I-TASSER results

I-TASSER results for job id Rv2548A

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

Input Sequence in FASTA format

>protein (124 residues)
MLPENLEQRVTALESQVRELADRVRASEQDAAAARVLAGAADRDVTEFVGEFRDFRRATI
GSFNALREDFTALREEMTERFSHVEERFSRVDDGFTEMRGKLDGAAAGQQRIVELIEQLI
ADQG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLPENLEQRVTALESQVRELADRVRASEQDAAAARVLAGAADRDVTEFVGEFRDFRRATIGSFNALREDFTALREEMTERFSHVEERFSRVDDGFTEMRGKLDGAAAGQQRIVELIEQLIADQG
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	9865579999999999999999999999999999998764556657899999999999999999999999999999997799999999876666787777644566778999999999997589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLPENLEQRVTALESQVRELADRVRASEQDAAAARVLAGAADRDVTEFVGEFRDFRRATIGSFNALREDFTALREEMTERFSHVEERFSRVDDGFTEMRGKLDGAAAGQQRIVELIEQLIADQG
Prediction	8557716531541463056155414446653322331322355415514541451353444424313541441355146425514543541551145134415334334530151045026588
	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

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
MLPENLEQRVTALESQVRELADRVRASEQDAAAARVLAGAADRDVTEFVGEFRDFRRATIGSFNALREDFTALREEMTERFSHVEERFSRVDDGFTEMRGKLDGAAAGQQRIVELIEQLIADQG

5cwmA1

0.15

0.14

0.92

0.95

MUSTER

----DPEDELKRVEKLVKEAEELLRQAKEKGS--EEDLEKALRTAEEAAREAKKVLEQAEKEGD--PEVALRAVELVVRVAELLLRIAKESGS--EEALERALRVAEEAARLAKRVLELAEKQG

5cwmA1

0.12

0.11

0.92

0.63

dPPAS

----DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTA-EEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGS-EEALERALRVAEEAARLAKRVLELAEKQG----

4z34A2

0.18

0.14

0.77

0.62

wdPPAS

-----IFGYVADLEDNWETLNDNLKVIEK-----------AD-NAAQVKDALTKMRAAALDAQKA----MKDFRHGFDILVGQIDDALKLANEG------KVKEAQAAAEQLKTTRNAYIQK--

4tkoB3

0.13

0.11

0.85

0.87

wMUSTER

-----LHISLSAKKLKVESLKKKREALREKLLQVEEKIKLVKLDWERYKSLFQK----LIP--RRKFEEVDTNLKVLLHEREYLEKSIQEINTEIKRAKKGIENARNEFKTIEELKK-------

4z34A2

0.18

0.14

0.77

0.73

wPPAS

-----IFGYVADLEDNWETLNDNLKVIEK-----------AD-NAAQVKDALTKMRAAALDAQKA----MKDFRHGFDILVGQIDDALKLANEG------KVKEAQAAAEQLKTTRNAYIQK--

5cwmA1

0.12

0.11

0.92

0.70

dPPAS2

----DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTA-EEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGS-EEALERALRVAEEAARLAKRVLELAEKQG----

5cwmA1

0.17

0.15

0.91

0.80

PPAS

----DPEDELKRVEKLVKEAEELLRQAKEKGS--EEDLEKALRTAEEAAREAKKVLEQAEKE-----DPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQG

1t6sA2

0.24

0.17

0.71

0.86

Env-PPAS

--------E-PEFADLVRQLLAPVIQRRLSRSMLEVLAVVAHQPVT--KGEIQQIRGASPD-----------------------YSIDRLLARGLIEVRGRAD--SPGRPLQYGTTEVFLDLFH

4tkoB3

0.12

0.10

0.85

0.88

MUSTER

-----LHISLSAKKLKVESLKKKREALREKLLQVEEKIKLVKLDWERYKSLFQKIPRRKFEEVDTNLKVLLHEREYLEKSIQEINTEIKRAKKGIENARNEFKTIEELKK--------------

5appA

0.07

0.06

0.98

0.61

dPPAS

QIEDKIEEILSKIYHIENEIARIKKLIQNVDVRSTENAARSRANEQKIAENKKAIEKADVEKNRADIAANSRAIATFRSSSQNIAALTTKMKQIEDKIEEILSKIYHIENEIARIKKLIKLH--

