I-TASSER results

I-TASSER results for job id Rv1332

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

Input Sequence in FASTA format

>protein (218 residues)
MPPVCGRRCSRTGEIRGYSGSIVRRWKRVETRDGPRFRSSLAPHEAALLKNLAGAMIGLL
DDRDSSSPSDELEEITGIKTGHAQRPGDPTLRRLLPDFYRPDDLDDDDPTAVDGSESFNA
ALRSLHEPEIIDAKRVAAQQLLDTVPDNGGRLELTESDANAWIAAVNDLRLALGVMLEIG
PRGPERLPGNHPLAAHFNVYQWLTVLQEYLVLVLMGSR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MPPVCGRRCSRTGEIRGYSGSIVRRWKRVETRDGPRFRSSLAPHEAALLKNLAGAMIGLLDDRDSSSPSDELEEITGIKTGHAQRPGDPTLRRLLPDFYRPDDLDDDDPTAVDGSESFNAALRSLHEPEIIDAKRVAAQQLLDTVPDNGGRLELTESDANAWIAAVNDLRLALGVMLEIGPRGPERLPGNHPLAAHFNVYQWLTVLQEYLVLVLMGSR
Prediction	CCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	99888777775455546888776665445567897799996899999999999999999857778899875788758888999999887898857778899887667776554558999999975589999999999999999878899679979999999999999999999998699888865689877568999999999999999999997789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MPPVCGRRCSRTGEIRGYSGSIVRRWKRVETRDGPRFRSSLAPHEAALLKNLAGAMIGLLDDRDSSSPSDELEEITGIKTGHAQRPGDPTLRRLLPDFYRPDDLDDDDPTAVDGSESFNAALRSLHEPEIIDAKRVAAQQLLDTVPDNGGRLELTESDANAWIAAVNDLRLALGVMLEIGPRGPERLPGNHPLAAHFNVYQWLTVLQEYLVLVLMGSR
Prediction	74442444144315145354430430444563744301030352014103400430241045567544543144034145445633523002200220244465555545445435521230241336402530153033004104766140404472043003000000010032141564446614774434212100100011010003013468
	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

CCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
MPPVCGRRCSRTGEIRGYSGSIVRRWKRVETRDGPRFRSSLAPHEAALLKNLAGAMIGLLDDRDSSSPSDELEEITGIKTGHAQRPGDPTLRRLLPDFYRPDDLDDDDPTAVDGSESFNAALRSLHEPEIIDAKRVAAQQLLDTVPDNGGRLELTESDANAWIAAVNDLRLALGVMLEIGPRGPERLPGNHPLAAHFNVYQWLTVLQEYLVLVLMGSR

3bjbB

0.18

0.12

0.67

1.26

dPPAS2

-------------------------------------------EEQRARHVRLEAAIELATEKELARVQHEVAKRAGVAI--------GTLYRYFPSVDQIDRGVGFKKSAESPQDAVYNVLVRATRGLLRRPALSTAIQSTSTANVASVP------DAGKVDRAFRQILDAAG--------------IEHPTEEDLTALRLLVQLWFGVIQSCLNGR

5fshA3

0.14

0.09

0.67

1.14

dPPAS2

-----------------------------------------DFALKEGVYGLARTLLHLAQEAKEEAAVLLQERLALLGRRPGLSPEEAEALRK---ALAELLPEEVRLPAKLGLLDLLAFLRLKGDEALGRLSLAELRGLAGALKGVHGFDVPSPKAVEGIARLAQGLLQDLEARTALGPLSPEPVPLGF---------------------------

5dw7A

0.14

0.13

0.93

0.69

MUSTER

LPHFLPARLNPLDEARAHSTTWAREMGMLEGSGVW--------EQSDLEAHDYGLLCAYTHPD---CDGPALSLITHFLEKYKRSQDRLAGKAHLDRLPLFMPLPEPRNPVEAGLADLWTRTVPAMSADWRRRFAVATEHLLNESMW-----ELNPVEYIEMRRKVGGAPWSAGLVEYATAEVPAAVAGTRPLRVLMETFSDAVHLRNDLFSYQREVE

5fshA3

0.14

0.10

0.69

0.65

dPPAS

-----------------------------------------DFALKEGVYGLARTLLHLAQEAKEEAAVLELLLQERLALLGRRPGLSPEEAEALRKALAELLPEEVRLPAKLGLLDLLAFLRLKGDEALGRLSLAELRGLAGALKGVHGFDVPSPKAVEGIARLAQGLLQDLEARTALGPLSPEPVPLGF---------------------------

