I-TASSER results

I-TASSER results for job id Rv0910

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

Input Sequence in FASTA format

>protein (144 residues)
MAKLSGSIDVPLPPEEAWMHASDLTRYREWLTIHKVWRSKLPEVLEKGTVVESYVEVKGM
PNRIKWTIVRYKPPEGMTLNGDGVGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPIG
MIVAAALRADIRESLQNFVTVFAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAKLSGSIDVPLPPEEAWMHASDLTRYREWLTIHKVWRSKLPEVLEKGTVVESYVEVKGMPNRIKWTIVRYKPPEGMTLNGDGVGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPIGMIVAAALRADIRESLQNFVTVFAG
Prediction	CCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCCCEEEEEEHCCCCEEEEEEEEEEEHCCEEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	987999999889999999999787777565655467875689877898899999985886568999999997995899999857886899999999859958999999984764666889999999999999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAKLSGSIDVPLPPEEAWMHASDLTRYREWLTIHKVWRSKLPEVLEKGTVVESYVEVKGMPNRIKWTIVRYKPPEGMTLNGDGVGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPIGMIVAAALRADIRESLQNFVTVFAG
Prediction	755253434162316301410231641541242144146645540443240333143452445040302414464402031433322414130303255620302032414332133302421243245404500540363278
	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

CCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCCCEEEEEEHCCCCEEEEEEEEEEEHCCEEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MAKLSGSIDVPLPPEEAWMHASDLTRYREWLTIHKVWRSKLPEVLEKGTVVESYVEVKGMPNRIKWTIVRYKPPEGMTLNGDGVGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPIGMIVAAALRADIRESLQNFVTVFAG

2m47A

0.17

0.98

2.38

MUSTER

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.16

0.98

3.08

dPPAS

SLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.17

0.97

3.79

wdPPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPK--SIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.16

0.98

3.47

wMUSTER

SLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.17

0.97

4.12

wPPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPK--SIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.17

0.98

5.03

dPPAS2

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.17

0.98

3.84

PPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2m47A

0.17

0.98

3.09

Env-PPAS

MPTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPGDKSIEEIEKRRLAAITGIPETLVAIQRILEV

2ns9A

0.19

0.18

0.97

2.10

MUSTER

LKRYEGSFEVSKTPEEVFEFLTDPKRFSRAFPGFKSVEVEDGS-----FTIELRLSLGPLDARVRASFEDLEKPSKATVKGSGRGALDFTLRFAVEPSGGGSRVSWVFEGNVGLAASMGGRVLDSLARRMINDVISGVKRELGE

2d4rA

0.14

0.13

0.97

2.61

dPPAS

-PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREG---ARTRSRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYETIPIFGGLLRKLVQKLQENVESLLKGLEERVLA

(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=0.68

Estimated TM-score = 0.80±0.09

Estimated RMSD = 3.3±2.3Å

Download Model 2

C-score=-1.43

Download Model 3

C-score=0.91

Download Model 4

C-score=-1.28

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	2m47A	0.880	1.61	0.157	0.965
2	3ie5B	0.750	3.03	0.099	0.979
3	3k3kA	0.722	3.02	0.129	0.938
4	2leqA	0.722	2.75	0.122	0.903
5	4xrtA2	0.721	3.16	0.100	0.965
6	3qtjA	0.717	3.13	0.130	0.944
7	3rd6A	0.715	2.54	0.101	0.896
8	2il5A	0.714	3.30	0.081	0.931
9	3klxA	0.713	3.28	0.129	0.944
10	3tfzA	0.712	3.25	0.116	0.938

(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	0.23	14	3nmnA	PYV	Rep, Mult	53,64,66,79,81,85,87,89,126,130,131
2	0.09	5	4n3eW	2AN	Rep, Mult	6,8,10,17,21,23,79,93,106
3	0.03	2	2e3rB	18C	Rep, Mult	21,27,31,33,52,54,55,57,60,81,87,106,110,116,122,123,126,127,130,131,134
4	0.02	1	2flhC	ZEA	Rep, Mult	21,23,53,64,66,79,93
5	0.02	1	1s5lK	CLA	Rep, Mult	11,12
6	0.02	1	2gkdA	NUC	Rep, Mult	118,121,122
7	0.02	1	3tvqA	DQH	Rep, Mult	56,62,64,81,86,118,122,123,126
8	0.02	1	2z9yA	DDR	Rep, Mult	21,27,30,54,64,80,106,110,130,134
9	0.02	1	3kv7B	ACT	Rep, Mult	29,48
10	0.02	1	2gkdA	NUC	Rep, Mult	124,125
11	0.02	1	2flhA	ZEA	Rep, Mult	22,68,72
12	0.02	1	1txcB	2AN	Rep, Mult	50,67,82,87,88

