I-TASSER results

I-TASSER results for job id Rv1546

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

Input Sequence in FASTA format

>protein (143 residues)
MASVELSADVPISPQDTWDHVSELSELGEWLVIHEGWRSELPDQLGEGVQIVGVARAMGM
RNRVTWRVTKWDPPHEVAMTGSGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPLG
SAAARAVKGDVEKSLKQFAELYG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MASVELSADVPISPQDTWDHVSELSELGEWLVIHEGWRSELPDQLGEGVQIVGVARAMGMRNRVTWRVTKWDPPHEVAMTGSGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPLGSAAARAVKGDVEKSLKQFAELYG
Prediction	CCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCCCEEEEEEEHCCCEEEEEEEEEEEHCCEEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	98699999978999999999978776766565456887578987679789999998578557999999999699589999996688689999999985995899999998576466688999999999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MASVELSADVPISPQDTWDHVSELSELGEWLVIHEGWRSELPDQLGEGVQIVGVARAMGMRNRVTWRVTKWDPPHEVAMTGSGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPLGSAAARAVKGDVEKSLKQFAELYG
Prediction	75525343425241630141023164254134214414654574244224134314344344403030341345440314252423141413030334752130203241433213330242124314540450164047238
	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

CCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCCCEEEEEEEHCCCEEEEEEEEEEEHCCEEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MASVELSADVPISPQDTWDHVSELSELGEWLVIHEGWRSELPDQLGEGVQIVGVARAMGMRNRVTWRVTKWDPPHEVAMTGSGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPLGSAAARAVKGDVEKSLKQFAELYG

2m47A

0.13

0.98

2.36

MUSTER

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKFSIEEIEKRRLAAITGIPETLV

2m47A

0.12

0.98

3.12

dPPAS

SLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKFSIEEIEKRRLAAITGIPETLV

2m47A

0.14

0.13

0.97

3.78

wdPPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPK--SIEEIEKRRLAAITGIPETLVAIQRILE

2m47A

0.12

0.98

3.33

wMUSTER

SLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKFSIEEIEKRRLAAITGIPETLV

2m47A

0.14

0.13

0.97

4.01

wPPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPK--SIEEIEKRRLAAITGIPETLVAIQRILE

2m47A

0.14

0.13

0.98

4.94

dPPAS2

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILE

2m47A

0.13

0.98

3.76

PPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKFSIEEIEKRRLAAITGIPETLV

2m47A

0.13

0.98

2.98

Env-PPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKFSIEEIEKRRLAAITGIPETLV

1t17A

0.13

1.00

2.22

MUSTER

MHRHVVTKVLPYTPDQLFELVGDVDAYPKFVPWITGTWNGRVDGAVSTVDAEAQVGFSFLREKFATRVRRDKDARSIDVSLLYGPFKRLNNGWRFMPEGDATRVEFVIEFKSALLDAMLAANVDRAAGKLIACFEARAQQLHG

2d4rA

0.14

0.13

0.97

2.81

dPPAS

-PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREG---ARTRSRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYEFGGLLRKLVQKLQENVESLLKGLEERVLAASS

(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 4 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=0.18

Estimated TM-score = 0.74±0.11

Estimated RMSD = 4.3±2.9Å

Download Model 2

C-score=-0.46

Download Model 3

C-score=-0.06

Download Model 4

C-score=-0.05

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	4xrtA2	0.820	2.18	0.121	0.979
2	1b6fA	0.802	2.38	0.129	0.979
3	3ie5B	0.800	2.44	0.100	0.979
4	4xrwA2	0.798	2.35	0.115	0.972
5	3tfzA	0.794	2.50	0.135	0.986
6	3k3kA	0.781	2.93	0.127	0.993
7	2rezA	0.776	2.67	0.135	0.986
8	3qtjA	0.772	2.76	0.099	0.986
9	2kf2A	0.772	2.82	0.064	0.986
10	1uw5A	0.769	2.77	0.058	0.972

(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	20	4n3eD	2AN	Rep, Mult	6,8,17,21,93,95,106,130,131,134
2	0.12	16	2flhB	ZEA	Rep, Mult	21,23,53,64,66,89,91,93,131,134
3	0.11	14	3nj1A	PYV	Rep, Mult	33,53,55,57,64,66,86,89,126,127
4	0.03	4	4a81A	2AN	Rep, Mult	6,8,20,79,93,106,108,124,127,128,131,132
5	0.03	3	3c0vC	TBR	Rep, Mult	70,72,76,92
6	0.02	2	4a8gA	DMX	Rep, Mult	20,21,24,27,51,77,79,93,106,131
7	0.01	1	3tgxA	MAN	Rep, Mult	17,18
8	0.01	1	3kv7B	ACT	Rep, Mult	29,48
9	0.01	1	3tvqA	DQH	Rep, Mult	56,62,64,81,86,116,122,123,126
10	0.01	1	4flfA	XXH	Rep, Mult	13,16
11	0.01	1	3nqnB	CA	Rep, Mult	1,3,4,132
12	0.01	1	2gkdA	NUC	Rep, Mult	118,121,122
13	0.01	1	2qimA	ZEA	Rep, Mult	4,5,6,121,124,125

