I-TASSER results

I-TASSER results for job id Rv2022c

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

Input Sequence in FASTA format

>protein (201 residues)
MNVPWENAHGGALYCLIRGDEFSAWHRLLFQRPGCAESVLACRHFLDGSPVARCSYPEEY
HPCVISRIALLCDSVGWTADVERISAWLNGLDRETYELVFAAIEVLEEEGPALGCPLVDT
VRGSRHKNMKELRPGSQGRSEVRILFAFDPARQAIMLAAGNKAGRWTQWYDEKIKAADEM
FAEHLAQFEDTKPKRRKRKKG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MNVPWENAHGGALYCLIRGDEFSAWHRLLFQRPGCAESVLACRHFLDGSPVARCSYPEEYHPCVISRIALLCDSVGWTADVERISAWLNGLDRETYELVFAAIEVLEEEGPALGCPLVDTVRGSRHKNMKELRPGSQGRSEVRILFAFDPARQAIMLAAGNKAGRWTQWYDEKIKAADEMFAEHLAQFEDTKPKRRKRKKG
Prediction	CCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCEEEEEEEEEHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCEEEEEEEHCCCCEEEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	998877778875789986446888999987477757887777654567776556888754445555434467656899998637889987999999999999999999898899987555688767776566554689876999999869967999986546787767749999999999999999999755566666569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MNVPWENAHGGALYCLIRGDEFSAWHRLLFQRPGCAESVLACRHFLDGSPVARCSYPEEYHPCVISRIALLCDSVGWTADVERISAWLNGLDRETYELVFAAIEVLEEEGPALGCPLVDTVRGSRHKNMKELRPGSQGRSEVRILFAFDPARQAIMLAAGNKAGRWTQWYDEKIKAADEMFAEHLAQFEDTKPKRRKRKKG
Prediction	872416423311000001143141034121424421431021223134431342544441232112313333450404040440350056036721430240042037323714202043064342550440214364442010000023623000000233446655126610530362055115515756566655678
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCEEEEEEEEEHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCEEEEEEEHCCCCEEEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MNVPWENAHGGALYCLIRGDEFSAWHRLLFQRPGCAESVLACRHFLDGSPVARCSYPEEYHPCVISRIALLCDSVGWTADVERISAWLNGLDRETYELVFAAIEVLEEEGPALGCPLVDTVRGSRHKNMKELRPGSQGRSEVRILFAFDPARQAIMLAAGNKAGRWTQWYDEKIKAADEMFAEHLAQFEDTKPKRRKRKKG

1wmiA

0.16

0.07

0.43

1.14

wdPPAS

--------------------------------------------------------------------------MTYRVKIHKVVKALQSLPKAHYRRFLEFRDILEYEPVPREKFDVIKLEGTGDLDLYRARL---GD--YRVIYSVNWKDKVIKILKLKPRGRA-----------------------------------

1wmiA

0.16

0.07

0.43

0.93

wPPAS

--------------------------------------------------------------------------MTYRVKIHKVVKALQSLPKAHYRRFLEFRDILEY-EPPREKFDVIKLEGTGDLDLYRARL---GD--YRVIYSVNWKDKVIKILKLKPRGRA-----------------------------------

2kheA

0.15

0.06

0.44

1.56

dPPAS2

--------------------------------------------------------------------------MGYRIEFDPAEKELEKLDREVARRILRFLRERVATLED-PRSLGEPLRGPELGRFWKYRVGD-----YRLICHIQDREATVLVLRVGHARDVYR---------------------------------

2kheA

0.15

0.06

0.44

1.13

wdPPAS

--------------------------------------------------------------------------MGYRIEFDPAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRV---GD--YRLICHIQDREATVLVLRVGHARDVYR---------------------------------

1wmiA

0.16

0.07

0.43

1.50

dPPAS2

--------------------------------------------------------------------------MTYRVKIHKVVKALQSLPKAHYRRFLEFRDILEYEPVPREKFDVIKLEGTGDLDLYRARL---GD--YRVIYSVNWKDKVIKILKLKPRGRA-----------------------------------

4bjaA

0.11

0.10

0.89

0.71

MUSTER

----WVGNESENPFDLALNKKDRTLLRETWQRLDDPKDIVGLIFLDIVND-IEPDLKKVFGVDRAPRAAMLKMP-KFGGHILRFYEFMEQLTSMLGTNLTGAWQLVRKTGRSVRQGFLEQNQNQMEKNYFEI-----------VINVFIER----LIPFLTGEQELNYTTSQITDVWKKFLNTVISQMTDSFELERAKQK-

