I-TASSER results

I-TASSER results for job id Rv2898c

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

Input Sequence in FASTA format

>protein (128 residues)
MTTLKTMTRVQLGAMGEALAVDYLTSMGLRILNRNWRCRYGELDVIACDAATRTVVFVEV
KTRTGDGYGGLAHAVTERKVRRLRRLAGLWLADQEERWAAVRIDVIGVRVGPKNSGRTPE
LTHLQGIG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTLKTMTRVQLGAMGEALAVDYLTSMGLRILNRNWRCRYGELDVIACDAATRTVVFVEVKTRTGDGYGGLAHAVTERKVRRLRRLAGLWLADQEERWAAVRIDVIGVRVGPKNSGRTPELTHLQGIG
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCEEEEEEEHCCCCEEEEEEEEHCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEHCCCCCCCCEEEEEHCCCC
Conf.Score	99875567899999999999999999898899875678997578999868998999999886689998897887999999999999999999979998875899999996899988766999985899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTLKTMTRVQLGAMGEALAVDYLTSMGLRILNRNWRCRYGELDVIACDAATRTVVFVEVKTRTGDGYGGLAHAVTERKVRRLRRLAGLWLADQEERWAAVRIDVIGVRVGPKNSGRTPELTHLQGIG
Prediction	86646534345204400410141047330401023142541101000334643000002032244542330131034511410240042003537465240000000000246665441404215638
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCEEEEEEEHCCCCEEEEEEEEHCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEHCCCCCCCCEEEEEHCCCC
MTTLKTMTRVQLGAMGEALAVDYLTSMGLRILNRNWRCRYGELDVIACDAATRTVVFVEVKTRTGDGYGGLAHAVTERKVRRLRRLAGLWLADQEERWAAVRIDVIGVRVGPKNSGRTPELTHLQGIG

3fovA

0.40

0.30

0.76

2.98

MUSTER

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRDA--LVAFVEVKARA--------YAVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPGAA

3fovA

0.37

0.27

0.73

4.75

dPPAS

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRD--ALVAFVEVKARAY--------AVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTAPDATP----------

3fovA

0.41

0.30

0.75

4.87

wdPPAS

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRDA--LVAFVEVKARAY--------AVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPG-A

3fovA

0.41

0.30

0.75

3.77

wMUSTER

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRDA--LVAFVEVKARA--------YAVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPG-A

3fovA

0.39

0.30

0.76

4.43

wPPAS

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRD--ALVAFVEVKARA--------YAVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPGAA

3fovA

0.37

0.27

0.73

15.05

dPPAS2

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRD--ALVAFVEVKARAY--------AVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTAPDATP----------

3fovA

0.39

0.30

0.76

3.99

PPAS

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRD--ALVAFVEVKARA--------YAVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPGAA

3fovA

0.39

0.30

0.76

4.30

Env-PPAS

--------------SAEASAADYLERQGYRILARRFKTRCGEIDLVAQRD--ALVAFVEVKARA--------YAVTPRQQSRIVAAAEAWLSRHPEHASELRFDAILIAPNTA-------PRHLPGAA

1ob8B

0.18

0.14

0.77

0.98

MUSTER

----------DIGKNAERELVSILRGEGFNAVR----PTNPLPDIFATKGN--TLLSIECKSTWENKV-----KVKEHQVRKLLDFLSM--------FTMKGVPLIAIKFKQVHEWRVLVPEKAEDII

4i8oA1

0.11

0.08

0.69

1.18

dPPAS

---RSYKNLNLVRANIETESRQFIENKNYSIQSIGPPGSRAGLRVVFTRPGVN-LATVDIFYNGD---GSTTIQYLTGANRSLGQELADHLFETI---------------------------------

