I-TASSER results

I-TASSER results for job id Rv0961

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

Input Sequence in FASTA format

>protein (115 residues)
MRVPSQWMISSRVTVAWNIVGYLVYAALAFVGGFAVWFSLFFAMATDGCHDSACDASYHV
FPAMVTMWIGVGAVLLLTLVVMVRNSSRGNVVIGWPFVGLLALGLVYVAADAVLH

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MRVPSQWMISSRVTVAWNIVGYLVYAALAFVGGFAVWFSLFFAMATDGCHDSACDASYHVFPAMVTMWIGVGAVLLLTLVVMVRNSSRGNVVIGWPFVGLLALGLVYVAADAVLH
Prediction	CCCCCCEEEHCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHCCCC
Conf.Score	9987644554455544568999999999988657999999998754776555677654454577788888899999999998745788748885688999999999886644459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MRVPSQWMISSRVTVAWNIVGYLVYAALAFVGGFAVWFSLFFAMATDGCHDSACDASYHVFPAMVTMWIGVGAVLLLTLVVMVRNSSRGNVVIGWPFVGLLALGLVYVAADAVLH
Prediction	7634542314441311032212211232233223312321121103421454314342311113123323332333110000023464230001123322333111201241338
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEHCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHCCCC
MRVPSQWMISSRVTVAWNIVGYLVYAALAFVGGFAVWFSLFFAMATDGCHDSACDASYHVFPAMVTMWIGVGAVLLLTLVVMVRNSSRGNVVIGWPFVGLLALGLVYVAADAVLH

5ezmA3

0.25

0.19

0.77

0.93

MUSTER

--SPRSW--------GKQLIGMAIVAACGLLASPVVATL----------NANHIPNS---FYRAYAVWVAVAFVVMLLGIAVARLLLRRGV---LPSVAVYAMGMYLGFTVALLH

5ezmA3

0.14

0.11

0.83

0.80

dPPAS

----------SPRSWGKQLIGMAIVAACGLLASPVVATL---------NANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAMGMYLGFTVALLGHETVGRPAS-

5ezmA3

0.21

0.16

0.76

0.78

wdPPAS

----------SPRSWGKQLIGMAIVAACGLLASPVVAT-----------ANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLR---RG----VLPSVAVYAMGMYLGFTVALLH

5ezmA3

0.26

0.19

0.75

1.00

wMUSTER

---------SPR-SWGKQLIGMAIVAACGLLASPVVAT-----------NANHIPNS---FYRAYAVWVAVAFVVMLLGIAVAR-LRRG----VLPSVAVYAMGMYLGFTVALLH

5ezmA3

0.24

0.18

0.75

0.67

wPPAS

--SPRSW--------GKQLIGMAIVAACGLLASPVVAT---------N-ANHIPNS----FYRAYAVWVAVAFVVMLLGIAVAR-LRRG----VLPSVAVYAMGMYLGFTVALLH

5ezmA3

0.20

0.16

0.77

0.96

dPPAS2

----------SPRSWGKQLIGMAIVAACGLLASPVVATL---------NANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLR---RG----VLPSVAVYAMGMYLGFTVALLH

5ezmA3

0.22

0.17

0.77

0.90

PPAS

--SPRSW--------GKQLIGMAIVAACGLLASPVVAT---------N-ANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLR---RG----VLPSVAVYAMGMYLGFTVALLH

3k13C1

0.16

0.14

0.84

0.74

Env-PPAS

--EINFVNIGERC----NVAGSRKFLRLVNEKKYDEALSIARQQVEDGALD-VNDDGLLDARTETTFLNLIS-EPEIARVPVI-DSSK---------WEVIEAGLKCLQGKSIVN

3jbrE

0.16

0.98

0.88

MUSTER

MS-PTEFCILVGIVLMTAVVEFTTQKEYSISAAAISVFSLGFLIMGTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKR-YYYSWSFACACAAFVLLFLGGISLR

4o6yA1

0.16

0.13

0.79

0.70

dPPAS

----------------------PIFMVVRVLGFIIAALVLTWTVHYRGGLALSSDNKDHIFVMMVIGLILFNGEAMLAYKSV--QGTKNLKKLVHLTLQLTAFILSLIGVWAALK

(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=-2.16

Estimated TM-score = 0.46±0.15

Estimated RMSD = 8.9±4.6Å

Download Model 2

C-score=-4.14

Download Model 3

C-score=-3.18

Download Model 4

C-score=-3.84

Download Model 5

C-score=-4.13

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	2p7vA	0.648	3.10	0.029	0.870
2	4e40A1	0.645	2.71	0.061	0.817
3	2y44A	0.642	2.72	0.026	0.817
4	3o6xA	0.637	3.17	0.071	0.861
5	2nyfA	0.633	3.37	0.103	0.887
6	1j3uA	0.632	3.14	0.046	0.852
7	4nleA3	0.631	3.55	0.096	0.878
8	5ezmA	0.628	2.92	0.139	0.878
9	1w27A3	0.627	3.50	0.074	0.896
10	4uosA	0.627	3.79	0.035	0.913