3cwrA

0.16

0.12

0.78

0.64

wdPPAS

--P---AV--PDAVVREGGAAATEG-SEAGIAKKTLYR----SGRADLIGLLVESWIAPIFPGFEADPQDAAAALERIVYDIAQSREAVSLFRLA--------------SDADLRNRFLPAYNAN-----IERSRRELARWLDQQASAGRPLPIPAERVADLLLSAVIAEPLRQITLGLRE----PLPAWDIAPRVADAVRLIA--------------

3e7qB

0.16

0.13

0.86

0.77

wMUSTER

NQEVRFSRLEACLKRHGFQGASVRK-AEAGVSVG-----LIDALVAEAYLAVTGRVMRLLRGAIDTAPGGARPRLS------------AFFEASF-SAELLDPQLLDAWLAFWGAVGSIEAIGRVHDHSYGEYRALLVGVLRQLAEEGG----WADFDAELAAISLSALLDGLWLESGLNPATF------TPRQGVQICEAWVDGLEAG--AHRRFRR

3e7qB

0.19

0.15

0.81

0.71

wPPAS

MNQE--VRFSRLPEQRKFQGASVR--AEAGVSVG-----LIDALVAEAYLAVTGRVMRLLRGAIDTAPGGARPRLSAF----SAELLDPQLLDAW---------------AFWGAVGSIEAIGRVHDHSYGEYRALLVGVLRQLAEEGG----WADFDAELAAISLSALLDGLWLESGLNPATF------TPRQGVQICEAWVDGLEAG---AHRRFR

3cwrA

0.11

0.08

0.73

1.14

dPPAS2

TEGVAG--IA-KKTLYRFASG-----------------------RADLIGLLVESWIAPIFPGFEADPQDAAAALERIV---------YDIAQAV------LSREAVSLFRLASDADLRNRFLPAYNANGIERSRRELARWLDQQASAGRPLPIPAERVADLLLSAVIAEPLRQITLGLRE----PLPAWDIAPRVADAVRLIA--------------

3e7qB

0.17

0.14

0.83

0.79

PPAS

MNQ--EVRFSRLPEQRKFQGASVRK-AEAGVSVGL------DALVAEAYLAVTGRVMRLLRGAIDTAPGGARPRLSAFFEASSAELLDPQLLDAWLAFW-----------GAVGSIEAIGRVHDHSYGEYRALLVGVLRQLAEEGGWADF----DAELAAISLSALLDGLWLESGLNP---------ATFTPRQGVQICEAWVDGLEAG---AHRRFR

2waaA2

0.12

0.11

0.91

0.70

Env-PPAS

-PQ---RKISVTCGE-AIDRVAGEDKNTRWWNARESYGMLTAKALDAQVQLVCWGGRGLIRSWNGKTDDANLPDFYQFTLGDTGQAPQWDHHRYQPDAIGTNDFSPGIPD--------RATYINTYTRFVRTLLDNQATIVLTEGAI------LNGDKKAALVSYIGETRQQLHSNRVFYASSSHHPGDNSDAHPTKDQHAAMARELTPQLRQIMDWL

(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=-2.40

Estimated TM-score = 0.43±0.14

Estimated RMSD = 11.0±4.6Å

Download Model 2

C-score=-2.85

Download Model 3

C-score=-4.11

Download Model 4

C-score=-4.80

Download Model 5

C-score=-3.22

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	3e7qB	0.664	3.61	0.126	0.872
2	3bcgA	0.640	4.10	0.093	0.881
3	5d18A	0.630	3.91	0.090	0.853
4	3lsjA	0.630	3.93	0.089	0.849
5	2fbqA	0.630	3.76	0.066	0.830
6	2uxuA	0.626	4.17	0.151	0.867
7	3c07A	0.620	4.04	0.069	0.839
8	1jt0A	0.619	3.65	0.051	0.803
9	5d1rA	0.618	4.06	0.057	0.839
10	3vibA	0.616	3.71	0.071	0.826

