINTDTDKIGGYRLKTTNIDIFVVLFGKRK-------------------------------------------------------------

4ifaA2

0.13

0.08

0.58

1.91

MUSTER

--------------------PLTPDKKQIENGNQQIFDLTNIIRSRH-NLPLLAWDQQTADVAIGHSKDKDN-NYFSHD-SPTLGTLGDRLQRGKVGFQAGENIAAQHSD---GVAALQGWLNSEGHRKNLLNEQFTGLGVGVYDK----FYTQNFIRK--------------------------------------------------------------

4ifaA2

0.13

0.08

0.58

2.62

dPPAS

---------------------PLTPDKKQIENGNQQIFDLTNIIRSRHNLPLLAWDQQTADVAIGHSKDKDN-NYFSHD-SPTLGTLGDRLQRGKVGFQAGENIAAQHS---DGVAALQGWLNSEGHRKNLLNEQFTGLGVGVYDK----FYTQNFIRK--------------------------------------------------------------

(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=-2.32

Estimated TM-score = 0.44±0.14

Estimated RMSD = 10.9±4.6Å

Download Model 2

C-score=-2.42

Download Model 3

C-score=-2.76

Download Model 4

C-score=-3.05

Download Model 5

C-score=-3.26

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	2vznA	0.495	3.44	0.141	0.602
2	1qnxA	0.492	3.37	0.128	0.597
3	1xtaA1	0.480	3.40	0.091	0.593
4	1smbA	0.476	3.10	0.182	0.566
5	2ddbB	0.467	3.37	0.096	0.570
6	1u53A	0.467	3.39	0.091	0.566
7	1t3tA2	0.432	5.85	0.028	0.756
8	1cfeA	0.430	3.17	0.103	0.525
9	1urjB1	0.422	5.53	0.087	0.724
10	1ve6A	0.421	5.92	0.048	0.729

(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	4	1hxpA	U5P	Rep, Mult	80,81,88,89,90,100
2	0.05	3	2cz8B	FAD	Rep, Mult	104,144,151,153
3	0.04	2	1gfnA	C8E	Rep, Mult	105,152
4	0.04	2	2h39B	ADQ	Rep, Mult	104,106,107,108,118
5	0.04	2	3kziA	CLA	Rep, Mult	37,41
6	0.04	2	4ac1X	ZN	Rep, Mult	78,124
7	0.02	1	3i9dW	MG	Rep, Mult	42,45
8	0.02	1	3qbmA	MG	Rep, Mult	130,133
9	0.02	1	2boqA	CA	Rep, Mult	69,81,83,85
10	0.02	1	1c4aA	SF4	Rep, Mult	118,120,122,125,127,153,202
11	0.02	1	1swiC	BNZ	Rep, Mult	59,63
12	0.02	1	5eteA	DIO	Rep, Mult	59,100,138
13	0.02	1	1c4aA	FES	Rep, Mult	67,68,69,70,80,81,103
14	0.02	1	2wse3	CLA	Rep, Mult	118,119,213
15	0.02	1	3v2d2	MG	Rep, Mult	70,74
16	0.02	1	3kdpB	III	Rep, Mult	89,90
17	0.02	1	4fe1F	CLA	Rep, Mult	32,36
18	0.02	1	3u3uC	EAH	Rep, Mult	40,44,47,105,117,118,121,122,127,131,154
19	0.02	1	2fhbA	GLC	Rep, Mult	89,91,99,157

	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	3d7uA	0.334	5.49	0.041	0.547	2.7.10.2	69
2	0.060	2veoB	0.407	5.37	0.056	0.661	3.1.1.3	NA
3	0.060	1ofdA	0.378	5.99	0.035	0.656	1.4.7.1	122
4	0.060	2pffB	0.397	5.65	0.067	0.679	2.3.1.86	114
5	0.060	1h19A	0.406	5.04	0.067	0.638	3.3.2.6	NA
6	0.060	2qr5A	0.422	5.89	0.048	0.733	3.4.19.1	NA
7	0.060	2e3xA	0.414	5.14	0.052	0.638	3.4.24.58	118,133
8	0.060	1e6yA	0.405	4.58	0.086	0.588	2.8.4.1	155
9	0.060	2fhbA	0.410	5.79	0.041	0.706	3.2.1.41	NA
10	0.060	1hr9F	0.398	5.62	0.044	0.683	3.4.24.64	115
11	0.060	2wk5A	0.314	5.71	0.042	0.543	2.4.2.4	NA
12	0.060	2pffA	0.416	5.59	0.055	0.720	2.3.1.41,2.3.1.86	NA
13	0.060	2ecfA	0.405	6.18	0.040	0.742	3.4.14.5	NA
14	0.060	1hr6D	0.402	5.51	0.039	0.679	3.4.24.64	NA
15	0.060	1z84A	0.416	5.21	0.051	0.661	2.7.7.12	NA
16	0.060	1t3tA	0.432	5.85	0.028	0.756	6.3.5.3	81
17	0.060	1kyaA	0.395	6.05	0.035	0.715	1.10.3.2	NA
18	0.060	1llwA	0.399	6.06	0.034	0.724	1.4.7.1	122
19	0.060	2gdkB	0.412	5.23	0.044	0.661	2.7.7.12	153

