I-TASSER results

I-TASSER results for job id Rv2628

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

Input Sequence in FASTA format

>protein (120 residues)
MSTQRPRHSGIRAVGPYAWAGRCGRIGRWGVHQEAMMNLAIWHPRKVQSATIYQVTDRSH
DGRTARVPGDEITSTVSGWLSELGTQSPLADELARAVRIGDWPAAYAIGEHLSVEIAVAV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSTQRPRHSGIRAVGPYAWAGRCGRIGRWGVHQEAMMNLAIWHPRKVQSATIYQVTDRSHDGRTARVPGDEITSTVSGWLSELGTQSPLADELARAVRIGDWPAAYAIGEHLSVEIAVAV
Prediction	CCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEHCCHCCCCEEEEHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHEEEEEEHC
Conf.Score	988787766665556644456667655555557888888775444466544466455336986999858855589999999988886789999999987775899999986446899869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSTQRPRHSGIRAVGPYAWAGRCGRIGRWGVHQEAMMNLAIWHPRKVQSATIYQVTDRSHDGRTARVPGDEITSTVSGWLSELGTQSPLADELARAVRIGDWPAAYAIGEHLSVEIAVAV
Prediction	864644534314222331212313422423234512141033335524533124025314753314034651343033114514343421541342144352420332043141414147
	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

CCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEHCCHCCCCEEEEHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHEEEEEEHC
MSTQRPRHSGIRAVGPYAWAGRCGRIGRWGVHQEAMMNLAIWHPRKVQSATIYQVTDRSHDGRTARVPGDEITSTVSGWLSELGTQSPLADELARAVRIGDWPAAYAIGEHLSVEIAVAV

3zxsA1

0.18

0.16

0.88

0.64

MUSTER

LTRLIDDLPALRAADPVVMAEVMEEGTYVPHHLAAMRKFARRLQER--GFRVAYSRLDDPD------TGPSIGAELLRRAAETGARE-AV-----ATRPGDWRLIEALEAM-PLPVRFLP

3m70A2

0.11

0.07

0.68

0.57

dPPAS

---------------------------------KKEDYFSKKYNTTAIHGDVVDAAKIISPCKVLDLGCGQ--GRNSLYLSLLGYDVTSWDHNENSIAF---LNETKEKENLNISTALY-

3zifN

0.17

0.13

0.79

0.57

wdPPAS

VTARLPKWSGSVKTG----SNMLGGV----VLPP---NSQAHRTETVGTEAT---RDNLHAEGAR--RPEDQTPYMILVEDSLGGLKRRMDLLEESNQQ---ATLNRLRTGLAA------

2e1yA1

0.17

0.15

0.89

0.65

wMUSTER

VATCDVLMAGADGMNTLSINGDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIHGGQSVII-----TDEIIDNIRRV---SPLA-PLHNYANL---SGIDAARHLFP-AVQVAV