(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=0.34

Estimated TM-score = 0.76±0.10

Estimated RMSD = 3.8±2.6Å

Download Model 2

C-score=-0.29

Download Model 3

C-score=-0.41

Download Model 4

C-score=-2.37

Download Model 5

C-score=-2.85

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	3fovA	0.695	1.38	0.402	0.758
2	2w4bA	0.669	3.54	0.087	0.969
3	3fhdA	0.635	3.72	0.098	0.906
4	1avqA	0.633	3.07	0.099	0.867
5	3k93A	0.630	3.53	0.104	0.898
6	1w36E2	0.630	3.57	0.074	0.906
7	2gw6A	0.624	2.88	0.066	0.781
8	3syyA	0.620	3.19	0.081	0.852
9	3u44B	0.618	3.73	0.058	0.914
10	1ob8B	0.599	2.49	0.189	0.742

(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	0.37	20	5d8uA	MN	Rep, Mult	13,44,59,60,79
2	0.05	3	2fkcA	CA	Rep, Mult	17,44
3	0.04	2	3slpB	QNA	Rep, Mult	8,10,13,62,64,76
4	0.02	1	1gef0	III	Rep, Mult	28,29,30,32,34,35,36,46,47,48,49,50,55,86
5	0.02	1	3a4kD	QNA	Rep, Mult	41,79,86
6	0.02	1	2wj0A	QNA	Rep, Mult	14,15,18,34

	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	2hb6B	0.520	4.45	0.107	0.867	3.4.11.1	NA
2	0.060	1l1lA	0.525	4.48	0.056	0.844	1.17.4.2	NA
3	0.060	2e52A	0.558	3.56	0.116	0.766	3.1.21.4	79
4	0.060	2gjwA	0.506	2.78	0.098	0.648	3.1.27.9	NA
5	0.060	1lbqA	0.519	4.33	0.061	0.859	4.99.1.1	NA
6	0.060	2oheA	0.496	3.09	0.093	0.656	3.1.27.9	NA
7	0.060	1tw8A	0.525	4.13	0.121	0.812	3.1.21.4	NA
8	0.060	2cvtA	0.502	4.62	0.048	0.797	1.17.4.1	NA
9	0.060	3kl9A	0.494	4.75	0.137	0.883	3.4.11.7	18,43
10	0.060	1az3B	0.542	4.02	0.062	0.836	3.1.21.4	62
11	0.060	1cw0A	0.497	4.26	0.143	0.789	3.1.-.-	NA
12	0.060	1dmuA	0.533	4.01	0.051	0.867	3.1.21.4	61
13	0.060	2cv8A	0.524	3.06	0.063	0.680	3.1.27.9	NA
14	0.060	2wghB	0.495	4.75	0.073	0.844	1.17.4.1	35,42
15	0.060	1avqA	0.633	3.07	0.099	0.867	3.1.11.3	61
16	0.060	1gytA	0.548	4.17	0.075	0.867	3.4.11.1	22
17	0.060	3ixzA	0.496	4.68	0.035	0.867	3.6.3.10	NA
18	0.060	2df5A	0.494	4.65	0.050	0.828	3.4.19.3	NA
19	0.060	2cv8B	0.543	2.93	0.061	0.695	3.1.27.9	124