2kheA

0.15

0.06

0.44

0.86

dPPAS

--------------------------------------------------------------------------MGYRIEFDPAEKELEKLDREVARRILRFLRERVATLED-PRSLGEPLRGPELGRFWKYRVGD-----YRLICHIQDREATVLVLRVGHARDVYR---------------------------------

2kc9A

0.15

0.07

0.46

0.90

wdPPAS

--------------------------------------------------------------------------MAYFLDFDEALKEWRKLGSTVREQLKKKLVEVLE------SPRINKLRG--MPDCYKIKLRSSG---YRLVYQVIDEKVVVFVISVGKAEAS-----EVYSEAVKRIL-------------------

5hhjA

0.13

0.12

0.91

0.62

wMUSTER

KPQPVRRKPDGGVRNLGVPTVTDRFIQQAIA---QVLTPIYEEQFHDHSYGFRPNRCAQQAILTALDMMNDGNDWIVDIDLEK-HDKLMTIIGRT-GDVISIVRKYLVSGIMIDDEYEDSIVGTPQGGLNELDKEMEKRGLNFVRYA----DDCIIMVG----------SEMSANRVMRNISRFIEEKLGLKVNMTKRPRG

2kheA

0.16

0.07

0.43

0.91

wPPAS

--------------------------------------------------------------------------MGYRIEFDPAEKELEKLDREVARRILRFLRERVAT-LEDPRSLGEPLRGPELGRFWKYRV---GD--YRLICHIQDREATVLVLRVGHARD----YR------------------------------

(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=-3.73

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.3±3.8Å

Download Model 2

C-score=-4.34

Download Model 3

C-score=-4.36

Download Model 4

C-score=-4.68

Download Model 5

C-score=-4.77

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	3rkoL	0.477	5.06	0.046	0.766
2	3rkoM	0.473	5.29	0.054	0.781
3	4he8L	0.470	5.28	0.083	0.781
4	5amqA	0.469	4.94	0.041	0.756
5	3vvnA	0.465	5.30	0.067	0.781
6	4av3A	0.462	5.19	0.065	0.736
7	3rkoN	0.460	5.60	0.087	0.791
8	3mktA	0.457	5.48	0.054	0.791
9	2dqmA	0.447	5.39	0.062	0.736
10	4a01A	0.446	5.16	0.051	0.741

(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	0.08	4	4fh2A	MA4	Rep, Mult	121,143,145,174
2	0.04	2	3qnfA	UUU	Rep, Mult	131,159,160
3	0.04	2	2a6sB	IPA	Rep, Mult	80,81,82,156,157,158
4	0.04	2	2aazA	UMP	Rep, Mult	133,143
5	0.04	2	5lcbN	BCL	Rep, Mult	174,177,181
6	0.04	2	3rkoL	LFA	Rep, Mult	98,101,102,132
7	0.04	2	2xquB	CVM	Rep, Mult	182,186
8	0.02	1	1gsaA	MG	Rep, Mult	119,131
9	0.02	1	3akkA	MG	Rep, Mult	128,149
10	0.02	1	3kisy	NUC	Rep, Mult	83,86,90,92,94,98,101,102,105,120,121,133,134,135,136,142,162,164
11	0.02	1	1qr0A	MG	Rep, Mult	80,82,108
12	0.02	1	3gdeA	PO4	Rep, Mult	27,125,131
13	0.02	1	3rkoN	LFA	Rep, Mult	85,86,89,99,100,103
14	0.02	1	3d5bG	MG	Rep, Mult	110,116
15	0.02	1	2v9jE	MG	Rep, Mult	81,143
16	0.02	1	2pg0B	FAD	Rep, Mult	91,92,96,98,163