(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	0.09	10	3abwB	22B	Rep, Mult	73,76,80,83,98,101,108
2	0.07	7	4xe5B	CLR	Rep, Mult	78,81,82,85
3	0.06	7	5dwkA	78N	Rep, Mult	37,63,66,67,70,75
4	0.05	6	2y02A	2CV	Rep, Mult	26,29,69,73,76
5	0.03	3	4brbD	78N	Rep, Mult	68,71,75,76,79,80
6	0.03	4	4i7zC	1E2	Rep, Mult	79,83
7	0.03	3	5d5aA	CLR	Rep, Mult	30,77,81
8	0.02	3	1ow7B	III	Rep, Mult	24,27,28,31,34,70,73,77,80,81
9	0.02	3	3zciA	BU9	Rep, Mult	57,60
10	0.02	2	3b71B	III	Rep, Mult	27,31,34,66,69,70,73,74,76
11	0.02	3	1ow6A	III	Rep, Mult	67,70,71,74,77
12	0.02	2	1j95A	TBA	Rep, Mult	66,100
13	0.02	2	3rrpA	LMR	Rep, Mult	7,8,9,14,18
14	0.01	1	2zs1B	MG	Rep, Mult	51,52
15	0.01	1	3erzD	HG	Rep, Mult	46,51,54
16	0.01	1	3f0fB	C5P	Rep, Mult	47,48
17	0.01	1	2jbsC	FMN	Rep, Mult	27,104,105,106
18	0.01	1	3dmrA	O	Rep, Mult	7,52
19	0.01	1	3b71A	III	Rep, Mult	21,24,77,80,84
20	0.01	1	1ow6A	III	Rep, Mult	99,102,103,106,109

	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	0.066	2h8aA	0.556	2.77	0.074	0.756	2.5.1.18	35,65
2	0.060	1k04A	0.565	3.33	0.119	0.800	2.7.10.2	75
3	0.060	1jswB	0.607	3.18	0.054	0.844	4.3.1.1	NA
4	0.060	3gzhA	0.590	3.90	0.097	0.896	4.3.2.2	5
5	0.060	1qleA	0.545	3.51	0.051	0.809	1.9.3.1	NA
6	0.060	1w27A	0.627	3.50	0.074	0.896	4.3.1.24	NA
7	0.060	2pg0A	0.577	3.58	0.087	0.861	1.3.99.3	NA
8	0.060	1c3cA	0.606	3.94	0.093	0.922	4.3.2.2	NA
9	0.060	2e9fB	0.610	4.15	0.066	0.913	4.3.2.1	NA
10	0.060	1k7wD	0.619	3.75	0.082	0.887	4.3.2.1	NA
11	0.060	3czoB	0.581	3.23	0.037	0.817	4.3.1.3	97
12	0.060	3gm1B	0.581	3.44	0.081	0.835	2.7.10.2	75,102,111
13	0.060	1dcnB	0.603	2.89	0.047	0.809	4.3.2.1	NA
14	0.060	1tj7A	0.623	3.64	0.047	0.896	4.3.2.1	NA
15	0.060	2ix6A	0.581	3.16	0.048	0.835	1.3.3.6	NA
16	0.060	1f1oA	0.606	3.41	0.056	0.878	4.3.2.2	NA
17	0.060	1jtnA	0.354	4.24	0.045	0.600	3.2.1.17	NA
18	0.060	1xmeA	0.584	3.54	0.097	0.852	1.9.3.1	NA
19	0.060	1yfmA	0.602	2.96	0.055	0.835	4.2.1.2	NA
20	0.060	2nyfA	0.633	3.37	0.103	0.887	4.3.1.5	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	0.13	0.592	3.06	0.07	0.81	5jdoA	GO:0016020 GO:0016021
1	0.09	0.584	3.17	0.04	0.82	3gtdA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0008152 GO:0016829 GO:0045239
2	0.09	0.620	3.73	0.11	0.91	1re5D	GO:0003824 GO:0016853 GO:0019619 GO:0047472
3	0.08	0.649	2.95	0.04	0.86	4xwjA	GO:0005737 GO:0006351 GO:0006355 GO:0010468 GO:0016989
4	0.08	0.636	3.41	0.11	0.89	1y2mB	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0052883
5	0.08	0.613	3.52	0.07	0.89	4c6gB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
6	0.07	0.622	3.12	0.06	0.86	4hgvA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
7	0.07	0.619	3.17	0.07	0.86	3tv2A	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
8	0.07	0.616	3.33	0.07	0.87	3nz4B	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
9	0.07	0.583	3.69	0.07	0.88	2x75A	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
10	0.07	0.607	3.18	0.05	0.84	1jswB	GO:0003824 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006531 GO:0008652 GO:0008797 GO:0016020 GO:0016829 GO:0051262
11	0.07	0.637	3.17	0.07	0.86	3o6xA	GO:0000166 GO:0003824 GO:0004356 GO:0006807 GO:0046872
12	0.07	0.584	3.68	0.10	0.87	4apbD	GO:0003824 GO:0004333 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0040007 GO:0045239 GO:0051262
13	0.07	0.623	3.64	0.05	0.90	1tj7A	GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262
14	0.07	0.532	3.46	0.06	0.80	1vdkA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
15	0.07	0.623	3.09	0.08	0.86	3e04D	GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0048873 GO:0051262 GO:0070062
16	0.07	0.606	3.94	0.09	0.92	1c3cA	GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626
17	0.07	0.627	3.50	0.07	0.90	1w27A	GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548
18	0.07	0.619	3.75	0.08	0.89	1k7wD	GO:0003824 GO:0004056 GO:0005212 GO:0006526 GO:0008652 GO:0016829 GO:0042450

Consensus prediction of GO terms

Molecular Function	GO:0004333	GO:0047472	GO:0016989	GO:0045548	GO:0052883
GO-Score	0.09	0.09	0.08	0.08	0.08
Biological Processes	GO:0006106	GO:0006099	GO:0019619	GO:0006355	GO:0006559	GO:0009800
GO-Score	0.09	0.09	0.09	0.08	0.08	0.08
Cellular Component	GO:0044424
GO-Score	0.46

(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.