4rhiA1

0.30

0.23

0.78

0.55

wPPAS

-------H-NVKGVTPRGWANRLGPVG--GPRRAPLLDFFLQSPR---DCDHYELT--IHDKGPIECPPETVFPVLNGQLDE-GTETP---------TSDEWGSLEASTELLE--VPVSV

3m70A2

0.11

0.07

0.68

0.52

dPPAS2

---------------------------------KKEDYFSKKYNTTAIHGDVVDAAKIISPCKVLDLGCGQ--GRNSLYLSLLGYDVTSWDHNENSIAF---LNETKEKENLNISTALY-

3sxnA2

0.19

0.17

0.94

0.63

PPAS

RLAQHPAAPGVRMLVPYDWRRTPGGLVRPDALWDDLLA---PESRRGGGELLYRVDRGPDGRRSAHV--ELTAVTADAHAALWRGLD-LIDRVSIGTHPHD-PLPYLLTDPRQAQVTASA

2lyxA

0.19

0.13

0.72

0.68

Env-PPAS

-GEETP----LVTARHMS---------KWE--EIAVKEAKKRYPLA-------QVLFKQKVWD--RKRKDEAVKQYHLTLREGSK------EFGVFVTISFDPYSQKV---NKIAILEEY

5cwmA1

0.15

0.14

0.95

0.62

MUSTER

----DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAE-EAARLAKRVLELAEKQG-

3zifN

0.12

0.10

0.82

0.55

dPPAS

VTARLPKWSGSVQ--DKTGSNMLGGVVLPPNS------QAHRTETVGTEATRDNLHAEGARRPEDQTPYMILVEDSLGGLKRR---MDLLEESNQQLLATLNRLRTGLAA----------

(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=-3.71

Estimated TM-score = 0.31±0.10

Estimated RMSD = 12.8±4.2Å

Download Model 2

C-score=-3.51

Download Model 3

C-score=-3.00

Download Model 4

C-score=-4.02

Download Model 5

C-score=-3.29

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	3kbcA	0.555	3.81	0.048	0.867
2	1e6vB2	0.546	4.16	0.053	0.867
3	3sqgB	0.545	4.05	0.035	0.867
4	1e6vA1	0.525	4.60	0.103	0.892
5	1e6yA3	0.522	4.67	0.086	0.892
6	1e6yE2	0.517	4.04	0.055	0.825
7	1hbnB2	0.515	4.25	0.078	0.858
8	5a8rB2	0.511	4.56	0.086	0.867
9	3hmjA	0.511	4.83	0.058	0.883
10	1e5mA	0.511	4.55	0.071	0.850

(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	0.07	4	1brrC	ARC	Rep, Mult	72,93,97
2	0.07	4	2z6iB	CA	Rep, Mult	96,99
3	0.05	3	4e97B	BME	Rep, Mult	40,43,52,55,56,111
4	0.05	3	3i8hS	MG	Rep, Mult	73,75
5	0.03	2	3sqgB	TP7	Rep, Mult	43,44,50,51,60
6	0.03	2	1e6vA	UUU	Rep, Mult	17,90,93
7	0.02	1	2qo3A	CER	Rep, Mult	25,27,38,108,114
8	0.02	1	1flcB	UUU	Rep, Mult	3,10,11,15
9	0.02	1	4iynA	MG	Rep, Mult	34,38
10	0.02	1	4y18A	III	Rep, Mult	45,46
11	0.02	1	3m2rD	F43	Rep, Mult	38,41,51
12	0.02	1	2o012	CLA	Rep, Mult	94,98
13	0.02	1	3hdlA	CA	Rep, Mult	9,57,64,67,70
14	0.02	1	1g4pA	MG	Rep, Mult	57,70
15	0.02	1	3q46A	MG	Rep, Mult	57,61
16	0.02	1	2ch1A	LLP	Rep, Mult	53,56
17	0.02	1	3d5dQ	MG	Rep, Mult	109,112,114