	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	1mhyD	0.417	5.11	0.040	0.672	1.14.13.25	NA
2	0.060	1ytmA	0.421	5.64	0.064	0.741	4.1.1.49	NA
3	0.060	2fahA	0.424	5.66	0.055	0.741	4.1.1.32	NA
4	0.060	2x1cA	0.436	5.60	0.063	0.746	2.3.1.164	185
5	0.060	1e1hC	0.288	5.53	0.049	0.488	3.4.24.69	48,82,84,158
6	0.060	1fziA	0.413	5.53	0.048	0.716	1.14.13.25	NA
7	0.060	2w2dA	0.424	5.00	0.089	0.677	3.4.24.69	NA
8	0.060	1bucA	0.417	5.52	0.056	0.726	1.3.99.2	NA
9	0.060	1jkyA	0.415	5.09	0.043	0.672	3.4.24.83	170
10	0.060	2gtqA	0.437	5.31	0.056	0.716	3.4.11.2	NA
11	0.060	1os1A	0.428	5.53	0.077	0.746	4.1.1.49	NA
12	0.060	2jifA	0.425	5.31	0.028	0.716	1.3.99.-	NA
13	0.060	1yrzA	0.419	5.62	0.057	0.726	3.2.1.37	NA
14	0.060	1yifA	0.419	5.61	0.057	0.726	3.2.1.37	122,157,159,174
15	0.060	1e1hD	0.236	4.66	0.076	0.353	3.4.24.69	NA
16	0.060	1o0sA	0.421	4.72	0.036	0.637	1.1.1.38	NA
17	0.060	2zciA	0.426	5.57	0.048	0.746	4.1.1.32	NA
18	0.060	1zxvA	0.417	5.03	0.062	0.662	3.4.24.83	NA
19	0.060	3d9dA	0.426	5.68	0.059	0.751	1.7.3.1	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	0.07	0.413	5.37	0.07	0.69	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
1	0.07	0.445	5.53	0.13	0.76	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
2	0.07	0.473	5.46	0.07	0.80	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
3	0.06	0.425	5.10	0.04	0.69	3efoB	GO:0000139 GO:0001701 GO:0002474 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0006810 GO:0006886 GO:0006888 GO:0008270 GO:0012507 GO:0015031 GO:0016020 GO:0016192 GO:0019886 GO:0030127 GO:0048208 GO:0048471
4	0.06	0.365	5.61	0.04	0.63	2ddsA	GO:0004767 GO:0005576 GO:0008081 GO:0016787 GO:0019835 GO:0044179
5	0.06	0.339	5.36	0.05	0.56	3aezA	GO:0000166 GO:0004594 GO:0004849 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006206 GO:0008152 GO:0015937 GO:0016301 GO:0016310 GO:0016740 GO:0040007 GO:0043097
6	0.06	0.320	5.84	0.04	0.59	3swxB	GO:0003824 GO:0008152 GO:0016853
7	0.06	0.320	5.20	0.05	0.53	3k6yA	GO:0001101 GO:0004252 GO:0005576 GO:0005618 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0009403 GO:0009405 GO:0016020 GO:0016021 GO:0016787
8	0.06	0.305	6.22	0.04	0.58	2af3C	GO:0005886 GO:0006085 GO:0008152 GO:0008959 GO:0016020 GO:0016407 GO:0016740 GO:0016746
9	0.06	0.301	6.33	0.07	0.57	4ew6A	GO:0016491 GO:0019151 GO:0055114
10	0.06	0.317	6.10	0.07	0.60	4fluA	GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0071897 GO:0090305
11	0.06	0.305	4.90	0.03	0.49	4i1tA	GO:0000166 GO:0001172 GO:0003968 GO:0016740 GO:0016779 GO:0019012 GO:0019079 GO:0030430 GO:0039694
12	0.06	0.321	5.88	0.03	0.55	2ddxA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0030247 GO:0033905 GO:0045493
13	0.06	0.304	5.06	0.04	0.50	4frfA	GO:0000166 GO:0000823 GO:0000824 GO:0005524 GO:0005634 GO:0005829 GO:0005886 GO:0008440 GO:0009555 GO:0009793 GO:0009846 GO:0009860 GO:0010183 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0047326 GO:0090406
14	0.06	0.290	5.60	0.04	0.50	4fu0A	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
15	0.06	0.308	5.50	0.06	0.52	2xi5A	GO:0000166 GO:0001172 GO:0003968 GO:0006351 GO:0016740 GO:0016779 GO:0019079 GO:0039694 GO:0046872
16	0.06	0.324	5.90	0.09	0.59	1tj7A	GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262
17	0.06	0.251	5.50	0.02	0.43	4f9gA	GO:0000166 GO:0002218 GO:0002230 GO:0002376 GO:0005737 GO:0005739 GO:0005741 GO:0005777 GO:0005783 GO:0005789 GO:0005794 GO:0005886 GO:0006915 GO:0008134 GO:0016020 GO:0016021 GO:0019901 GO:0030659 GO:0031625 GO:0032092 GO:0032479 GO:0032481 GO:0032608 GO:0033160 GO:0035438 GO:0035458 GO:0042802 GO:0042803 GO:0042993 GO:0045087 GO:0045944 GO:0048471 GO:0051607 GO:0061507 GO:0071360
18	0.06	0.359	5.78	0.04	0.63	4xr7A	GO:0000288 GO:0000289 GO:0000932 GO:0003676 GO:0004518 GO:0004527 GO:0004535 GO:0005737 GO:0006301 GO:0006397 GO:0016787 GO:0031251 GO:0090305 GO:0090503

Consensus prediction of GO terms

Molecular Function	GO:0048037	GO:0050136
GO-Score	0.37	0.37
Biological Processes	GO:0006119	GO:0022904
GO-Score	0.37	0.37
Cellular Component	GO:0071944
GO-Score	0.37

(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.