	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	0.152	2vq5A	0.728	2.75	0.133	0.944	4.2.1.78	27,46,48
2	0.060	1im0A	0.544	4.30	0.055	0.832	3.1.1.32,3.1.1.4	75
3	0.060	1bibA	0.517	3.66	0.065	0.720	6.3.4.15	NA
4	0.060	1sczA	0.528	4.53	0.068	0.853	2.3.1.61	NA
5	0.060	1ndoA	0.658	3.35	0.076	0.923	1.14.12.12	132,140
6	0.060	1xl7B	0.515	4.54	0.063	0.832	2.3.1.137	NA
7	0.060	1ordA	0.529	4.65	0.045	0.846	4.1.1.17	20,133
8	0.060	1b5sA	0.535	4.42	0.049	0.860	2.3.1.12	NA
9	0.060	2ii4A	0.534	4.77	0.044	0.888	2.3.1.168	NA
10	0.060	3l60A	0.541	4.34	0.059	0.867	2.3.1.12	NA
11	0.060	1kfqB	0.533	3.34	0.073	0.741	5.4.2.2	NA
12	0.060	3en1A	0.650	3.47	0.083	0.930	1.14.12.11	NA
13	0.060	2b1xA	0.636	3.66	0.066	0.909	1.14.12.12	NA
14	0.060	3e2dA	0.503	4.70	0.030	0.846	3.1.3.1	NA
15	0.060	1eg9A	0.659	3.34	0.076	0.923	1.14.12.12	NA
16	0.060	1yaaA	0.512	4.66	0.072	0.811	2.6.1.1	18,134
17	0.060	1y791	0.511	4.92	0.057	0.867	3.4.15.5	5
18	0.060	1q23B	0.526	4.66	0.068	0.860	2.3.1.28	NA
19	0.060	3mebA	0.504	4.34	0.065	0.811	2.6.1.1	NA
20	0.060	2ewnA	0.548	3.77	0.064	0.748	6.3.4.15	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	0.762	2.71	0.09	0.97	2flhB	GO:0006952 GO:0009607
1	0.32	0.769	2.38	0.10	0.94	1z94B	GO:0006950
2	0.31	0.722	2.97	0.11	0.93	2leqA	GO:0006950
3	0.28	0.802	2.45	0.14	0.99	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
4	0.26	0.710	2.87	0.07	0.91	2m89A	GO:0006950
5	0.25	0.760	2.82	0.10	0.99	4q0kA	GO:0006952 GO:0009607 GO:0009740
6	0.24	0.697	2.98	0.11	0.90	1xn5A	GO:0006950
7	0.24	0.747	2.60	0.15	0.92	3q63F	GO:0006950
8	0.23	0.730	2.94	0.16	0.96	3pu2B	GO:0006950
9	0.23	0.775	2.54	0.10	0.97	2bk0A	GO:0006952 GO:0009607
10	0.23	0.684	2.47	0.09	0.83	4fpwA	GO:0006950
11	0.23	0.770	2.51	0.09	0.96	3q64A	GO:0006950
12	0.22	0.780	2.42	0.07	0.96	3putB	GO:0006950
13	0.22	0.744	2.79	0.12	0.94	4n0gC	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
14	0.22	0.758	2.69	0.11	0.97	2wqlA	GO:0006952 GO:0009607
15	0.21	0.749	2.92	0.10	0.96	2ldkA	GO:0006950
16	0.21	0.776	2.71	0.10	0.99	4c9iA	GO:0006952 GO:0009607
17	0.21	0.780	2.67	0.14	0.99	4a80A	GO:0005737 GO:0006952 GO:0009607
18	0.21	0.757	2.81	0.11	0.99	1e09A	GO:0006952 GO:0009607
19	0.20	0.772	2.62	0.12	0.96	2il5A	GO:0006950
20	0.20	0.733	3.09	0.09	0.96	1xfsA	GO:0006950
21	0.20	0.745	2.41	0.11	0.91	3rd6A	GO:0006950
22	0.19	0.754	2.96	0.12	0.99	5c9yA	GO:0006952 GO:0009607
23	0.19	0.676	3.05	0.11	0.87	2luzA	GO:0006950
24	0.19	0.733	2.79	0.21	0.93	3eliA	GO:0006950
25	0.19	0.713	3.20	0.11	0.99	4m9bA	GO:0006952 GO:0009607
26	0.19	0.714	2.62	0.09	0.91	2lcgA	GO:0006950
27	0.18	0.705	3.15	0.12	0.96	2l9pA	GO:0006950
28	0.18	0.758	2.89	0.11	0.99	4c94A	GO:0006952 GO:0009607
29	0.18	0.712	3.17	0.09	0.98	4gy9A	GO:0006952 GO:0009607 GO:0009736 GO:0009877
30	0.18	0.745	2.97	0.11	0.98	5amwA	GO:0006952 GO:0009607
31	0.17	0.699	2.99	0.10	0.88	2nn5A	GO:0006950
32	0.16	0.711	2.66	0.12	0.88	1xn6A	GO:0006950
33	0.16	0.746	2.83	0.07	0.96	1xuvA	GO:0006950
34	0.15	0.793	2.48	0.11	0.98	5i8fA	GO:0006952 GO:0009607
35	0.14	0.731	3.18	0.11	0.99	1ifvA	GO:0006952 GO:0009607 GO:0016787
36	0.13	0.752	2.58	0.14	0.96	2vneA	GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
37	0.13	0.753	2.62	0.07	0.95	3otlA	GO:0006950
38	0.13	0.729	3.09	0.12	0.99	1tw0A	GO:0006952 GO:0009607
39	0.13	0.764	2.98	0.09	0.99	3kdhA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
40	0.12	0.727	3.07	0.10	0.97	2qimA	GO:0006952 GO:0009607 GO:0046872
41	0.10	0.727	2.90	0.12	0.96	3uidA	GO:0006950

Consensus prediction of GO terms

Molecular Function	GO:0016741
GO-Score	0.55
Biological Processes	GO:0044249	GO:0016999	GO:0009607	GO:0006952
GO-Score	0.55	0.55	0.39	0.39
Cellular Component
GO-Score

(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.