I-TASSER results

I-TASSER results for job id Rv0163

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

Input Sequence in FASTA format

>protein (151 residues)
MAALPAPEKLLRSDFPVLWPVGTRWADNDMFGHLNNAVYYQLFDTAINAWINTSTGVDPL
AMPVLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVTYRLGVFKEPDDAGVITALGH
WVHVYVDRTSRRPVPIPEAIRSLLSTACVSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAALPAPEKLLRSDFPVLWPVGTRWADNDMFGHLNNAVYYQLFDTAINAWINTSTGVDPLAMPVLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVTYRLGVFKEPDDAGVITALGHWVHVYVDRTSRRPVPIPEAIRSLLSTACVSG
Prediction	CCCCCCCCCCCCCCCCEEEEEEHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCCEEEEEEEEEHCCCCCCEEEEEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHCCC
Conf.Score	9988877656654688899999753435689975557899999999999999988998545785789999997885566799689999999997698899999999878888689999999999997888988899999999999986569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAALPAPEKLLRSDFPVLWPVGTRWADNDMFGHLNNAVYYQLFDTAINAWINTSTGVDPLAMPVLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVTYRLGVFKEPDDAGVITALGHWVHVYVDRTSRRPVPIPEAIRSLLSTACVSG
Prediction	8664565653437613041504020110333100110331431130002003531324246462210014230403320516340203030451442303010201446565330103030100002376543350265025204612378
	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

CCCCCCCCCCCCCCCCEEEEEEHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCCEEEEEEEEEHCCCCCCEEEEEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHCCC
MAALPAPEKLLRSDFPVLWPVGTRWADNDMFGHLNNAVYYQLFDTAINAWINTSTGVDPLAMPVLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVTYRLGVFKEPDDAGVITALGHWVHVYVDRTSRRPVPIPEAIRSLLSTACVSG

2o6tA

0.44

0.42

0.96

4.05

MUSTER

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.41

0.40

0.97

5.96

dPPAS

--HMATAPRPLREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.44

0.42

0.96

5.49

wdPPAS

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.44

0.42

0.96

4.95

wMUSTER

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.44

0.42

0.96

4.93

wPPAS

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.44

0.42

0.96

6.25

dPPAS2

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

2o6tA

0.44

0.42

0.96

4.67

PPAS

MATAPRP---LREQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGLDIQGGEVIGLVVSSSCDYFAPVAFPQRIEMGLRVARLGNSSVQYELALFLEGQ--REACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS-

5byuA

0.25

0.21

0.85

4.66

Env-PPAS

----------EINKIIHKKTFDIAWGDMDALGHVNNARYFDYFQEARIDWLRELDIK--MTGQTGPVVIHVACTFLKPIVYPATVTIHSKVNSLGNSSMIMDHDLYQE----ETLMAQGVSKIVWIDYTQNKSVPLPDIIRNLV-------

5byuA

0.25

0.21

0.85

3.67

MUSTER

----------EINKIIHKKTFDIAWGDMDALGHVNNARYFDYFQEARIDWLRELDIK--MTGQTGPVVIHVACTFLKPIVYPATVTIHSKVNSLGNSSMIMDHDLYQEET----LMAQGVSKIVWIDYTQNKSVPLPDIIRNLV-------

5byuA

0.25

0.21

0.85

5.39

dPPAS

----------EINKIIHKKTFDIAWGDMDALGHVNNARYFDYFQEARIDWLRELDIK--MTGQTGPVVIHVACTFLKPIVYPATVTIHSKVNSLGNSSMIMDHDLYQE----ETLMAQGVSKIVWIDYTQNKSVPLPDIIRNLV-------

(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=1.39

Estimated TM-score = 0.91±0.06

Estimated RMSD = 2.1±1.7Å

Download Model 2

C-score=-3.79

Download Model 3

C-score=-3.97

Download Model 4

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	2o6tA	0.931	1.01	0.418	0.967
2	2xemA	0.816	2.25	0.135	0.934
3	2w3xE	0.813	1.96	0.109	0.907
4	2oafB	0.793	2.07	0.212	0.907
5	5eo4A	0.791	2.17	0.161	0.894
6	3ck1A	0.788	2.01	0.218	0.881
7	1s5uE	0.787	2.07	0.172	0.881
8	2nujA	0.784	2.22	0.184	0.907
9	3qy3A	0.783	1.62	0.287	0.854
10	1z54A	0.771	1.86	0.238	0.861

(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	0.44	45	5byuG	COA	Rep, Mult	67,68,69,95,96,97,98,122,124,126,131,133
2	0.32	26	1wn3C	HXC	Rep, Mult	29,30,31,33,34,36,75,76,77,78,114
3	0.07	12	4m20C	COA	Rep, Mult	44,67,68,69,126,127
4	0.03	3	2xemB	SSV	Rep, Mult	47,48,50,66,89,91,101,144
5	0.02	4	3p3iA	FAH	Rep, Mult	44,67,68,123
6	0.01	1	2oiwA	MG	Rep, Mult	26,28
7	0.01	1	2cyeA	ZN	Rep, Mult	29,33
8	0.01	2	2w3xC	POP	Rep, Mult	19,20,21,45