(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	0.47	0.695	1.38	0.40	0.76	3fovA	GO:0003676 GO:0004518 GO:0090305
1	0.39	0.635	3.72	0.10	0.91	3fhdA	GO:0003677 GO:0004518 GO:0004527 GO:0046872 GO:0090305
2	0.14	0.644	3.50	0.10	0.91	3k93A	GO:0003677 GO:0004518 GO:0090305
3	0.13	0.624	2.88	0.07	0.78	2gw6A	GO:0000213 GO:0005634 GO:0005654 GO:0005730 GO:0006388 GO:0006397 GO:0008033 GO:0090501 GO:0090502
4	0.12	0.513	2.48	0.14	0.65	2zyzC	GO:0000213 GO:0003676 GO:0004518 GO:0006388 GO:0090305 GO:0090501 GO:0090502
5	0.10	0.669	3.54	0.09	0.97	2w4bA	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004527 GO:0016032 GO:0016787 GO:0030430 GO:0039595 GO:0039657 GO:0042025 GO:0090305
6	0.08	0.633	3.13	0.08	0.86	3sz4A	GO:0003677 GO:0004518 GO:0004527 GO:0046872 GO:0090305
7	0.07	0.630	3.57	0.07	0.91	1w36B	GO:0000166 GO:0000287 GO:0000724 GO:0003677 GO:0004003 GO:0004386 GO:0004518 GO:0004519 GO:0004527 GO:0005524 GO:0006281 GO:0006302 GO:0006310 GO:0006974 GO:0008854 GO:0009338 GO:0016787 GO:0032508 GO:0044355 GO:0046872 GO:0090305
8	0.07	0.618	3.16	0.10	0.87	3sm4C	GO:0003677 GO:0004518 GO:0004527 GO:0016787 GO:0046872 GO:0090305
9	0.06	0.564	3.77	0.08	0.86	3u44A	GO:0000166 GO:0000724 GO:0003677 GO:0003690 GO:0004003 GO:0004386 GO:0004518 GO:0004527 GO:0005524 GO:0006281 GO:0006302 GO:0006974 GO:0008408 GO:0016787 GO:0032508 GO:0090305
10	0.06	0.563	3.67	0.08	0.84	4cejA	GO:0000166 GO:0000724 GO:0003677 GO:0003690 GO:0004003 GO:0004386 GO:0004518 GO:0004527 GO:0005524 GO:0006281 GO:0006302 GO:0006974 GO:0008408 GO:0016787 GO:0032508 GO:0090305
11	0.06	0.400	4.59	0.07	0.72	1dhrA	GO:0001889 GO:0004155 GO:0005737 GO:0005739 GO:0005829 GO:0006559 GO:0006729 GO:0010044 GO:0010288 GO:0016491 GO:0033762 GO:0035690 GO:0042803 GO:0043005 GO:0055114 GO:0070062 GO:0070402 GO:0070404
12	0.06	0.325	5.51	0.07	0.66	4zw9A	GO:0005215 GO:0005355 GO:0005536 GO:0005886 GO:0005887 GO:0005975 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0019852 GO:0022857 GO:0022891 GO:0033300 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:1904659
13	0.06	0.321	4.63	0.04	0.54	1s5pA	GO:0005737 GO:0006476 GO:0006935 GO:0008270 GO:0016787 GO:0034979 GO:0034983 GO:0036047 GO:0036048 GO:0036049 GO:0036054 GO:0036055 GO:0046872 GO:0070403
14	0.06	0.365	4.61	0.13	0.64	4i1vA	GO:0000166 GO:0004140 GO:0005524 GO:0005737 GO:0015937 GO:0016301 GO:0016310 GO:0016740
15	0.06	0.367	5.25	0.09	0.72	4upkA	GO:0003824 GO:0006793 GO:0008152 GO:0008484 GO:0016787 GO:0042578
16	0.06	0.409	4.61	0.07	0.70	2b20A	GO:0005506 GO:0005737 GO:0006826 GO:0008849 GO:0016787
17	0.06	0.344	5.25	0.07	0.70	3n2oA	GO:0003824 GO:0006527 GO:0006596 GO:0008295 GO:0008792 GO:0016829 GO:0016831 GO:0046872
18	0.06	0.389	4.94	0.06	0.69	5c1sA	GO:0005525 GO:0005622 GO:0007264
19	0.06	0.348	4.93	0.03	0.63	4axnA	GO:0004553 GO:0004568 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0016892	GO:0004549	GO:0004527	GO:0046872
GO-Score	0.47	0.47	0.47	0.39	0.39
Biological Processes	GO:0090305	GO:0000394	GO:0008033
GO-Score	0.76	0.47	0.47
Cellular Component	GO:0005730	GO:0005654
GO-Score	0.13	0.13

(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.