I-TASSER results

I-TASSER results for job id Rv2704

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

Input Sequence in FASTA format

>protein (142 residues)
MSASRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQA
GATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAY
VGSAVADRNSGAGPKDPSPAGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSASRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYVGSAVADRNSGAGPKDPSPAGG
Prediction	CCCCCEEHCCCCCCCCCCCCCCEEEHCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEEHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9988768758998877888774799899999967899999999999999999999999989986646899998588678999999999995999985677778877999977999999997777888888888888888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSASRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYVGSAVADRNSGAGPKDPSPAGG
Prediction	8656354143774155323202003344201000101447504400420052043005316242430010101022273054015004520773310100010251336702000200011343455556674454445768
	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

CCCCCEEHCCCCCCCCCCCCCCEEEHCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEEHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCC
MSASRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYVGSAVADRNSGAGPKDPSPAGG

3i7tA

1.00

0.83

4.28

MUSTER

---SRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

3i7tA

1.00

0.83

5.56

dPPAS

---SRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

1oniA

0.27

0.25

0.90

5.23

wdPPAS

SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPGVAEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAAL-PKGSRIEIEAVAIQGPLTTASL-------------

3i7tA

1.00

0.82

4.70

wMUSTER

----RTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

1oniA

0.27

0.25

0.90

4.29

wPPAS

SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPGVAEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAAL-PKGSRIEIEAVAIQGPLTTASL-------------

3i7tA

1.00

0.83

5.30

dPPAS2

---SRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

3i7tA

1.00

0.83

4.43

PPAS

---SRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

3i7tA

1.00

0.83

4.96

Env-PPAS

---SRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYV---------------------

1oniA

0.27

0.25

0.90

4.00

MUSTER

SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPGVAEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAALP-KGSRIEIEAVAIQGP-------LTTASL------

1oniA

0.27

0.25

0.90

5.17

dPPAS

SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPGVAEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAAL-PKGSRIEIEAVAIQGPLTTASL-------------

(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=0.67

Estimated TM-score = 0.80±0.09

Estimated RMSD = 3.3±2.3Å

Download Model 2

C-score=-1.21

Download Model 3

C-score=-2.44

Download Model 4

C-score=-2.25

Download Model 5

C-score=0.34

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	1oniA	0.829	1.44	0.268	0.894
2	2ig8B	0.782	2.20	0.250	0.887
3	3i7tA	0.779	1.32	0.992	0.831
4	1x25B	0.770	1.55	0.269	0.838
5	2b33A	0.768	1.43	0.288	0.831
6	2dyyD	0.766	1.36	0.325	0.824
7	1jd1A	0.763	1.51	0.271	0.831
8	1xrgB	0.762	1.56	0.297	0.831
9	3m1xA	0.758	1.43	0.267	0.817
10	1qd9A	0.758	1.37	0.293	0.817

(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	0.63	26	1oniC	BEZ	Rep, Mult	20,34,36,107,114
2	0.14	6	2uynA	2KT	Rep, Mult	34,36,114
3	0.12	8	3du7C	HOS	Rep, Mult	80,83,84,98,100
4	0.10	6	3i3fC	BUA	Rep, Mult	15,20,34,108
5	0.04	4	3d01H	PG5	Rep, Mult	110
6	0.01	1	3d01A	PG5	Rep, Mult	79,81
7	0.01	1	3i3fA	LEA	Rep, Mult	98,99,100
8	0.01	1	2b33B	CA	Rep, Mult	39
9	0.01	1	1oniB	BEZ	Rep, Mult	74,77,80,100
10	0.01	1	2uyjA	EDO	Rep, Mult	20,34
11	0.01	1	3vczB	MG	Rep, Mult	76,78