	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	0.299	1lo8A	0.760	2.20	0.114	0.874	3.1.2.23	39,102
2	0.179	1y7uA	0.624	2.87	0.143	0.781	3.1.2.20	44,69
3	0.077	3ir3A	0.573	2.94	0.073	0.695	4.2.1.-	123
4	0.066	1mkaA	0.563	2.92	0.082	0.729	4.2.1.60	NA
5	0.066	1z6bA	0.547	2.50	0.035	0.669	4.2.1.-	NA
6	0.060	2ownB	0.723	2.43	0.125	0.854	3.1.2.14	36,78
7	0.060	2gllA	0.587	2.64	0.056	0.729	4.2.1.-	NA
8	0.060	1a39A	0.439	4.94	0.071	0.729	3.2.1.4	51
9	0.060	2hx5A	0.746	2.03	0.153	0.848	3.1.2.-	89
10	0.060	3khpC	0.559	3.46	0.116	0.729	1.-.-.-	NA
11	0.060	2jfdA	0.353	4.85	0.029	0.623	2.3.1.85	NA
12	0.060	1tbuB	0.518	2.10	0.061	0.589	3.1.2.2	NA
13	0.060	1u1zB	0.579	2.79	0.066	0.722	4.2.1.-	NA
14	0.060	1pn4D	0.547	3.46	0.042	0.729	4.2.1.-	NA
15	0.060	2vz8B	0.508	3.17	0.015	0.675	2.3.1.85	NA
16	0.060	1iq6B	0.560	2.55	0.103	0.662	4.2.1.17	136
17	0.060	2qq2C	0.647	3.08	0.113	0.815	3.1.2.2	38
18	0.060	2pffB	0.574	3.60	0.072	0.781	2.3.1.86	88
19	0.060	1gpiA	0.412	5.13	0.038	0.715	3.2.1.91	123
20	0.060	2c2iA	0.562	2.66	0.096	0.675	4.2.1.17	104
21	0.060	3b7kC	0.617	3.51	0.120	0.828	3.1.2.1	45
22	0.060	2uv8G	0.576	3.65	0.067	0.781	2.3.1.86	NA
23	0.060	2v1oE	0.642	3.02	0.120	0.801	3.1.2.2	51,92
24	0.060	3el6A	0.512	3.16	0.058	0.682	4.2.1.61	84

(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	0.40	0.725	2.40	0.30	0.85	2cyeC
1	0.33	0.710	2.21	0.16	0.83	1njkA	GO:0006635 GO:0016787 GO:0047617
2	0.31	0.761	2.21	0.11	0.87	1lo7A	GO:0016787 GO:0018739
3	0.31	0.771	1.86	0.24	0.86	1z54A	GO:0016787
4	0.31	0.762	2.31	0.14	0.88	2hljA	GO:0016740 GO:0016746
5	0.30	0.759	1.44	0.21	0.82	2egiC	GO:0016787
6	0.29	0.739	2.33	0.18	0.85	3r87A	GO:0016787
7	0.29	0.787	2.07	0.17	0.88	1s5uE	GO:0005886 GO:0006629 GO:0016020 GO:0016787 GO:0016790
8	0.28	0.758	2.02	0.15	0.86	2hx5A	GO:0016787 GO:0016790 GO:0042372
9	0.26	0.719	1.74	0.11	0.79	3hm0A	GO:0016787 GO:0016790
10	0.26	0.741	2.30	0.21	0.85	2oiwA
11	0.24	0.755	2.05	0.13	0.85	2pzhA	GO:0006629 GO:0016787
12	0.23	0.761	2.31	0.13	0.88	4k00A	GO:0004778 GO:0016290 GO:0016787 GO:0016790 GO:0042372 GO:0047617
13	0.17	0.729	2.68	0.10	0.87	2essA	GO:0006633 GO:0016790
14	0.14	0.611	2.79	0.20	0.74	2gvhB	GO:0016787
15	0.07	0.616	1.13	0.19	0.65	2egiI	GO:0016787
16	0.06	0.311	4.91	0.04	0.50	4ervA	GO:0005216 GO:0005219 GO:0005262 GO:0005509 GO:0005516 GO:0005783 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0015278 GO:0016020 GO:0016021 GO:0016529 GO:0031090 GO:0033017 GO:0034220 GO:0043231 GO:0051209 GO:0051289 GO:0055085 GO:0070588 GO:0071277 GO:0071286 GO:0071313 GO:0071318 GO:1903779
17	0.06	0.296	5.64	0.03	0.59	5d80B	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
18	0.06	0.253	4.10	0.07	0.39	2lkzA	GO:0000166 GO:0000245 GO:0000381 GO:0000398 GO:0003676 GO:0003677 GO:0003723 GO:0003729 GO:0005634 GO:0005654 GO:0005681 GO:0006396 GO:0006397 GO:0006915 GO:0008270 GO:0008285 GO:0008380 GO:0042981 GO:0043065 GO:0044822 GO:0046872
19	0.06	0.247	5.32	0.04	0.47	2g77B	GO:0000042 GO:0000139 GO:0000166 GO:0003924 GO:0005525 GO:0005794 GO:0005796 GO:0006810 GO:0006891 GO:0006914 GO:0007264 GO:0015031 GO:0016020 GO:0048705 GO:0070062 GO:1903358 GO:1903434 GO:2000156 GO:2000785
20	0.06	0.228	5.12	0.04	0.40	2dizA	GO:0003756 GO:0005783 GO:0005788 GO:0006457 GO:0016853 GO:0034976 GO:0043066 GO:0043202 GO:0043277 GO:0045454 GO:0070062
21	0.06	0.739	2.36	0.22	0.86	2gf6A
22	0.06	0.220	5.42	0.02	0.39	1eo1A

Consensus prediction of GO terms

Molecular Function	GO:0047617	GO:0018739	GO:0016746
GO-Score	0.33	0.31	0.31
Biological Processes	GO:0006635
GO-Score	0.33
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.