(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=-2.02

Estimated TM-score = 0.47±0.15

Estimated RMSD = 8.7±4.6Å

Download Model 2

C-score=-2.76

Download Model 3

C-score=-1.90

Download Model 4

C-score=-3.95

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	2j0oA	0.780	1.94	0.078	0.935
2	1xzpA	0.765	2.44	0.104	0.927
3	3gehA	0.763	2.50	0.068	0.944
4	3geiA2	0.759	2.57	0.068	0.944
5	5doqA	0.759	2.59	0.065	1.000
6	2ga0A	0.757	2.62	0.083	0.976
7	2yevA2	0.757	2.37	0.068	0.944
8	3caxA	0.754	2.32	0.066	0.960
9	1sj8A	0.753	2.22	0.086	0.935
10	1qleC	0.751	2.37	0.066	0.935

(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	8	5da5E	GOA	Rep, Mult	51,55,84
2	0.09	8	3u3cA	III	Rep, Mult	18,21,22,25,116
3	0.05	4	1fapB	RAP	Rep, Mult	24,28,32,103,106,107,110,113
4	0.05	4	2avkA	FEA	Rep, Mult	21,24,58,59,62,76,80,111,112,115,116,119
5	0.05	4	5dirD	MLE	Rep, Mult	48,52,55,84,87,91,112
6	0.05	4	4xefA	III	Rep, Mult	18,22,26,29,32,106,109,113,116
7	0.03	3	1qhjA	PH1	Rep, Mult	16,17,20,21,24,25,59
8	0.03	3	5doqA	HEB	Rep, Mult	52,55,56,59,60,62,63,77,80,81,84,113,116
9	0.03	3	2eikC	CD	Rep, Mult	32,35,99,103
10	0.02	2	3qbgA	22B	Rep, Mult	56,57,60,74,81,88
11	0.01	1	3sjqC	PHU	Rep, Mult	34,37
12	0.01	1	3sxkA	BCT	Rep, Mult	27,28,29
13	0.01	1	2zxwC	CDL	Rep, Mult	14,21,120
14	0.01	1	1ezvC	HEM	Rep, Mult	17,20,56,59,60,62,68,73,74,77,78,80,116,119,120,123