	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	1ufyA	0.475	3.40	0.108	0.662	5.4.99.5	NA
2	0.060	1cpyA	0.427	4.95	0.096	0.739	3.4.16.5	NA
3	0.060	3kizB	0.554	2.95	0.081	0.725	6.3.3.1	11,106
4	0.060	1w0iA	0.499	4.24	0.094	0.768	2.3.1.41	NA
5	0.060	3a31A	0.497	3.94	0.070	0.768	6.1.1.3	54
6	0.060	2pffD	0.499	4.81	0.106	0.810	2.3.1.86	53
7	0.060	1qf6A	0.497	4.64	0.050	0.817	6.1.1.3	NA
8	0.060	1ivyA	0.498	4.34	0.037	0.782	3.4.16.5	NA
9	0.060	1t3tA	0.578	3.67	0.063	0.810	6.3.5.3	NA
10	0.060	2zodB	0.567	2.74	0.075	0.718	2.7.9.3	23
11	0.060	3h8eA	0.502	3.87	0.068	0.711	3.4.11.1	NA
12	0.060	1hp4A	0.493	4.03	0.053	0.753	3.2.1.52	NA
13	0.060	1kogH	0.435	4.61	0.049	0.739	6.1.1.3	47,114
14	0.060	1yhtA	0.493	4.22	0.050	0.768	3.2.1.52	NA
15	0.060	2veoB	0.502	4.37	0.066	0.768	3.1.1.3	37,42
16	0.060	1ac5A	0.496	4.36	0.058	0.789	3.4.16.6	NA
17	0.060	1h7rA	0.497	4.37	0.064	0.789	4.2.1.24	NA
18	0.060	2vhhC	0.493	4.27	0.084	0.775	3.5.1.6	NA
19	0.060	3fd5B	0.559	3.22	0.095	0.761	2.7.9.3	NA
20	0.060	2btuA	0.501	2.84	0.058	0.648	6.3.3.1	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	0.64	0.779	1.32	0.99	0.83	3i7tA	GO:0005886
1	0.48	0.745	1.49	0.26	0.81	1qu9A	GO:0005737 GO:0005829 GO:0008652 GO:0009082 GO:0009097 GO:0009636 GO:0016020 GO:0016787 GO:0019239 GO:0042802 GO:0051082
2	0.42	0.829	1.44	0.27	0.89	1oniA	GO:0001822 GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005739 GO:0005777 GO:0005829 GO:0006449 GO:0007420 GO:0016787 GO:0016892 GO:0017148 GO:0030324 GO:0033993 GO:0036041 GO:0042803 GO:0043167 GO:0044822 GO:0046914 GO:0050680 GO:0070062 GO:0070314 GO:0090502 GO:1902074 GO:1904012 GO:1904013
3	0.42	0.802	1.35	0.28	0.86	1qahA	GO:0001822 GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005739 GO:0005777 GO:0005829 GO:0007420 GO:0016787 GO:0016892 GO:0017148 GO:0030324 GO:0033993 GO:0036041 GO:0042803 GO:0043167 GO:0044822 GO:0046914 GO:0050680 GO:0070062 GO:0070314 GO:0090305 GO:0090502 GO:1902074 GO:1904012 GO:1904013
4	0.38	0.807	1.44	0.28	0.87	1nq3A	GO:0004518 GO:0004519 GO:0009986 GO:0016787 GO:0090305
5	0.34	0.693	1.49	0.30	0.76	2cwjA	GO:0016787
6	0.34	0.758	1.37	0.29	0.82	1qd9A	GO:0005737 GO:0008652 GO:0009082 GO:0009097 GO:0009636 GO:0016787 GO:0019239 GO:0046360
7	0.34	0.763	1.51	0.27	0.83	1jd1A	GO:0005634 GO:0005737 GO:0005739 GO:0005758 GO:0005829
8	0.33	0.743	1.82	0.28	0.84	1pf5A
9	0.30	0.778	1.51	0.28	0.85	3v4dF	GO:0006212 GO:0016491 GO:0019740 GO:0055114
10	0.14	0.758	1.48	0.24	0.82	2uyjA	GO:0006566 GO:0016787 GO:0042802 GO:0070689
11	0.14	0.757	1.49	0.23	0.82	3quwA	GO:0005739 GO:0005759 GO:0009097 GO:0032543
12	0.10	0.682	1.17	0.22	0.73	3lybB
13	0.06	0.394	5.20	0.05	0.75	3ozqA	GO:0005615
14	0.06	0.408	4.71	0.04	0.66	3dwcB	GO:0004180 GO:0004181 GO:0006508 GO:0016787
15	0.06	0.276	5.49	0.05	0.53	3tswB	GO:0001825 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005921 GO:0005923 GO:0007043 GO:0007605 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0016327 GO:0019904 GO:0030054 GO:0035329 GO:0043296 GO:0045177 GO:0046581 GO:0090557 GO:0098609 GO:0098641 GO:1901350
16	0.06	0.440	5.20	0.05	0.82	1flgA	GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
17	0.06	0.288	3.92	0.04	0.42	4lowA	GO:0006729 GO:0008124
18	0.06	0.271	3.66	0.10	0.37	4q2qA	GO:0001825 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005921 GO:0005923 GO:0007043 GO:0007605 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0016327 GO:0019904 GO:0030054 GO:0035329 GO:0043296 GO:0045177 GO:0046581 GO:0090557 GO:0098609 GO:0098641 GO:1901350

Consensus prediction of GO terms

Molecular Function	GO:0044822	GO:0042803	GO:0016892	GO:1904012	GO:0036041	GO:0046914	GO:1904013	GO:0051082	GO:0019239
GO-Score	0.66	0.66	0.66	0.66	0.66	0.66	0.66	0.48	0.48
Biological Processes	GO:0050680	GO:0007420	GO:0030324	GO:0090502	GO:1902074	GO:0033993	GO:0017148	GO:0001822	GO:0070314	GO:0008652	GO:0009097	GO:0009636	GO:0006449
GO-Score	0.66	0.66	0.66	0.66	0.66	0.66	0.66	0.66	0.66	0.48	0.48	0.48	0.42
Cellular Component	GO:0005829	GO:0005777	GO:0070062	GO:0005634	GO:0005739	GO:0005886	GO:0009986
GO-Score	0.82	0.66	0.66	0.66	0.66	0.64	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.