I-TASSER results

I-TASSER results for job id Rv2307B

[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)
MEEVPTGPPAMGHRACGGQKAAFPTRMNSGVEKMYKNSIAIAIGTLTMAVEFSMVSANAE
PAPPPGQDPHMPNSAMGYCPGGGFGGITGWGYCDGIRYPDGSYWHQVRVPAPFVGTTLTL
SCVIDDGSPVPPLAAPGSCGGGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MEEVPTGPPAMGHRACGGQKAAFPTRMNSGVEKMYKNSIAIAIGTLTMAVEFSMVSANAEPAPPPGQDPHMPNSAMGYCPGGGFGGITGWGYCDGIRYPDGSYWHQVRVPAPFVGTTLTLSCVIDDGSPVPPLAAPGSCGGGA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHCCCCCCCEEEEEHCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCCCCC
Conf.Score	98889999887778887765554444554678888899999999999998745565668999999999999999877899999986456799788568998756777765665566589999868999999999999998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MEEVPTGPPAMGHRACGGQKAAFPTRMNSGVEKMYKNSIAIAIGTLTMAVEFSMVSANAEPAPPPGQDPHMPNSAMGYCPGGGFGGITGWGYCDGIRYPDGSYWHQVRVPAPFVGTTLTLSCVIDDGSPVPPLAAPGSCGGGA
Prediction	86634744443354313445442334135224413424012101101111223333353534555564343342333203434323122212044461351331242313232334413030114644463434445434658
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHCCCCCCCEEEEEHCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCCCCC
MEEVPTGPPAMGHRACGGQKAAFPTRMNSGVEKMYKNSIAIAIGTLTMAVEFSMVSANAEPAPPPGQDPHMPNSAMGYCPGGGFGGITGWGYCDGIRYPDGSYWHQVRVPAPFVGTTLTLSCVIDDGSPVPPLAAPGSCGGGA

4n0nA3

0.17

0.15

0.89

0.78

MUSTER

ASEYVEGPPGSG-------KTFH---LVKDVLAVVGSALVVPTHASMLDCINKLKQAGADPYVVPKYTVLFPRPGSG----NITVRLPQVGTSEGETFVDVAYFSPVDLARILT--QGRVKGYGDLNGCVGPASVPRNLLEPL

3zifR

0.19

0.13

0.69

0.70

dPPAS

--EIPTPQPQMGAAAGASQDYSTRMNWFSAGPDMIHDVNNIRDAQNRILMTQSAIGGIGSRQFVEEFVPAVYLNPYSGPPD---------------SYPDQFIRHYNVYSNSVSG----------------------------

3zifR

0.24

0.15

0.64

0.82

wdPPAS

--EIPT-PPQMGA--AAGASQDYSTRMNDMIHDVNNIRDAQNRILMTQSAIGGIGSRQFVEEFVPAVYLNPYSGP----PD---------------SYPDQFIRHYNVYSNSVSG----------------------------

1w2rA

0.15

0.13

0.84

0.82

wMUSTER

AEAISCGSPPPGRISYYSTPIAVGTVISGT--RLIEKSL--------LCITKDKVDGTWDKPA-----PKQYFNKYSSCPIVPGGYKIR----GSTPYRHGDS--TFACKTNFSGNKS-VWC-QANNMWGPTRLPSVFPLEQK

3zifR

0.25

0.15

0.62

0.79

wPPAS

--EIPT-PPQMGA--AAGASQDYSTRMNDMIHDVNNIRDAQNRILMTQSAIGGIGSRQFVEEFVPAVYLNPYSGP----PD---------------SYPD------------FI-RHY--NVYSNSG----------------

3zifR

0.24

0.15

0.64

0.90

dPPAS2

--EIPT-PPQMGA--AAGASQDYSTRMNDMIHDVNNIRDAQNRILMTQSAIGGIGSRQFVEEFVPAVYLNPYSGP----PD---------------SYPDQFIRHYNVYSNSVSG----------------------------

3zifR

0.24

0.15

0.64

0.81

PPAS

--EIPT-PPQMGA--AAGASQDYSTRMNDMIHDVNNIRDAQNRILMTQSAIGGIGSRQFVEEFVPAVYLNPYSGP----PD---------------SYPDQFIRHYNVYSNSVSG----------------------------

3sojA

0.14

0.10

0.76

0.68

Env-PPAS

----------------------------SHMKERAAIIESMNIIGNVKASIQNDINNNLDISQQTYDTP------TGTVTGSTSGATIDINLSQTSPFTNDNDIIRLSGVV-VSGSTFQWTCSHNNASTLTASNVPHTCSSSA

4h04A3

0.09

0.08

0.89

0.72

MUSTER

-TPVDAGIYDIPQLKSISKGPWELITTPDGYYQMK----DTVSGKCLA--LFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANEKWQIRAD---KDGK----YTISPALTQ--QRLAIATGNEQNIDLETHRPAAGTVA

4n0nA3

0.12

0.11

0.91

0.65

dPPAS

ASEYVEGPPGSGHLVKDVLAVVGSATLVVPTHASMLDCINKLKQAGADPYFVVPKYTVLDFPRPGSGNITVRLPQVGTSEG--------ETFVD-----EVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVPRNLWLRH

(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=-3.96

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.0±3.9Å

Download Model 2

C-score=-4.26

Download Model 3

C-score=-4.44

Download Model 4

C-score=-5.00

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	1tf1A	0.469	4.87	0.054	0.797
2	1ko3A	0.458	5.08	0.056	0.825
3	2y8nA	0.457	4.48	0.054	0.776
4	1vi9A	0.455	4.69	0.058	0.755
5	1yleA	0.454	4.13	0.061	0.706
6	1hmwA	0.452	4.57	0.015	0.748
7	1bxrA	0.452	4.33	0.038	0.727
8	5b6aA	0.451	4.89	0.041	0.783
9	2g7uA2	0.450	5.05	0.054	0.790
10	3ixzA1	0.449	4.32	0.083	0.720

(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	0.08	4	1jdbE	GLN	Rep, Mult	20,21,24,39,40,43
2	0.08	4	1jdbH	GLN	Rep, Mult	43,89,90,91,101,102
3	0.08	4	5ezmA	MPG	Rep, Mult	41,44
4	0.06	3	4hytD	CLR	Rep, Mult	43,47,50
5	0.04	2	3s5yB	NAG	Rep, Mult	73,84,98,100
6	0.04	2	1sqpE	PLX	Rep, Mult	35,38
7	0.04	2	3efoB	ZN	Rep, Mult	79,93,111,122
8	0.02	1	3lunB	CA	Rep, Mult	80,81,82
9	0.02	1	1f5fA	ZN	Rep, Mult	105,126
10	0.02	1	1eakA	CA	Rep, Mult	57,58,81,83,85
11	0.02	1	1sumB	FE	Rep, Mult	32,36

	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	1xrtA	0.336	5.16	0.064	0.615	3.5.2.3	NA
2	0.060	1ac5A	0.442	4.75	0.061	0.790	3.4.16.6	NA
3	0.060	1hn0A	0.442	4.68	0.080	0.734	4.2.2.20	13
4	0.060	2zo4A	0.438	5.45	0.117	0.839	3.-.-.-	NA
5	0.060	2b0tA	0.433	4.98	0.064	0.748	1.1.1.42	21
6	0.060	3fwnA	0.437	5.11	0.071	0.790	1.1.1.44	NA
7	0.060	2f89F	0.419	4.90	0.031	0.699	2.5.1.1,2.5.1.10	NA
8	0.060	1yleA	0.454	4.13	0.061	0.706	2.3.1.109	NA
9	0.060	1bxrA	0.452	4.33	0.038	0.727	6.3.5.5	23
10	0.060	2zj7A	0.383	5.46	0.046	0.734	3.1.1.3	26
11	0.060	2yyyA	0.435	5.20	0.050	0.790	1.2.1.59	NA
12	0.060	3fmrB	0.438	4.67	0.031	0.748	3.4.11.18	15
13	0.060	1xdpA	0.436	4.98	0.042	0.762	2.7.4.1	28,35
14	0.060	3d6nA	0.439	5.40	0.038	0.860	3.5.2.3	NA
15	0.060	2f8zF	0.436	5.01	0.022	0.741	2.5.1.10,2.5.1.1	125
16	0.060	1cb8A	0.450	4.56	0.015	0.748	4.2.2.5	NA
17	0.060	1ko2A	0.457	5.10	0.064	0.825	3.5.2.6	NA
18	0.060	3h8iA	0.432	4.82	0.067	0.741	1.6.99.3	63
19	0.060	1vi9A	0.455	4.69	0.058	0.755	2.7.1.35	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	0.12	0.420	5.38	0.07	0.81	1m2xA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
1	0.07	0.469	4.87	0.05	0.80	1tf1A	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0006974 GO:0042802 GO:0045892
2	0.07	0.435	5.24	0.04	0.78	3mq0B	GO:0003677 GO:0006351 GO:0006355
3	0.07	0.445	5.06	0.07	0.82	1a8tA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
4	0.07	0.445	5.18	0.04	0.80	2o99C	GO:0003677 GO:0003700 GO:0005829 GO:0006097 GO:0006351 GO:0006355 GO:0045892
5	0.07	0.441	4.94	0.08	0.80	4bp0A	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046872
6	0.07	0.439	5.09	0.07	0.77	3obfA	GO:0003677 GO:0006351 GO:0006355
7	0.07	0.451	4.81	0.06	0.77	2g7uA	GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
8	0.07	0.439	5.25	0.08	0.83	3faiA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
9	0.07	0.442	5.18	0.06	0.82	2yntA	GO:0046872
10	0.07	0.439	5.08	0.07	0.80	3sd9A	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046677 GO:0046872
11	0.07	0.441	5.15	0.06	0.80	4wd6A	GO:0046872
12	0.07	0.403	5.30	0.02	0.80	4ad9A	GO:0004521 GO:0005739 GO:0005759 GO:0008270 GO:0016787 GO:0046872 GO:0090502
13	0.07	0.420	5.17	0.09	0.78	2o0yC	GO:0003677 GO:0006351 GO:0006355
14	0.06	0.436	5.11	0.03	0.77	1ysqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
15	0.06	0.438	4.82	0.05	0.75	1yspA	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
16	0.06	0.444	5.04	0.06	0.80	2m5cA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
17	0.06	0.412	4.78	0.04	0.73	4chlB	GO:0005506 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0006749 GO:0016491 GO:0046872 GO:0050313 GO:0051213 GO:0055114 GO:0070221 GO:0070813
18	0.06	0.445	5.13	0.04	0.80	1mkmB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892

Consensus prediction of GO terms

Molecular Function	GO:0003676	GO:0016812	GO:0046914
GO-Score	0.37	0.36	0.36
Biological Processes	GO:0010468	GO:2000112	GO:0006351	GO:1903506	GO:0044248	GO:0042221	GO:0016999
GO-Score	0.37	0.37	0.37	0.37	0.36	0.36	0.36
Cellular Component	GO:0044464
GO-Score	0.30

(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.