	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	0.248	1tqgA	0.675	2.05	0.099	0.815	2.7.13.3	47,92,108
2	0.233	3eabA	0.487	2.92	0.024	0.685	3.6.4.3	16,19
3	0.214	2kk1A	0.624	2.72	0.093	0.790	2.7.10.2	61,85,114
4	0.185	3gm1B	0.691	2.73	0.119	0.895	2.7.10.2	76
5	0.172	3eziA	0.547	3.08	0.082	0.790	2.7.13.3	20,118
6	0.129	2ksfA	0.576	3.36	0.078	0.806	2.7.13.3	119
7	0.118	2npuA	0.580	2.61	0.050	0.758	2.7.11.1	NA
8	0.060	1yisA	0.622	3.75	0.041	0.968	4.3.2.2	NA
9	0.060	1k04A	0.530	3.02	0.057	0.726	2.7.10.2	49,105,107
10	0.060	1i5nD	0.647	2.40	0.061	0.790	2.7.13.3	58,73
11	0.060	3cxhN	0.719	3.12	0.049	0.976	1.10.2.2	NA
12	0.060	1vdkA	0.646	3.39	0.083	0.968	4.2.1.2	NA
13	0.060	1g4uS	0.618	2.94	0.065	0.871	3.1.3.48	NA
14	0.060	2epoA	0.632	3.04	0.026	0.839	3.2.1.52	42
15	0.060	2r25A	0.624	2.57	0.030	0.798	2.7.13.3	62,66
16	0.060	3gzhA	0.620	3.94	0.024	0.976	4.3.2.2	NA
17	0.060	3g4xA	0.641	2.52	0.057	0.815	1.15.1.1	18,118
18	0.060	3no9A	0.649	3.44	0.084	0.960	4.2.1.2	84
19	0.060	2epoB	0.632	3.05	0.026	0.839	3.2.1.52	42
20	0.060	2pfmA	0.622	3.67	0.041	0.992	4.3.2.2	NA
21	0.060	2wlaA	0.617	2.22	0.071	0.742	1.16.3.1	NA
22	0.060	1yfmA	0.663	3.41	0.121	1.000	4.2.1.2	NA
23	0.060	2htnG	0.638	2.78	0.069	0.782	1.16.3.1	57
24	0.060	1jtnA	0.325	4.37	0.052	0.516	3.2.1.17	NA
25	0.060	1q0mD	0.648	2.41	0.076	0.815	1.15.1.1	18
26	0.060	3ee4A	0.617	2.83	0.039	0.798	1.17.4.1	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	0.25	0.780	1.94	0.08	0.94	2j0oA	GO:0005576 GO:0009405
1	0.19	0.765	2.44	0.10	0.93	1xzpA	GO:0000166 GO:0002098 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0030488 GO:0046872
2	0.18	0.453	2.50	0.03	0.56	3cp1A	GO:0005198 GO:0019031
3	0.15	0.761	2.62	0.07	0.95	3geiC	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0046872
4	0.14	0.640	3.61	0.05	0.94	2izpA	GO:0005576 GO:0009405
5	0.14	0.763	2.50	0.07	0.94	3gehA	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0046872
6	0.11	0.682	3.38	0.07	0.98	3geiA	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0046872
7	0.11	0.635	3.70	0.06	0.94	2jaaA	GO:0005576 GO:0009405
8	0.11	0.689	3.13	0.08	0.92	2ym9A	GO:0005576 GO:0009405
9	0.10	0.627	3.76	0.09	0.95	3zqeB	GO:0005576 GO:0006810 GO:0008565 GO:0009405 GO:0015031
10	0.09	0.652	3.43	0.10	0.98	2p7nA	GO:0009405
11	0.08	0.599	3.49	0.07	0.88	2e87A	GO:0005525
12	0.08	0.514	4.06	0.09	0.81	3bhqA	GO:0003677 GO:0006351 GO:0006355
13	0.08	0.457	2.98	0.08	0.61	1fxkB	GO:0005737 GO:0006457 GO:0016272 GO:0051082
14	0.07	0.615	3.80	0.09	0.92	3jctb	GO:0000054 GO:0000166 GO:0005525 GO:0005634 GO:0005730 GO:0006364 GO:0030687 GO:0042254 GO:0042273 GO:1902626
15	0.07	0.758	2.73	0.08	1.00	4aurA	GO:0005525
16	0.07	0.357	5.22	0.09	0.69	1zcaA	GO:0000166 GO:0001664 GO:0001701 GO:0003924 GO:0004871 GO:0005525 GO:0005834 GO:0005925 GO:0007165 GO:0007186 GO:0007188 GO:0007264 GO:0007266 GO:0008360 GO:0010762 GO:0016020 GO:0019001 GO:0030154 GO:0031526 GO:0031683 GO:0031752 GO:0032006 GO:0032434 GO:0035556 GO:0042493 GO:0042733 GO:0046872
17	0.07	0.428	4.38	0.06	0.71	3ftqA	GO:0000145 GO:0000166 GO:0000775 GO:0000776 GO:0000777 GO:0000910 GO:0002036 GO:0003924 GO:0005525 GO:0005634 GO:0005694 GO:0005730 GO:0005737 GO:0005819 GO:0005826 GO:0005856 GO:0005876 GO:0005886 GO:0005930 GO:0005938 GO:0007049 GO:0007067 GO:0007224 GO:0009986 GO:0015629 GO:0015630 GO:0016020 GO:0030234 GO:0030496 GO:0031105 GO:0031175 GO:0031513 GO:0032154 GO:0032391 GO:0032880 GO:0032947 GO:0035869 GO:0042384 GO:0042802 GO:0042995 GO:0043209 GO:0045202 GO:0048471 GO:0050790 GO:0051258 GO:0051301 GO:0060170 GO:0070062
18	0.07	0.638	3.60	0.06	0.97	3zqbA	GO:0005576 GO:0006810 GO:0008565 GO:0009405 GO:0015031
19	0.06	0.432	4.11	0.06	0.68	1jalA	GO:0000166 GO:0005524 GO:0005525 GO:0016887 GO:0043022 GO:0043023 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0005525	GO:0003924	GO:0046872
GO-Score	0.31	0.31	0.31
Biological Processes	GO:0001510	GO:0002097	GO:0009405
GO-Score	0.38	0.38	0.36
Cellular Component	GO:0005576	GO:0036338	GO:0005737
GO-Score	0.36	0.36	0.31

(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.