(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	0.15	0.495	3.44	0.14	0.60	2vznA	GO:0005576
1	0.10	0.479	3.15	0.19	0.57	4aiwA	GO:0000139 GO:0005576 GO:0005794 GO:0010634 GO:0010718 GO:0016020 GO:0042803 GO:0070062 GO:0070374
2	0.08	0.492	3.37	0.13	0.60	1qnxA	GO:0005576
3	0.07	0.472	3.69	0.10	0.60	3mz8A	GO:0005576
4	0.07	0.477	3.78	0.09	0.60	1wvrA	GO:0005576
5	0.07	0.474	3.71	0.08	0.61	1rc9A	GO:0005576
6	0.07	0.487	3.38	0.10	0.61	3q2uA	GO:0005576 GO:0005886 GO:0016020 GO:0016021
7	0.07	0.467	3.39	0.09	0.57	4nuiA	GO:0005576 GO:0046872
8	0.06	0.467	3.37	0.10	0.57	2ddbB	GO:0005576 GO:0046872
9	0.06	0.430	3.17	0.10	0.52	1cfeA	GO:0005576 GO:0006952 GO:0009607 GO:0031640 GO:0050832
10	0.06	0.499	3.91	0.09	0.63	3nt8A	GO:0005576
11	0.06	0.305	4.09	0.02	0.42	4jgoB	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0030435
12	0.06	0.306	5.78	0.04	0.53	5er8A	GO:0003824 GO:0004311 GO:0008152 GO:0008299 GO:0016740 GO:0016829 GO:0046872
13	0.06	0.243	4.92	0.05	0.38	2khcA	GO:0000166 GO:0000381 GO:0002121 GO:0003676 GO:0003723 GO:0003729 GO:0003730 GO:0005634 GO:0005737 GO:0006378 GO:0007281 GO:0007286 GO:0007319 GO:0007476 GO:0014881 GO:0016604 GO:0017148 GO:0030727 GO:0031536 GO:0031965 GO:0036099 GO:0042078 GO:0043186 GO:0045214 GO:0046011 GO:0048477 GO:2000738
14	0.06	0.249	4.97	0.07	0.38	4ffuI	GO:0016491 GO:0055114
15	0.06	0.233	4.46	0.06	0.34	1c2nA	GO:0009055 GO:0015979 GO:0020037 GO:0046872 GO:0055114
16	0.06	0.224	4.80	0.05	0.33	4yuuQ2	GO:0005509 GO:0009523 GO:0009654 GO:0015979 GO:0019898
17	0.06	0.203	4.99	0.03	0.32	4a53A	GO:0000932 GO:0003729 GO:0005737 GO:0010494 GO:0031087 GO:0033962
18	0.06	0.200	4.26	0.04	0.28	1q38A	GO:0001525 GO:0001775 GO:0001932 GO:0002020 GO:0002576 GO:0002931 GO:0005178 GO:0005518 GO:0005576 GO:0005577 GO:0005578 GO:0005604 GO:0005605 GO:0005615 GO:0005793 GO:0006953 GO:0007044 GO:0007155 GO:0007160 GO:0007161 GO:0008201 GO:0008284 GO:0008347 GO:0008360 GO:0009611 GO:0010193 GO:0010628 GO:0010952 GO:0016324 GO:0016504 GO:0018149 GO:0022617 GO:0030198 GO:0030335 GO:0031012 GO:0031093 GO:0033622 GO:0034446 GO:0035924 GO:0035987 GO:0036120 GO:0042060 GO:0042802 GO:0043066 GO:0045340 GO:0045773 GO:0048146 GO:0050900 GO:0050921 GO:0051384 GO:0070062 GO:0070372 GO:0071222 GO:0071288 GO:0071333 GO:0071347 GO:0071380 GO:0071560 GO:0071773 GO:0072562 GO:1904237 GO:2001202

Consensus prediction of GO terms

Molecular Function	GO:0042803
GO-Score	0.10
Biological Processes	GO:0010718	GO:0010634	GO:0070374
GO-Score	0.10	0.10	0.10
Cellular Component	GO:0005576
GO-Score	0.38

(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.