	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	0.067	2vq5A	0.651	3.90	0.081	0.938	4.2.1.78	24,48,92
2	0.060	2ihwA	0.539	4.55	0.045	0.840	2.3.1.168	NA
3	0.060	1q23B	0.507	4.95	0.045	0.854	2.3.1.28	NA
4	0.060	1kfqB	0.497	3.93	0.099	0.750	5.4.2.2	NA
5	0.060	3b9jC	0.488	4.68	0.036	0.799	1.17.3.2,1.17.1.4	NA
6	0.060	3kvnX	0.501	4.63	0.030	0.806	3.1.1.1	74
7	0.060	1sczA	0.525	4.55	0.030	0.833	2.3.1.61	NA
8	0.060	3l60A	0.552	4.41	0.060	0.847	2.3.1.12	NA
9	0.060	3igyB	0.510	4.76	0.095	0.854	5.4.2.1	NA
10	0.060	1z01A	0.614	4.36	0.079	0.958	1.14.13.61	NA
11	0.060	1wqlA	0.603	3.94	0.061	0.910	1.14.12.-	23
12	0.060	2de6B	0.600	4.39	0.057	0.951	1.14.12.-	20
13	0.060	1vlbA	0.486	4.88	0.049	0.833	1.2.99.7	NA
14	0.060	2b1xA	0.617	3.91	0.058	0.917	1.14.12.12	NA
15	0.060	2e1qA	0.516	4.95	0.049	0.875	1.17.3.2,1.17.1.4	NA
16	0.060	1yaaB	0.507	4.63	0.073	0.812	2.6.1.1	39
17	0.060	2ckjA	0.486	5.22	0.070	0.868	1.17.1.4,1.17.3.2	NA
18	0.060	1uliC	0.602	4.14	0.068	0.910	1.14.12.18	23
19	0.060	3b9jI	0.274	4.91	0.065	0.465	1.17.1.4,1.17.3.2	NA
20	0.060	1eadA	0.526	4.49	0.085	0.826	2.3.1.12	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	0.23	0.678	3.39	0.14	0.92	4n0gC	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
1	0.19	0.686	3.55	0.11	0.96	4c94A	GO:0006952 GO:0009607
2	0.17	0.695	3.39	0.11	0.96	4q0kA	GO:0006952 GO:0009607 GO:0009740
3	0.16	0.681	3.71	0.08	0.97	4c9iA	GO:0006952 GO:0009607
4	0.15	0.691	3.48	0.11	0.96	2flhB	GO:0006952 GO:0009607
5	0.12	0.722	3.02	0.13	0.94	3k3kA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042802 GO:0042803 GO:0043086 GO:0080163
6	0.12	0.725	3.32	0.11	0.98	5i8fA	GO:0006952 GO:0009607
7	0.12	0.670	3.94	0.11	0.97	4m9bA	GO:0006952 GO:0009607
8	0.11	0.708	3.19	0.15	0.94	3nefA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
9	0.11	0.671	3.80	0.11	0.96	2wqlA	GO:0006952 GO:0009607
10	0.11	0.678	3.88	0.09	0.97	1tw0A	GO:0006952 GO:0009607
11	0.11	0.679	3.76	0.11	0.94	4gy9A	GO:0006952 GO:0009607 GO:0009736 GO:0009877
12	0.11	0.702	3.50	0.12	0.96	4oicA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
13	0.10	0.683	3.70	0.10	0.97	1e09A	GO:0006952 GO:0009607
14	0.10	0.709	3.38	0.13	0.95	3kdhA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
15	0.10	0.687	3.45	0.13	0.94	3rt0C	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
16	0.10	0.671	3.81	0.09	0.96	2vneA	GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
17	0.10	0.691	3.46	0.14	0.94	3ojiB	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
18	0.10	0.668	3.69	0.09	0.96	5amwA	GO:0006952 GO:0009607

Consensus prediction of GO terms

Molecular Function	GO:0019888	GO:0060089	GO:0046983	GO:0033293	GO:0019212	GO:0042562	GO:0042802
GO-Score	0.47	0.47	0.47	0.47	0.47	0.47	0.47
Biological Processes	GO:0009607	GO:0006952	GO:0043666	GO:0071215	GO:0044092	GO:0010476
GO-Score	0.52	0.52	0.47	0.47	0.47	0.35
Cellular Component	GO:0043231	GO:0071944	GO:0016020
GO-Score	0.47	0.47	0.35

(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.