(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	0.11	7	3g1mA	RF3	Rep, Mult	60,74,75,78,79,136,137,140,167,170,171,174,203
2	0.05	3	3whbA	DCC	Rep, Mult	49,52,53,56,123,126,127,130,131,133,134,160,161,163,164,167,171
3	0.05	3	2uxuB	NAR	Rep, Mult	56,78,95,139,162,163,166,170
4	0.03	2	3jwrA	IBM	Rep, Mult	88,91
5	0.03	2	1usyF	HIS	Rep, Mult	203,207
6	0.03	2	1jumA	BER	Rep, Mult	55,56,59,80,131,134,167
7	0.03	2	4ojjC	MG	Rep, Mult	45,121
8	0.03	2	1jt0A	QNA	Rep, Mult	95,167,169,170,173,174
9	0.02	1	1gzmA	C8E	Rep, Mult	57,60
10	0.02	1	3fz3A	CA	Rep, Mult	28,170,171
11	0.02	1	4ev6E	MG	Rep, Mult	60,136
12	0.02	1	3hiyB	MG	Rep, Mult	88,97
13	0.02	1	3c9iB	XE	Rep, Mult	210,214
14	0.02	1	1jt0C	QNA	Rep, Mult	142,160,161,162,165,166
15	0.02	1	1bjyB	CTC	Rep, Mult	169,173,176
16	0.02	1	2wtfA	CA	Rep, Mult	105,108

	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	3ffzA	0.420	6.05	0.064	0.761	3.4.24.69	NA
2	0.060	1auiA	0.413	5.96	0.031	0.734	3.1.3.16	126
3	0.060	3c8yA	0.418	4.85	0.059	0.642	1.12.7.2	73,171,186
4	0.060	1xzwB	0.424	5.94	0.075	0.752	3.1.3.2	NA
5	0.060	1kbpA	0.413	5.95	0.040	0.729	3.1.3.2	NA
6	0.060	1wdpA	0.412	5.30	0.070	0.665	3.2.1.2	NA
7	0.060	2qtcB	0.388	5.89	0.077	0.647	1.2.4.1	113
8	0.060	2fonB	0.417	4.89	0.020	0.642	1.3.3.6	NA
9	0.060	1cb7B	0.420	4.71	0.071	0.619	5.4.99.1	NA
10	0.060	2qf7A	0.426	5.74	0.034	0.734	6.4.1.1	NA
11	0.060	2uv8G	0.425	5.25	0.058	0.679	2.3.1.86	NA
12	0.060	2a06C	0.363	5.66	0.060	0.615	1.10.2.2	174
13	0.060	3gpbA	0.415	5.88	0.074	0.702	2.4.1.1	93
14	0.060	1y791	0.444	5.09	0.056	0.679	3.4.15.5	45
15	0.060	2pywA	0.438	5.19	0.051	0.702	2.7.1.100	NA
16	0.060	2uxwA	0.432	6.13	0.046	0.789	1.3.99.-	NA
17	0.060	2qllA	0.404	5.73	0.056	0.688	2.4.1.1	93
18	0.060	2z1qB	0.420	6.04	0.033	0.766	1.3.99.3	NA
19	0.060	1w07B	0.429	5.30	0.021	0.679	1.3.3.6	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	0.21	0.664	3.61	0.13	0.87	3e7qB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
1	0.19	0.618	3.99	0.06	0.82	2qibA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.18	0.626	4.20	0.15	0.87	2uxhA	GO:0003677 GO:0006351 GO:0006355
3	0.17	0.603	3.64	0.08	0.78	3g7rB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
4	0.14	0.600	4.10	0.06	0.82	3kz9B	GO:0003677 GO:0006351 GO:0006355
5	0.13	0.622	3.67	0.10	0.81	4ichA	GO:0003677 GO:0006351 GO:0006355
6	0.12	0.600	3.66	0.09	0.78	2np5A	GO:0003677 GO:0006351 GO:0006355
7	0.10	0.592	3.81	0.07	0.79	3crjA	GO:0003677
8	0.10	0.609	4.06	0.09	0.83	2id6A	GO:0003677 GO:0006351 GO:0006355
9	0.10	0.604	4.10	0.06	0.83	2pbxA
10	0.08	0.630	3.76	0.07	0.83	2fbqA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714
11	0.08	0.632	3.98	0.06	0.85	3c07A	GO:0003677 GO:0006351 GO:0006355
12	0.08	0.635	3.82	0.06	0.85	3vibC	GO:0003677 GO:0006351 GO:0006355
13	0.07	0.612	4.08	0.08	0.84	3p9tA	GO:0003677 GO:0006351 GO:0006355
14	0.07	0.600	3.61	0.08	0.79	2g3bA	GO:0003677 GO:0006351 GO:0006355
15	0.07	0.585	3.85	0.14	0.78	4l62A	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
16	0.07	0.588	3.77	0.07	0.77	3knwA	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.571	4.37	0.06	0.81	1rktA	GO:0003677 GO:0006351 GO:0006355
18	0.07	0.586	4.03	0.10	0.78	3f1bA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003700
GO-Score	0.62	0.47
Biological Processes	GO:0006355
GO-Score	0.62
Cellular Component
GO-Score

(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.