	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	1qlvA	0.482	4.24	0.090	0.850	2.3.1.74	27
2	0.060	3il7A	0.481	4.39	0.000	0.783	2.3.1.180	NA
3	0.060	3dysB	0.468	3.24	0.045	0.675	3.1.4.35	53,110
4	0.060	1wl4A	0.477	4.51	0.093	0.808	2.3.1.9	44
5	0.060	1y37A	0.475	4.99	0.088	0.892	3.8.1.3	105
6	0.060	1pjrA	0.388	4.65	0.057	0.683	3.6.4.12	NA
7	0.060	1hbmA	0.516	4.08	0.078	0.825	2.8.4.1	NA
8	0.060	3kzuA	0.506	4.58	0.080	0.842	2.3.1.41	NA
9	0.060	1tqyA	0.506	4.80	0.089	0.858	2.3.1.41	NA
10	0.060	1zklA	0.468	3.61	0.046	0.692	3.1.4.17	NA
11	0.060	1tedA	0.468	4.40	0.035	0.750	2.3.1.74	NA
12	0.060	1ox0A	0.506	4.81	0.042	0.867	2.3.1.41	NA
13	0.060	2ebdA	0.481	4.84	0.066	0.825	2.3.1.180	NA
14	0.060	3dsiA	0.472	4.91	0.027	0.867	4.2.1.92	39,105,114
15	0.060	1e6yA	0.500	4.68	0.089	0.858	2.8.4.1	120
16	0.060	1bucA	0.464	4.71	0.034	0.767	1.3.99.2	110
17	0.060	1gytJ	0.469	4.78	0.047	0.875	3.4.11.1	94,102
18	0.060	2wgdA	0.487	4.71	0.042	0.850	2.3.1.41	NA
19	0.060	1ehyA	0.472	4.75	0.073	0.867	3.3.2.10	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	0.07	0.565	3.89	0.08	0.88	4ky0C	GO:0015293 GO:0016020 GO:0016021 GO:0055085
1	0.07	0.500	4.43	0.12	0.85	1e6yA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
2	0.06	0.516	4.08	0.08	0.82	1hbmA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
3	0.06	0.504	4.36	0.09	0.84	1e6vA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
4	0.06	0.396	4.69	0.09	0.69	2heiB	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0005768 GO:0005769 GO:0005886 GO:0006810 GO:0007032 GO:0007264 GO:0015031 GO:0016020 GO:0019003 GO:0019882 GO:0030100 GO:0030139 GO:0030742 GO:0031901 GO:0042470 GO:0048227 GO:0070062
5	0.06	0.549	3.61	0.05	0.85	4x2sC	GO:0015293 GO:0016020 GO:0016021 GO:0055085
6	0.06	0.413	4.31	0.04	0.68	3grpD	GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
7	0.06	0.307	5.95	0.07	0.69	1im8A	GO:0002098 GO:0005737 GO:0008757 GO:0016300 GO:0016740 GO:0016743 GO:0030488 GO:0032259 GO:1904047
8	0.06	0.545	4.05	0.04	0.87	3sqgB	GO:0015948 GO:0016740 GO:0050524
9	0.06	0.426	4.51	0.03	0.75	1e6yE	GO:0015948 GO:0016740 GO:0050524
10	0.06	0.365	4.97	0.04	0.64	1n6oA	GO:0000166 GO:0001726 GO:0003924 GO:0005525 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0005886 GO:0006810 GO:0006897 GO:0006909 GO:0007264 GO:0007596 GO:0008021 GO:0010008 GO:0015031 GO:0015629 GO:0016020 GO:0016023 GO:0019001 GO:0019003 GO:0030100 GO:0030139 GO:0030424 GO:0030425 GO:0030670 GO:0031410 GO:0031901 GO:0036465 GO:0036477 GO:0042470 GO:0042995 GO:0043025 GO:0043195 GO:0043679 GO:0045022 GO:0045121 GO:0045335 GO:0045921 GO:0051036 GO:0051489 GO:0070062 GO:0098559 GO:2000286 GO:2000300 GO:2000785
11	0.06	0.368	4.61	0.07	0.67	2yriA	GO:0003824 GO:0008483 GO:0016740
12	0.06	0.361	4.62	0.06	0.66	4gekG	GO:0002098 GO:0008168 GO:0016300 GO:0016740 GO:0016743 GO:0030488 GO:0032259 GO:1904047
13	0.06	0.419	4.45	0.06	0.74	1e6vB	GO:0015948 GO:0050524
14	0.06	0.349	4.62	0.09	0.66	2bydA	GO:0000287 GO:0005737 GO:0005829 GO:0008897 GO:0015939 GO:0016740 GO:0019878 GO:0046872 GO:0070062
15	0.06	0.336	5.08	0.02	0.65	2i6iA	GO:0004725 GO:0005737 GO:0006470 GO:0016311 GO:0016791 GO:0035335
16	0.06	0.367	4.63	0.10	0.63	4dydA	GO:0000166 GO:0003857 GO:0006631 GO:0016491 GO:0055114 GO:0070403
17	0.06	0.422	4.33	0.04	0.72	5a0yB	GO:0015948 GO:0016740 GO:0050524
18	0.06	0.354	4.45	0.09	0.61	2bp7B	GO:0003824 GO:0003863 GO:0008152 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0050497
GO-Score	0.36	0.36
Biological Processes	GO:0043447	GO:0015975	GO:0009061	GO:0015947
GO-Score	0.36	0.36	0.36	0.36
Cellular Component	GO:0016021	GO:0005886	GO:0030139	GO:0070062	GO:0031901	GO:0042470
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07

(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.